title: DeSUMOylation limits the rapid transcriptional reprogramming induced by anthracyclines in Acute Myeloid Leukemias

city: Montpellier

first: Denis

last: Tempé

address: 1919 route de Mende

country: France

institute: CNRS

summary: Genotoxicants have been used for decades as front-line therapies against cancer on the basis of their DNA-damaging actions. However, some of their non-DNA-damaging effects are also instrumental for killing dividing cells. We report here that the anthracycline Daunorubicin (DNR) but not the nucleoside analog Cytarabine, the two main drugs used to treat Acute Myeloid Leukemia (AML), induces rapid (3 hours) and broad transcriptional changes in AML cells. The regulated genes are particularly enriched in genes controlling cell proliferation and death, as well as inflammation and immunity. These transcriptional changes are preceded by DNR-dependent deSUMOylation of chromatin proteins, in particular at active promoters and enhancers. Surprisingly, accelerating deSUMOylation dampens DNR-induced transcriptional reprogramming. Quantitative proteomics shows that proteins that are deSUMOylated in response to DNR are mostly transcription factors, transcriptional co-regulators and chromatin organizers. Among them, the CCCTC-binding factor CTCF is highly enriched at SUMO-binding sites found in cis-regulatory regions. This is notably the case at the promoter of the DNR-induced NFKB2 gene. Although DNR does not modify CTCF binding on chromatin in general and at NFKB2 promoter in particular, it leads to a SUMO-dependent reconfiguration of chromatin loops engaging CTCF- and SUMO-bound NFKB2 promoter with distal cis-regulatory regions.

overall_design: Cut&run targeting CTCF in HL60 cells treated with 1 μM DNR and 0.5 μM ML-792 for 2 hrs.

first: Mathias

last: Boulanger

first: Mays

last: Aqrouq

first: Chamseddine

last: Kifagi

first: Marko

last: Ristic

first: Dana

last: Akl

first: Rawan

last: Hallal

first: Aude

last: Carusi

first: Ludovic

last: Gabellier

first: Marion

last: de Toledo

first: Jon-Otti

last: Sigurdsson

first: Tony

last: Kaoma

first: Charlotte

last: Andrieu-Soler

first: Thierry

last: Forné

first: Eric

last: Soler

first: Yosr

last: Hicheri

first: Elise

last: Gueret

first: Laurent

last: Vallar

first: Jesper

last: Olsen

first: Guillaume

last: Cartron

first: Marc

last: Piechaczyk

last: Bossis


title: Low-level repressive histone marks fine-tune stemness gene transcription in neural stem cells [scRNA-seq]

status: Public on Jun 23 2023

city: Stanford

first: Arjun

last: Rajan

state: California

address: 265 Campus Drive

department: Developmental Biology

country: USA

institute: Stanford University

type: Expression profiling by high throughput sequencing

summary: Coordinated regulation of stemness gene activity by transcriptional and translational controls poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of stemness gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes stemness gene transcription in stem cells, a mechanism likely conserved from flies to humans.

overall_design: scRNA-seq was performed on RFP+ sorted cells from 96hr drosophila larval brains expressing RFP+ in type II neural stem cell lineages.

first: Lucas

last: Anhezini

first: Noemi

last: Rives-Quinto

first: Megan

last: Neville

first: Elizabeth

last: Larson

first: Stephen

last: Goodwin

first: Melissa

last: Harrison

first: Cheng-Yu

last: Lee


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ChIP-seq]

city: Kansas City

first: Julia

last: Zeitlinger

institute: Stowers Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: While enhancers are often regulated at the level of accessibility by pioneer factors, promoters tend to be constitutively accessible and poised for activation by paused Pol II — thus are often not considered as sites of developmental regulation. Here we show that the accessibility of promoters and the acquisition of paused Pol II can also be subject to developmental regulation by pioneer factors. We show that Lola-I, a Drosophila zinc finger transcription factor, is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene expression. Lola-I mediates this function by binding to the edges of the promoter nucleosomes, which leads to their depletion, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers, providing further evidence that promoters and enhancers display unexpectedly similar characteristics.

overall_design: scRNA-seq, RNA-seq, ChIP-seq, ATAC-seq or MNase-seq was performed in Drosphila embryos.

first: Vivekanandan

last: Ramalingam


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [scRNA-Seq]


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [RNA-Seq]


title: Inferring gene regulatory networks via transcriptional profiles as associated dynamical attractors

city: MERCED

first: Ruihao

last: Li

state: CA

address: 5200 NORTH LAKE ROAD

department: QSB/MCB

institute: University of California, Merced

type: Non-coding RNA profiling by high throughput sequencing

summary: Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. Numerous methods exist for profiling mRNA transcript levels and identifying protein-DNA binding interactions at the genome-wide scale. These enable researchers to determine the structure and output of transcriptional regulatory networks, but uncovering the complete structure and regulatory logic of GRNs remains a challenge. The field of GRN inference aims to meet this challenge using computational modeling to derive the structure and logic of GRNs from experimental data and to encode this knowledge in Boolean networks, Bayesian networks, ordinary differential equation (ODE) models, or other modeling frameworks. However, most existing models do not incorporate dynamic transcriptional data since it has historically been less widely available in comparison to “static” transcriptional data. We report the development of an evolutionary algorithm-based ODE modeling approach that integrates kinetic transcription data and the theory of attractor dynamics analysis to infer GRN architecture and regulatory logic. Our method outperformed six leading GRN inference methods, all of which do not incorporate kinetic transcriptional data in predicting regulatory connections among TFs when applied to a small-scale engineered synthetic GRN in S. cerevisiae. Moreover, we have shown the potential of our method to predict unknown transcription profiles that would be produced upon genetic perturbation of the GRN governing a two-state phenotypic switch in C. albicans. We established an iterative refinement strategy to facilitate candidate selection for experimentation and the experimental results in turn provide validation or improvement for the model. In this way, our GRN inference approach can expedite the development of a sophisticated mathematical model that accurately describes the structure and dynamics of the in vivo GRN.

overall_design: Use the 5' capped short mRNA abundances as the promoter strengths for each gene across genome in Candida albicans white and opaque wildtype cells

first: Mohammad

last: Qasim


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development

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

overall_design: Refer to individual Series


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ATAC-seq INTACT]


overall_design: Screen single knockouts and created double knockouts in Candida albicans white-opaque switch core circuit to verify model prediction.

first: Morgan

last: Quail


title: Identification of specific miRNAs in the seminal plasma extracellular vesicles from fertile and subfertile rabbit bucks

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

summary: In this study, the methods to isolate and identify extracellular vesicles (EVs) including exosomes, from the seminal plasma (SP) of 3 fertile (F) and subfertile (S) bucks have been developed. Additionally, we investigated whether specific miRNA abundance differences between F and SF bucks could serve as fertility biomarkers. Ultracentrifugation and size exclusion chromatography analysis have made it possible to isolate different SP-EVs concentrations (8.53x10^11 ± 1.04x10^11 and 1.84x10^12 ± 1.75x10^11 particles/ml of SP; p=0,008), with a similar average size (143.9 ± 11.9 and 115.5 ± 2.4 nm; p=0.7422) in F and S males, respectively. Particle size was not significantly correlated with any kinetic parameter. Also, EVs have been identified by electron microscopy and their marker proteins by Western blot. The concentration of SP-EVs was positively correlated with the percentage of abnormal forms (r=0.94; p<0.05) and with the percentage of immotile spermatozoa (r=0.88; p<0.05). A total of 18 miRNAs were differentialy expressed (FC>2, FDR<0.05) in F vs. S groups. SP from F and S males contains EVs with different miRNA cargo that could be used as biomarkers for male fertility.

overall_design: 14 sexually mature male California x New Zealand white rabbits of 10-12 months of age were used. An ejaculate was collected from these animals twice a week with an artificial vagina for 1 month (8 ejaculates from each animal). The macroscopic quality of each ejaculate was assessed, discarding the ejaculates with abnormal colors (yellow or red) and low volumes (<0.2 ml). Sperm viability was also evaluated with the eosin staining test and the percentage of abnormal forms, concentration, and kinetic parameters (CASA program) were assessed, observing a minimum of 200 cells in each of the 3 replicates that were analyzed from each ejaculate. In the CASA system settings, a 70% straightness index (STR) was defined for progressive motility, and mean velocities (VAP) of <10 µm/s <25 µm/s <50 µm/s for slow, medium, and fast SPZ, respectively. From these analyses, 3 males of high and 3 of low seminal quality were chosen for Seminal Plasma-EVs (SP-EVs) isolation and their miRNA content identification.

first: Osama

last: Sakr

first: Karina

last: Cañón-Beltrán

first: Yulia

middle: N

last: Cajas

first: Radek

last: Prochazka

first: Dimitrios

last: Rizos

first: Pilar

middle: G

last: Rebollar


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [MNase-seq]


title: SUMO2/3 CHIP-Seq in  HL-60 cells treated or not with cytarabine or daunorubicine

first: Mathias

last: Boulanger

department: IGMM

summary: SUMOylation, a post-translational modification of the ubiquitin family plays key roles in Acute Myeloid Leukemias response to therapies, in particular through the regulation of gene expression. We have investigated here how daunorubicine (DNR) and cytarabine (Ara-C), the two main drugs used for Acute Myeloid Leukemia treatment, affect the distribution of SUMO on chromatin in the HL-60 cell lines. We found that DNR but not Ara-C leads to a massive decrease in the presence of SUMOylated proteins on the chromatin, in particular at promoters and enhancers, where they are enriched.

overall_design: ChIP-Seq with SUMO2/3 antibodies were performed in pooled triplicate in HL-60 cells treated or not for 2 hours with DNR or AraC.

first: Chamseddine

last: Kifagi

first: Guillaume

last: Bossis


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ATAC-seq]

overall_design: ScRNAseq, RNAseq,Tissue Specific ChIP-Seq or Whole embryo ChIP-Seq and ATAC-Seq was performed in Drosphila embryos.


