title: Menin is a ‘reader’ of histone H3 lysine 79 methylation (RNA-Seq)

city: Hong Kong

first: Jason

last: Wong

address: L1-51, 21 Sassoon Road

department: School of Biomedical Sciences

institute: The University of Hong Kong

summary: Methylation of histone H3 lysine-79 is an epigenetic mark for gene regulation in development, cellular differentiation and disease progression. However, it remains poorly understood how this histone mark is translated into downstream effects due to the lack of knowledge of H3K79 methylation ‘readers’. Here, we develop a nucleosome-based photoaffinity probe to capture proteins that recognize H3K79 dimethylation (H3K79me2) in nucleosomal context. In combination with a quantitative proteomics approach, this probe identifies menin as a bona fide “reader” for H3K79me2. Menin directly and selectively binds to the nucleosome with H3K79me2 mark in vitro. In cells, menin is tightly associated with this histone mark on chromatin, particularly in gene bodies. Reading H3K79me2 at intragenic enhancers, menin promotes gene transcription, likely by mediating enhancer–promoter interactions.

overall_design: MCF7 cells were treated with EPZ5676 or DMSO control. RNA-seq was performed in triplicates for each condition.

first: Xiang

middle: D

last: Li

first: Xiucong

last: Bao


title: Menin is a ‘reader’ of histone H3 lysine 79 methylation

status: Public on Feb 17 2023

country: China

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: A balance of de novo and maintenance activities governs epigenetic inheritance of CG methylation in Arabidopsis transposons

city: Norwich

first: David

middle: B.

last: Lyons

state: Norfolk

address: Colney Lane

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

type: Expression profiling by high throughput sequencing

summary: Dnmt1/MET1 methyltransferases mediate the epigenetic inheritance of cytosine methylation within CG dinucleotides (mCG). These enzymes use a semiconservative mechanism previously expected to produce binary present/absent methylation patterns. However, we show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic mCG is quantitatively associated with transposon expression and is stably inherited across many generations. We develop a mathematical model that estimates the rates of semiconservative maintenance failure and de novo methylation at each transposon, demonstrating that mCG can be stably inherited at any level via a dynamical balance of these activities. We find that DRM2 – the core methyltransferase of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic de novo mCG, with de novo rates orders of magnitude higher than previously thought, whereas chromomethylases make smaller contributions. Our results demonstrate that mCG epigenetic inheritance in plant heterochromatin is highly dynamic, with CG sites frequently switching methylation states.

overall_design: Bisulfite sequencing was carried out on inbred h1ddm1 mutants and compound methyltransferase mutants to monitor changes in methylation over transgenerational time.  RNA-seq was carried out on an early generation (F3) set of h1ddm1 and control sibling cohort to measure differences in transposon transcription.

middle: B


title: Hypoxia potentiates the inflammatory fibroblast phenotype promoted by pancreatic cancer cell-derived cytokines

status: Public on Feb 18 2023

city: Chicago

first: Simon

last: Schwoerer

address: 900 E 57th St

country: USA

institute: University of Chicago

summary: Cancer-associated fibroblasts (CAFs) are a major cell type in the stroma of solid tumors and can exert both tumor-promoting and tumor-restraining functions. This functional heterogeneity is correlated with the existence of transcriptionally distinct subpopulations of CAFs. While CAF heterogeneity can be driven in part by tumor cell-produced cytokines, other determinants shaping CAF identity and function are largely unknown. Here, we investigated the role of hypoxia in regulating CAF heterogeneity in PDAC

overall_design: RNA-sequencing of PSC cells expressing a control sgRNA (R26-sg1) or HIF-1a targeting sgRNA (HIF1a-sg2), cultured in normoxia (20% O2) or hypoxia (0.5% O2) for 48h

last: Schwörer

first: Craig

last: Thompson


title: Menin is a ‘reader’ of histone H3 lysine 79 methylation (ChIP-Seq)

overall_design: MCF7 cells were treated with EPZ5676 or DMSO control. ChIP-seq were performed in duplicates with matched input control for each condition and antibody.

middle: W


title: Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast

city: Seattle

first: Mosur

middle: K

last: Raghuraman

state: WA

address: Foege Bldg, 3720 15th Ave NE

department: Genome Sciences Box 355065

institute: University of Washington

type: Genome variation profiling by genome tiling array

summary: Ribosomal DNA (rDNA) is organized as large arrays of tandem repeats that vary in copy number from a few dozen to hundreds.  In the budding yeast Saccharomyces cerevisiae, each rDNA repeat includes a potential origin of replication.  Previous work has led to the model that the rDNA replication origins compete for limiting replication initiation factors with origins in the rest of the genome, suggesting that reduction in rDNA copy number would reduce competition for these limiting factors and therefore promote origin usage in the rest of the genome.  To test this hypothesis, we compared genome-wide replication in strains with either wild type rDNA copy number of ~180 (“180 rDNA”) or just ~35 copies (“35 rDNA”) by performing dense-to-light isotope transfer experiments to physically separate replicated, hybrid-density (HL or heavy-light) DNA from unreplicated, HH (heavy-heavy) DNA in cell samples collected at different times in S phase.  Contrary to our expectations, we find that although there are no apparent differences in non-rDNA origin activity between the two strains, the 35 rDNA strain shows a genome-wide delay in progression through S phase compared to the 180 rDNA strain.

overall_design: To profile genome-wide replication, we grew cells in isotopically dense (13C-glucose, 15N-ammonium sulfate) for ≥7 population doublings.  We then arrested the cells in G1 using a-factor, filtered and resuspended the cells in isotopically light (12C, 14N) medium, then released them into S phase by addition of Pronase.  We collected samples at intervals through the ensuing S phase (30,35,40,45,50 min for 35 rDNA strain; 25,30,35,40,45,55 min for 180 rDNA strain).  We extracted the DNA, and digested it with a restriction enzyme.  Unreplicated (HH) DNA was separated from replicated (HL) DNA by ultracentrifugation in cesium chloride gradients, which were subsequently drip-fractionated.  Small aliquots of each fraction were hybridized on a slot blot with a [32P]-labeled whole-genome probe, both to identify fractions with HH and HL DNA and to quantify the percent replication in each S phase sample.  For each sample, we then pooled all the HH fractions and labeled the DNA with Cy3, likewise labeled the HL DNA with Cy5, and co-hybridized the pair to a microarray.  After extraction of hybridization intensities, we used the known % replication values from the slot blot analysis to normalize the overall % replication in each sample, with an added correction for the percentage of cells in the population that successfully completed S phase (obtained from the maximum % replication seen at the end of S phase from the slot blot analysis).  The normalized % replication values were loess-smoothed with a window of 22 kb and plotted as a function of chromosome coordinate with a step size of 500 bp.  For a detailed description of this protocol, see Peng et al. (2014), Methods Mol Biol 1170:477-99 (PMCID: PMC4338859).

