title: PIGA mutation and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

summary: Progression of duodenal polyposis into cancer is an important cause of morbidity and mortality in the inherited tumour syndromes Familial Adenomatous Polyposis (FAP) and MUTYH-associated Polyposis (MAP), yet this process remains poorly understood. This study aimed to identify genes that are mutated in FAP and MAP duodenal adenomas and to characterise the cellular consequences for duodenal tumorigenesis.

overall_design:
We performed whole transcriptome sequencing were used to identify putative drivers of duodenal tumorigenesis in 70 duodenal adenomas from patients with FAP and MAP.
Grant:
NIH/NCI
R03 CA176788-01A1
Discovering New Targets for Chemoprevention in Familial Adenomatous
Polyposis
Vilar-Sanchez, Eduardo / University of Texas MD Anderson Cancer Center

last: Vilar


title: Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells

status: Public on Jul 24 2023

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [ChIP-seq]

summary: Zfp296 KO profoundly affects the gene expression patterns of ESCs. ZFP296 belongs to the C2H2-type ZF family. To map the ZFP296 binding sites across the whole genome, chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed.

overall_design: ChIP-seq for Ty1-tagged ZFP296 expressed in Zfp296-KO #98 ESCs.

first: Jun-ichi

last: Miyazaki

first: Satsuki

first: Hiroyuki

last: Yamano


title: Distribution of RNA polymerase II and changes of carbo-terminal phosphorylation sites after INTS11 knockdown

status: Public on Jul 25 2023

city: Kunming City

first: Jiangyang Li

last: Jingyang Li

state: Yunnan Province

address: School of Life Science, Yunnan University, Chenggong District

department: School of Life Science

country: China

institute: Yunnan Universiity

summary:
As Integrator is tightly associated with RNAPII-CTD, it is critical to understand how the RNAPII engaged and conducted within the active gene promoter for divergent transcription.   We thus employed RNAPII ChIP-seq (Chromatin Immuno-precipitation with RNAPII antibody) to determine the distribution of the total RNAPII and its phosphorylation isoforms.
Total RNA polymerase II and its carbon terminal phosphorylation(RNA polymerase II-ctd-Tyr-1，RNA polymerase II-ctd-ser-2) before and after INTS11 knockdown in HCT116-INTS11-AID cells changes chromatin immunoprecipitation DNA sequencing (ChIP-seq).

overall_design: See the distribution of RNA polymerase II and RNA Polymerase II-CTD-TYR-1 under induction

first: L

last: Fan

first: Y

last: Jiao

last: Jingyang

first: S

last: Wenhao

first: H

last: Daoheng


title: Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [RNA-seq-2]

summary: Zfp296-KO ESCs grew as flat colonies and could not form teratomas, but could contribute to germline-competent chimeric mice. To analyze the molecular mechanisms causing these unique phenotypes, we compared gene expression profiles among wild-type (WT), Zfp296-KO, and Zfp296-rescue ESCs by RNA-sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT, Zfp296-KO #156, and Zfp296-rescue #10 ES cells.


title: Surprising mechanisms and regulatory roles of yeast transcription factors

status: Public on Aug 01 2023

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

country: USA

institute: Fred Hutchinson Cancer Center


title: Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [RNA-seq-1]

summary: Zfp296-KO ESCs grew as flat colonies and could not form teratomas, but could contribute to germline-competent chimeric mice. To analyze the molecular mechanisms causing these unique phenotypes, we compared gene expression profiles among wild-type (WT), Zfp296-KO, and Zfp296-rescue ESCs by RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from WT, Zfp296-KO #98, and Zfp296-rescue #22 ES cells.


title: Mitochondrial clearance and HSF-1 activity are coupled to promote proteostasis capacity, organismal robustness and longevity in response to fasting

status: Public on Jul 20 2023

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

summary: In this experiment, we aimed to determine the gene expression changes associated with a single period of transient fasting early in life in C. elegans.

overall_design: C. elegans worms (N2 laboratory wild-type strain) were synchornised by egg-laying, grown at 20C and removed from food (OP50) at the mid-L4 stage for 24 hours. Following this, animals were returned to food and allowed to recover for another 24 hours, after which they were exposed to heat shock (35C, 30 minutes) or kep at 20C. Worms were collected and snap frozen before RNA was extracted using an RNeasy kit (Qiagen).

first: Nikolaos

last: Tataridas-Pallas


title: Methylation studies in multiple human tissues N16

status: Public on Aug 05 2023

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

summary:
An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from human postmortem tissue samples.
n=661 tissues. Adipose, Lung, Blood, Bone marrow, Heart, Kidney, Liver, Spleen, Lymph node, Skeletal muscle, Pituitary gland,

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Genome annotations of the array can be downloaded from https://github.com/shorvath/MammalianMethylationConsortium

first: Andrew

middle: J

last: Levine


title: Apolipoprotein E2 protects against aging-induced neuronal endosomal dysfunction through enhanced exosome secretion

status: Public on Jul 31 2023

city: Orangeburg

first: Paul

last: Mathews

state: NY

address: 140 Old Orangeburg Rd.

department: Psychiatry

institute: New York University Grossman School of Medicine

summary: In 12-month-old APOE targeted-replacement mice, we report that overall differences in gene expression were the most prominent when comparing the protective APOE2 to the other two alleles, with fewer differences found when comparing the risk-neutral APOE3 and disease-promoting APOE4 alleles. When compared with either APOE3 or APOE4, differential expression of genes within the endosomal pathways is a prominent feature of APOE2 expression in the brain. We hypothesized that the protective effects of APOE2 are mediated through the endosomal pathway during aging. In contrast to Alzheimer’s disease and APOE4 models, we detected normal morphology and abundance of early endosomes within cortical neurons of APOE2 targeted-replacement mice during aging despite decreased rab5b recruitment to early endosomes. Similarly, the morphology and abundance of retromer-associated vesicles was normal in APOE2 mice, despite reduced recruitment of vesicle-associated VPS35. Significantly, we observed increased brain extracellular levels of endosome-derived exosomes in APOE2 compared with APOE3 mice during aging, indicative of an enhanced endosomal cargo clearance to the extracellular space that contributes to a homeostatic balance of endosomal functions. Our findings thus demonstrate that APOE2 effectively offsets endosomal pathway changes during aging to preserve its integrity by enhancing exosome biogenesis, mitigating age-driven endosomal dysfunction that contributes to Alzheimer’s disease risk.

overall_design: Hemibrain genetic profiles of targeted-replacement APOE2, APOE3, and APOE4 mice at 12 months of age

first: Katherine

middle: Y

last: Peng

first: Braison

last: Liemisa

first: Jonathan

last: Pasato

first: Sai

middle: C

last: Penikalapati

first: Melissa

last: Alldred

first: Monika

last: Pawlik

first: Adriana

last: Heguy

first: Stephen

middle: D

last: Ginsberg

first: Efrat

last: Levy

middle: M


title: UBR5 Forms Ligand-Dependent Complexes on Chromatin to Regulate Nuclear Hormone Receptor Binding

city: Boston

first: Jared

last: Brown

state: MA

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

institute: Dana Farber Cancer Institute


title: Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure (rat sample)

status: Public on Jul 17 2023

first: Daisuke

last: Motooka

summary: Non-canonical Wnt signaling activated by Wnt5a and Wnt11 is required for the development of second heart field cardiac progenitor cells in mice. However, the pathophysiological role of non-canonical Wnt signaling in the adult heart has not been fully elucidated. Here we show that cardiomyocyte-specific Wnt5a knockout mice exhibit improved systolic function and reduced expression of mechanosensitive genes including Nppb compared to control mice when subjected to pressure overload. In cultured cardiac myocytes, Wnt5a knockdown reduces the upregulation of Nppb gene expression and YAP nuclear translocation induced by cyclic cell stretch. Wnt5a knockdown-induced Nppb downregulation in response to cell stretch is rescued by inhibition of Hippo pathway, and the rescue effect of Hippo inhibition is canceled by YAP knockdown. These results collectively suggest that Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure.

overall_design: mRNA profiles obtained from neonatal rat ventricular cardiomyocytes

first: Masayoshi

last: Iwasaki

last: Okuzaki


title: Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure (mouse sample)

overall_design: mRNA profiles obtained from control and Wnt5aCKO hearts


title: Effect of INTS11, INTS9, CPSF73 knockdown on transcription

first: Jiangyang Li

last: Jingyang Li

summary:
As a key component for transcription, Transcriptional results of INTS11 knockdown were analyzed by chromatin associated RNA sequencing (ChrRNA-seq).
We used ChrRNA-seq, 4sU-seq and TT-seq data of HCT116-INTS11-AID cells under normal condition, induction condition and recovery condition, and HCT116-INTS9-AID cells, Chrna-seq data of HCT116-CPSF73-AID cells before and after protein knockdown were analyzed for gene expression profile.

overall_design: Changes of pre-mRNA after INTS11 knockdown. Early genetic changes under induction

first: L

last: Fan

first: D

last: Yunkun

first: Y

last: Jiao

last: Jingyang


title: UBR5 Forms Ligand-Dependent Complexes on Chromatin to Regulate Nuclear Hormone Receptor Binding [RNA-Seq]

summary: Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are important therapeutic targets in malignancy. Hormone binding triggers NR activation and their subsequent proteasomal degradation through unknown ligand-dependent ubiquitin ligase machinery. NR degradation is therapeutically relevant: the oncogenic PML-RARA fusion between PML and the retinoic acid receptor (RARA) drives acute promyelocytic leukemia and degradation of PML-RARA induced by all-trans-retinoic acid (ATRA) is required for anti-tumor activity. Our work establishes UBR5-driven NR degradation as an integral regulator of transcriptional signaling by nuclear hormones.

overall_design: RNA sequencing (RNA-seq) was performed for NB4 and A549 cells. Samples were prepared and sequenced in biological duplicate across multiple times following treatment. Treatment consisted of application of ATRA (NB4 cells) or Dexamethasone (A549 cells). For each cell type, 2 control genotypes (2 knockdowns of luciferase) and two test genotypes (2 typs of UBR5 knockdown) were parepared for each treatment condition.

last: Tsai

first: Jacob

last: Aguirre

first: Vivian

last: Focht

first: Yen-Der

last: Li

first: Georg

last: Kempf

first: Lukas

last: Kater

first: Brittany

last: Sandoval

first: Charles

last: Zou

first: Justine

last: Rutter

middle: A

last: Donovan

first: Quinlan

last: Sievers

first: Paul

last: Park

first: Jevon

last: Cutler

last: Hatton

first: Elizabeth

last: Ener

first: Micah

middle: T

last: Sperling

first: Mikolaj

last: Slabicki

first: Peter

middle: G

last: Miller

first: Roger

last: Belizaire

first: Adam

middle: S

first: Scott

last: Armstrong

first: Eric

last: Fischer

first: Nicolas

last: Thomä

first: Benjamin

last: Ebert


title: Age-related histone loss and altered histone acetylation in mouse retinal pigment epithelium.