title: Differential gene expression analysis to investigate prostate tumor responses to intratumoral immunotherapies.

city: London

first: Efthymia

last: Papaevangelou

address: Guy's Hospital

department: Peter Gorer Department of Immunobiology

country: United Kingdom

institute: King's College London

summary: Purpose: Next-generation sequencing (NGS)-derived transcriptome profiling (RNA-seq) is a powerful tool for analysing cellular pathways involved in treatment responses. In this study, RNA-seq was used to perform differential gene expression (DEG) and gene ontology (GO) analyses in prostate tumors treated with different immunotherapies and their combination. This was in order to investigate which pathways are activated and mediate the therapeutic effect.  Methods: Mice with TRAMP-C2 subcutaneous prostate tumors were treated with either HBSS (control) or cyto-IL-15 or the STING agonist ADU-S100 or combination of ADU-S100 and cyto-IL-15. At day 6, tumors were removed and RNA was harvested to be used for RNA sequencing with Illumina NovaSeq. Using DESeq2, a comparison of gene expression between the treatment cohorts was performed and the Wald test was used to generate p-values and Log2 fold changes. GO analysis was performed on the statistically significant genes by implementing GeneSCF software using Fisher exact test. The mgi GO list was used to cluster the set of genes based on their biological process.   Results: DEG analysis shown that more than 1,000 genes were differentially expressed in tumors 6 days after treatment with ADU-S100 or its combination with cyto-IL-15 (1,040 genes for ADU-S100 compared to control; 1,141 genes for combination compared to control). Most of the differentially expressed genes were upregulated (>70% in both comparisons). cyto-IL-15 led to differential expression of 96 genes compared to control. Differential expressed genes included Cxcl11 involved in immune cell recruitment and activation, and genes encoding granzymes a and b, which are proteases released by cytotoxic T cells and natural killer (NK) cells to kill cancer cells. In the control versus ADU-S100 or combination comparisons, GO analysis revealed that the majority of genes were involved in processes such as cellular responses to interferon-γ and β, complement activation, innate immune response, phagocytosis, and B cell signalling and activation.   Conclusions: This study provides valuable insights in differential expression and activation of genes and cellular pathways involved in eliciting responses to immunotherapies in mouse prostate tumors. Using NSG and more specifically RNAseq-based transcriptome characterization, a detailed quantitative and qualitative analysis on how novel therapies exert their efficacy in tumors can be achieved and uncover the specific biological processes and functions contributing to the anti-tumor effects.

overall_design: Prostate tumor mRNA profiles from mice treated with either HBSS (control), cyto-IL15, ADU-S100 or combination of cyto-IL15 plus ADU-S100  using 3 replicates (3 tumors) in each group.

first: Ana

middle: M

last: Esteves

first: Prokar

last: Dasgupta

first: Christine

last: Galustian


title: SUMOylation controls Daunorubicin-regulated gene expression in the Acute Myeloid Leukemia cell line HL-60

summary: SUMOylation, a post-translational modification of the ubiquitin family plays key roles in Acute Myeloid Leukemias response to therapies, in particular through the regulation of gene expression. We have investigated here how inhibition of SUMOylation with ML-792 affects gene daunorubicine (DNR-)-regulated gene expression. We found that inhibition of SUMOylation limits DNR-induce up- or down-regulation of gene expression.

overall_design: RNA-seq were performed in triplicates in HL-60 cells treated for 3 hours with DMSO (mock), DNR (1µM), ML-792 (0,5µM) and the combination of ML-792 (0,5µM) and DNR (1µM)


title: SUMOylation regulates daunorubicin-induced changes in the long-range interactions between NFKB2 promoter and distant genomic regions in HL-60 cells

summary: SUMOylation, a post-translational modification of the ubiquitin family plays key roles in Acute Myeloid Leukemias response to therapies, in particular through the regulation of gene expression. We have found that the NFKB2 gene is rapidly induced by DNR in the HL-60 cell line and inhibition of SUMOylation limits is induction. To decipher how SUMOylation controls DNR-induced NFKB2 expression, we analyzed the dynamic of the 3D conformation of the NFKB2 gene using Circularized Chromosome Conformation Capture (4C). We found that the NFKB2 promoter interacts with four distal regions. DNR induced a loss of one of the interaction and the gain of a new interaction. Inhibition of SUMOylation with ML-792 did not affect the interactions between NFKB2 promoter and distal genomic regions. However, inhibition of SUMOylation prevented DNR-regulated changes in the 3D architecture of the locus.

overall_design: The 4C approaches was performed in 3 biological replictes in HL-60 after 2 hours of treatment with DMSO (mock), DNR (1µM), ML-792 (0,5µM) and the combination of ML-792 (0,5µM) and DNR (1µM). The NFKB2 gene promoter has been used as a viewpoint for the technique.


title: Astrocytic response mediated by the CLU rs11136000 risk allele inhibits OPC proliferation and myelination in a human iPSC model

city: Duarte

first: Yanhong

last: Shi

address: 1500 E Duarte Road

institute: City of Hope

summary:
Purpose: To study whether and how CLU rs11136000 associates with Alzheimer’s disease (AD) in astrocytes and affects their function.
Methods: Different genotypes of astrocytes were differentiated from human isogenic iPSCs which used CRISPR/Cas9 editing, and total RNA was isolated and sequenced.
Results: We identified 271 up-regulated genes (Fold-change ≥ 2, p<0.05) versus 176 down-regulated genes (Fold-change ≤ 0.5, p<0.05).
Conclusion: CLU expression and IFN response were up-regulated in C/C astrocytes.

first: Zhenqing

last: Liu


title: Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ChIP-seq INTACT]

first: Julia

last: Zeitlinger

first: Vivekanandan

last: Ramalingam


title: SUMO controls the rapid transcriptional reprogramming induced by chemotherapies in Acute Myeloid Leukemias


title: IL-3 receptor signaling suppresses chronic intestinal inflammation by controlling mechanobiology and tissue egress of regulatory T cells

status: Public on Jun 22 2023

city: Erlangen

first: Mark

last: Dedden

state: Bayern

address: Schwabachanlage 12

department: Department of Medicine 1

country: Germany

institute: Universitätsklinikum Erlangen

summary: We studied the impact of Il3r deficiency on freshly isolated thymocytes of steady-state IL3R alpha deficient and wildtype mice.

overall_design: RNA-sequencing of murine steady-state Interleukin-3 (IL-3) receptor alpha deficient (Il3ra-/-) and wildtype (Il3ra+/+) thymocytes of 3 mice per group.

first: Karen

middle: A

last: Ullrich

first: Tanja

last: Müller

first: Markus

middle: F

last: Neurath

first: Sebastian

last: Zundler


title: Emergent mechanical control of vascular morphogenesis

city: Cambridge

first: Robert

middle: D.

last: Kamm

state: MA

address: 77 Massachusetts Avenue Bldg NE47-321

department: Department of Mechanical Engineering

institute: Massachusetts Institute of Technology

summary: mRNA profiles of endothelial cells and fibroblasts undergoing vasculogenesis under juxtacrine co-culture vs. monoculture.

first: Jordan

last: Whisler

first: Roger


title: Distinguishing Keratoacanthoma from Well-Differentiated Cutaneous Squamous Cell Carcinoma Using Single-cell Spatial Pathology

city: Detroit

first: Jesse

last: Veenstra

address: One Ford Place

institute: Henry Ford Health

summary: We used RNAseq to identify key differences in transcriptomes between keratoacanthoma and well-differentiated cutaneous squamous cell carcinoma, which suggested divergent keratinocyte populations between each tumor.

overall_design: FFPE blocks from biopsy-proven KA and cSCC (n=10/group) were used for TruSe RNA Exome (Illumina) at 40M reads/sample following quality control (Novogene).

first: David

last: Ozog

first: Ian

last: Loveless

first: Indra

last: Adrianto

first: Peter

last: Dimitrion

first: Kalpana

last: Subedi

first: Ben

last: Friedman

first: Li

last: Zhou

first: Qing-Sheng

last: Mi


title: Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Supplentary Fig. 4)

city: Bordeaux

first: Julian

last: Boutin

state: Nouvelle Aquitaine

address: 146 rue Leo Saignat

institute: INSERM U1312 BRIC

type: Genome variation profiling by genome tiling array

summary: ABRAXAS2 gene editing by CRISPR-Cas9 nuclease or before editing in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS or without cell sorting and large rearrangements confirmation in chromosome 10q.

overall_design: Three-condition experiment,edited or no edited HFF vs Illumina reference CGH-Array. Fluorescent positive cell bulk or bulk without cell sorting after ABRAXAS2 gene editing or before editing.

first: Samuel

last: Amintas


title: Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 3d)

summary: SORSC1 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

overall_design: Three-condition experiment, HFF vs Agilent control DNA, Two Fluorescent-positive clones  after SORSC1 gene editing and bulk before editing

first: Perrine

last: Pennamen


title: Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 5e)

summary: ABRAXAS2 or SORSC1 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF KO P53 for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

overall_design: Two-condition experiment, florescent-positive clones HFF KO P53 edited  vs fluorescent-negative HFF KO P53  edited bulk  after ABRAXAS2 or SORSC1 gene editsing.


title: Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 4C)

summary: ADRA2A or CPXM2 or TRUB1 or VCL or PLEKHA1 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

overall_design: Five-condition experiment,edited HFF vs control clone 6 WT HFF. Fluorescent positive cell bulk after ADRA2A or CPXM2 or TRUB1 or VCL or PLEKHA1  gene editing.


title: Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 3b)

overall_design: One condition experiment, Florescent positive cell bulk HFF vs Fluorescent negative HFF cell bulk after SORSC1 gene editing.


title: Human HFF cells large rearranements detection after CRISPR-Cas9 nuclease (Fig.2c)

summary: ABRAXAS2 gene editing by CRISPR-Cas9 nuclease in heterozygous HFF for UROS inactivation. Fluorescent positive cell sorting for UROS and large rearrangements confirmation in chromosome 10q.