first: Gina

middle: M

last: Alvino

first: Elizabeth

middle: X

last: Kwan

first: M

first: Bonita

middle: J

last: Brewer


title: Effects of ccf-1 RNAi on C. elegans response to cadmium and acrylamide

city: Saskatoon

first: Cheng-Wei

last: Wu

state: SK

address: 52 Campus Drive

country: Canada

institute: University of Saskatchewan

summary: In a genome-wide RNAi screen to identify activators of numr-1, a cadmium responsive gene involved in RNA splicing regulation, we isolated ccf-1 as a gene that is required for cadmium-induced numr-1 activation. The ccf-1 gene encodes a deadenylase within the CCR4-NOT complex that generally serves to suppress gene expression by initiating mRNA degradation. However, a role for ccf-1 as a positive regulator of stress-induced gene expression remains to be characterized. Silencing of ccf-1 inhibits various classes of cadmium-inducible genes including several glutathione-s-transferase (gst) and heat shock protein genes. RNAi knockdown of ccf-1 significantly reduces lifespan and decreases survival in cadmium, implicating a role for ccf-1 in aging and stress protection. The ccf-1 gene is also required for resistance against acrylamide with RNAi depletion of ccf-1 inhibiting acrylamide-induced gst induction, decreasing survival in acrylamide stress, and increasing C. elegans sensitivity to acrylamide-induced neurodegeneration. Using RNA-sequencing, we observed that ccf-1 regulates ~28-35% of all genes induced by cadmium (500 out of 1802 DEG) or acrylamide (296 out of 851 DEG) by >2-fold. Clustering analysis of ccf-1 dependent cadmium or acrylamide up-regulated genes indicate significant enrichment to glutathione and cytochrome P450 metabolism, suggesting a central role for ccf-1 in regulating antioxidant defense across different stressors. Using a CCF-1::GFP translational reporter, we find that CCF-1 is broadly expressed in the intestine, muscle, and hypodemis. Interestingly, CCF-1::GFP strongly localizes to the intestinal nuclei, implicating a potential nuclear role for CCF-1 in transcriptional regulation that is distinct for its deadenylase function in the cytoplasm

overall_design: Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq.


title: Fumarate induces vesicular release of mtDNA to drive innate immunity

city: London

first: Shamith

last: Samarajiwa

address: ICTEM Building, Hammersmith Campus, Du Cane Road,

department: Genetics and Genomics Section  Department of Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: Fumarate Hydratase (FH) is an enzyme of the Tricarboxilic Acid Cycle (TCA) that catalyzes the conversion of fumarate into malate. In the last decade, studies have revealed FH as a bona fide tumour suppressor whose mutations cause Hereditary leiomyomatosis and renal cell carcinoma (HLRCC). Loss of FH in the kidney elicits several oncogenic signalling cascades through the accumulation of the oncometabolite fumarate. Yet, whilst the long-term consequences of FH loss have been extensively described, the acute response to FH loss has not been investigated due, in part, to the lack of a suitable model. Here, we generated a new inducible mouse model to investigate the chronology of the murine homologue of FH, Fh1, loss in the adult kidney.

overall_design: Mice were of mixed genetic background C57BL/6 and 129/SvJ. Fh1fl/fl (Pollard et al., 2008) and R26Creert2 (Hameyer et al., 2007) mice were crossed to generate animals homozygous for the conditional LoxP-exon3/4-LoxP Fh1 allele and expressing the Cre–recombinase-ert2 fusion under control of the ROSA26 promoter (Fh1 fl/fl; R26 Creert2/Creert2). Littermate controls lacked the LoxP-exon3/4-LoxP allele but also expressed the Cre-ert2 allele under the control of the ROSA26 promoter (Fh1 +/+; R26 Creert2/Creert2). Control mice were induced and sacrificed at the same time as their experimental littermates. Briefly, 12-weeks old animals received 3 x 2mg tamoxifen via intraperitoneal injection (every other day; starting at day 0 of induction), the kidneys were collected at day 5 and day 10 post-induction and total RNA was prepared for sequencing.

first: Vincent

last: Zecchini

first: Dora

last: Bihary

first: Christian

last: Frezza


title: Influenza A virus modulation of Streptococcus pneumoniae infection using ex vivo transcriptomics in a human primary lung epithelial cell

status: Public on Feb 16 2023

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

summary: Deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), alone, together, and after coincubation with Influenza A virus pH1N1.

sample_organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

overall_design: Total RNA was isolated from EF3030 and nHBEC, alone and after co-culture with pH1N1 over time. Ribosomal RNA was depleted and the remaining RNA was reverse-transcribed into a cDNA library for Illumina sequencing. Reads were mapped to the EF3030,and the human genome.

first: Kevin

middle: S

last: Harrod

first: Jennifer

middle: L

last: Tipper

first: Carlos

last: Orihuela

first: Adonis

last: D'Mello

first: Jessica

middle: R

last: Lane

first: Eriel

last: Martínez

first: Holly

middle: N

last: Roussey

first: Hervé

last: Tettelin


title: Pol II Preferentially Regulates Ribosomal Protein Expression by Trapping Disassociated Subunits [TT-seq]

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: Pol II has been recognized as a passively regulated holoenzyme. However, whether Pol II plays specific regulatory roles remain unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, Specific Degradation of Disassociated Subunits (SDDS), we demonstrated that dRPB3 functions as a regulatory component of Pol II to enable the preferential control of 3’ end processing of ribosomal protein genes directly through N-terminal domain of RPB3. Machine learning analysis of large-scale genomic features revealed that the little elongation complex helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3’ end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that Pol II gains specific regulatory functions by trapping disassociated subunits.

overall_design:
We performed ChAR-seq, TT-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours; refer to individual Series. For TT-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the HEK293T cells were used as the spike-in cells.
This dataset includes the TT-seq data.

first: Yuanjun

last: Li

first: Jie

last: Huang

first: Lijun

last: Bao

first: Junyi

last: Zhu

first: Wenjia

last: Duan


title: scRNA-seq of cancer and CD8+ cells during early metastasis identifies targetable subpopulations and immune evasion mechanisms

city: Singapore

first: Yiqun Elaine

last: Cao

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identified a sub-population of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunted tumor invasion in patient-derived cultures. Furthermore, scRNAseq analyses of tumor-infiltrating CD8+ T-lymphocytes showed two distinct trajectories to T-cell dysfunction, corroborated by their clonal architecture based on single-cell T-cell receptor sequencing. By determining key modulators of these trajectories, followed by validation using external datasets and functional experiments, we uncovered a novel role for SOX4 in mediating T-cell exhaustion. Finally, interactome-analyses between pre-metastatic tumor-cells and CD8+ T-lymphocytes uncovered a putative role for the Midkine pathway in immune-modulation; this was confirmed by scRNAseq of tumors from humanized mice. Aside from specific findings, this study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.