status: Public on Jul 15 2023

city: Johnson City

first: Mark

middle: Ellsworth

last: Kleinman

state: Tennessee

address: Quillen College of Medicine

department: Department of Surgery

institute: East Tennessee State University


title: Age-related histone loss and altered histone acetylation in mouse retinal pigment epithelium. [Total RNA]

summary: Histones are pivotal carriers of epigenetic information through post-translational modifications (PTMs), crucial for regulating gene expression, proper cellular function and maintaining cell identity. Perturbations in histone levels within the aging genome can profoundly impact chromatin structure and gene expression profiles. In this study, we examined the effects of age-related changes on histone levels and histone acetylation in the retinal pigment epithelium (RPE) and retina of mice. Our findings revealed a global reduction in histones H1, H2A, H2B, H3, and H4 within the aged RPE/choroid, while the neural retina remained unaffected. Transcriptome analysis unveiled a significant downregulation of histone genes in the aged RPE/choroid, including key components of the histone locus body (HLB) complex involved in histone pre-mRNA processing. Knockdown of HINFP, a critical HLB component, in human RPE cells resulted in histone loss, induction of senescence, and upregulation of senescence-associated secretory phenotype (SASP) markers. Replicative aging of human RPE cells exhibited progressive histone loss and acquisition of the SASP phenotype. Immunostaining of human retina sections demonstrated a gradual decline in histones within the aging RPE. Additionally, aging in mice RPE/choroid led to diminished global histone acetylation levels, particularly H3K14ac, H3K56ac, and H4K16ac marks. These alterations in histone acetylation were metabolically driven and correlated with changes in acetyl-CoA abundance. Collectively, our findings highlight the characteristic loss of histones as a hallmark of aging in the RPE/choroid, shedding light on potential mechanisms linking histone dynamics, cellular senescence, and age-related functional changes in RPE cells.

overall_design:
We conducted transcriptome analysis on RNA-Seq data derived from the RPE/choroid of young (1-2 months) and aged (20-24 months) mice (n=3 per group).
Submitter states that raw data files were lost due to central server crash

first: Sushil

middle: K

last: Dubey

first: Rashmi

first: Kyung

last: Jung

first: Subhash

last: Prajapati

first: Xinan

last: Liu

first: Jinze

middle: E


title: Zfp296 knockout enhances chromatin accessibility and induces a unique state of pluripotency in embryonic stem cells [ATAC-seq]

first: Daisuke

last: Motooka

summary: To explore the molecular mechanism underlying transcriptional repression by ZFP296, we performed genome-wide analysis of chromatin accessibility (ATAC-seq).

overall_design: ATAC-seq for wild-type, Zfp296-knockout #98, and Zfp296-rescue #22 ESCs.

first: Jun-ichi

last: Miyazaki

first: Satsuki

first: Hiroyuki

last: Yamano


title: Genome-wide localization of SMAD2/3 and JUN family protein and epigenetic landscapes in human breast cell line treated with or without TGF-β.

status: Public on Jul 14 2023

summary: The non-receptor tyrosine kinase SRC is overexpressed in various human cancers, however, transcriptional mechanisms underlying SRC expression is poorly understood. In this study, we found that transforming growth factor-β (TGF-β), which is abundantly secreted in tumor microenvironment, upregulates SRC protein and mRNA expression. To clarify the molecular mechanisms underlying TGF-β-induced SRC expression, we analyzed the genome-wide localization of SMAD2/3 and JUN family protein and epigenetic landscapes in human breast cell lines. These results showed that a novel TGF-β-responsive enhancer, which localizes at intragenic region of SRC, is activated via TGF-β/SMAD pathway and upregulates SRC expression.

overall_design: Chromatin immunoprecipitation and DNA sequencing (ChIP-Seq) for H3K4me3, H3K27Ac, SMAD2, SMAD3, JUN, and JUNB in MCF10A and H3K27Ac in BT-549. Cells were treated with or without TGF-β (10 ng/ml) for 24h.

first: Soshi

last: Noshita

last: Okuzaki


title: Age-related histone loss and altered histone acetylation in mouse retinal pigment epithelium. [polyA RNA]

overall_design: We performed transcriptome profiling of ribosomal RNA depleted poly(A) enriched sequencing data from RPE/choroid of young (1-2 months) and aged (20-24 months) mice (n=3 per group).


title: Systematic interrogation of CRISPR-based antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide-, and strain-specific factors influencing antimicrobial activity

city: Paris

first: David

last: Bikard

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address this knowledge gap by systematically interrogating the use of CRISPR antimicrobials against multidrug-resistant and hypervirulent strains of Klebsiella pneumoniae. Comparing different Cas nucleases, we found that AsCas12a exhibited robust targeting across different strains. The elucidated modes of escape from this nuclease varied widely, restraining opportunities to enhance killing. We also encountered individual guide RNAs yielding different extents of clearance across strains. The differences were attributed to improper RNA folding, leading to inefficient DNA cleavage and subsequent repair via homologous recombination. To explore features that could improve targeting across strains, we performed a genome-wide screen in different K. pneumoniae strains that yielded guide design rules and trained an algorithm for predicting guide efficiency. Finally, we showed that Cas12a antimicrobials can be exploited to eliminate K. pneumoniae when encoded in phagemids delivered by T7-like phages. Altogether, our results highlight the importance of evaluating antimicrobial activity of CRISPR antimicrobials across relevant strains and define critical parameters for efficient CRISPR-based targeting.

sample_organism:
Escherichia coli
Klebsiella pneumoniae

platform_organism:
Escherichia coli
Klebsiella pneumoniae

overall_design: A library (11,900 targets and 100 non-targeting guides) was designed to target a non-redundant collection of complete genomes of Klebsiella pneumoniae, by randomly choosing targets with a proper TTTV PAM shared by all the genomes in the collection. The library was prepared in E. coli MG1655, transfered to E. coli MFDpir, and delivered by conjugation to 3 K. pneumoniae strains (NTUH-K2044, KPPR1 and SB5442). Samples were harvested after induction with 1 nM anhydrotetracycline (aTc) at time zero, 3 hours and 16 hours. Finally, plasmids were extracted from 10 mL of these cultures and the donor strain culture. The samples were prepared for amplicon sequencing and sequencing was then performed with Illumina sequencing primers using a NextSeq 500 benchtop sequencer

first: Solange

last: Miele

first: Elena

last: Vialetto

first: Chase

last: Beisel


title: Gene expression profiles in the epithelial cells from the different parts of the colon in mice

summary: We investigated the difference of gene expression profiles in the epithelial cells between the different parts of the colon in C57BL/6J mice.

overall_design: Intestinal epithelial cells from the different parts of the colon in C57BL/6J mice.

first: Ryu

last: Okumura

first: Shota

last: Okamoto

first: Mugen

last: Taniguchi


title: Gene expression profiles in the colonic epithelial cells from mice deficient in the function of St6galnac6, B3galt5 and B3gnt7

summary: To investigate the effect of deficiency of glycosyltransferases on the intestinal epithelial cells, we analyzed the gene expression profiles in colonic epithelial cells of mice deficient in the function of St6galnac6, B3galt5 and B3gnt7.

overall_design: Intestinal epithelial cells from the colon of wild-type, St6galnac6-/-, B3galt5D116A and B3gnt7-/- C57BL/6J mice.

first: Ayaka

last: Nakatani


title: An intersectional genetic cell depletion unravels the unique role of Th1-Treg cells in tumor immunity

status: Public on Jul 13 2023

summary: The immune system comprises various cell types including regulatory T (Treg) cells, and their subsets. Since most of inducible depletion of immune cells for the functional analysis rely on a single protein or gene, it is no longer optimal for the analysis of cell subsets defined by multiple genes. Here we create the Cre- and Flp-double recombinase-dependent intersectional genetic VeDTR mouse system that can selectively label and inducibly deplete a subpopulation of Treg cells called T helper 1 (Th1)-Treg cells. Characterization of Th1-Treg cells using the VeDTR mice revealed the high resistance under oxidative stress, which was required for Th1-Treg cells to accumulate in tumor tissues. Moreover, short-term depletion of Th1-Treg cells only led to anti-tumor immunity but not autoimmunity, whereas that of whole Treg cells did both. Collectively, we have established a novel intersectional genetic immune cell depletion system to reveal unique features of Th1-Treg cells in tumor immunity.

overall_design: To characterize the difference between Th1-Treg cells and non-Th1-Treg cells, we analyzed gene expression pattern of YFP+ CD4+ CD25+ T cells (YFP+ Treg cells) and YFP- CD4+ CD25+ T cells (YFP- Treg cells) in the spleens of Foxp3-Cre/Tbx21-Flp/VeDTR(LF) mice.

first: Masaaki

first: Masahiro

last: Yamamoto


title: Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes

status: Public on Jul 12 2023

city: Saarbrücken

first: Annika

last: Engel

state: Saarland

address: Campus E2 1

department: Center for Bioinformatics

country: Germany

institute: Saarland University

summary: Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound healing support, oral therapies, and anti-tumour treatments. While its applications shown promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus applied non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (5 time points spanning 2 hours), we compared the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, miR-223-3p also exhibited an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single blood cell sequencing revealed the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.

overall_design: Single-cell peripheral blood mononuclear cells: Four C57BL/6 wild-type mice were anaesthetized. The two mice of the treatment group were irradiated with NTP for 10 minutes using anatmospheric pressure argon plasma jet. The other two mice belonging to the control group were equally anaesthetized but remained unexposed to non-thermal plasma. The blood of the four mice was collected after a period of 120 min from the vena cava.

first: Nicole

last: Ludwig

first: Friederike

last: Grandke

first: Viktoria

last: Wagner

first: Fabian

last: Kern

first: Tobias

last: Fehlmann

first: Georges

middle: P

last: Schmartz

first: Ernesto

last: Aparicio-Puerta

first: Barbara

last: Walch-Rückheim

first: Matthias

last: Hannig

first: Stefan

last: Rupf

first: Eckart

last: Meese

middle: W

last: Laschke

first: Andreas

last: Keller


type: Non-coding RNA profiling by high throughput sequencing

summary:
This SuperSeries is composed of the SubSeries listed below.
Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.