overall_design: Three-condition experiment,edited HFF vs Agilent control DNA or control HFF. Fluorescent positive cell bulk and two fluorescent-positive clones, #1 and #2 after ABRAXAS2 gene editing.


title: SR9243 (LXR antagonist) and T3 effects on clownfish larvae

city: Onna-son

first: Natacha

last: Roux

state: Okinaw

address: 1919-1 Tancha

country: Japan

institute: OIST

summary:
Investigate the effects of SR9243 and T3 on Amphiprion ocellaris larvae
Amphiprion larvae were treated for 5 days at 10-7M SR9243 and at 10-7M T3

overall_design: Comparative gene expression analysis of RNA-seq data of SR9243, T3 and control (DMSO solvant) larvae

first: Saori

last: Miura

first: Mélanie

last: Dussenne

first: Yuki

last: Tara

first: Shu-Hua

last: Lee

first: Simon

last: de Bernard

first: Mathieu

last: Reynaud

first: Pauline

last: Salis

first: Agneesh

last: Barua

first: Adbelhay

last: Boulahtouf

first: Patrick

last: Balaguer

first: Karine

last: Gauthier

first: Davidl

last: Lecchini

first: Yann

last: Gibert

first: Laurence

last: Besseau

first: Vincent

last: Laudet


title: T3 effects on clownfish larvae

city: Lyon

address: 30 rue Pré Gaudry

institute: AltraBio

summary:
Investigate the effects of thyroid hormone on Amphiprion ocellaris larvae
Amphiprion larvae were treated for 2 days at 10-7M T3

overall_design: Comparative gene expression analysis of RNA-seq data T3 treated larvae and control (DMSO solvant) larvae


title: Volatile organic compounds emitted by the biocontrol agent Pythium oligandrum contribute to ginger plant growth and disease resistance

city: Nanjing

first: Paul

last: Daly

state: Jiangsu

address: 50 Zhongling St

country: China

institute: Jiangsu Academy of Agricultural Sciences

summary: The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycetes-caused diseases such as Pythium myriotylum-caused rhizome rot in ginger leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using N. benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass content. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones, and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stress and the mechanisms of action of P. oligandrum as a biocontrol agent.

overall_design: Transcriptome analysis was performed on leaf blades from three ginger (Zingiber officinale) plants exposed to volatile compounds from Pythium oligandrum for 21 days using a plastic pot-glass jar apparatus whereby P. oligandrum was grown in the glass-jar and ginger was grown in the plastic pot placed on top of the glass jar. For the control, leaf blades were sampled from three ginger plants that were not exposed to P. oligandrum volatile compounds using the same plastic pot-glass jar apparatus whereby nothing was grown in the glass-jar and ginger was grown in the plastic pot placed on top of the glass jar.

first: Taha

last: Sheikh

first: Dongmei

last: Zhou

last: Wang

first: Siqiao

last: Chen

first: Sheng

last: Deng

first: Haider

last: Ali

first: Sarfraz

last: Hussain

first: Yishen

last: Zhao

first: Waseem

last: Raza

first: Xian

last: Wen

first: Xiaoyu

first: Jinfeng

last: Zhang

first: Lunji

first: Hui

last: Feng

first: Lihui

last: Wei


title: MPI effects on clownfish larvae

first: Simon

last: de Bernard

summary:
Investigate the effects of goitrogenous compound on Amphiprion ocellaris larvae
Amphiprion larvae were treated for 19 days with a mix of Methimazole, potassium perchlorate and iopanoic acid

overall_design: Comparative gene expression analysis of RNA-seq data MPI treated larvae and control (DMSO solvant) larvae

first: Natacha

last: Roux

first: Saori

last: Miura

first: Mélanie

last: Dussenne

first: Yuki

last: Tara

first: Shu-Hua

last: Lee

first: Mathieu

last: Reynaud

first: Pauline

last: Salis

first: Agneesh

last: Barua

first: Adbelhay

last: Boulahtouf

first: Patrick

last: Balaguer

first: Karine

last: Gauthier

first: Davidl

last: Lecchini

first: Yann

last: Gibert

first: Laurence


title: Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells [RNA-Seq]

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

summary: Cancer cells can only rarely be reprogrammed to induced pluripotent stem cells (iPSCs) using the overexpression of the transgenes Oct4, Sox2, Klf4, and Myc. Those cancer cells that have been reprogrammed seem to only partially complete the process and are locked in an intermediate state. There are barriers that block cancer cells from reprogramming, but the nature of those barriers is unclear. In this work, we immortalized mouse embryonic fibroblasts (MEFs) using a variety of  transgenes and discovered several immortalized cell lines that remain compatible with reprogramming. We utilise the different lines to explore the factors that are compatible with reprogrmming and those that block reprogramming to pluripotent stem cells

overall_design: MEFs were immortalized with combinations of: oncogenes (Myc, Hras, Mef2d, p53DD), viral factors (SV40T, E1A), apoptotic factors (Bcl2), and an engineered epigenetic factor (Hdac7SA; serines 178, 344, and 479 substituted with alanine, to block nuclear export (Luo et al., 2019)). The MEFs were passaged for at least a month to remove untransformed wildtype MEFs, then the cells were reprogrammed using OSKM (Oct4, Sox2, Klf4, c-Myc) transgenes to reprogram. Cells were reprogrammed in serum+ vitamin C and in various inhibitor cocktails against: MEK (PD; PD0325901), GSK3 (CHIR; CHIR99021), ROCK (Y; Y23637), G9a (BIX; BIX-01294), and Histone deacetylases (TSA)). Reprogrammed cells were sorted using GFP driven from the 'OG2' reporter.

first: Xiuling

last: Fu


title: Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Lack of relevant disease animal models and cell lines hampers our understanding of hepatoblastoma and identification of therapeutic targets. We report a liver-specific MYC-driven hepatoblastoma murine model that faithfully recapitulates the pathological features of mixed fetal and embryonic hepatoblastoma, with transcriptomics resembling the high-risk gene signatures of human disease. Single-cell RNA-sequencing (scRNA-seq) and spatiotranscriptomics identify a subpopulation of hepatoblastoma cells with high levels of adult hemoglobin genes. After deriving a cell line from the mouse model, we mapped the cancer dependency genes using CRISPR-Cas9 and identified druggable targets shared with human hepatoblastoma (i.e., CDK7, CDK9, PRMT1, PRMT5). Our screen also discovered oncogenes and tumor suppressive genes in hepatoblastoma that engage multiple cancer signaling pathways. Chemotherapy is the mainstay of human hepatoblastoma. Genetic map of doxorubicin response by CRISPR-Cas9 identified modifiers whose loss-of-function synergizes (PRKDC) and antagonizes (Polycomb repressive complex 2) the effect of chemotherapy. Combination of PRKDC inhibitor and chemotherapy greatly enhances therapeutic efficacy. Our studies have provided useful disease models and potential therapeutic targets of hepatoblastoma.

overall_design: Examination of gene profile changes by comparing normal liver tissue and liver tumor tissue with RNA-seq.

first: Jie

last: Fang

first: Shibiao

last: Wan

first: Yiping

last: Fan

first: Jun

last: Yang


title: Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells

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

overall_design: Refer to individual Series


title: Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [ATAC-seq]

city: Daejeon

first: YEONWOO

last: KIM

address: 291 Daehak-ro, Yuseong-gu

department: Department of Biological Sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Liver cancer, particularly hepatocellular carcinoma (HCC), poses a significant global threat to human lives. To advance the development of innovative diagnostic and treatment approaches, it is essential to examine the hidden features of HCC, particularly its 3D genome architecture, which is not well understood. In this study, we investigated the 3D genome organization of four HCC cell lines—Hep3B, Huh1, Huh7, and SNU449—using in situ Hi-C and ATAC-seq. Our findings revealed that HCCs had elevated long-range interactions compared to HMECs, both intra- and interchromosomal. Unexpectedly, they displayed cell line-specific compartmental modifications at the Mb scale, which could aid in determining HCC subtypes. At the sub-Mb scale, we observed a decrease in intra-TAD interactions and chromatin loops in HCCs compared to HMECs. Lastly, we discovered a correlation between gene expression and 3D chromatin architecture in SLC8A1, which encodes the sodium-calcium antiporter known to induce apoptosis. Our findings suggest that HCCs have a distinct 3D genome organization that is different from normal and other cancer cells. Overall, we take this as evidence that genome organization plays a crucial role in cancer phenotype determination. Further exploration of epigenetics in HCC will lead us to a better understanding of specific gene regulation mechanisms and uncover novel targets for cancer treatments.

overall_design: Genome-wide distribution of chromatin accessibility in Human mammary epithelial cells (HMECs, as a control) and the hepatocellular carcinoma cell lines (Hep3B, Huh1, Huh7, SNU449). Please note that each processed data was generated from  two technical replicates.

first: Yeonwoo

last: Kim

first: Hyeokjun

first: Daeyoup


title: Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma [Hi-C]

overall_design: The 3D chromatin organization of human mammary epithelial cells (HMECs, as a control) and four hepatocellular carcinoma cell lines were analyzed via Hi-C sequencing. Please note that each processed data was generated from two biological replicates.

last: Lee


title: The role of Itgb1 in islet development

first: Hung Ping

last: Shih

address: 1500 East Duarte Road

summary: Pancreatic development requires appropriate environmental cues, in which ECM-Integrin signaling plays a central role in the process. Specifically, we investigated how ECM-Integrin signaling in Ngn3+ cell (endocrine progenitors) regulates islet architecture and functions. Here we showed disruption of ECM-Integrin signaling affects beta cell functional maturation and potential non-autonomous regulation around islets.

overall_design: Four biological replicates were analyzed for wildtype and Itgb1 mutant

first: Hung-Ping

first: Ya-Ting

last: Chang


title: Methyl-CpG binding domain 2 (Mbd2) is an Epigenetic Regulator of Autism-Risk Genes and Cognition [Bisulfite-Seq]