overall_design: Examining the tumor microenvironment of primary and early metastatic from treatment-naïve patient with head and neck squamous cell cancers

first: Hong

last: Quah

first: Elaine

middle: Y

first: N

middle: G

last: Iyer


title: Single-cell transcriptomics to define Plasmodium falciparum stage-transition in the mosquito midgut

city: Stockholm

first: Mubasher

last: Mohammed

state: Stockholm lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

country: Sweden

institute: Stockholm University

summary:
Malaria inflicts the highest rate of morbidity and mortality among the vector-borne diseases. The dramatic bottleneck of parasite numbers that occurs in the gut of the obligatory mosquito vector provides a promising target for novel control strategies. Using single-cell transcriptomics, we analyzed Plasmodium falciparum development in the mosquito gut, from unfertilized female gametes through the first 20 hours post blood feeding, including the zygote and ookinete stages. This study revealed the temporal gene expression of the ApiAP2 family of transcription factors, and of parasite stress genes in response to the harsh environment of the mosquito midgut. Further, employing structural protein prediction analyses we found several upregulated genes predicted to encode intrinsically disordered proteins (IDPs), a category of proteins known for their importance in regulation of transcription, translation and protein-protein interactions. IDPs are known for their antigenic properties and may serve as suitable targets for antibody or peptide-based transmission suppression strategies. In total, this study uncovers the P. falciparum transcriptome from early-to-late parasite development in the mosquito midgut, inside its natural vector, which provides an important resource for future malaria transmission-blocking initiatives.

Single-cell data can be visualized interactively via https://mubasher-mohammed.shinyapps.io/shinyapp/

In-house bash, R code scripts and data that were implemented in this study are available on GitHub https://github.com/ANKARKLEVLAB/Single-cell-P.falciparum-midgut .

overall_design: Plasmodium falciparum NF54 gametocyte producing cell line were committed to sexual stages (gametocytes) and pooled to 1% gametocytaemia and 50% hematocrit. Gametocyte were membrane fed to Anopheles gambiae adult mosquitoes and dissected at time points; 2, 4, 8, 12 and 20 hours post infection, parasites were then isolated using Micromanupulation based on Anti-Pfs25 antibody conjugated to Alexa-flour-488 anti-mouse IgG (H+L) and Hoechst 33342 stain. cDNA libraries were prepared using SMART-seq2 protocol and ScRNA-seq high-through put data were then analyzed using various computational tools.

first: Johan

last: Ankarklev

last: Henriksson


title: Human Hematopoietic Stem Cell Vulnerability to Ferroptosis

city: Boston

first: Jiawei

last: Zhao

state: Massachusetts

address: 1 Blackfan Circle

institute: Boston Children's Hospital


title: Spermiogenesis alterations in the absence of CTCF revealed by single cell RNA sequencing

city: Mexico city

first: Aarón

last: Vázquez-Jiménez

state: Mexico city

address: Periferico Sur 4809

country: Mexico

institute: INMEGEN

summary: In this work, we performed single cell RNA sequencing in spermatogenic cells without CTCF. We uncovered defects in transcriptional programs that explain the severity of the damage in the produced sperm. At early stages of spermatogenesis, transcriptional alterations are mild. As germ cells go throughout the specialization stage or spermiogenesis, transcriptional profiles become more altered. We found spermatid defects that support the alterations in the transcriptional profiles, and thus we conclude that CTCF depletion alters several transcriptional profiles mostly during spermiogenesis. Our data highlights the importance of CTCF at the different stages of spermatogenesis.

overall_design: Testis mRNA profile of 12-15 weeks old Wild Type (Ctcf wt/wt) and Ctcf-cKO (Stra8-iCre-Ctcf f/Δ ) mice

first: Ulises

last: Torres-Flores

first: Fernanda

last: Díaz-Espinosa

first: Tayde

last: López-Santaella

first: Rosa

last: Rebollar-Vega

first: Ian

last: Taylor

first: Rosario

last: Ortiz-Hernández

first: Olga

last: Echeverría

first: Gerardo

middle: H

last: Vázquez-Nin

first: María

middle: C

last: Gutierrez-Ruiz

first: Inti

middle: A

last: De la Rosa-Velázquez

first: Osbaldo

last: Resendis-Antonio

first: Abrahan

last: Hernández-Hernandez


title: Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease

city: Kiel

first: Elisa

last: Rosati

address: Rosalind-Franklin Strasse 12

department: Institute of Clinical Molecular Biology

country: Germany

institute: University of Kiel


title: Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease [bulk TCR-seq]

summary: Alcohol-associated liver disease is accompanied by changes in the intestinal mycobiome. How fungal dysbiosis contributes to liver disease is not clear. T-helper (Th17) cells mediate immune responses against fungi, but the interleukin 17 (IL17) pathway has been associated with pathogenesis of alcohol-associated liver disease. Here, we demonstrate that Candida albicans (C. albicans)-specific Th17 cells are increased in the circulation and present in the liver of patients with alcohol-associated liver disease. Chronic ethanol administration to mice results in migration of C. albicans-reactive Th17 cells from the intestine to the liver. The antifungal agent nystatin reduced intestinal fungal overgrowth, decreased C. albicans-specific Th17 cells in the liver, and reduced features of ethanol-induced liver disease in mice. Transgenic mice that express a T-cell receptor (TCR) reactive to Candida antigens develop more severe ethanol-induced liver disease than transgene-negative littermates; disease severity was reduced by administration of an antibody against IL17 to the TCR transgenic mice. Adoptive transfer of C. albicans-reactive Th17 cells exacerbated ethanol-induced liver disease in wild-type mice. IL17 receptor A (IL17ra) signaling in Kupffer cells was required for the effects of C. albicans-reactive Th17 cells. Our findings indicate that ethanol increases C. albicans-reactive Th17 cells, which contribute to alcohol-associated liver disease.

overall_design: For bulk TCR repertoire analyses one liver biopsy and sorted CD4+ T cells from blood were processed for the same two patients use for single-cell analysis

first: Suling

last: Zeng

first: Carina

last: Saggau

first: Berith

last: Messner

first: Yi

last: Duan

first: Phillipp

last: Hartmann

first: Shengyun

last: Ma

first: Wendy

last: MenHuang

first: Jihyung

last: Lee

first: Sung

first: Carvalho-Gontijo

last: Raquel

first: Vivian

last: Zhang

first: Joseph

middle: P

last: Hoffmann

first: Jay

last: Kolls

first: Eyal

last: Raz

first: David

last: Brenner

first: Tatiana

last: Kisseleva

first: Salomé

last: LeibundGut-Landmann

first: Petra

last: Bacher

first: Peter

last: Stärkel

first: Bernd

last: Schnabl


title: Candida albicans-specific Th17 cell-mediated response contributes to alcohol-associated liver disease [scRNA & scTCR-seq]

first: Elisa

last: Rosati

overall_design: For single-cell gene transcriptomics, two ALD patients were analyzed. CD154+ cells isolated from PBMCs were isolated by ARTE and further purified by FACS sorting. Data produced include single-cell gene expression (GEX) and single-cell TCR.