overall_design: Refer to individual Series


title: Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation

status: Public on Jul 11 2023

city: Waltham

first: Ajay

last: Larkin

address: 415 South St

department: MCB

institute: Brandeis University

summary: This SuperSeries is composed of the SubSeries listed below.


overall_design: MiRNA sequencing data: 55 C57BL/6 wild-type mice were anaesthetized. The left ear of the 28 mice in the treatment group was irradiated with NTP for 10 minutes using anatmospheric pressure argon plasma jet. The 27 mice of the control group were equally anaesthetized but remained unexposed to non-thermal plasma. Right and left ears of treatment and control mice were collected after 0, 10, 30, 60, and 120 minutes. Analysing was done using the miRNA sequencing data.

first: Dominic

last: Henn


title: UBR5 Forms Ligand-Dependent Complexes on Chromatin to Regulate Nuclear Hormone Receptor Binding [ChIP-Seq]

first: Jared

last: Brown

summary: Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are important therapeutic targets in malignancy. Hormone binding triggers NR activation and their subsequent proteasomal degradation through unknown ligand-dependent ubiquitin ligase machinery. NR degradation is therapeutically relevant: the oncogenic PML-RARA fusion between PML and the retinoic acid receptor (RARA) drives acute promyelocytic leukemia and degradation of PML-RARA induced by all-trans-retinoic acid (ATRA) is required for anti-tumor activity. We identify a Leu-X-X-Leu-Leu (LxxLL) binding motif that associates with a conserved degron in RARA. A high-resolution crystal structure of the RARA ligand binding domain in complex with this LxxLL motif shows how UBR5 binding is mutually exclusive with nuclear co-activator engagement. Our work establishes UBR5-driven NR degradation as an integral regulator of transcriptional signaling by nuclear hormones.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed for RARA and UBR5 in NB4 cells and GR and UBR5 in A549 cells. Control samples for each cell type (DMSO) as well as treatment samples following application of ATRA and DEX in NB4 and A549 cells respectively. Separate preparations of DEX treated A549 cells were sequenced both 15 minutes and 24 hours post-treatment. Samples of the NB4 cell conditions were prepared in biological duplicate. Fractions of each sample were sequenced absent precipitation as matched input datasets.

first: Jonathan

last: Tsai

first: Jacob

last: Aguirre

first: Vivian

last: Focht

first: Yen-Der

last: Li

first: Georg

last: Kempf

first: Lukas

last: Kater

first: Brittany

last: Sandoval

first: Charles

last: Zou

first: Justine

last: Rutter

first: Katherine

last: Donovan

first: Quinlan

last: Sievers

first: Paul

last: Park

first: Jevon

last: Cutler

last: Hatton

first: Elizabeth

last: Ener

first: Micah

last: Sperling

first: Mikolaj

last: Slabicki

first: Peter

last: Miller

first: Roger

last: Belizaire

first: Adam

first: Scott

last: Armstrong

first: Eric

last: Fischer

first: Nicolas

last: Thomä

first: Benjamin

last: Ebert


title: Analysis of transcriptomics and metabolomics reveal glutathione pathway contributed to laccase production of medicinal fungi Cerrena unicolor 87613

status: Public on Jul 10 2023

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

summary: In this project, the transcriptomic data was obtained from the 6-day and 10-day submerged cultures of Cerrena unicolor sp. 87613 under PDA media, respectively. C.unicolor is reported to be an important medicinal fungus as well as an efficient laccase producer. Interestingly, C.unicolor sp.87613 presented a highest laccase production with ~420 U/mL at fermentation day 6, while the laccase production was reduced by ~27% at fermentation day 10. Therefore, these collected data were used to unveil the potential regulatory mechanism of laccase production. Besides, these transcriptomic data also provide essential data source for a better understanding of C.unicolor in various aspects.

overall_design: To investigate the property of C.unicolor 87613 in high-efficiency production of laccase, we collected the submerged cultures from fermentation day 6 and day 10, respectively. We then performed transcription profiling analysis using data obtained from RNA-sequencing of 6 different samples incubated with glucose at two time points as well as 6 samples incubated with fructose.

last: Zhang

first: Ting-Ting

last: Qiu

first: Wu-Wei-Jie

last: Yang


title: CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

overall_design: Uterine-placental interface tissue (also called metrial glands) were used from gd 15.5 (n=3 pregnancies) and 19.5 rat placentation sites (n= 3pregnancies)

first: Ha

last: Vu

first: Regan

last: Scott

first: Geetu

last: Tuteja

first: Michael

last: Soares


title: Wnt5a-YAP signaling axis mediates mechanotransduction in cardiac myocytes and contributes to the transition to heart failure

first: Daisuke

last: Motooka

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation [RNA-seq]

first: Ajay

last: Larkin

summary: Stress can spur the redistribution of histone modifications to establish novel phenotypes. We do not understand how cells leverage existing epigenetic pathways to establish and maintain new gene expression states that enhance fitness and cell survival. H3K9 methylation promotes epigenetic silencing in fission yeast (S. pombe). Heterochromatin establishment depends on the H3K9 methyltransferase, Clr4 and is opposed by two major two heterochromatin regulators, Epe1, a putative H3K9 demethylase and Mst2, an H3K14 acetyltransferase. We designed an inducible system in mst2D cells to toggle Epe1 availability on-demand and trigger heterochromatin misregulation thus initiating an adaptive epigenetic response. Following Epe1 depletion, we mapped transcriptome and H3K9me3 changes as a function of time. Although Epe1 could be removed in ~30 minutes, the population of cells took two orders of magnitude longer to establish an adaptive phenotype. Similarly, re-expressing Epe1 did not switch cells back to their initial state. Instead, cells exhibit unique transcriptional signatures during recovery that encode adaptive memory that is both reversible and tunable.  Our results reveal that the slow kinetics of chromatin state changes enable bet-hedging for cells to identify optimal adaptive solutions while hysteresis within the gene regulatory network encodes cellular memory.

overall_design: Comparative gene expression profiling analysis of RNA-seq data, performed in triplicate, under several genotypic backgrounds. Epe1-deg strains contained a modified, suppressible epe1 gene locus. Epe1 was suppressed and samples were drawn at 24 hour time intervals. Recovery samples had Epe1 returned, following 120 hours of Epe1 depletion. Short recovery was 24 hours +Epe1, medium recovery was 48 hours +Epe1. Other strains were grown in neutral media.

first: Colin

last: Kunze

first: Melissa

last: Seman

first: Alex

last: Levashkevich

first: Justin

last: Curran

first: Dionysus

last: Morris-Evans

first: Sophia

last: Lemieux

first: Ahmad

last: Khalil

first: Kaushik

last: Ragunathan


title: A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

summary: Antisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes bear great potential in the fight against antimicrobial resistance and for precision microbiome editing. The development of such antisense antibiotics has primarily focused on using phosphoramidite morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based therapy in general. Here, we compare seven chemically distinct 10mer-ASOs, all designed to target the same essential acpP mRNA upon delivery with a KFF-peptide carrier into Salmonella, comparing PNA, PMO, phosphorothioate modified-DNA (PTO), 2’-methoxylated RNA (RNA-OMe), 2’-methoxyethylated RNA (RNA-MOE), 2’-fluorinated RNA (RNA-F) and 2’-locked RNA (LNA). Our systematic analysis using a variety of in vitro and in vivo methods to evaluate ASO uptake, target pairing and bacterial killing suggests that only PNA and PMO make it into Salmonella to cause bacterial growth inhibition. However, given their high target binding and translational repression activity in vitro, ASOs based on LNA and RNA-MOE appear to be promising candidates for antisense antibiotics that will require the identification of an efficient carrier.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Salmonella cells after 15 min exposure to several nucleotide mimics fused to the KFF pepide targeting the essential gene acpP. 2 replicates and 10 conditions

first: Chandradhish

last: Ghosh

first: Linda

last: Popella

first: Dhamodharan

last: Venugopalan

first: Lars

last: Barquist

first: Claudia

last: Höbartner

first: Jörg

last: Vogel


title: Analysis of differentially expressed genes after EGFR-TKI treatment

status: Public on Jul 04 2023

city: Nanjing

first: Feng

last: Jiang

state: Jiangsu

address: Baiziting 42

institute: Jiangsu Institute of Cancer Research

overall_design: H1975 cells treated with DMSO or Osi (1000 nM)  for 0, or 72 hours


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [RNA-seq 2]

status: Public on Jul 02 2023

first: Xiaoxu

last: Liu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: The P-TEFb-containing super elongation complex (SEC) plays the essential role in transcriptional elongation control. The AF4/FMR2 family members AFF1 and AFF4 are the central scaffold proteins of SEC, associated with different human diseases. However, their specific roles in transcriptional control remain unclear. Here, we report that AFF1 and AFF4 show distinct genomic distribution patterns around TSS. AFF1 binds upstream of TSS, while AFF4 is enriched downstream of TSS. Pol II occupancies are reduced genome-widely after depletion of AFF1, but not AFF4. Interestingly, in a subset of active genes with broad AFF4 binding signature, AFF4 disruption causes slow elongation and early termination, while AFF1 deletion mirrors the transcriptional defects observed in the fast Pol II mutant. Furthermore, AFF4 knockdown leads to increased AFF1 levels at chromatin, and vice versa. In summary, our data demonstrate that AFF1 and AFF4 function, to some extent, antagonistically to ensure proper Pol II transcription.

overall_design: Expression profiling by high throughput sequencing. RNA-seq was performed in WT ，AFF1 KO and AFF4 KO serum-induced HCT116 cells for two replicates.

first: Chengqi

last: Lin


title: HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation [ChIP-seq]

status: Public on Jul 03 2023

city: ShangHai

first: Jialun

last: Li

address: NO. 500 Dongchuan Road, Minhang distinct

institute: WuHu Hospital, East China Normal University

summary: Lysine succinylation is one of the major post-translational modifications occurred on histones and is believed to have significant roles in regulation of chromatin structure and function. Currently, histone desuccinylation is widely believed to be exerted by the members of SIRT family deacetylases. Here, we report that histone desuccinylation is in fact primarily catalyzed by the class I HDAC1/2/3. Inhibition or depletion of HDAC1/2/3 resulted in marked increase of global histone succinylation, whereas ectopic expression of HDAC1/2/3 but not their deacetylase inactive mutants downregulated global histone succinylation. We demonstrated that the class I HDAC1/2/3 complexes have robust histone desuccinylase activity in vitro. Genomic landscape analysis revealed that histone succinylation is highly enriched at gene promoters and inhibition of HDAC activity results in marked elevation of promoter histone succinylation. Furthermore, integrated analysis revealed that the promoter histone succinylation positively correlates with the transcriptional activity. Collectively, we demonstrate that the class I HDAC1/2/3 but not the SIRT family proteins are the major histone desuccinylases particularly important for promoter histone desuccinylation. Our study thus sheds new light on the role of histone succinylation in transcriptional regulation.

overall_design:
Chromatin immunoprecipitation DNA-sequencing (ChlP-seg) for pan-Ksu and H3K23su as well as the histone modifications H3K27ac,H3K4me3 in both control and TSA treated HeLa cells.All ChIP-seq experiments were carried out with three independent biological samples.