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

type: Methylation profiling by high throughput sequencing

summary: The Methyl-CpG-Binding Domain Protein family has been implicated in neurodevelopmental disorders. The Methyl-CpG-binding domain 2 (Mbd2) binds methylated DNA and was shown to play an important role in cancer and immunity. Some evidence linked this protein to neurodevelopment. However, its exact role in neurodevelopment and brain function is mostly unknown.   Here we show that Mbd2-deficiency in mice (Mbd2-/-) results in deficits in cognitive, social and emotional functions. Mbd2 binds regulatory DNA regions of neuronal genes in the hippocampus and loss of Mbd2 alters the expression of hundreds of genes with a robust down-regulation of neuronal gene pathways. Further, a genome-wide DNA methylation analysis found an altered DNA methylation pattern in regulatory DNA regions of neuronal genes in Mbd2-/- mice. Differentially expressed genes significantly overlap with gene-expression changes observed in brain of Autism Spectrum Disorder (ASD) individuals. Notably, down-regulated genes are significantly enriched for human ortholog ASD risk-genes. Observed hippocampal morphological abnormalities were similar to those found in individuals with ASD and ASD rodent models. Mbd2 knockdown partially recapitulates  the behavioral phenotypes observed in Mbd2-/- mice.   These findings suggest Mbd2 is a novel epigenetic regulator of genes that are associated with ASD in humans. Mbd2 loss causes behavioral alterations that resemble those found in ASD patients.

overall_design: Pools of hippocampi from wild-type and mice hippocmapi were subjected to genome-wide bisulfite-sequencing with replicates (8-10 mice/group), in addition targeted bisulfite-sequencing from 3-5 mice/groups were done on an additional cohort

first: Sonia

last: Do Carmo

first: Yehoshua

last: Enuka

first: Daniel

last: Sapozhnikov

first: Lindsay

last: Welikovitch

first: Niaz

last: Mahmood

first: Shafaat

last: Rabbani

first: Liqing

last: Wang

first: Jonathan

last: Britt

first: Wayne

middle: W

last: Hancock

first: Yosef

last: Yarden

first: Moshe

last: Szyf


title: Methyl-CpG binding domain 2 (Mbd2) is an Epigenetic Regulator of Autism-Risk Genes and Cognition [RNA-seq]

overall_design: RNA from wild-type and Mbd2-/- mice hippocmapi was-sequenced

middle: D

last: Carmo


title: Methyl-CpG binding domain 2 (Mbd2) is an Epigenetic Regulator of Autism-Risk Genes and Cognition


title: Methyl-CpG binding domain 2 (Mbd2) is an Epigenetic Regulator of Autism-Risk Genes and Cognition [ChIP-seq]

overall_design: Pools of hippocampi from wild-type and knockout mice were subjected to Mbd2 ChIP-seq.


title: Low-level repressive histone marks fine-tune stemness gene transcription in neural stem cells

city: Stanford

first: Arjun

last: Rajan

address: 265 Campus Drive

institute: Stanford University

type: Expression profiling by genome tiling array


title: A Transcriptomic and Proteomic Atlas of Obesity and Type 2 Diabetes in Cynomolgus Monkeys

city: South San Francisco

first: Xianglong

last: Zhang

address: 1120 Veterans Blvd

institute: Amgen Inc

summary: Obesity and type 2 diabetes (T2D) remain major global healthcare challenges and developing therapeutics necessitate using nonhuman primate models. Here, we present transcriptomic and proteomic analyses of all the major organs of cynomolgus monkeys with spontaneous obesity or T2D in comparison to healthy controls. Molecular changes occur predominantly in the adipose tissues of obesity individuals, while extensive expression perturbations of T2D individuals are observed in many tissues, such as liver, kidney, brain, and heart. Immune response-related pathways are upregulated in obesity and T2D, whereas metabolism and mitochondrial pathways are downregulated. Incorporating human single-cell RNA sequencing findings corroborates the role of macrophages and monocytes in obesity. Moreover, we highlight some potential therapeutic targets including SLC2A1 and PCSK1 in obesity as well as SLC30A8 and SLC2A2 in T2D. Our findings provide insights into the tissue-specific molecular foundations of obesity and T2D and reveal the mechanistic links between these two metabolic disorders.

overall_design: Studied the transcriptomics and proteomics of 27 tissues from cynomolgus monkeys with obesity and Type 2 diabetes and matched controls.

first: Ying

last: Lei

first: Oliver

last: Homann

first: Marina

last: Stolina

first: Songli

first: Murielle

last: Véniant

first: George

last: Hu

first: Yi-Hsiang

last: Hsu


title: How enhancers regulate wavelike gene expression patterns

status: Public on Jun 21 2023

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

summary: A key problem in development is to understand how genes turn on or off at the right place and right time during embryogenesis. Such decisions are made by non-coding sequences called 'enhancers.' Much of our models of how enhancers work rely on the assumption that genes are activated de novo as stable domains across embryonic tissues. Such a view has been strengthened by the intensive landmark studies of the early patterning of the anterior-posterior (AP) axis of the Drosophila embryo, where indeed gene expression domains seem to arise more or less stably. However, careful analysis of gene expression patterns in other model systems (including the AP patterning in vertebrates and short-germ insects like the beetle Tribolium castaneum) painted a different, very dynamic view of gene regulation, where genes are oftentimes expressed in a wavelike fashion. How such gene expression waves are mediated at the enhancer level is so far unclear. Here, we establish the AP patterning of the short-germ beetle Tribolium as a model system to study dynamic and temporal pattern formation at the enhancer level. To that end, we established an enhancer prediction system in Tribolium based on time- and tissue-specific ATAC-seq and an enhancer live reporter system based on MS2 tagging. Using this experimental framework, we discovered several Tribolium enhancers, and assessed the spatiotemporal activities of some of them in live embryos. We found our data consistent with a model in which the timing of gene expression during embryonic pattern formation is mediated by a balancing act between enhancers that induce rapid changes in gene expression patterns (that we call 'dynamic enhancers') and enhancers that stabilize gene expression patterns (that we call 'static enhancers'). However, more data is needed for a strong support for this or any other alternative models.

overall_design: Embryos were collected 23-26 hours after egg lay (AEL) or 26-29 hours AEL and prepared for ATAC seq analysis. Biological replicates were collected in triplicates per timepoint. Samples were subjected to paired end sequencing (2x 150bp) on an Illumina NovaSeq 6000.

first: Christine

last: Mau

first: Heike

last: Rudolf

first: Frederic

last: Strobl

first: Benjamin

last: Schmid

first: Timo

last: Regensburger

first: Ralf

last: Palmisano

first: Ernst

last: Stelzer

first: Ezzat

last: El-Sherif


title: Transcription modulates chromatin dynamics and locus configuration sampling

city: Edinburgh

first: Giada

last: Forte

address: Peter Guthrie Tait Road

institute: The University of Edinburgh


title: Identification of the RNA targets of RBM5 and transcriptome analysis of the brain of wild-type and R6/2 (Huntington's disease) mice

city: Copenhagen

first: Nicolas

last: Fossat

address: Blegdamsvej 3B

country: Denmark

institute: University of Copenhagen

summary: Using the Cross-linking immuno-precipitation (CLIP) methodology combined with high throughput sequencing analysis, we have identified the RNA targets of the RNA-binding protein RBM5 in the brain of wild-type and R6/2 (Huntington's disease model) adult mice. In parallel, transcriptome analysis was performed by RNA-sequencing using brain samples from the same animals.

overall_design: Mouse brains were harvested from three wild-type and three R6/2 12-weeks old male mice. Each brain was longitudinally bisected into two equivalent halves. Both halves were gently dissociated and homogenized. One half was exposed to UV254 for cross-linking and processed for CLIP and high throughput sequencing (CLIP-Seq) following a protocol previously published (PMID: 24407355). Briefly, after the first steps including gentle lysis and controlled RNA fragmentation, the lysate was divided into three equal fractions and each fraction was incubated with magnetic beads coupled with rabbit anti-RBM5 antibodies (AbR; ref# HPA018011, Sigma), mouse anti-RBM5 antibodies (AbM; ref# sc-515419, Santa Cruz) or non-specific antibodies (IgG) before the rest of the protocol was performed. Isolated RNAs were then processed for library preparation and high throughput sequencing (single-end reads, 150bp; Illumina MiSeq), resulting in 18 raw fastq files (NFO120-A to NFO120-R) and one xlsx processed file (CLIP-Seq_processed-data). Total RNA was extracted from a small portion of the non-cross-linked half of the brain and processed for RNA-Sequencing (paired-end reads, 2 x75bp; Illumina NextSeq500) according to standard protocol, and resulting in 48 raw fastq files (eight for each sample: NFO136-2 to NFO136-9) and one xlsx processed file (RNA-Seq_processed-data). For each experiment – CLIP-Seq and RNA-Seq – all samples were processed in parallel.

first: Meeli

last: Mullari

first: Niels

middle: H

last: Skotte

first: Andrea

last: Asenjo-Martinez

first: David

middle: T

last: Humphreys

first: Jens

last: Bukh

first: Agnete

last: Kirkeby

first: Troels

middle: K

last: Scheel

first: Michael

middle: L

last: Nielsen


title: Mutant APC reshapes plasma membrane cholesterol-dependent Wnt proteolipid condensate structure-function and feedforward oncogenic β-catenin signaling

city: College Station

first: Destiny

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

summary: Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. Here, we demonstrate the role of oncogenic APC in increasing plasma membrane free cholesterol and rigidity, thereby modulating Wnt signaling hubs. This results in an overactivation of Wnt signaling in the colon. Finally, using the Drosophila sterol auxotroph model, we demonstrate the unique ability of exogenous free cholesterol to disrupt plasma membrane homeostasis and drive Wnt signaling in a wildtype APC background. Collectively, these findings provide a mechanistic link between oncogenic APC, loss of plasma membrane homeostasis and CRC development.