first: Suling

last: Zeng

first: Carina

last: Saggau

first: Berith

last: Messner

first: Yi


title: Pol II Preferentially Regulates Ribosomal Protein Expression by Trapping Disassociated Subunits [ChIP-seq]

first: Xiong

last: Ji

overall_design:
We performed ChAR-seq, TT-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours; refer to individual Series. For TT-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the HEK293T cells were used as the spike-in cells.
This dataset includes the ChIP-seq data.

first: Yuanjun

last: Li

first: Jie

last: Huang

first: Lijun

last: Bao

first: Junyi

last: Zhu

first: Wenjia

last: Duan


title: Cross-tissue correlations of genome-wide DNA methylation in Japanese live human brain and their blood, saliva, and buccal epithelial tissues

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

country: Japan

institute: University of Fukui

type: Methylation profiling by genome tiling array

summary: Neuroepigenetics considers genetic sequences and the interplay with environmental influences to elucidate vulnerability risk for various neurological and psychiatric disorders. However, evaluating DNA methylation of brain tissue is challenging owing to the issue of tissue specificity. Consequently, peripheral surrogate tissues were used, resulting in limited progress compared with other epigenetic studies, such as cancer research. Therefore, we developed databases to establish correlations between the brain and peripheral tissues in the same individuals. Four tissues, resected brain tissue, blood, saliva, and buccal mucosa (buccal), were collected from 19 patients (aged 13–73 years) who underwent neurosurgery. Moreover, their genome-wide DNA methylation was assessed using the Infinium HumanMethylationEPIC BeadChip arrays to determine the cross-tissue correlation of each combination. These correlation analyses were conducted with all methylation sites and with variable CpGs, and with when these were adjusted for cellular proportions. For the averaged data for each CpG across individuals, the saliva–brain correlation (r = 0.90) was higher than that for blood–brain (r = 0.87) and buccal–brain (r = 0.88) comparisons. Among individual CpGs, blood had the highest proportion of CpGs correlated to the brain at nominally significant levels (19.0%), followed by saliva (14.4%) and buccal (9.8%). These results were similar to the previous IMAGE-CpG results; however, the correlation analysis between the correlation coefficients of the datasets revealed a relatively low degree of correlation (brain vs. blood: r = 0.27, saliva; r = 0.18, and buccal; r = 0.24). To the best of our knowledge, this is the fourth study in the literature initiating the development of databases for correlations between the brain and peripheral tissues in the same individuals. We present the first database developed from an Asian population, specifically Japanese samples (AMAZE-CpG), which would contribute to interpreting individual epigenetic study results from various Asian populations.

overall_design: Bisulfite-converted brain, blood, saliva, and buccal DNA from the 19 brain surgery patients were hybridized into the Illumina Infinium Methylation EPIC Kit array

first: Akemi

last: Tomoda


title: Pleiotrophin drives a pro-metastatic immune niche within the breast tumor microenvironment

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

summary: Here, we evaluated the effect of Pleiotrophin (PTN) depletion on tumor microenvironment. For this, we utilized a mouse monoclonal antibody against PTN, 3B10. We tested its therapeutic efficacy in 2 mouse breast cancer models, 4T1 (orthotopic, 4th mammary fat pad) and MMTV-PyMT (genetic model). Tumors from control IgG(C44) treated and 3B10 treated mice were sent for RNA sequencing to evaluate transcriptional changes. Additionally, PTN was knocked down in E0771 and E0771-LG syngeneic breast cancer lines. To evaluate transcriptional changes due to PTN depletion, shCtrl and PTN KD cells from E0771 and E0771-LG were evaluated by RNA sequencing. Overall, our results from these 4 sets of experiments show that depletion or blocking PTN results in inflammation related transcript changes suggesting function of PTN in immune regulation.

overall_design: Breast cancer tumors (4T1 & MMTV-PyMT) or cells (E0771 or E0771-LG) were treated with 3B10 or depleted of PTN.

first: Debolina

last: Ganguly

first: Rolf

last: Brekken

first: Anton

last: Wellstein


title: Effect of donepezil on lung fibrosis related pulmonary hypertension

city: Zhuzhou

first: Guo

last: Yuan

address: No. 116, Changjiang South Road, Tianyuan District

institute: Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University

summary: This study is designed to investigate the protective function of cholinesterase inhibitor Donepezil (DON) in regulating Group III pulmonary hypertension (PH).

overall_design: Lung fibrosis related PH model was established by single intratracheal instillation of bleomycin (BLM), and then DON (1mg/kg, Selleck, USA) was intraperitoneal injected daily from the first day to day 21 as therapeutic protocol. At the end of the study, lung tissue in each group subjected to RNA sequencing to identify the differential expression genes and reveal the underlying mechanism.

first: Yuan

last: Guo

first: Yuzi

last: He

first: Zhu

last: Chen


title: The transcriptomic profile of primary cells isolated from intestinal muscle layers in 2D or 3D culture conditions and with different culture media

status: Public on Feb 15 2023

city: Palo Alto

first: James

last: Dunn

state: California

address: 453 Quarry Road, Office 454H

institute: Stanford University

summary: The intestinal muscle layers execute various gut wall movements to achieve controlled propulsion and mixing of intestinal content. Engineering intestinal muscle layers with complex contractile function is critical for developing bioartificial intestinal tissue to treat patients with short bowel syndrome. A living intestinal muscle patch is created for the first time in vitro to generate three distinct motility patterns and display multiple digesta manipulations. Developing such intestinal muscle patches combines a differentiation medium and a 3D scaffold. Next-generation RNA sequencing was performed across primary cells isolated from the intestinal muscle layers that were further cultured with/without the differentiation medium or with/without the 3D scaffold to characterize the effect of the medium and the scaffold on the transcriptomic profile of the cells. We found that the successful generation of the contracting intestinal muscle patch relies on both biological factors in the medium and environmental cues from the scaffold. In cooperation, the medium and the scaffold both greatly enhance the differentiation and maturity of the enteric neurons. Separately, the medium profoundly impacts ion transport activities. The scaffold markedly reshapes cell communication and protein binding.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for primary cells isolated from the intestinal muscle layers and cultured in different media and with/without a 3D electrospun gelatin scaffold. Samples of the intestinal muscle strips were included as a positive control. Three biologically independent replicates for each condition. Two technical replicates for each sample.

first: Qianqian

last: Wang

first: Jiafang

first: Elmira

last: Tokhtaeva

first: Zhen

first: Martín

last: Martín

first: Xuefeng

middle: B

last: Ling


title: Expression data from Arabidopsis suspension cells overexpressing ATHB8-GFP

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

institute: the university of tokyo

summary: ATHB8 is a member of HD-ZIP III family transcription factors and has a important role in vascular development. However, how ATHB8 regulates vascular development is still a mystery.  Here, we identified specific genes downstream of  ATHB8-GFP with transformed suspension culture cells in microarray experiments.