UPDATE: [06-06-2024] The Sample titles and treatments were corrected, and the .bw files were reassociated with the Samples accordingly.

first: Lu

last: Lu

first: Lingling

first: Jiemin

last: Wong


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [ChIP-seq 1]

overall_design: Genome binding/occupancy profiling by high throughput sequencing

first: Chenqi


title: Mapping the dynamics of epigenetic adaptation during heterochromatin misregulation [ChIP-seq]

first: Ajay

last: Larkin

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) for H3K9me3

first: Colin

last: Kunze

first: Melissa

last: Seman

first: Alex

last: Levashkevich

first: Justin

last: Curran

first: Dionysus

last: Morris-Evans

first: Sophia

first: Ahmad


title: Sensitivity of splicing factor mutant hematopoietic cells to GSK-3 inhibition

status: Public on Jun 28 2023

city: Philadelphia

first: Peter

last: Klein

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

summary: Recurrent mutations in the splicing factors SRSF2 and SF3B1 are common in myelodysplasia (MDS) and acute myeloid leukemia (AML). These mutations are invariably heterozygous, as cells with splicing factor mutations nevertheless depend on wild-type splicing activity. Disrupting splicing further is lethal, suggesting a therapeutic vulnerability for splicing factor mutant hematopoietic neoplasms. Glycogen synthase kinase-3 (GSK-3) phosphorylates multiple splicing factors, including SRSF2 and SF3B1, and regulates the splicing of a broad range of mRNAs in human cells. Inhibition of GSK-3 disrupts splicing and promotes cell death in hematopoietic cells with heterozygous mutations in SRSF2 or SF3B1 and not in cells with wild-type splicing factors. To characterize how GSK-3 inhibition alters splicing and leads to cell death in SRSF2P95H/+ and SF3B1K700E/+ cells, we have performed deep RNA sequencing on K562 cells with SRSF2P95H/+ or SF3B1K700E/+ knocked into the endogenous locus (provided by Omar Abdel-Wahab (Wang et al; PMID 30799057) and treated with the GSK-3 inhibitor CHIR99021. Parental cells with wild-type splicing factors were included as controls. RNA-Seq data were further analyzed through the rMATS pipeline to assess changes in mRNA splicing (Liu et al, 2023).

overall_design: To investigate the functional consequences of GSK-3 inhibition on gene expression and splicing, we performed deep RNA-sequencing (RNA-seq) of parental K562 and isogenic SRSF2P95H/+ and SF3B1K700E/+ lines treated with DMSO or GSK-3 inhibitor Chir99021.

first: Xiaolei

first: John

last: Tobias


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [RNA-seq]

first: Xiaoxu

overall_design: Expression profiling by high throughput sequencing. RNA-seq was performed in WT and AFF4 MT serum-induced HCT116 cells for two replicates.

first: Chengqi


title: Functional analysis of Caspase-4 in non-small cell lung cancer cells

status: Public on Jun 21 2023

city: Kitakyushu, Fukuoka

first: Yosuke

last: Chiba

address: 1-1 Iseigaoka, Yahatanishi-ku

institute: University of Occupational and Environmental Health

summary: To clarify the role of Caspase-4 in non-small cell lung cancer cells, Caspase-4 overexpressing and knockout cells in NCI-H292 cells were established and each was analyzed by RNAseq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NCI-H292 cells and its CASP4 overexpressing/CASP4 knockout.

first: Tomomitsu

last: Doi

first: Motoyoshi

last: Endo


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [ChIP-seq 2]


title: HDAC1/2/3 Are Major Histone Desuccinylase Critical for Promoter Desuccinylation

first: Jialun


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation


title: In vitro differentiated CD56-positive ILC transcriptional profiling via scRNA-seq

status: Public on Jun 30 2023

city: LUND

first: Dang

middle: Nghiem

last: Vo

address: B12 Biomedical Center, Klinikgatan 26

department: Department of Laboratory Medicine

country: Sweden

institute: Lund University

summary: The innate cytotoxic Natural Killer (NK) cells emerged during hematopoiesis through a linear model of human NK development, yet how in vitro model of NK differentiation recapitulates in vivo process is largely under-explored. Here, we established that NK cell trajectory in vitro can be divided into 4 stages by sequential acquisition of CD161, CD56 and CD94 in which CD56 bifurcation can separate Stage 3a (CD56-) as ILC-precursor that can further give rise to stage 3b (CD56+) and stage 4 (CD94+). Re-plating results together with clonal tracing between S3b, S4 and ILC3 subsets supported a diverging developmental point between NK and ILC3 lineages occurs at the S3a stage and accompanied by the loss of the ILC3 potential as NK cell maturation progress from S3b toward S4. Single-cell transcriptomic and RNA-velocity connected the NK cytotoxic trajectory with a coordinated network of transcription factors (TFs) that are highly compatible with primary NK cell gene program.

overall_design:
CD56-positive ILC generated from in vitro differentiation culture after 4 weeks, further undegone column-purification for Lineage-postive cells removal. Purifed CD56-positive ILC cells are subjected to transcriptomic profiling via single-cell RNA sequencing with 10X Genomics platform.
-----------------------------
Authors state:
raw FASTQ files cannot be uploaded due to compliance with GDPR guildlines for human samples.

middle: N

first: Ewa

last: Sitnicka


title: Phosphodiesterase 10A inactivation protects against doxorubicin-induced cardiotoxicity and concomitantly inhibits tumor growth

status: Public on Jun 22 2023

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

summary: Phosphodiesterase 10A (PDE10A), by degrading cAMP/cGMP, play critical roles in cardiovascular biology/disease. Cardiotoxicity is a clinical complication of chemotherapy. We aim to determine the role of PDE10A in cancer growth and cardiotoxicity induced by doxorubicin (DOX), a chemotherapy drug. We found that PDE10A deficiency/inhibition alleviated DOX-induced cardiotoxicity in C57Bl/6J mice, including myocardial atrophy, apoptosis, and dysfunction. RNAseq study revealed several PDE10A-regulated signaling associated with DOX-induced cardiotoxicity. In cancer cells, PDE10A inhibition increased the death, decreased the proliferation, and potentiated the effect of DOX in various cancer-cell lines. Importantly, in nude mice with implanted ovarian cancer xenografts, PDE10A inhibition attenuated tumor growth while protected against DOX-induced cardiotoxicity. In isolated cardiomyocytes (CMs), PDE10A contributed to DOX-induced CM death via promoting mitochondrial dysfunction, and to CM atrophy via potentiating foxo3 signaling. Collectively, our study elucidates a novel role for PDE10A in cardiotoxicity and cancer growth in vitro and in vivo, and suggest that PDE10A inhibition may represent a novel strategy in cancer therapy.

overall_design: To identify transcriptomes that are regulated by DOX and PDE10A in mouse hearts, we performed whole genome transcriptome profiling via RNA-seq with heart samples from both PDE10A-WT and PDE10A-KO mice treated with or without DOX. Comparative gene expression profiling analysis of RNA-seq data for hearts from PDE10A-WT/Vehicle (WT/Veh), PDE10A-WT/DOX (WT/DOX), PDE10A-KO/Vehicle (KO/Veh), and PDE10A-KO/DOX (KO/DOX) groups.

first: Si

last: Chen

first: Jiawei

first: Wenting

last: Du

first: Deanne

last: Mickelsen

first: Hangchuan

last: Shi

first: Han

last: Yu

first: Sparsh

last: Kumar

first: Chen

last: Yan


title: Young bone marrows transplantation rejuvenates immune cells, attenuate cerebral Aβ accumulation and related pathologies in Alzheimer’s disease model mouse

status: Public on Jun 27 2023

city: Chongqing

first: Yun-feng

last: Tu

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing

department: Daping Hospital

institute: Third Military Medical University

summary: Immunesenescence contributes to systematic aging and participates in the pathogenesis of Alzheimer’s disease (AD). To define the potential of immune rejuvenation in AD therapy, we reconstituted the immune systems of aged APP/PS1 mice through bone marrow transplantation (BMT). Single cell RNA sequencing (ScRNA-seq) of peripheral blood mononuclear cells (PBMCs) indicated that young BMT reverse the expression of aging- and AD-related genes in multiple cell types of PBMCs. Plasma proteome profiling also indicated the reduction of the plasma level of senescence-associated secretory phenotype (SASP) proteins after young BMT. Young BMT significantly reduced central and peripheral Aβ levels, alleviated brain Aβ plaque burden, neuronal degeneration, neuroinflammation, and behavioral deficits in the aged APP/PS1 mice. These effects occurred with the improved Aβ capacity of peripheral monocytes. Collectively, our study demonstrated that rejuvenation of immune system could decrease brain Aβ deposition and other AD-type pathologies, representing a potential therapeutic approach for AD.

overall_design: In order to rejuvenate the peripheral immune system, we established a model of heterochronic BMT. Old (9-month) recipient APP/PS1 mice (YTg BMCs group) were irradiated (with head-shielding) prior to injection of donor bone marrow cells from young (2-month) donor APP/PS1 mice. The mice were feeded for 3 an additional months. To investigate the cellular mechanisms by which young BMT contributes to immune rejuvenation, we isolated and compared, at single cell resolution, the PBMCs from YTg BMCs APP/PS1 mice, with corresponding cells from the young (2-month, control YTg) and old (12-month, control OTg) APP/PS1 mice without BMT.