overall_design: YAMC (Apc+/+), IMCE (Apc-/+) and IMCE Bcat (Apc-/+ Bcat-/+) mouse cell lines derived from the colonic epithelium were employed to elucidate the effect of oncogenic mutant APC on the expression of cholesterol homeostasis related genes. To achieve this, three independent biological replicates (n=3 per group) were utilized to establish the enrichment of multiple cholesterol homeostasis pathway genes in mutant APC and compared to WT APC (control) samples. Furthermore, the effect of aberrant dysregulation of Wnt signaling was also examined by comparing the dysregulation magnitude of cholesterol homeostatic genes across all cell lines,i.e., YAMC< IMCE<IMCE Bcat. Similarly, a colorectal cancer mouse model was utilized to examine the effect of mutant oncogenic APC on the expression of cholesterol homeostasis related genes in vivo. To achieve this, primary colonic crypts from the epithelium of heterozygous (AGC) and homozogous (AfGC) mutant APC mice (n=4 per group) were utilized to establish the enrichment of multiple cholesterol homeostasis pathway genes and compared to WT APC control mice (GC, n=4). Furthermore, the effect of aberrant dysregulation of Wnt signaling was also examined by comparing the dysregulation magnitude of cholesterol homeostatic genes across all mice genotypes (GC< AGC<AfGC).

first: Alfredo

last: Erazo-Oliveras

first: Mónica

last: Muñoz-Vega

first: Jennifer

middle: S

last: Goldsby

first: Robert

last: Chapkin


title: Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation [ChIP-seq]

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

institute: Tongji University

summary: To investigate the potential target genes regulated by the interaction of Zhx1-hnRNPA1 at CP stage. Samples from day 6 of cardiomyocyte differentiation in the 46C-Ctrl and Zhx1-KO groups were collected. Gene expression levels were quantitated by RNA-seq analysis, and the potential target genes were identified by ChIP-seq analysis.

overall_design: Examination of the potential target genes regulated by the interaction of Zhx1-hnRNPA1 at CP stage.

first: Yang

last: Chen


title: Low-level repressive histone marks fine-tune stemness gene transcription in neural stem cells [CUT&Tag]

first: Arjun

last: Rajan

summary: Coordinated regulation of stemness gene activity by transcriptional and translational controls poise stem cells for a timely cell-state transition during differentiation. Although important for all stemness-to-differentiation transitions, mechanistic understanding of the fine-tuning of stemness gene transcription is lacking due to the compensatory effect of translational control. We used intermediate neural progenitor (INP) identity commitment to define the mechanisms that fine-tune stemness gene transcription in fly neural stem cells (neuroblasts). We demonstrate that the transcription factor FruitlessC (FruC) binds cis-regulatory elements of most genes uniquely transcribed in neuroblasts. Loss of fruC function alone has no effect on INP commitment but drives INP dedifferentiation when translational control is reduced. FruC negatively regulates gene expression by promoting low-level enrichment of the repressive histone mark H3K27me3 in gene cis-regulatory regions. Identical to fruC loss-of-function, reducing Polycomb Repressive Complex 2 activity increases stemness gene activity. We propose low-level H3K27me3 enrichment fine-tunes stemness gene transcription in stem cells, a mechanism likely conserved from flies to humans.

overall_design: CUT&RUN experiments are performed in duplicate in fly larval neuroblast enriched brains endogenously tagged with fruC::myc using the following antibodies: myc, fruCOM, Su(H), trl, Su(z)12, Caf-1, H3K4me3, H3K9me3, H3K27me3, H3K27ac, iGG. Complementary experiments were performed in neuroblast enriched fruC-/- brains for H3K4me3, H3K27me3, and H3K27ac.

first: Lucas

last: Anhezini

first: Noemi

last: Rives-Quinto

first: Megan

last: Neville

first: Elizabeth

last: Larson

first: Stephen

last: Goodwin

first: Melissa

last: Harrison

first: Cheng-Yu

last: Lee


title: Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation [RNA-seq]


title: Muscle denervation promotes functional interactions between glial and mesenchymal cells through NGFR and NGF

city: La jolla

first: Chiara

last: Nicoletti

address: 10901 North Torrey Pines Road

department: Development, Aging and Regeneration Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: We have performed parallel scRNA-seq and snATAC-seq analysis of skeletal muscles subjected to sciatic nerve transection to delineate cell type-specific patterns of gene expression and chromatin accessibility at different time-points post-denervation. This analysis revealed that, unlike muscle injury, denervation leads to the selective activation of specific muscle-resident cell types, such as glial cells and a population of mesenchymal cells marked by the expression of Thy1/CD90.

overall_design: For each time-point post denervation (namely, 2, 5 and 15 days p.d., as well as the non-denervated control (abbreviated as Non-DEN in all figures and tables), 1 wild-type male C5Bl6/N mice at 3 months of age was used for each of the two biological replicates. After sciatic nerve transection, we collected two muscles downstream to the sciatic nerve, the tibialis anterior (TA) and gastrocnemius (GA) muscles. Cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using either scRNAseq (for Non-DEN, DEN2d, DEN5d and DEN15d timepoints) or snATAC-seq (for Non-DEN and DEN5d timepoints).

first: Pier

last: Puri

first: Xiuqing

last: Wei


title: RNA Polymerase II CTD is dispensable for transcription in vivo and required for termination

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

summary: The largest subunit of RNA polymerase (Pol) II harbors a evolutionary conserved C-Terminal-Domain (CTD), composed of a repetition of heptapeptides, central in the transcriptional process. Here, we have analysed the transcriptional phenotypes of a CTD-∆5 mutant that carries a large CTD truncation. Unexpectedly, our results indicate that this mutant can widely transcribe genes in living cells but displays an extreme pervasive phenotype with severely impaired termination, similar to but more severely impaired than previously characterized mutations of CTD tyrosine residues. The CTD-∆5 mutant has also lost its interactions with the Mediator and Integrator complexes involved in activation of transcription and maturation of RNAs. Examination of long-distance interactions and CTCF binding pattern in CTD-∆5 did not indicate major changes in TAD domains or borders. Our data demonstrate that the CTD is largely dispensable for the act of transcription per se in living cells. We propose a model in which CTD-depleted Pol II has a lower entry rate into DNA but becomes extremely pervasive once engaged in transcription, resulting in a global loss of termination.

overall_design: This study was performed in a human Raji cell line. It contains ChIP-seq data for HA-tagged RNA Pol II, H3K4me1, H3K4me3 and CTCF as well as RNA-seq data for PolyA-RNA and chromatin-associated RNA (ChrRNA) and HiC data. All sequencing were performed in paired-end sequencing runs.

first: Yousra

last: Yahia

first: Alexia

last: Pigeot

middle: Z

last: El Aabidine

first: Nilay

last: Shah

first: Nezih

last: Karazu

first: Ignasi

last: Forné

first: Stefan

last: Krebs

first: Helmut

last: Blum

first: Cyril

last: Esnault

first: Tom

last: Sexton

first: Axel

last: Imhof

first: Dirk

last: Eick

first: Jean-Christophe

last: Andrau


title: LY6E is a pan-coronavirus restriction factor in the respiratory tract

city: New. York

first: Katrina

last: Mar

address: 417 E 68th St

institute: MSKCC

summary: LY6E is an antiviral restriction factor that inhibits coronavirus spike-mediated fusion, but the cell types in vivo that require LY6E for protection from respiratory coronavirus infection are unknown. Here, we used a panel of seven conditional Ly6e knockout mice to define which Ly6e-expressing cells confer control of airway infection by murine coronavirus and SARS-CoV-2. Loss of Ly6e in Lyz2-expressing cells, radioresistant Vav1-expressing cells, and non-hematopoietic cells increased susceptibility to murine coronavirus. Global conditional loss of Ly6e expression resulted in clinical disease and higher viral burden after SARS-CoV-2 infection, but little evidence of immunopathology. We show that Ly6e expression protected secretory club and ciliated cells from SARS-CoV-2 infection and prevented virus-induced loss of an epithelial cell transcriptomic signature in the lung. Our study demonstrates that lineage confined rather than broad expression of Ly6e sufficiently confers resistance to disease caused by murine and human coronaviruses.

overall_design: RNA from homogenized lungs was prepared from 6 uninfected wildtype mice (homozygous or heterozygous for Ly6e-flox), 4 uninfected Ly6e KO mice, 7 SARS-CoV-2 infected wildtype mice, and 7 SARS-CoV-2 infected Ly6e KO mice. Lungs were harvested from SARS-CoV-2 infected mice 3 days after intranasal inoculation.

middle: B

first: Alexandra

middle: I

last: Wells

first: Marley

middle: C

last: Caballero Van Dyke

last: Lopez

first: Jennifer

last: Eitson

first: Wenchun

last: Fan

first: Natasha

last: Hanners

first: Bret

last: Evers

first: John

last: Shelton

last: Schoggins


title: Factors controlling somatic reprogramming of transformed tumorigeneic cells to induced pluripotent-like stem cells [ATAC-seq]

first: Andrew

last: Hutchins

overall_design: MEFs were immortalized with combinations of: oncogenes (Myc, Hras, Mef2d, p53DD), viral factors (SV40T, E1A), apoptotic factors (Bcl2), and an engineered epigenetic factor (Hdac7SA; serines 178, 344, and 479 substituted with alanine, to block nuclear export (Luo et al., 2019)). The MEFs were passaged for at least a month to remove untransformed wildtype MEFs. MEFs were treated with the MEK inhibitor (PD; PD0325901), or a Histone deacetylase inhibitor (TSA).

first: Xiuling

last: Fu


title: Spatial Transcriptomics correlated Electron Microscopy

city: Munich

first: Peter

last: Androvic

state: Bavaria

address: Feodor-Lynen-Strasse 17

institute: LMU Hospital, Institute for Stroke and Dementia Research

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Euo is a developmental regulator that represses late genes and activates midcycle genes in C. trachomatis