overall_design: To identify genes downstream of ATHB8, we collected three samples at 24h with or without estrogen with triplicates.

first: Kuninori

last: Iwamoto

first: Hiroo

last: Fukuda


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1 [Foxp1 cTG scRNA-seq]

city: Salt Lake City

first: Monica

middle: L.

last: Vetter

state: UT

department: Neurobiology & Anatomy

institute: University of Utah

summary: Transitions in competence underlie the ability of CNS progenitors to generate a diversity of neurons and glia. Retinal progenitor cells in mouse generate early-born cell types embryonically and late-born cell types largely postnatally. We find that the transition from early to late progenitor competence is regulated by Jarid2. Loss of Jarid2 results in extended production of early cell types and extended expression of early progenitor genes. Jarid2 can regulate histone modifications, and we find reduction of repressive mark H3K27me3 on a subset of early progenitor genes with loss of Jarid2, most notably Foxp1. We show that Foxp1 regulates the competence to generate early-born retinal cell types, promotes early and represses late progenitor gene expression, and is required for extending early retinal cell production after loss of Jarid2. We conclude Jarid2 facilitates progression of retinal progenitor temporal identity by repressing Foxp1, which is a primary regulator of early temporal patterning.

overall_design: Single cell gene expression comparison of Foxp1 cTG and control in P0 mouse retina.

first: Jianmin

last: Zhang

first: Jacqueline

last: Roberts

first: Fei

last: Chang

first: Joon

last: Schwakopf


title: Effect of depletion of p53 and BACH1 on gene expression in human tongue squamous cell carcinoma cell line Cal-33.

city: New York

first: Wei

last: Gu

state: NY

address: 1130 St. Nicholas Ave.

institute: Columbia University

summary:
To investigate how BACH1 and p53-R175H regulate metastasis-related genes, we transiently transfected Cal-33 cells with control or p53 or BACH1 siRNA to knock down these genes expression.
We then performed gene expression profiling analysis using data obtained from RNA-seq of these knockdown cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cal-33 cells and its KD derivatives (p53 knockdown and BACH1 knockdown).

first: Su

last: Zhenyi

first: Gu

last: Wei


title: RELA tunes innate-like interferon I/III responses in human T cells

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

summary: In innate immune cells, intracellular sensors such as cGAS-STING stimulate type I/III interferon (IFN) expression, which promotes antiviral defense and immune activation. However, how IFN-I/III expression is controlled in adaptive cells is poorly understood. Here, we identify a transcriptional rheostat orchestrated by RELA that confers human T cells with innate-like abilities to produce IFN-I/III. Despite intact cGAS-STING signaling, IFN-I/III responses are stunted in CD4+ T cells compared with dendritic cells or macrophages. We find that lysine residues in RELA tune the IFN-I/III response at baseline and in response to STING stimulation in CD4+ T cells. This response requires positive feedback driven by cGAS and IRF7 expression. By combining RELA with IRF3 and DNA demethylation, IFN-I/III production in CD4+ T cells reaches levels observed in dendritic cells. IFN-I/III production provides self-protection of CD4+ T cells against HIV infection and enhances the elimination of tumor cells by CAR T cells. Therefore, innate-like functions can be tuned and leveraged in human T cells.

overall_design: To study transcriptional response to cGAMP, samples were harvested five hours following cGAMP (6 μg/ml) stimulation of activated CD4+ T cells. For RELA and RELA K5R analysis,activated CD4+T cells transduced with either pTRIP-SFFV-GFP or pTRIP-SFFV-GFP-RELA or pTRIP-SFFV-GFP-RELA K5R were harvested 4 days post-transduction. Total RNA was extracted (Macherey-Nagel #740955.50) and RNA integrity was verified using Agilent Bioanalyzer (Agilent RNA 6000 Nano kit #5607-1511), all samples had a RIN >9. RNA sequencing libraries were prepared from 500 ng of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit. A first step of polyA selection using magnetic beads was performed to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and ligated to the TruSeq indexed adapters. PCR amplification was performed to create the final cDNA library (with 13 cycles). After quantification of PCR products, sequencing was carried out using 2*100 cycles (paired-end reads, 100 nucleotides) on a Novaseq6000 instrument, targeting 25M clusters.

first: Nadia

last: Jeremiah

first: Kévin

last: De Azevedo


title: A druggable signaling hub of choroid plexus immune-secretory function

city: new haven

first: Kristopher

last: Kahle

state: CT

address: 333 ceder st

department: Department of Neurosurgery

institute: Yale university

summary: Integrated multi-omics investigation of novel rat models of acquired hydrocephalus, Blood or bacteria in CSF trigger similar choroid plexus (ChP) immune-secretory responses, Crosstalk between ChP immune and epithelial cells drives CSF hypersecretion and ventriculomegaly, Repurposed systemic immunomodulators ameliorate acquired hydrocephalus, Identification of a druggable hub of ChP function relevant for multiple neurological diseases.

overall_design: Examine the effect of IVH and LPS on ChP

middle: T

first: Emre

last: Kiziltug

first: M Shahid

last: Mansuri

first: Jason

last: Karimy

first: Stephanie

last: Robert


title: Consensus molecular subtypes as biomarkers of FU/FA maintenance therapy with or without panitumumab in RAS wild-type metastatic colorectal cancer (PanaMa, AIO KRK 0212).

city: Berlin

first: Arndt

last: Stahler

address: Chariteplatz 1

department: Medical Department of Hematology, Oncology and Cancer Immunology

institute: Charite Universitaetsmedizin Berlin

summary: Customized Nanostring PanCancer Progression Panel performed on FFPE tumor tissue derived from treatment naive metastatic colorectal cancer patients included into the randomized phase 2 PanaMa trial.

overall_design: Treatment naive patients with RAS wild-type metastatic colorectal cancer received 12 cycles of FOLFOX plus Panitumumab induction treatment and were then randomized to receive maintenance consisting of 5-fluorouracil and folinic acid with or without panitumumab; mRNA was extracted from 307 patients from tissue obtained before treatment start.

first: Dominik

last: Modest


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1 [Jarid2 cKO CUT&RUN]

first: Monica

last: Vetter

overall_design: Genomic location of H3K27me3 enrichment in Jarid2 cKO and control e18.5 retinas determined by CUT&RUN.

first: Jianmin

last: Zhang

middle: M


title: Single-cell RNA-seq of human liver samples

city: Innsbruck

first: Stefan

last: Salcher

address: Anichstraße 35

department: Internal Medicine V

country: Austria

institute: Medical University of Innsbruck

summary: We performed in-depth serial immune cell mapping of human donor livers before and after normothermic machine perfusion (NMP) as well as after reperfusion to specifically investigate the source of immunomodulatory cytokines/chemokines and the dynamics of immune activation at the single-cell level.

overall_design: In-depth serial immune cell mapping of eight human donor livers before and after normothermic machine perfusion (NMP) as well as after repserfusion was applied to specifically investigate the source of immunomodulatory cytokines/chemokines and the dynamics of immune activation at the single-cell level. We validated and visualized our findings by multiplex immunofluorescent (IF) staining in liver biopsies.