first: Pu-Yang

last: Sun

first: Jie

last: Liu

first: Yun-Feng

first: Yan-Jiang

last: Wang


title: Simultaneous Profiling of Chromatin-Associated RNA at Targeted DNA Loci and RNA-RNA Interactions through TaDRIM-Seq

status: Public on Jun 08 2023

city: Wuhan

first: guoting

last: chen

address: 1 Shizishan Street, Hongshan District

institute: National Key Laboratory of Crop Genetic Improvement

summary: The enormous variety of different RNAs are transcribed from eukaryotic genome. Some RNAs, particular long non-coding RNAs (lncRNAs),  enrich on chromatin via transcribed RNAs to retain at their transcription site (Cis-acting RNAs) and recruited to different genomic regions (Trans-acting RNAs), which play significant roles in regulating gene transcription, epigenomic modifications and mediating chromatin states. Here, we developed TaDRIM-Seq (Targeted DNA-associated RNA and RNA-RNA Interactions Mapping by Sequencing) method to capture RNA-DNA  on specific protein region and RNA-RNA spatial interactions in nuclei. We performed TaDRIM-Seq of antibodies H3, H3K9ac and H3K27me3 in rice and H3K4me3 and CTCF in human K562 cells, to identify chromatin-interacting RNAs and RNA-RNA interactions.

sample_organism:
Homo sapiens
Oryza sativa Indica Group

platform_organism:
Homo sapiens
Oryza sativa Indica Group

overall_design: We report TaDRIM-Seq technique PG-Tn5-mediated targeted DNA element and proximity ligation to simultaneously detect chromatin-associated RNAs in diverse regions of the genome and RNA-RNA spatial interactions in nuclei.

first: Cheng

last: Ding

first: Guoting


title: Nucleosomal DNA has topological memory

status: Public on Jun 05 2023

city: Barcelona

first: Joaquim

last: Roca

address: Baldiri Reixach 4-15

department: IBMB

country: Spain

institute: CSIC

summary: One elusive aspect of the chromosome architecture is how it constrains the DNA topology. Nucleosomes stabilise negative DNA supercoils by restraining a DNA linking number difference (∆Lk) of about -1.26. However, whether this capacity is uniform across the genome is unknown. Here, we calculated the ∆Lk restrained by over 4000 nucleosomes in yeast cells. To achieve this, we placed each nucleosome in a circular minichromosome and performed Topo-seq, a high-throughput procedure to inspect the topology of circular DNA libraries in one gel electrophoresis. We found that nucleosomes inherently restrain distinct ∆Lk values depending on their genomic origin. Nucleosome DNA topologies differ at gene bodies (∆Lk=-1.29), intergenic regions (∆Lk=-1.23), rDNA genes (∆Lk=-1.24) and telomeric regions (∆Lk=-1.07). Nucleosomes near the transcription start and termination sites also exhibit singular DNA topologies. Our findings demonstrate that nucleosome DNA topology is imprinted by its native chromatin context and persists when the nucleosome is relocated.

overall_design:
A library of 4000 nucleosomes (NucLib) hosted in circular minichromosomes was inspected using Topo-seq. Nucleosomal DNAs were eluted from two gel sections (Topo-seq-A, Topo-seq-B) and sequenced to calculate the ∆Lk restrained by each nucleosome.

Each sample (NucLib, Topo-seq-A, Topo-seq-B) has been sequenced twice (replicate 1 & 2) and the number of reads of each sample combined into a unique dataset for the analyses.

first: Joana

last: Segura

first: Ofelia

last: Díaz-Ingelmo

first: Belen

last: Martínez-García

first: Alba

last: Ayats-Fraile

first: Christoforos

last: Nikolaou


title: IL22RA2 is a Smad7 target mediating alleviation of dermatitis and psoriatic phenotypes in mice

status: Public on Jun 12 2023

city: Aurora

first: Ben-Zheng

last: Li

state: CO

department: Department of Physiology and Biophysics

institute: University of Colorado Anschutz Medical Campus

summary: Long-term management of inflammatory skin diseases is challenging because of side effects from repeated use of systemic treatments or topical corticosteroids. This study sought to identify novel mechanisms and developmental therapeutics for these diseases using genetic models and pharmacological approaches. We found mice overexpressing Smad7 in keratinocytes, but not mice overexpressing the N-terminal domain of Smad7 (N-Smad7), were resistant to imiquimod (IMQ)-induced Th1/17 and Th2 type inflammation. We generated a truncated Smad7 protein encompassing C-terminal Smad7 and PY motif fused with cell-penetrating Tat peptide (Tat-PYC-Smad7). Topically applied Tat-PYC-Smad7 to inflamed skin entered cells upon contact and attenuated IMQ-, 2,4-dinitrofluorobenzene-induced atopic dermatitis (AD) and tape-stripping inflammation (TS). RNAseq analyses of mouse skin exposed to these insults identified that in addition to inhibiting TGFβ/NFκB, Smad7 blunted IL22/STAT3 activation and associated pathogenesis, which is due to Smad7 transcriptionally upregulating IL22 antagonist IL22RA2. Mechanistically, Smad7 facilitated nuclear translocation and DNA binding of C/EBPβ to IL22RA2 promoter for IL22RA2 transactivation. Consistent to the above observations in mice, transcript levels of IL22RA2 were increased in human atopic dermatitis and psoriasis lesions with clinical remission. Our study identified the anti-inflammation functional domain of Smad7 and suggests mechanism and feasibility for developing Smad7-based biologics as a topical therapy for skin inflammatory disorders.

overall_design: Comparative gene expression profiling analysis using data obtained from RNA-seq data for K5.Smad7 transgenic and wildtype dorsal IMQ skin on day 6, and Tat-PYC-Smad7 and vehicle-treated  IMQ, AD and TS dorsal skin on day 6.

first: Yao

last: Ke

first: Khoa

last: Nguyen

first: Donna

first: Suyan

first: Christian

last: Young

first: Xiao-Jing


title: Tripartite motif 8 promotes hepatocellular carcinogenesis by mediating ubiquitination and degradation of hepatocyte nuclear factor 1α

status: Public on Jul 08 2023

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

summary: To explore the underlying mechanism of TRIM8 in HCC, a RNA sequencing was conducted to obtain the differentially expressed genes (DEGs) between TRIM8-KO and WT HepG2 cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TRIM8-knockout and wild-type HepG2 cells

first: Yu

last: Peng

first: Hui

last: Qian

first: Wenping

last: Xu


title: Alcohol-Induced Alterations in Sperm Noncoding RNAs Persist After One Month Cessation and Correlate with Indicators of Epididymal Mitochondrial Dysfunction I

status: Public on Jun 13 2023

city: College Station

first: Michael

last: Golding

state: Texas

address: Veterinary Research Building, Bldg 1197, Rm 334, 588 Raymond Stotzer Pkwy

department: Veterinary Physiology & Pharmacology

institute: Texas A&M University

summary:
Background
Chronic preconception paternal alcohol use modifies the sperm epigenome, inducing fetoplacental growth defects in the offspring of exposed males. A crucial outstanding question in the field of paternal epigenetic inheritance concerns the resilience of the male reproductive tract and the germline's capacity to recover and correct sperm-inherited epigenetic errors after stressor withdrawal.
Objectives
We set out to determine if measures of the sperm-inherited epigenetic program revert to match the control treatment one month after withdrawing daily alcohol treatments.
Materials and Methods
Using a voluntary access model, we exposed C57Bl6/J males to 10% alcohol for ten weeks, withdrew alcohol treatment for four weeks, and used RNA sequencing to examine gene expression patterns in the caput section of the epididymis. We then compared the abundance of sperm small RNA species between treatments.
Results
In the caput section of the epididymis, chronic alcohol exposures induced changes in the transcriptional control of genetic pathways related to mitochondrial function, oxidative phosphorylation, the generalized stress response (EIF2 signaling), and Sirtuin signaling. Subsequent analysis identified region-specific, alcohol-induced changes in mitochondrial DNA copy number across the epididymis, which correlated with increases in the mitochondrial DNA content of alcohol-exposed sperm. Notably, in the corpus section of the epididymis, increases in mitochondrial DNA copy number persisted one month after alcohol cessation. Analysis of sperm noncoding RNAs between Control and Alcohol-Exposed males one month after alcohol withdrawal revealed a ~100-fold increase in mir-196a, a microRNA induced as part of the Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2)-driven cellular antioxidant response.
Discussion and Conclusion
Our data reveal that alcohol-induced epididymal mitochondrial dysfunction and differences in sperm noncoding RNA content persist after alcohol withdrawal. Further, differences in mir-196a and sperm mitochondrial DNA copy number may serve as viable biomarkers of adverse alterations in the sperm-inherited epigenetic program.

overall_design: RNA seq on EtOH treated and EtOH ceased isolated caput portions of the epididymis

first: Alexis

last: Roach

first: Sanat

last: Bahdsalve

first: Sam

last: Higgins

first: Destani

last: Derrico

first: Kara

last: Thomas

first: Ali

last: Basel


title: RNA-sequencing analysis of SD rat abdominal wall treated with adhesive or non-adhesive implant

status: Public on Jun 01 2023

city: Cambridge

first: Hyunwoo

last: Yuk

email: hyunwoo@mit.edu, hyunwooyuk@gmail.com

address: 77 Massachusetts Ave.

institute: MIT

summary: We utilize bulk RNA-seq to profile the mRNA expression in day 3 and day 14 post-implantation of SD rat abdminal wall treated with adhesive or non-adhesive implants

overall_design: Adhesive or non-adhesive implant was implanted to the abdominal wall of SD rat. The tissue was collected on day 3 or day 17 post-implntation for downstream analyses. mRNA profile from abdominal wall treated with adhesive implant (n=4) and non-adhesive implant (n=4) were examined for each time points (day 3 and day 14 post-implantation).

first: Jingjing

last: Wu

first: Georgios

last: Theocharidis


title: Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation [ChiP-seq 3]

first: Xiaoxu

last: Liu

overall_design: Genome binding/occupancy profiling by high throughput sequencing. CSTF2 ChIP-seq in WT,  AFF4 MT and AFF4 KO serum-induced HCT116 cells.

first: Chengqi

last: Lin


title: Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas

city: Houston

first: Jeffrey

middle: Andrew

last: How

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

institute: The University of Texas MD Anderson Cancer Center

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Comprehensive analysis of cellular senescence in the central nervous system revealed microglial senescence and its involvement in demyelinating diseases

status: Public on May 25 2023

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Cellular senescence is a state of irreversible cell-cycle arrest caused by various cellular stressors. Accumulating evidence indicates that cellular senescence is one of the key factors causing age-related tissue dysfunction in various organs. However, the features of cells that undergo cellular senescence and their significance in neural impairment are still unclear in the central nervous system. We showed that microglia, particularly in the white matter, undergo cellular senescence in the brain and spinal cord during ageing and in disease models involving demyelination through comprehensive investigations utilizing single-cell transcriptome analysis and various mouse models. Microglial senescence is predominantly detected in disease-associated microglia (DAM), which emerge with ageing and in neurodegenerative diseases. Knockouts of the p16INK4a gene, a key inducer of cellular senescence, ameliorated the neuroinflammatory phenotype in damaged spinal cords in mice. Finally, we showed that commensal bacteria promote the accumulation of senescent microglia and DAM associated with ageing. These results advanced our understanding of cellular senescence’s role in the central nervous system and opened new strategies for treating age-related neural disorders.