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

institute: University of California Irvine

summary: The pathogenic bacterium Chlamydia reproduces via an unusual intracellular developmental cycle in which it converts from a dividing form (reticulate body or RB) to an infectious form (elementary body or EB). The transcription factor Euo has been proposed as a developmental regulator in C. trachomatis because it repressed a number of late chlamydial promoters, which are transcribed during RB-to-EB conversion. To define the Euo regulon, we performed a genome-wide study that combined Euo DNA Immunoprecipitation-seq (DIP-seq) studies with RNA-seq analysis of HeLa cells infected with an Euo-overexpressing C. trachomatis strain. We demonstrate that Euo directly regulates ~7% of C. trachomatis genes. However, only about half were downregulated (28/61; 45.9%) by Euo overexpression while paradoxically the other half were upregulated (33/61; 54.1%). Intriguingly, all downregulated genes were late genes, while the majority of upregulated genes were midcycle genes, which are transcribed during RB replication. DIP analysis showed that Euo occupancy sites were restricted to the core promoter region for downregulated genes, but were located over a wider region immediately upstream of the promoter for upregulated genes. We also found that Euo controls its own expression through a negative feedback mechanism. Electron microscopy analysis of cells infected with the Euo-overexpressing strain showed fewer EBs, consistent with a block in RB-to-EB conversion, as well as fewer and larger RBs. Together, these findings broaden the role of Euo as a developmental regulator that functions as both a transcriptional repressor of late genes and a transcriptional activator of midcycle genes in C. trachomatis.

overall_design: Total RNA from C. trachomatis infected HeLa cells purified, rRNA depleted, total cDNA constructed and sequenced

first: Owais

last: Rashid

first: Ming

last: Tan

first: Cuper

last: Ramirez


title: Subfunctionalized expression drives evolutionary retention of ribosomal protein paralogs Rps27 and Rps27l in vertebrates

city: Palo Alto

first: Maria

last: Barna

address: 240 Pasteur Dr, BMI 4500

department: Genetics

summary: The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.

overall_design: Ribosome profiling of the total ribosome fraction and FLAG-immunoprecipitated (IP) ribosome fraction from Rps27-FLAG, Rps27l-FLAG, and untagged wild-type (WT) control mouse embryonic stem cells (mESCs). IP ribosome fractions from Rps27-FLAG and Rps27l-FLAG mESCs represent Rps27- and Rps27l-containing ribosomes, respectively. All samples were collected in triplicate.

first: Adele

last: Xu


title: Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with alpha amanatin treatment to inhibit transcription

first: Giada

last: Forte

summary: NG-Capture-C profiling of chromatin interactions (using DpnII 3C and Oligo nucleotide sequence capture followed by Next generation sequencing) of enhancers, promoters and CTCF/Rad21 binding sites throughout a ~600kb region of the mouse Pax6 locus in β-TC3 cells treated with alpha amanitin. β-TC3 cell are a mouse pancreatic β cell derived from mouse insulinoma.

overall_design: β-TC3 mouse cells were analysed after being treated either with alpha amanitin or with mock treatment (PBS alone).  Two separate panels of capture oligos were used (denoted the CTCF pool and the PROM pool), with two biological replicates generated in each case.

first: G

first: A

last: Buckle

first: S

last: Boyle

first: D

last: Marenduzzo

first: N

last: Gilbert

first: C

last: Brackley


title: Cooperative regulation of Zhx1 and hnRNPA1 drives the cardiac progenitor-specific transcriptional activation during cardiomyocyte differentiation.

first: Li

last: Jianguo


title: Characterisation by Next generation Capture-C of Pax6 locus in a mouse cell line with bleomycin treatment to relieve topological stress

overall_design: β-TC3 mouse cells were analysed after being treated either with bleomycin or with mock treatment (PBS alone).  Two separate panels of capture oligos were used (denoted the CTCF pool and the PROM pool), with two biological replicates generated in each case.


title: Effect of cholesterol  overload on gene expression of hepatic macrophages isolated from normal and NASH livers.

status: Public on Jun 20 2023

city: Nagoya

first: Michiko

last: Itoh

state: Aichi

address: Furo-cho, Chikusa-ku

department: Research Institute of Environmental Medicine

institute: Nagoya University

summary: Hepatocyte death plays a critical role in the disease progression from simple steatosis to non-alcoholic steatohepatitis (NASH). We have previously reported that hepatocyte death locally induces phenotypic changes in the macrophages surrounding the corpse and remnant lipids, thereby promoting liver fibrosis in a murine model of NASH. Here, we demonstrated free cholesterol was accumulated in macrophages around dead hepatocytes containing cholesterol crystals. In vitro experiments revealed that cholesterol-induced lysosomal stress triggered profibrotic activation in macrophages predisposed to the steatotic microenvironment. This study provides evidence that dysregulated cholesterol metabolism in macrophages would be a novel mechanism of NASH.

overall_design: Hepatic macrophages were isolated from normal livers of wild-type mice fed a standard diet or steatotic livers of MC4R-KO mice fed a Western diet for 6 to 10 weeks using anti-F4/80 antibodies and magnetic separation columns. Macrophages were treated with cholesterol crystals at a dose of 500 μg/ml for 24 hours. RNA sequencing analysis was performed to compare the response to lysosomal stress induced by cholesterol crystals.

first: Yasuyoshi

last: Oka

first: Tomoo

last: Ogi

first: Takayoshi

last: Suganami


title: ASH2L Regulates Postnatal Neurogenesis through Onecut2-mediated Inhibition of TGF-β Signaling Pathway

city: beijing

first: Peipei

last: liu

address: No. 25-1 West Beisihuan Rd, Haidian District, Beijing

department: State Key Laboratory of Stem cells and Reproductive Biology

institute: institute of zoology,Chinese academy of sciences

summary: We applied whole transcriptome analysis of P7 NSPCs  from WT/Ash2l-iKO mice to gain insight into genes that might be dysregulated and transcriptionally different after Ash2l deletion.

overall_design: Total RNA was extracted from the FACS-sorted NSPCs that collected from freshly dissociated P7 cortex Nestin-CreERT2; Ash2lf/f; tdTomato and Nestin-CreERT2; tdTomato mice, in four biological replicates, using Illumina Hiseq4000.

first: Ya-Jie


title: On salt stress PLETHORA signalling maintains root meristems

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

summary: Salinity represses plant root growth, resulting in reduced biomass of agricultural plants. Little is known about how plants maintain root growth and development to counteract salt stress. SOS2-mediated PLT1/2 phosphorylation stabilizes PLT1/2, which is critical for root apical meristem maintenance under salt stress.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for gl1 and sos2-2 mutant.

first: Rong

last: Hao

first: Wenkun

last: Zhou

first: Yan

last: Guo


title: Immunological modifications following chemotherapy are associated with delayed recurrence of ovarian cancer

city: Detroit

first: Gil

middle: G.

last: Mor

state: Michigan

address: 275 E. Hancock

department: C.S. Mott Center for Human Growth and Development

institute: Wayne State University School of Medicine

summary: This study was conducted to determine why some high grade serous ovarian cancer (HGSOC) patients recur earlier than others following treatment

overall_design: Tumor samples were obtained from twenty-four patients diagnosed with FIGO Stage III / IV HGSOC before and after they were treated with 6 cycles of Carboplatin and Paclitaxel

first: Nicholas

last: Adzibolosu

first: Ayesha

last: Alvero

first: Rouba

last: Ali-Fehmi

first: Radhika

last: Gogoi

first: Logan

last: Corey

first: Roslyn

last: Tedja

first: Hussein

last: Chehade

first: Vir

first: Robert

last: Morris

first: Matthew

last: Anderson

first: Julie

last: Vitko

first: Clarissa

last: Lam

first: Douglas

last: Craig

first: Sorin

last: Dragichi

first: Thomas

last: Rutherford


title: Spatial Transcriptomics correlated Electron Microscopy [MERFISH]

first: Peter

last: Androvic

summary: Current spatial transcriptomics methods provide molecular and spatial information but no morphological readout. Here, we present STEM - a method that correlates multiplexed error-robust FISH with electron microscopy from neighboring tissue sections of the same sample. STEM links transcriptional and spatial organization of single cells with ultrastructural morphology of the tissue in vivo. Using STEM to characterize demyelinated white-matter lesions allowed us to link morphology of myelin-laden foamy microglia to transcriptional signature. Moreover, we revealed that interferon-response microglia have unique morphology and are enriched near CD8 T-cells.

overall_design: Brain sections were collected from mice after unilaterally induced demyelination injury and analyzed by MERFISH

first: Ozgun

last: Gokce


title: Genomic innovation and horizontal gene transfer shaped plant colonization and biomass degradation strategies of a globally prevalent fungal pathogen

city: Richmond

first: Jonathan

middle: Michael

last: Plett

state: NSW

address: Bourke St. Entrance, Building L9

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

summary: Members of the fungal genus Armillaria are necrotrophic pathogens with efficient plant biomass-degrading strategies. Armillaria species are some of the largest terrestrial organisms on Earth that cause tremendous losses in diverse ecosystems. Despite their global importance, how Armillaria evolved pathogenicity in a clade of dominantly non-pathogenic wood-degraders (Agaricales) remains elusive. Here, using new genomic data, we show that Armillaria species, in addition to widespread gene duplications and de novo gene origins, acquired at least 1,025 genes via 124 horizontal gene transfer (HGT) events, primarily from Ascomycota donors. Functional and expression data suggest that HGT might have affected plant biomass-degrading and virulence abilities of Armillaria, two pivotal traits in their lifestyle. HGT provides an explanation for their soft-rot like biomass degrading strategy, which is which is markedly different from the primarily white rot decay mechanism of related species. Combined multi-species expression data revealed extensive regulation of horizontally acquired and wood-decay related genes, putative virulence factors as well as novel conserved pathogenicity-induced small secreted proteins (PiSSPs), two of which were experimentally verified to induce necrosis in live plants. Overall, this study details how evolution knitted together horizontally and vertically inherited genes in complex adaptive traits, such as plant biomass degradation and pathogenicity in one of the most influential fungal pathogens of temperate forest ecosystems.