first: Theresa

last: Hautz

first: Margot

last: Fodor

first: Gregor

last: Sturm

first: Anna

last: Mair

first: Manuel

last: Trebo

first: Gerold

last: Untergasser

first: Sieghart

last: Sopper

first: Zlatko

last: Trajanoski

first: Rupert

last: Oberhuber

first: Andreas

last: Pircher

last: Wolf

last: Schneeberger


title: Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

type: Expression profiling by genome tiling array

summary:
To investigate which cellular functions may be perturbed along the branches of a synthetic evolutionary tree obtained by incremental deletions of large genomic regions, we subjected six Bacillus subtilis strains to transcriptome profiling.
These six strains are : MS (~3.98 Mbp), which is already a genome-reduced derivative of the B. subtilis 168  (~4.22 Mbp) and the root of our evolutionary tree; MGP254 (~2.73 Mbp), the farthest genome-reduced strain; MGP234 (~2.81 Mbp), another terminal leaf in our tree; MGP181 (~2.87 Mb) and MGP192 (~2.85 Mbp), two intermediate strains in the ancestor lineage common to MGP254 and MGP234; and finally MGP229 (2.82 Mbp), an intermedidate strain between MGP192 and MGP254 (i.e. an ancestor of MGP254 but not MGP234).
The vast majority of genes conserved in the six strains displayed no differential expression, showing the robustness of the cell transcriptional network against massive genome reduction.
Among deregulated genes, more than half could be explained by loss of known functions and aberrant transcription at deletion boundaries.
An unexpected common feature in genome-reduced strains was the upregulation of genes involved in cell responses to oxidative stresses.

sample_organism: Bacillus subtilis subsp. subtilis str. 168

overall_design: The transcriptome of each strain was assessed by separate hybridization of two RNA samples extracted  from two independent cultures (biological duplicates).

first: Kosei

last: Tanaka

first: Etienne

last: Dervyn

first: Matthieu

last: Jules

first: Philippe

last: Noirot

first: Cyprien

last: Guérin


title: Caenorhabditis briggsae SDC-2 and DPY-27 ChIP-seq

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

summary: ChIP-seq for the SDC-2 and DPY-27 subunits of the dosage compensation complex in C. briggsae

overall_design: ChIP-seq

first: Qiming

last: Yang

first: Te-Wen

last: Lo

first: Katjusa

last: Brejc

first: Caitlin

last: Schartner

first: Edward

last: Ralston

first: Denise

last: Lapidus


title: Systemic Hypoxemia Induces Cardiomyocyte Hypertrophy and Right Ventricular Specific Induction of Proliferation

city: Philadelphia

first: Jaslyn

last: Johnson

state: Pennsylvania

address: 3500 N. Broad Street

department: Cardiovascular

institute: Lewis Katz School of Medicine, Temple University

summary: A recent study suggests that systemic hypoxemia in adult male mice can induce cardiac myocytes to proliferate. The goal of the present experiments was to confirm these results, provide new insights on the mechanisms that induce adult cardiomyocyte cell cycle re-entry, and to determine if hypoxemia also induces cardiomyocyte proliferation in female mice. We also analyzed gene expression using data obtained from RNAseq of ventricular heart tissue from male and female mice subjected to either normoxia or hypoxia.

overall_design: Male and female mice in the Hypoxia group were placed in a hypoxia chamber and the oxygen was lowered by 1% every day for 14 days to reach 7% oxygen. The animals remained in 7% oxygen for 2 weeks before terminal studies. Mice in the normoxia group remained at room air (20.9% oxygen) for 4 weeks before terminal studies. Hearts were collected and snap frozen in liquid nitrogen. Frozen ventricular samples of the hearts were used in RNAseq. We performed comparative gene expression profiling analysis of RNA-seq data on male and female mice subjected to either normoxia or hypoxia.

first: Yijun

first: Zilin

last: Bian


title: Transcriptome profiling at four stages of turbot development from phylotypic to post-metamorphic stages [RNA-seq]

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

summary: Metamorphosis is a widely studied post-embryonic process in which many tissues undergo dramatic modifications to adapt to the new adult lifestyle. Flatfish represent a good example of metamorphosis in teleosts. During flatfish metamorphosis, organ regression and neo-formation occur, being the most remarkable change the migration of one of the eyes to the other side of the body. In order to create a useful and reliable tool to advance the molecular study of metamorphosis in flatfish, we generated a chromatin accessible atlas as well as gene expression profile during four developmental stages ranging from a phylotypic stage to a post-metamorphic stage. We identified 29,019 accessible regions of chromatin and 3,253 differentially expressed genes. We found stage-specific regulatory regions and gene expression profile, supporting the quality of the results. Our work provides strongly reproducible data for further studies to elucidate the regulatory elements that ensure successful metamorphosis.

overall_design: RNAseq experiments in different developmental stages in Scophthalmus maximus

last: Guerrero-Peña

first: Paula

last: Suarez-Bregua

first: Alejandro

last: Gil-Gálvez

first: Silvia

last: Naranjo

first: Luis

last: Méndez-Martínez

first: Ricardo

last: Tur

first: Pablo

last: García-Fernández

first: Juan

middle: J

last: Tena

first: Josep

last: Rotllant


title: Transcriptomes of Neural Stem and Progenitor Cells from the subgranular zone (SGZ) of Wild Type (NTG) and 3xTg-AD mice at juvenile age

city: Ottawa

first: Ruth

last: Slack

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

summary:
The goals of this study are to compare transcriptome profiling (RNA-seq) in wild-type (NTG) and 3xTg-AD mice, to determine the transcriptomal changes of neural stem and progenitor cells (NSPC) from the SGZ at early stages of Alzheimer's Disease in a mouse model.
Methods: A tamoxifen (TAM)-inducible Nestin-CreERT2;ROSA26-EYFP reporter mouse line  was cross-bred with NTG or 3xTG-AD mice to label NSPC upon TAM administration. YFP-positive NSPCs were sorted through FACS (Fluorescence-Activated Cell Sorting) 10 days after TAM from NTG; Nestin-CreERT2;ROSA26-EYFP and 3xTg-AD;Nestin-CreERT2;ROSA26-EYFP mice. RNA was extracted with RNeasy Micro Kit and deep-sequenced on the NovaSeq SP flowcell SR200 platform. The sequence reads of Fastq files that passed quality filters were aligned to the mouse genome (build mm10) using hisat2. Samtools was used to index the BAM files. DESeq2 was used to establish differential gene expression between NTG and 3xTg-AD samples.
Results: We mapped about 48 million sequence reads per sample to the mouse genome (build mm10) and identified 1391 genes that were differentially expressed in the 3xTg-AD, with 720 down- and 671 up-regulated. Genes were considered significantly different between two genotypes if they meet the following criteria: 1) adjusted p-value < 0.05, and 2) log2 fold change > 0.5 or < -0.5.
Conclusions: Gene ontology analysis of differentially expressed genes uncovered several pathways that may contribute to early neural stem cell decline in the 3xTg mice. Our results revealed very early perturbations in the SGZ neurogenic niche in the 3xTg mouse model of AD, manifested by intrinsic molecular changes in neural stem and progenitor cells (NSPC) at juvenile age, resulting in dysregulated neural stem cell homeostasis.