overall_design: Young and old GF and SPF mice (young GF, 2 months, N = 2; young SPF, 2 months, N   = 2; old GF, 22 months, N = 2; old SPF, 22 months) were anaesthetized by intraperitoneal injection of three anaesthetic agents and heparin and transcardially perfused with ice-cold HBSS containing heparin. The brains were cut in sagittal midlines and the cerebral hemispheres were roughly minced by scissors, followed by digestion according to the standard protocol of Neural tissue dissociation kits (P). The brain homogenate was filtered through a 70 µm cell strainer, and cell debris was removed by centrifugation according to the standard protocol of Debris Removal Solution. The cells in HBSS with 1% BSA were then treated on ice with CD16/32 FcR-blocking reagent for 10 minutes, followed by 15 minutes of staining with fluorescence-conjugated antibodies. The following antibodies were used (all antibodies were purchased from BioLegend): Fluorescein isothiocyanate (FITC)-conjugated anti-Cd45 (cat#: 103108) and allophycocyanin (APC)-conjugated anti-Cd11b (cat#: 101212). Before sorting, cells were filtered through a 40 µm cell strainer and stained with propidium iodide (PI). PI-negative, Cd45-low, and Cd11b-positive cells were sorted into 1.5 ml Protein LoBind Tubes containing 1% BSA in HBSS and then centrifuged. After removal of the supernatant, the remaining pellet was lysed and total RNA was isolated according to the standard protocol of the RNeasy Micro Kit. Full-length cDNA was prepared using a SMART-Seq HT Kit (Takara Bio, Japan) according to the manufacturer's instructions. According to the SMARTer kit instructions, an Illumina library was then prepared using a NexteraXT DNA Library Preparation Kit (Illumina). An Illumina NovaSeq 6000 sequencer (Illumina) were used for DNA Sequencing. Generated reads were mapped to the mouse (mm10) reference genome using TopHat v2.1.1. Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1.

first: Tatsuyuki

last: Matsudaira

first: Sosuke

last: Nakano

first: Eiji

last: Hara


title: Single-cell transcriptomics of human cholesteatoma identifies an activin A-producing osteoclastogenic fibroblast subset inducing bone destruction

status: Public on May 29 2023

summary: To elucidate the mechanism underlying bone erosion in cholesteatoma, we performed scRNA-seq using human cholesteatoma tissues surgically resected from patients. We focused on pathogenic fibroblasts or keratinocytes, and therefore CD45-negative cells were collected for scRNA-seq analysis to exclude hematopoietic cell lineages. As there are no “normal” tissues in the middle ear that correspond to cholesteatoma, retroauricular skin at the incision site was used as the control for analysis of cholesteatoma. We dentified a characteristic pathogenic fibroblast subset with abundant expression of inhibin βA.

overall_design: Expression profiling by high throughput sequencing

first: K

last: Shimizu

first: D

last: Okuzaki

first: J

last: Kikuta


title: Spatial transcriptomics of de novo NEPC and ARPC

status: Public on May 17 2023

summary: We analyze and report the differences in gene expression between de novo NEPC and ARPC using spatial gene expression analysis techniques (Visium CytAssist, 10x genomics).

overall_design: Formalin-fixed, paraffin-embedded (FFPE) samples of resected prostate specimen

first: Ryuta

last: Watanabe

first: Noriyoshi

last: Miura

first: Mie

last: Kurata

first: Riko

last: Kitazawa

first: Tadahiko

last: Kikugawa

first: Takashi

last: Saika


title: Tissue-intrinsic beta-catenin signals antagonize Nodal-driven anterior visceral endoderm differentiation

status: Public on May 19 2023

city: Leiden

first: Christian

last: Schröter

state: Zuid-Holland

address: Einsteinweg 55

department: Cell Systems and Drug Safety

country: Netherlands

institute: Leiden University, Leiden Academic Centre for Drug Research

summary: The anterior-posterior axis of the mammalian embryo is laid down by the anterior visceral endoderm (AVE), an extraembryonic signaling center that is specified within the visceral endoderm. Current models posit that AVE differentiation is promoted globally by epiblast-derived Nodal signals, and spatially restricted by a BMP gradient established by the extraembryonic ectoderm. Here, we report spatially restricted AVE differentiation in bilayered embryo-like aggregates made from mouse embryonic stem cells that lack an extraembryonic ectoderm. Notably, clusters of AVE cells also form in pure visceral endoderm cultures upon activation of Nodal signaling, indicating that tissue-intrinsic factors can restrict AVE differentiation. We identify β-catenin activity as a tissue-intrinsic factor that antagonizes AVE-inducing Nodal signals. Together, our results show how an AVE-like population can arise through interactions between epiblast and visceral endoderm alone. This mechanism may be a flexible solution for axis patterning in a wide range of embryo geometries, and provide robustness to axis patterning when coupled with signal gradients.

overall_design: We performed single cell RNA sequencing on cells obtained from three types of multicellular aggregates: bilayered embryo-like aggregates (BELAs), VE cysts and Epi cysts.

first: Sina

last: Schumacher

first: Max

last: Fernkorn

first: Michelle

last: Marten


title: Mi-2β knockout enhanced response of B16F10 cells to IFN-γ

status: Public on May 23 2023

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Mi-2β-knockout and non-target control B16F10 cell lines were created using a clustered regular interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. Total RNA was extracted from Mi-2β knockout and control B16F10 cells, which were treated with IFN-γ (10ng/mL) for 24 hours, for microarray assay. The experimental group cells were cultured in triplicate. The experiment was comprised of 6 Mouse Gene 2.0 ST arrays.

overall_design: Mi-2β-knockout and non-target control B16F10 cell lines were cultured in triplicates.

first: Bo

last: Zhu

first: Rutao

last: Cui


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [scRNA-seq PDX MLL-7]

status: Public on May 14 2023

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: This study characterized the effect of WEE1 kinase inhibition using AZD1775 treatment on single-cell gene expression profile using the 10x Genomics protocol in the acute lymphoblastic leukemia cells

overall_design:
scRNA-seq samples were generated from NSG mice transplanted with PDX MLL-7 treated for 24 hours (2 doses) with 120 mg/kg AZD1775 (HY-10993). 4 hours after the last dose mice were sacrificed and bone marrow cells were viably frozen. Before the library preparation, freshly thaw alive hCD45pos hCD19pos mCD45neg bone marrow cells were sorted and proceeded to 10x library protocol. For combination treatments, animals were treated with 6 days of AZD1775 (MedChemExpress) at 120mg/kg alone or with Dasatinib for 3 days (MedChemExpress) at 50 mg/kg. Vehicle animals received 6 days of 5% DMSO, 40% PEG 300, 5% Tween 80 and 50% NaCl solution (all from Sigma-Aldrich). Animals were sacrificed by cervical dislocation 20 hours after the last treatment. Using fresh bone marrow cells from day 6 sequentially treated samples, the cells were FACS sorted like the shorter time point and then proceeded to the 10x library protocol.

***RAW data not provided due to patient privacy concerns***

first: Mari

last: Lahnalampi

first: Ton

last: Falques-Costa

first: Alena

last: Malyukova

first: Anna

last: Hagström

first: Olle

last: Sangfelt


title: Therapeutic targeting of metabolic vulnerabilities in cancers with MLL3/4-COMPASS epigenetic regulator mutations

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Epigenetic alterations due to abnormalities in the enzymatic machineries modifying chromatin, are frequently reported in developmental diseases and in a variety of human cancers. However, the cellular dependency and functional outcome of epigenetic alterations during these processes have not been fully elucidated.  In this study, we depleted two of the most frequently mutated epigenetic factors, the MLL3 and MLL4 components of the COMPASS family, in mouse embryonic stem cells (mESCs) to investigate the cellular vulnerabilities when enhancer functions are compromised as the result of MLL3-4/COMPASS loss.  CRISPR dropout screens revealed synthetic lethality of purine and pyrimidine nucleotide synthesis pathway suppression in cells with MLL3/4 loss. We observed a metabolic usage shift towards purine synthesis in Mll3/4 knockout mESCs. Subsequently, Mll3/4 KO cells exhibited enhanced sensitivity to purine synthesis inhibitor lometrexol, which induced unique gene expression signature changes in Mll3/4 KO cells. A tandem mass tag (TMT) proteomics profiling further identified upregulation of purine metabolism factors in Mll3/4KO cells. We also identified the top MLL3/4 target genes coinciding with suppression of the purine metabolism pathway. Finally, in vivo cancer studies show that tumors mutated for MLL3 and/or MLL4 are very sensitive to purine synthesis inhibitor lometrexol in culture and in animal models of cancer. Taken together, we depict a metabolic dependency map for cells deficient for epigenetic factors and provide insights into cancer treatments related to epigenetic alterations corresponding with MLL3/4 COMPASS malfunction.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We depleted two of the most frequently mutated epigenetic factors, the MLL3 and MLL4 components of the COMPASS family, in mouse embryonic stem cells (mESCs) to investigate the cellular vulnerabilities when enhancer functions are compromised as the result of MLL3-4/COMPASS loss.

first: Zibo

last: Zhao


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [GROseq]

summary: Nascent transcription and enhancer activity was studied using GRO-seq in the acute lymphoblastic leukemia cell line RS4;11 upon inhibition of the WEE1 kinase.

overall_design: GRO-seq profiles were generated from RS4;11 cell line after 4, 10 and 24 h WEE1 inhibition by AZD1775. DMSO treated cells were used as controls.


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [scMultiome]

summary: This study characterized the effect of WEE1 kinase inhibition using AZD1775 treatment on single-cell accessible chromatin and gene expression profile using the 10x Genomics multiome protocol (ATAC + Gene Expression Assay) in the acute lymphoblastic leukemia cell line RS4;11 that represents the KMT2A-rearranged subtype.

overall_design: scMultiome-seq samples were generated from cells treated for 10 h with AZD1775(Wee1i) or vehicle (DMSO) using the 10x Genomics Chromium platform and protocols generating scRNA-seq and scATAC-seq from the same cells.