sample_organism:
Eucalyptus grandis
Armillaria luteobubalina

overall_design: In total 28 samples were analysed by RNA-sequencing of which 20 samples included 4 replicates each of 5 timepoints of symbiosis between Eucalyptus grandis and Armillaria luteobubalina (24 hours pre-symbiosis, and 24 hrs, 48 hrs, 1 week, 2 week post contact). The remaining eight samples included RNA from axenically grown A. luteobubalina and E. grandis. All organisms and symbiotic compartment was performed on ½ strength Modified Melin Norkans Medium (with 1g/L of glucose rather than 5 g/L).

middle: M

first: Johanna

last: Wong-Bajracharya

first: Neha

last: Sahu

first: Laszlo

last: Nagy


title: Spatial Transcriptomics correlated Electron Microscopy [scRNA-Seq]

summary: Current spatial transcriptomics methods identify cell types and states in a spatial context but lack morphological information. Electron microscopy, in contrast, provides structural details at nanometer resolution without decoding the diverse cellular states and identity.  STEM address this limitation by correlating multiplexed error-robust FISH with electron microscopy from adjacent tissue sections. Using STEM to characterize demyelinated lesions in mice, we were able to bridge spatially resolved transcriptional data with morphological information on cell identities. This approach allowed us to link the morphology of foamy microglia and interferon-response microglia with their transcriptional signatures.

overall_design: CD11b+ cells were isolated by flow-cytometry from brain white and grey matter of control mice and mice with white-matter demyelination injury induced by lysophosphatidylcholine injection and analyzed by scRNA-Seq


title: Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes [scRNA-seq]

city: PHILADELPHIA

first: XING`

last: JI

state: PA

address: 3401 Civic Center Blvd

institute: Children's hospital of Philadelphia

summary: Type I diabetes (T1D) impairs bone accrual in patients, but the mechanism is unclear.  Here in a murine monogenic model for T1D, we demonstrate that diabetes suppresses bone formation resulting in a rapid loss of both cortical and trabecular bone.  Single-cell RNA sequencing uncovers metabolic dysregulation in bone marrow osteogenic cells of the diabetic mice.  In vivo stable isotope tracing reveals impaired glycolysis in diabetic bone that is highly responsive to insulin stimulation.  Remarkably, deletion of the insulin receptor reduces cortical but not trabecular bone.  Increasing glucose uptake by overexpressing Glut1 in osteoblasts exacerbates bone defects in T1D mice.  Conversely, activation of glycolysis by Pfkfb3 overexpression preserves both trabecular and cortical bone mass in the face of diabetes.  The study identifies defective glucose metabolism in osteoblasts as a pathogenic mechanism for osteopenia in T1D, and furthermore implicates boosting osteoblast glycolysis as a potential anabolic therapy.

overall_design: single-cell RNA-sequencing profiling of endosteal cells from WT and Akita at 8 weeks and 20weeks, n=1 for each genotype

first: Xing

last: Ji

first: Fanxin

last: Long


title: Cell Line-Specific Features of 3D Chromatin Organization in Hepatocellular Carcinoma

city: Daejeon

first: YEONWOO

last: KIM

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

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


title: Single Cell Transcriptomic Analysis in a Mouse Model of Barth Syndrome Reveals Cell-Specific Alterations in Gene Expression and Intercellular Communication

city: Boston

first: Gayani

last: Perera

address: 800 Washington Street

department: MCRI

institute: Tufts Medical Center

summary: To identify novel, cell-specific, pathological pathways that mediate heart dysfunction in Barth Syndrome, we performed single-nucleus RNA-sequencing (snRNA-seq) on wild type and Tafazzin-knockout mouse hearts.

overall_design: Four wild type and four Tafazzin-knockout mouse hearts were sampled to analyze using snRNA-seq.

first: Michael

last: Chin

first: Liam

last: Power


title: Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes


title: Dynamic changes in the transcriptome of tRNA-derived small RNAs related with fat metabolism II

city: Chengdu

first: mailin

last: gan

state: Sichuan

address: No. 211, Huimin Road, Wenjiang District, Chengdu, Sichuan, China

institute: Sichuan Agricultural University

summary: The prevalence of obesity and overweight is steadily rising, posing a significant global challenge for humanity. The fundamental cause of obesity and overweight lies in the abnormal accumulation of adipose tissue. While numerous regulatory factors related to fat deposition have been identified in previous studies, a considerable number of regulatory mechanisms remain unknown. tRNA-derived small RNAs (tsRNAs), a novel class of non-coding RNAs, have emerged as significant regulators in various biological processes. In this study, we obtained small RNA sequencing data from subcutaneous white adipose tissue and omental white adipose tissue of lean and obese pigs. In addition, we similarly obtained tsRNAs profiles from scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epigonadal white adipose tissue (eWAT) of normal mice. Finally, we successfully identified a large number of expressed tsRNAs in each tissue type and identified tsRNAs conserved in different adipose tissues of pigs and mice. These datasets will be a valuable resource for elucidating the epigenetic mechanisms of fat deposition.

overall_design: So to investigate the role of tsRNAs in fat deposition, we collected subcutaneous white adipose tissue and omental white adipose tissue from both Qingyu pig (obese pig) and Yorkshine (lean pig) and obtained their tsRNAs sequencing data. In addition, we also obtained tsRNAs sequencing data of scapular brown adipose tissue (BAT), inguinal white adipose tissue (iWAT) and epigonadal white adipose tissue (eWAT) from normal C57BL/6j mice.

first: Tianci

last: Liao

first: Mailin

last: Gan

first: Linyuan

last: Shen

first: Li

last: Zhu


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [Placenta_TFAP2C_ChIP]

city: Kansas City

first: Boryana

last: Koseva

state: MO

address: 2420 Pershing Road

department: CMRI

institute: Children's Mercy Hospital

summary: The extravillous trophoblast (EVT) cell lineage is a key feature of placentation and critical for spiralartery remodeling and successful pregnancy. Our knowledge of transcriptional regulation driving EVT cell development is limited. Here, we mapped the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem (TS) cells and their transition into the differentiated EVT cell lineage. We identified that chromatin accessibility in intergenic regions was more extensive in EVT cells than in TS cells in the stem state, which is indicative of increased enhancer-driven gene regulation. Using reference epigenome annotation, we noted that 18% of the chromatin landscape in EVT cells was uncharted. We linked regulatory regions to their cognate target genes and characterized the three-dimensional organization of the TS cell functional genome by Hi-C. Integrational analysis of chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enabled identification of transcription factors and regulatory mechanisms associated with EVT cell lineage development. Subsequent analyses elucidated functional roles forTFAP2C,EPAS1,SNAI1, andDLX6in the regulation of EVT cell lineage development.EPAS1was identified as an upstream regulator of EVT cell transcription factors, includingSNAI1andDLX6, and was found to be upregulated in idiopathic recurrent pregnancy loss. Collectively, we have revealed activation of a dynamic regulatory network that provides a framework for understanding EVT cell specification in trophoblast cell lineage development and human placentation.

overall_design: ChIP was performed on CT27 human TS cells in three replicates using the SimpleChiP Enzymatic Chromatin IP kit (Cell Signaling Technology. Anti-rabbit AP-2 gamma antibody (1:50, 2320, Cell Signaling) was used in the analysis.

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

first: Ayelen

last: Moreno-Irusta

first: Ross

last: McNally

first: Emily

last: Wesley

first: Khursheed

last: Iqbal

first: Warren

last: Cheung

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Lydic

last: Michael

first: Holoch

last: Kristin

first: Courtney

last: Marsh

middle: J

last: Soares

first: Elin

last: Grundberg


title: ELL3 promotes stem cell native to primed transition through LINE-based enhancers [4C-seq]

city: Nanjing

first: Xiaoxu

last: Liu

address: 2 Sipailou

department: Institute of Life Sciences

institute: Southeast University

summary: Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos. Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure. ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells. We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

first: Chenqi

last: Lin


title: Determination of steady-state transcriptome modifications associated with repeated homotypic stress in the rat rostral posterior hypothalamic region

city: Boulder

first: Serge

last: Campeau

address: 2860 Wilderness Place

department: Psychology and Neuroscience

institute: University of Colorado Boulder

summary: Chronic stress is epidemiologically correlated with physical and psychiatric disorders. Whereas many animal models of chronic stress induce symptoms of psychopathology, repeated homotypic stress typically fails to induce these symptoms and may even protect against the effects of subsequent stress exposures. Recent results indicate that the rostral posterior hypothalamic (rPH) region is a significant component of the brain circuitry underlying response reductions (habituation) associated with repeated homotypic stress. To test whether posterior hypothalamic transcriptional regulation associates with the behavioral modifications induced by repeated homotypic stress, RNA-seq was performed in the rPH dissected from adult male rats that experienced either no stress, 1, 3, or 7 stressful loud noise exposures. Plasma samples displayed reliable increases of corticosterone in all stressed groups, with the smallest increase in the group exposed to 7 loud noises, indicating significant habituation compared to the other stressed groups. While no differentially expressed genes were detected 24-hrs after a single loud noise exposure, 36 and 405 transcripts were differentially expressed between the control vs 3-stress and control vs 7-stress groups, respectively, which correlated with the corticosterone habituation observed. Gene ontology analyses indicated multiple significant functional terms related to neuron differentiation, neural membrane potential, pre- and post-synaptic elements, chemical synaptic transmission, vesicles, axon guidance and projection, glutamatergic and GABAergic neurotransmission. Some of the differentially expressed genes (Zmat4, Dlx6) encoded transcription factors that were independently predicted by transcription factor enrichment analysis to target other differentially regulated genes in the set. A similar experiment employing in situ hybridization histochemical analysis in additional animals validated the direction of change of the 5 transcripts investigated (Camk4, Gabrb2, Gad1, Grin2a and Slc32a) with a high level of temporal and regional specificity for the rPH. In aggregate, the results suggest that distinct patterns of gene regulation are obtained in response to repeated homotypic vs. heterotypic stress regimens; they also point to a significant reorganization of the rPH region that may critically contribute to the phenotypic modifications associated with repeated homotypic stress habituation.