overall_design: mRNA profiles of FACS-sorted neural stem and progenitor cells (NSPC) from wild type (NTG) and 3xTg-AD mice at 5 weeks of old

first: Yubing

last: Liu

middle: S


title: Pol II Preferentially Regulates Ribosomal Protein Expression by Trapping Disassociated Subunits [RNA-seq]

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

institute: Peking University

summary: Pol II has been recognized as a passively regulated holoenzyme. However, whether Pol II plays specific regulatory roles remain unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, Specific Degradation of Disassociated Subunits (SDDS), we showed that dRPB3 functions as a regulatory component of Pol II to enable the preferential control of 3’ end processing of ribosomal protein genes. Machine learning analysis of large-scale genomic features revealed that the little elongation complex helps to determine the functional specificity of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3’ end processing. Furthermore, the coordination between RPB3 and ribosomal proteins was widespread in diverse tissues and cancer cells. These findings suggest that Pol II gains specific regulatory functions by trapping disassociated subunits.

overall_design:
We performed ChAR-seq, TT-seq, RNA-seq, and ChIP-seq to investigate the roles of various specialized subunits in transcription and post-transcriptional regulation. The V6.5 mouse ES (mES) cell line was used for all the high-throughput analyses. Degron mES cells were pretreated with 1 μg/ml Doxycycline for 12h to induce TIR1 expression, and treated with or without 500 μM IAA for different hours; refer to individual Series. For TT-seq, ChAR-seq, and RNA-seq, the Drosophila S2 cells were used as the spike-in cells, and for ChIP-seq, the HEK293T cells were used as the spike-in cells.
This dataset includes the RNA-seq data.

first: Yuanjun

last: Li

first: Jie

last: Huang

first: Lijun

last: Bao

first: Junyi

last: Zhu

first: Wenjia

last: Duan


title: Photoreceptor survival in CEP290-retinopathy by Reserpine involves modulation of proteostasis

city: Bethesda

first: Matthew

last: Brooks

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Photoreceptor cell death is a major cause of incurable vision loss in retinal degeneration, with little to no treatment options available. To identify drug candidates to maintain photoreceptor survival, we performed an unbiased high-throughput screening of over 6,000 bioactive small molecules using retinal organoids differentiated from induced pluripotent stem cells of rd16 mice, which phenocopy Leber congenital amaurosis (LCA) 10 caused by CEP290 mutations. Five positive hits including the lead compound Reserpine were further validated by the improvement of photoreceptor maintenance and survival in organoid cultures and in vivo retina. Subsequent investigation revealed misregulation of autophagy in degenerative retina, which is associated with compromised primary cilium biogenesis. Reserpine largely restored the balance between autophagy and the ubiquitin-proteasome system, and improved primary cilium assembly in vitro and in vivo. This study identified effective drug candidates for treatment of retinal degeneration and highlights the impact of proteostasis in photoreceptor cell death.

overall_design: The generation and characterization of the familial control, LCA-1 and LCA-2 iPSC lines have been previously reported (Shimada et al., 2017). Human retinal organoid differentiation was performed as previously described (Regent et al., 2020). Total RNA was purified from homogenized retinal organoids using TriPure isolation reagent (Roche). Quality of isolated RNAs was assessed using Bioanalyzer RNA 6000 nano assays (Agilent) and high-quality total RNA (RNA integrity number ≥7.5) were used for construction of mRNA sequencing library. 100ng total RNA were used to construct the strand-specific libraries using TruSeq RNA Sample Prep Kit-v2 (Illumina).

first: Holly

last: Chen

first: Manju

last: Swaroop

first: Samantha

last: Papal

first: Anupam

middle: K

last: Mondal

first: Gregory

last: Tawa

first: Florian

last: Regent

first: Hiroko

last: Shimada

first: Kunio

last: Nagashima

first: Natalia

last: de Val

first: Samuel

last: Jacobson

first: Wei

last: Zhang

first: Anand


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1 [H3K27me3 CUT&RUN E14.5 and P0]

first: Monica

last: Vetter

overall_design: Genomic location of H3K27me3 relative to IgG in wild type e14.5 and P0 retinas determined by CUT&RUN.

first: Jianmin

first: Jacqueline

last: Roberts

first: Fei

last: Chang

first: Joon

last: Schwakopf

middle: L


title: Transcriptional profiling of Cd169-lineage lymph node macrophages

city: Darlinghurst

first: Tri

middle: Giang

last: Phan

state: New South Wales

address: 384 Victoria St

department: Immunology Division

country: Australia

institute: Garvan Institute

summary: Tingible body macrophages (TBMs) exist in lymph node B cell follicles and are responsible for clearing apoptotic B cells. Our data suggests that TBMs are of Cd169-lineage. We isolated cells from Cd169Cre/+.Tdtomatofl/fl reporter mice and transcriptionally profiled them to identify putative TBMs and chacterise their development and function relative to other LN cells of the Cd169 lineage.

overall_design: Cd169Cre/+.Tdtomatofl/fl mice were immunised with  hen egg lysozyme (HEL). Lymph nodes were harvested from 2 unimmunised and 2 immunised mice 9 days later. The cells were stained with CITE-seq antibodies and hashtags, and  Tomato pos CD11b hi cells were isolated by Fluorescence-activated cell sorting (FACS). As the cells were hashtagged, all samples were combined and split cross two 10X capture reactions

middle: g

first: Akira

last: Nguyen

first: Abigail

last: Grootveld


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1 [Jarid2 scRNA-Seq]

overall_design: Single cell gene expression comparison of Jarid2 cKO and control in E18.5 mouse retina, performed in duplicate.