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [scRNA-seq]

summary: This study characterized the effect of WEE1 kinase inhibition using AZD1775 treatment on single-cell gene expression profile using the 10x Genomics protocol in the acute lymphoblastic leukemia cell lines RS4;11 (KMT2A-rearranged subtype) and Nalm6 (other subtype).

overall_design: scRNA-seq samples were generated from 24 h after AZD1775 using the 10X Genomics Chromium platform and protocols. DMSO treated cells were used as controls. Parallel cell cultures from RS4;11 cells were processed for scATAC-seq.


title: Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [ATAC-seq]

status: Public on May 11 2023

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

summary: The precisely orchestrated differentiation of chondrocytes during skeleton development is a critical determinant of human height and body shape. Disruptions of this process can cause severe skeletal abnormalities. The ultimate size and shape of each of over 200 bones depends on the intricate spatiotemporal regulation of chondrogenic and chondrocyte differentiation genes, but the genomic architecture coordinating these events remains poorly defined. Here we provide a comprehensive map of transcriptional enhancers specifically active in chondrocytes and show that they provide a mechanistic framework through which noncoding genetic variants can influence human stature. We isolated limb and trunk fetal chondrocytes from mice with a Col2a1 fluorescent regulatory sensor and used RNA-seq to identify 780 genes that are specifically expressed during chondrogenesis. To create cell type-specific enhancer maps, we performed ATAC-seq to map open chromatin regions and ChIP-seq for H3K27ac, an enhancer-associated histone modification, and identified 2'704 putative chondrogenic enhancer regions. Most of these enhancers (74%) showed pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. We found that chondrogenic enhancers are enriched for the binding of several chondrogenic transcription factors including SOX9. Moreover, we find that genetic variation overlapping chondrogenic enhancers explains a higher fraction of the heritability of human adult height than the one overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci each exhibited a significant reduction of cognate gene expression, therefore demonstrating their functional importance. This data provides a comprehensive mapping of the chondrogenic enhancer repertoire, paving the way to interpreting the role of non-coding sequence polymorphisms in phenotypic variation and bone diseases.

overall_design: We devised a Col2a1 fluroescent reporter approach to sort chondrocytes from embryonic trunk and limbs. We validate the specfici of the reproter using scRNAseq. We then analyse Col2a1-GFP positive and negative cells to profile their transcriptome, open chromatin and H3K27ac coverage to define enahncers and asssooicated genes.

first: Fabrice

last: Darbellay


title: Investigation of SARS-CoV-2 variants that escape from cellular immunity in the absence of humoral immunity

status: Public on May 12 2023

first: Daisuke

last: Motooka

state: Osaka

summary: X-linked agammaglobulinemia (XLA) is a primary immunodeficiency causing a lack of immunoglobulin production. A COVID-19 patient with XLA showed persistent infection for more than 239 days, representing the longest duration yet reported, in whom SARS-CoV-2 evolved increased proliferative capacity. We identify a mutation of SARS-CoV-2 that is responsible for the immune escape from the cellular immunity of this patient, as well as the TCR that could recognize the wild type antigen but not the correspoinding mutant antigen.

overall_design: We stimulated the PBMC from the donor with SARS-CoV-2 peptides that cover the mutation identified from the patient for 12 days, sorted the T cells and analyzed the cells by single-cell TCR and RNA sequencing. We reconstituted a highly expanded TCR into a reporter cell line, and identified its epitope.

first: Xiuyuan

last: Lu

first: Yu-chen

last: Liu

last: Okuzaki

first: Sho

last: Yamasaki


title: Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [ChIP-seq]


title: Chloroplast nucleoid is organized by membrane association of transcribed genes [ATAC]

status: Public on May 10 2023

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

summary: Chloroplasts are organelles responsible for photosynthesis. They originated form a procaryotic ancestor in the process of endosymbiosis and contain their own genomes. The chloroplast genome is packaged into a chromatin-like structure known as the nucleoid. The internal arrangement of the nucleoid, molecular mechanisms of DNA packaging and connection of the nucleoid structure to gene expression remain poorly understood. We show that Arabidopsis thaliana chloroplast nucleoids have a unique organization driven by DNA binding to the thylakoid membranes. Membrane association of specific DNA regions is correlated with high levels of transcription, high protein occupancy and reduced DNA accessibility. Genes with low levels of transcription are further away from the membranes, have lower protein occupancy and higher DNA accessibility. Gene-specific disruption of transcription in sigma factor mutants causes a corresponding reduction in membrane association, indicating that RNA polymerase activity causes DNA tethering to the membranes. We propose that transcription organizes the chloroplast nucleoid into a transcriptionally active membrane-associated core and a less active Periphery.

overall_design: The data consists of 11 replicates of ptATAC-seq on nucleoids and naked plastid DNA.

first: V

first: Andrzej

last: Wierzbicki


title: Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [scRNA-seq]


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia

first: Merja

last: Heinäniemi


title: Pre-Hypertrophic Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development [RNA-seq]


title: Targeted suppression of siRNA biogenesis in Arabidopsis pollen [RNA-seq]

status: Public on May 07 2023

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

institute: Institut Jean-Pierre Bourgin - INRAE

summary: We used the RNaseIII-like protein RTL1 to suppress siRNA biogenesis specifically in Arabidopsis pollen, and found distinct siRNA subsets produced in the sperm and vegetative cell lineages via the RNA polymerase IV (Pol IV).

overall_design: RNA sequencing of Arabidopsis pollen


title: Targeted suppression of siRNA biogenesis in Arabidopsis pollen [bisulfite-seq]

type: Methylation profiling by high throughput sequencing

overall_design: Whole-genome bisulfite sequencing of Arabidopsis pollen


title: Targeted suppression of siRNA biogenesis in Arabidopsis pollen


title: CpG island turnover is associated with evolutionary changes in enhancer activity

city: New Haven

first: James

middle: P.

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale University

summary: Changes in the activity of transcriptional enhancers have been shown to influence phenotypic variation across species. However, it remains challenging to identify the sequence features associated with species differences in enhancer activity. Here we assessed the contribution of orphan CpG islands (oCGIs), which are regions enriched in CpG dinucleotides that are known to recruit chromatin modifiers and components of the transcriptional machinery. We integrated oCGIs in nine mammals with previously ascertained maps of chromatin modifications across multiple tissues, and found that species-specific oCGIs significantly co-localize with species-specific histone modification peaks. We focused on one enhancer of interest (hs754) which contains an oCGI in human but not in mouse, and overlaps an H3K27ac peak in the developing human brain, but not in mouse. We generated a humanized mouse model and profiled the locus using ChIP-seq, finding increased deposition of the histone modifications H3K27ac and H3K4me3 and gained CTCF binding sites in the humanized enhancer. ChIP-seq data for H3K27me3 was also generated and was not included in the final study, but is deposited here. We also measured gene expression in the humanized mouse and did not find any changes associated with the humanized enhancer, although using the datasets described above we found that genes near enhancers with species-specific oCGIs and species-specific activity show a species bias in expression. This work identifies oCGI turnover as a mechanism affecting mammalian enhancer evolution.

overall_design: ChIP-seq (H3K27ac, H3K4me3, H3K27me3, and CTCF) and RNA-seq were performed using developing diencephalon tissue (E11.5 and E17.5) from wild type and hs754-humanized mouse lines. The number of replicates for each genotype are as follows: 3 replicates for E17.5 ChIP-seq; 2 replicates for E11.5 ChIP-seq; 4 replicates for E11.5 and E17.5 RNA-seq.

first: A

last: Kocher

first: J


title: Chloroplast nucleoid is organized by membrane association of transcribed genes [ChIP]

overall_design: The data consists of 3 replicates of ptChIP of RpoB protein in Arabidopsis thaliana Col-0 wild type, during light and darkness.


title: BoDV-1 infection during neuronal differentiation

status: Public on May 03 2023

summary: Borna disease virus (BoDV-1) is a highly neurotropic RNA virus, which causes neurobehavioral disturbances such as abnormal social activities and memory impairment. In this study, we investigated the effects of BoDV-1 infection on neuronal differentiation and transcriptome of differentiated neuronal cells using persistently BoDV-1-infected SH-SY5Y (SB) cells. Differentiated neuronal cells exhibited transcriptomic changes of genes related to neurite outgrowth and antiviral immune system.

overall_design: SH-SY5Y (SHSY) and BoDV-1-infected SH-SY5Y (SB) cells were treated with 10 µM retinoic acid (RA) for 2 days. Total RNA was isolated from the cells and subjected to RNA-seq analysis.

first: Tomoyuki

last: Honda

first: Teng

last: Da


title: Lupus autoantibodies initiate a maladaptive homeostasis sustained by HMGB1:RAGE signaling and reversed by LAIR-1:C1q signaling

status: Public on May 01 2023

first: Joshua

last: Levin

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

summary: Cognitive impairment is a frequent manifestation of neuropsychiatric systemic lupus erythematosus (NPSLE), present in up to 80% of patients and leading to a diminished quality of life.  We have developed a model of lupus-like cognitive impairment which is initiated when anti-DNA, anti-N-methyl D-aspartate receptor (NMDAR) cross- reactive antibodies, which are present in 30% of SLE patients, penetrate the hippocampus.  This leads to immediate, self-limited excitotoxic death of CA1 pyramidal neurons followed by loss of dendritic arborization in the remaining CA1 pyramidal neurons and impaired spatial memory.  Both microglia and C1q are required for dendritic loss.  Here we show that this pattern of hippocampal injury creates a maladaptive homeostasis that is sustained for at least one year.  It requires HMGB1 secretion by neurons to bind RAGE, a receptor for HMGB1 expressed on microglia, and leads to decreased expression of microglial LAIR-1, an inhibitory receptor for C1q.  The angiotensin converting enzyme (ACE) inhibitor captopril, which can restore a healthy homeostasis, microglial quiescence, and intact spatial memory, leads to upregulation of LAIR-1. This paradigm highlights HMGB1:RAGE and C1q:LAIR-1 interactions as pivotal pathways in the microglial–neuronal interplay that defines a physiologic versus a maladaptive homeostasis.

overall_design: Microglia of NPSLE-like (DNRAb+), control (DNRAb-), and captopril-treated NPSLE-like (DNRAb+ with Captopril) mice were isolated from the hippocampus by fluorescence-activated cell sorting (FACS) according to CD45 and CD11b signal and analyzed using scRNAseq.

first: Kaitlin

last: Carroll

first: Mark

last: Mizrachi

first: Sean

last: Simmons

first: Jeffrey

last: Wingard

first: Bahtiyar

last: Toz

first: Nazila

last: Tehrani

first: Aida

last: Zarfeshani

first: Nina

last: Kello

first: Czeslawa

last: Kowal

first: Bruce

last: Volpe

first: Betty

last: Diamond


title: Targeted suppression of siRNA biogenesis in Arabidopsis pollen [small RNA-seq]

first: Filipe

last: Borges

overall_design: Small RNA sequencing of Arabidopsis pollen


title: MRC5_miRs-treatment_NC-miR_vs_miRs

status: Public on Apr 26 2023

first: Daisuke

last: Motooka

summary: Six different miRs were administered to MRC5, and samples with miRs or parent were compared.