overall_design: Gene expression profiling of RNA-seq data generated from 4 groups (n=6/group) of independent rat brains in the rostral posterior hypothalamic region after control, 1, 3 or 7 30-loud noise presentations.

first: Connor

last: McNulty

first: Jacob

last: Stanley

first: Anthony

middle: N

last: Gerber

first: Sarah

last: Sasse

first: Robin

last: D Dowell


title: GATA3 induces the pathogenicity of Th17 cells via regulation of GM-CSF expression

city: Bethesda

first: Jinfang

last: Zhu

state: MD

address: 10 Center Drive, Building 10, Room 11D02

department: National Institute of Allergy and Infectious Disease

institute: National Institutes of Health

summary: To investigate the effects of a late deletion of Gata3 on CD4 T cell gene expression profiles in experimental autoimmune encephalomyelitis, we performed a RNA-Seq analysis of Gata3-sufficient (i.e., Cd45.1/Cd45.2 or vehicle treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 fl/fl) and Gata3-deficient (i.e., tamoxifen-treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl) CNS-infiltrating CD4+ effector T cells from mixed congenic co-transfer recipient mice. We performed a gene expression profiling analysis using data obtained from RNA-seq from 2 mixed congenic adoptive transfer receipient vehicle-treated mice and 2 mixed congenic adoptive transfer receipient tamoxifen-treated mice for a total of 8 biological samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CNS infiltrating CD3+CD4+CD44 high T effector cells from vehicle or tamoxifen treated mixed congenic transfer recipient Tcra-/- mice. Vehicle-treated Cd45.1/Cd45.2 effector T cells, vehicle-treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl effector T cells, tamoxifen-treated Cd45.1/Cd45.2 effector T cells, and tamoxifen-treated Cd45.2/Cd45.2 Cre-ERT2 Gata3 Fl/Fl effector T cells were collected and studied.

first: Matthew

last: Butcher


title: ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ATAC-seq]

summary: Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naÃ¯ve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naÃ¯ve-primed transition through regulating the young LINE-1 based enhancers.

overall_design: ATAC-seq

first: Chengqi


title: Genetic activation of glycolysis in osteoblasts preserves bone mass in type I diabetes [bulkRNA-seq]

first: XING`

last: JI

overall_design: WT and Akita at 20 weeks, n=4 for each genotype

first: Xing

last: Ji

first: Fanxin

last: Long


title: R-loop dependent promoter-proximal termination ensures genome stability [PRO-seq]

city: Shanghai

first: Jiwei

last: Chen

address: 130 DongAn Road

institute: Fudan University

summary: Precise regulation of transcription is essential to maintain genome integrity, yet key mechanisms coordinating transcription, genome stability and downstream cellular functions remain incomplete. Here we report the identification of SOSS-INTAC, a stable association of the genome stability regulator Sensor of Single-stranded DNA (ssDNA) (SOSS) complex and transcription regulator Integrator-PP2A (INTAC). Via SSB1-mediated ssDNA recognition at its targets, SOSS-INTAC stimulates early termination of transcription and thus attenuates paused Pol II-induced formation of R-loops to prevent its aberrant accumulation that has the risk of increasing chromatin accessibility and compromising genome stability. SOSS-INTAC-mediated attenuation of R-loops is greatly enhanced by SSB1's unique property of forming liquid-like condensates. In contrast, preventing SSB1 condensation through deletion or cancer-associated mutation within its intrinsically disordered region (IDR) leads to pervasive accumulation of R-loops at a genome-wide level. Thus, our study highlights the genomic surveillance function of SOSS-INTAC that enables timely transcriptional termination to constrain aberrant R-loop accumulation and ensure genomic stability.

overall_design: PRO-seq with 2 biological replicates in DLD-1 cells.

first: Congling

last: Xu

first: Chengyu

last: Li

first: Yan

last: Xiong

first: Huasong

last: Lu

first: Fei

middle: X


title: R-loop dependent promoter-proximal termination ensures genome stability

overall_design: Refer to individual Series


title: R-loop dependent promoter-proximal termination ensures genome stability [KAS-seq]

overall_design: KAS-seq with 2 biological replicates in DLD-1 cells.


title: Global Epigenome and Transcriptome Maps of Human Trophoblast Cell Lineage Development [Placenta_ChIP]

first: Boryana

last: Koseva

overall_design: ChIP was performed on a hTSC line,TSCT-1 (CT27), established in our previous study (Okae et al. Cell Stem Cell 2018) using the ChIP Reagents (NIPPON GENE).

first: Kaela

last: Varberg

first: Esteban

last: Dominguez

first: Ayelen

last: Moreno-Irusta

first: Ross

middle: P

last: McNally

first: Emily

last: Wesley

first: Khursheed

last: Iqbal

first: Warren

last: Cheung

first: Hiroaki

last: Okae

first: Takahiro

last: Arima

first: Lydic

last: Michael

first: Holoch

last: Kristin

first: Courtney

last: Marsh

first: Michael

last: Soares

first: Elin

last: Grundberg


title: Thymic epithelial cell potency and fate in early organogenesis assessed by single cell transcriptional and functional analysis. [10x Genomics]

city: oxford

first: Sam

last: Palmer

address: mathematics institute, radcliffe observatory quarter

institute: university of Oxford

summary: During development, cortical (c) and medullary (m) thymic epithelial cells (TEC) arise from the third pharyngeal pouch endoderm.  Current models suggest that within the thymic primordium most TEC exist in a bipotent/common thymic epithelial progenitor cell (TEPC) state able to generate both cTEC and mTEC, at least until embryonic day 12.5 (E12.5) in the mouse.  This view however, is challenged by recent transcriptomics and genetic evidence.  We therefore set out to investigate the fate and potency of TEC in the early thymus.  Here using single cell (sc) RNAseq we identify a candidate mTEC progenitor population at E12.5, consistent with recent reports.  Via lineage-tracing we demonstrate this population is mTEC fate-restricted, validating our bioinformatics prediction.  Using potency analyses we also establish that most E11.5 and E12.5 progenitor TEC are cTEC-fated.  Finally we show that overnight culture causes most if not all E12.5 cTEC-fated TEPC to acquire functional bipotency, and provide a likely molecular mechanism for this changed differentiation potential.  Collectively, our data overturn the widely held view that a common TEPC predominates in the E12.5 thymus, showing instead that sublineage-primed progenitors are present from the earliest stages of thymus organogenesis but that these early fetal TEPC exhibit cell-fate plasticity in response to extrinsic factors.  Our data provide a significant advance in understanding of fetal thymic epithelial development and thus have implications for thymus-related clinical research, in particular research focussed on generating TEC from pluripotent stem cells.

overall_design: E12.5 and E13.5 wild type (WT), E12.5 and E13.5 Rosa26CreERt2;iFoxn1 (iFoxn1; called enforced Foxn1) and E12.5 and E13.5 Rosa26CreERt2 (called Cre-only)  fetal thymi were microdissected.  The samples processed for library preparation were as follows: (i) Freshly isolated wild type E12.5 and E13.5 and E12.5 iFoxn1 and Cre-only lobes were dissociated to single cell suspensions using TrypLE Express (Life Technologies 12604013) as above and immediately processed for library preparation; (ii) E12.5 wild type, iFoxn1 and Cre-only lobes were cultured overnight as intact lobes at the air-liquid interface (i.e. standard fetal thymic organ culture [FTOC] conditions, called FTOC), then processed to single cell suspensions using TrypLE Express; and (iii)  E12.5 wild type, iFoxn1 and Cre-only lobes were dissociated to single cell suspensions and cultured overnight as monolayers (called monolayer), then harvested using TrypLE Express.

first: An

last: Chengrui

first: Alison

last: Farley

first: Dong

last: Liu

first: Anastasia

last: Kousa

first: Paul

last: Rouse

first: Viktoria

last: Major

first: Joanna

last: Sweetman

first: Jan

last: Morys

first: Andrea

last: Corsinotti

first: Jennifer

last: Nichols

last: Ure

first: Renee

last: McLay

first: Luke

last: Boulter

first: Jon

last: Chapman

first: Simon

middle: R

last: Tomlinson

first: Clare

last: Blackburn


title: R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

first: Jiwei

last: Chen

overall_design: CUT&Tag sequencing for Rloop, rH2AX, XRN2, MTR4, DIS3 and EXOSC10 in DLD-1 cells.

first: Congling

last: Xu

first: Chengyu

last: Li

first: Yan

last: Xiong

first: Huasong

last: Lu

first: Fei


title: R-loop dependent promoter-proximal termination ensures genome stability [ATAC-seq]

overall_design: ATAC-seq with 2 biological replicates in DLD-1 cells.


title: Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain (RNA-Seq)

city: Montreal

first: Arthur

middle: Jules

last: Gouhier

state: Quebec

address: 110 Avenue des Pins

country: Canada

institute: IRCM

summary: Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL- isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggest complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.

overall_design: RNA-seq in AtT-20 cell line

first: Virginie

last: Bascunana

first: Audrey

last: Pelletier

first: Amandine

last: Bemmo

first: Aurelio

last: Balsalobre

first: Jacques

last: Drouin


title: Transcriptional profiling of IRF8 KO B cell differentiation

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

summary: To understand the gene expression programs regulated by IRF8 in B cells responding to LPS stimulation we generated IRF8 deficient B cells by CRISPR/Cas9.  IRF8 knockout and wild-type CD43- splenic B cells were isolated and directly used for RNA-seq (naive B cells) or simulated to differentiate with LPS, IL2, and IL5 for 3 days.  At this time activated Bcells and plasmablasts were sorted for RNA-seq.

overall_design: IRF8 knockout B cells and WT B cells representing naïve, activated B cells, and plasmablasts were isolated in triplicate for RNA-seq

first: Christopher

middle: D


title: ELL3 promotes stem cell native to primed transition through LINE-based enhancers [RNA-Seq]

first: Xiaoxu

last: Liu

summary: Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

overall_design: RNA-Seq

first: Chengqi

last: Lin