overall_design: MiRs transfection to MRC5

first: Hirofumi

last: Yamamoto


title: c-MAF_KO_vs_WT_AOM_DSS

summary: Chemical carcinogenesis experiments were performed on MAF knockout and wild-type mice by administering AOM/DSS.

overall_design: Chemical carcinogenesis experiments


title: Mechanistic study of Wee1 kinase inhibition with AZD1775 exposes drug targetable vulnerabilities in acute B-lymphoblastic leukemia [scATAC-seq]

first: Merja

last: Heinäniemi

summary: This study characterized the effect of WEE1 kinase inhibition using AZD1775 treatment on single-cell accessible chromatin and gene expression profile in the acute lymphoblastic leukemia cell line RS4;11 that represents the KMT2A-rearranged subtype.

overall_design: scATAC-seq samples were generated from 24 h after AZD1775 (Wee1i) using the 10x Genomics Chromium platform and protocols. DMSO treated cells were used as controls. Parallel cell cultures were processed for scRNA-seq.

first: Mari

last: Lahnalampi

first: Alena

last: Malyukova

first: Olle

last: Sangfelt


title: Antitumor Activity of Galaxamide Involved in Cell Apoptosis and Stemness by Inhibiting Wnt/β-catenin Pathway in Cervical Cancer.

status: Public on Apr 03 2023

city: Guangzhou

first: Yang

last: Guang

state: Guangdong

address: No. 601 West Huangpu Avenue, Tianhe District

institute: Jinan University

summary: Background and Purpose: Our previous work reported that galaxamide, a cyclopeptide extracted from the seaweed Galaxaura filamentosa, showed antiproliferative activity against HeLa cells by MTT assay. However, the therapeutic effects in vivo and potential mechanisms to eliminate cervical cancer cells remain unknown.  Experimental Approach: HeLa cells were obtained as a cervical carcinoma in vitro model. The growth-inhibitory effects of galaxamide in HeLa cells and xenograft mouse models were investigated. RNA-seq was employed to analyse the main target of galaxamide in HeLa cells. Immunostaining, qRT‒PCR and Western blotting were applied to test the pharmacological effects in vitro and in vivo.  Key Results: Galaxamide significantly inhibited cell growth, colony formation, migration, and invasion and induced cell apoptosis by inhibiting the Wnt signalling pathway in HeLa cells. RNA sequencing revealed that galaxamide regulated stemness via the Wnt6 signalling pathway in HeLa cells. By analysing The Cancer Genome Atlas database (TCGA), Wnt6 was found to be negatively/positively correlated with stemness- and apoptosis-related genes in human cervical cancer. Cancer stem-like cells (CSCs) isolated and enriched from HeLa cells demonstrated elevated Wnt6 and β-catenin genes compared with nonstem HeLa cells. After galaxamide treatment, CSCs showed abrogation of sphere-forming ability, along with inhibition of stemness-related and Wnt pathway genes. Galaxamide treatment was accompanied by the induction of apoptosis in HeLa cells, which was consistent with the results in BALB/c nude mice.  Conclusion and Implications: Our results provide preclinical evidence that suppression of stemness by downregulating the Wnt signalling pathway is the molecular mechanism by which galaxamide effectively inhibits cell growth and induces apoptosis in cervical cancer cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HeLa cells of control  and HeLa cells treated with galaxamide.

first: Ping

last: Li

first: Guang

last: Yang

first: Yunbiao

last: He

first: Yingxing

last: Chen


title: Single-cell RNA sequencing for the effects of Commd3 deficiency and celastrol treatment on humoral immune responses

status: Public on Mar 31 2023

summary: To profile the global effects of Commd3 deficiency on humoral immune responses, CD45+ cells from the draining lymph nodes (LNs) of CreERT2Commd3flox/+ and CreERT2Commd3flox/flox mice were subjected to single-cell RNA sequencing (scRNA-seq) at 7 days after immunization. We found that Commd3 deletion a week before immunization reduced only the proportion of germinal center B cells with minimal transcriptomic changes in B cell populations. Celastrol treatment in WT mice a week before immunization also selectively reduced the proportion of GC B cells with little impact on the transcriptomes, whereas none of the detectable immune cell populations were significantly affected by celastrol treatment in the immunized COMMD3C170A/C170A mice.

overall_design: Mice received subcutaneous injections of NP-CGG at both sides of the abdomen and tail base (100 μg NP-CGG in total), and the inguinal LNs were collected at 7 days after immunization. Live CD45+ cells sorted from the LNs were subjected to scRNA-seq. To test the effects of Commd3 deletion, CreERT2Commd3flox/+ and CreERT2Commd3flox/flox mice were treated with tamoxifen for 3 consecutive days from 9 days before immunization. To test the effects of celastrol treatment, WT or COMMD3C170A/C170A mice received intraperitoneal injections of vehicle [PBS containing 2% dimethyl sulfoxide] or celastrol (1 mg/kg, twice a week at 2- and 3-day intervals) from 7 days before immunization.

first: Taiichiro

last: Shirai

first: Yu-Chen

last: Liu

last: Okuzaki

first: Kazuhiro

last: Suzuki


title: RNA-sequencing analysis of lung tissue from monocrotaline-induced pulmonary arterial hypertension rats

status: Public on Apr 14 2023

city: 咸阳

first: yangfan

last: jia

state: 陕西

address: 中国陕西省杨凌区

institute: 西北农林科技大学

summary: To investigate the genes associated with the progression pulmonary arterial hypertension，lung tissues of rats treated either with PBS buffer or monocrotaline (50mg/kg）were harvested for RNA-sequencing.

overall_design: Each treatment contains 4 biological replicates.

first: Ang

last: Luo

first: Haiyang

last: Tang


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [ChIP-seq]

first: Evgeny

last: Deforzh

state: MA

address: 60 Fenwood Rd, Brigham and Women's Hospital Neurology Department, 9th Floor

department: Neurology

institute: Brigham and Women's Hospital

summary: A growing number of studies describe multiple functions of lncRNAs in chromatin that support their active roles in normal and disease-specific gene expression. We identified a specific enhancer-associated LINC01116 (named HOXDeRNA), which targeted activation transformed human astrocytes into glioma-like cells. Using a combination of RNA-Seq, ChIRP-Seq, and ChIP-Seq, we defined the transcriptomic and epigenetic changes underlying the transformation. We demonstrate that HOXDeRNA binds in trans to the promoters of 44 glioma-specific transcription factors distributed throughout the genome and derepresses them by removing the Polycomb 2 complex. This process is mediated by the RNA G-quadruplex structure of HOXDeRNA. Moreover, HOXDeRNA-induced astrocyte transformation is accompanied by the activation of glioma-specific super-enhancers enriched for binding sites of glioma master transcription factors SOX2 and OLIG2, and multiple oncogenes such as EGFR, PDGFR, BRAF, and miR-21. Our results help reconstruct the sequence of events underlying the process of astrocyte transformation and suggest a driving role of HOXDeRNA eRNA in gliomagenesis.

overall_design: We investigated the epigenetic status of HOXDeRNA-occupied genes in control or HOXDeRNA-active astrocytes, using H3K27Ac (#4353, Cell Signaling) as the mark of active chromatin state, and H3K27Me3 (#9733, Cell Signaling) and EZH2 (Cat. 39002, Active Motif) as the marks associated with repressed chromatin.


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [ChiRP-Seq]

overall_design: ChiRP-Seq were performed on Glioma Stem Cells (GBM4, GBM6, GBM8)  and HOXDeRNA-activated astrocytes to capture all direct interactions between the HOXDeRNA and genomic DNA


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Analysis of the Combined Effect of rs699 and rs5051 on Angiotensinogen Expression and Hypertension

status: Public on Apr 07 2023

city: Indianapolis

first: Nick

last: Powell

state: United States

address: 950 W. Walnut St.

institute: IUSM

summary: RNA from primary hepatocytes from pooled or individual donors was crosslinked to microRNA and Argonaute and pulled down for sequencing analysis.

overall_design: RNA-seq

first: Todd

middle: C

last: Skaar


title: NK co-culture CRISPR screen in the 721.221 B-cell lymphoblast

status: Public on Mar 29 2023

city: Bethesda

first: Xiaoxuan

last: Zhuang

state: MD

address: 10 Center Dr, RM 6N105

institute: NIH

summary: Therefore, to gain a deeper understanding of the interaction between NK cells and B-cell malignancies, we performed here a genome-wide CRISPR screen in the 721.221 cell line (referred to as 221), an EBV-transformed lymphoblastoid B-cell line. This cell line had been selected for the loss of classical HLA-I genes [14] and is therefore sensitive to lysis by NK cells. As expected, the loss of ligands for NK activation receptors resulted in reduced sensitivity. However, deletion of a few other genes, including Signal Peptide Peptidase-Like 3 (SPPL3), had the greatest impact on resistance to lysis by NK cells. Here, we describe how SPPL3 is a crucial controller of the interaction between NK cells and their targets. We found that the increased amount of complex N-glycans in SPPL3-deleted tumor cells limits the binding of NK cell receptors and facilitates immune evasion. We further identified glycosyl transferases that were responsible for the resistant phenotype through a secondary screen in SPPL3-deleted cells and analysis of mutations that restored sensitivity to lysis by NK cells.

overall_design: GeCKO V2 library-transduced 221 cells were selecteted by co-culturing with NK cells. 221 cells expressing CRIPSR library but not co-cultured with NK cells were used as control.  For glycosylation-focused secondary CRISPR screen, the glycoGene library was used. SPPL3-deleted or sgNT 221 cells expressing lentiBlast-Cas9 were transduced with library. Cells were treated with doxycycline for 10 days to induce sgRNA expression before co-incubation with NK cells. For RNA-seq analysis, transcriptome of SPPL3-KO and control (sgNT) 221 cells were compared.

first: Eric

middle: O

last: Long


title: Genome-wide activation of a glioma cancerous transcription program and super-enhancers by a single enhancer HOXDeRNA [RNA-seq]

overall_design: mRNA-Seq was performed on fetal human astrocytes, Immortalized dCas9 expressing astrocytes (NHA) transduced with sgRNA non-targeting control and custom-made Edit-R CRISPRa human HOXDeRNA lentiviral sgRNAs