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1

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

overall_design: Refer to individual Series


title: Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1 [Foxp1 cKO bulk RNA-seq]

overall_design: Gene expression comparison, by bulk RNA-sequencing, of triplicate Foxp1 cKO and control littermates during early retinal development (e16.5).


title: γ-Linolenic acid in maternal milk drives cardiac metabolic maturation

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

summary: The goal of this study was to compare the transcriptome profile (RNA-seq) of perinatal hearts of cardiomyocyte-specific RXRab-deficient (edKO) and WT mice, to identify genes that are controlled by the expression of the TF RXRa and RXRb.

overall_design: Hearts from wild type (WT) and cardiomyocyte-specific RXRab-/- (edKO) P0 newborns were collected and analyzed by RNASeq.

first: A

last: Paredes

first: M


title: Small RNA sequencing of Aspergillus fumigatus

status: Public on Feb 14 2023

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

type: Non-coding RNA profiling by high throughput sequencing

summary: Aspergillus fumigatus is an important human pathogen and a leading fungal killer. This study aimed to determine the small RNA repertoire of A. fumigatus in conidia and mycelium grown for 24 or 48 hours in liquid culture.

overall_design: Total RNA was isolated using a Roboklon RNA Isolation kit from Aspergillus fumigatus conidia and mycelium growth in Aspergillus minimal media for 24 or 48 hours. Small RNA was then enriched using a Zymo RNA Clean and Concentrate kit before treatment with NEB RppH enzyme to remove cyclic phosphates and facilitate library prepration. Libraries were prepared using NEB Small RNA Sequencing Library Prepration Kits and 50 nt single end sequencing was performed by Eurofins.

middle: G

first: Abdulrahman

last: Kelani


title: Metabolic maturation of neonatal hearts driven by γ-linolenic acid in maternal milk

summary:
Birth is the first metabolic challenge that cardiomyocytes need to overcome as they reshape their fuel preference from glucose to fatty acids (FA) to optimize energy production in postnatal life. This adaptation is partly triggered by drastic post-partum environmental changes, yet the molecular players responsible for orchestrating cardiomyocyte maturation remain unknown. Here, we discover that maternal metabolite γ-linolenic acid (GLA) support this transition. Specifically, colostrum GLA acts as an agonist for Retinoid X Receptors (RXR), a family of ligand-activated transcription factors expressed from embryonic life in cardiomyocytes. Mice lacking RXR in embryonic cardiomyocytes showed an aberrant chromatin landscape that prevented the induction of RXR-dependent FA metabolism genes (mtFAH signature). This results in a defective metabolic transition with blunted mitochondrial lipid-derived energy production and enhanced glucose consumption, which ultimately leads to perinatal lethal cardiac dysfunction. In vitro GLA supplementation in cardiomyocytes induced the expression of mtFAH signature in a RXR-dependent manner. Altogether, our study uncovers GLA/RXR axis as the fundamental mechanism by which maternal physiology commands metabolic functioning in perinatal hearts.

This SuperSeries is composed of the SubSeries listed below.


title: mRNA-seq of Aspergillus fumigatus RNAi double knockouts

summary: The RNA interference (RNAi) pathway has evolved numerous functionalities in eukaryotes, with many on display in Kingdom Fungi. RNAi can regulate gene expression, facilitate drug resistance, or even be altogether lost to improve virulence potential in some fungal pathogens. In the WHO fungal priority pathogen, Aspergillus fumigatus, the RNAi system is known to be intact and functional. To extend our limited understanding of A. fumigatus RNAi, we performed a multi-condition mRNA-seq analysis comparing expression of several RNAi double knockout mutants with the wild-type strain in conidia and mycelium grown for 24 or 48 hours. The analysis linked the A. fumigatus dicer-like enzymes and RNA-dependent RNA polymerases to regulation of conidial ribosome biogenesis. Cumulatively, A. fumigatus RNAi appears to play an active role in defense against double-stranded RNA species alongside a previously unappreciated housekeeping function in regulation of conidial ribosomal biogenesis genes.

overall_design: Comparative gene expression profiling analysis of poly(A) RNA-seq data for double knockouts (𝚫dclA/B, 𝚫ppdA/B, 𝚫rrpA/B) in the RNAi pathway of Aspergillus fumigatus conidia, 24-h-mycelium, and 48-h-mycelium.

first: Xiaoqing

last: Pan


title: Oncogenic YAP mediates changes in chromatin accessibility and activity that drive cell cycle gene expression and cell migration

city: Wuerzburg

first: Carsten

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

institute: University of Wuerzburg

summary: YAP, the key protein effector of the Hippo pathway, is a transcriptional co-activator that controls the expression of cell cycle genes, promotes cell growth and proliferation and regulates organ size. YAP modulates gene transcription by binding to distal enhancers, but the mechanisms of gene regulation by YAP-bound enhancers remain poorly understood. Here we show that constitutive active YAP5SA leads to widespread changes in chromatin accessibility in untransformed MCF10A cells. Newly accessible regions include YAP-bound enhancers that mediate activation of cycle genes regulated by the Myb-MuvB (MMB) complex. By CRISPR-interference we identify a role for YAP-bound enhancers in phosphorylation of Pol II at Ser5 at MMB-regulated promoters, extending previously published studies that suggested YAP primarily regulates the pause-release step and transcriptional elongation. YAP5SA also leads to less accessible 'closed' chromatin regions, which are not directly YAP-bound but which contain binding motifs for the p53 family of transcription factors. Diminished accessibility at these regions is, at least in part, a consequence of reduced expression and chromatin-binding of the p53 family member ΔNp63 resulting in downregulation of ΔNp63-target genes and promoting YAP-mediated cell migration. In summary, our studies uncover changes in chromatin accessibility and activity that contribute to the oncogenic activities of YAP.

overall_design: ATAC-seq and ChIP-seq of MCF10A-YAP5SA cells as well as RNA-seq and CUT&RUN-seq of MCF10A-ER-YAP2SA-MY-COMP cells or MCF10A_Y5SA cells, respectively. CnR-seq and ChIP-seq of MCF10A-YAP5SA cells.

first: Stefan

last: Gaubatz

first: Maria

middle: C

last: Fetiva

first: Franziska

last: Liss


title: Gene silencing dynamics are modulated by transiently active regulatory elements [ChIP-seq II]

first: Marit

middle: W.

last: Vermunt

state: PA

address: 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Phildelphia

summary: Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during erythroid maturation, and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de-novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via engagement of the FOG1/NuRD deacetylase complex, as revealed by study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.

overall_design: Chromatin Immuno Precipitation (ChIP)-Sequencing at different time points of erythroid differentiation

middle: W


title: Infiltration of inflammatory macrophages and neutrophils and widespread pyroptosis in lung drive influenza lethality in nonhuman primates

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary:
We established a model by which precise doses of H5N1 influenza could be delivered via aerosol into the lower lungs of macaques.
We then allowed the animals to progress to an endpoint, collected organs, sorted cells, and performed RNA seq specifically on whole lung, interstitial macrophages, alveolar macrophages or neutrophils.

overall_design: Compared mock infected animals to H5N1 infected animals

first: Jacqueline

last: Corry

first: Gwenddolen

last: Kettenburgolen Kettenburg

first: Amit

middle: A

last: Upadhyay

first: Megan

last: Wallace

first: Michelle

last: Marti

first: Elizabeth

middle: R

last: Wonderlich

first: Stephanie

last: Bissel

first: Kyndal

last: Goss

first: Timothy

last: Sturgeon

first: Simon

last: Watkins

first: Douglas

last: Reed

first: Steven

middle: E

last: Bosinger

last: Barratt-Boyes


title: Upregulation of GALNT7 in prostate cancer modifies O-glycosylation and promotes tumour growth

city: Newcastle upon Tyne

first: Jennifer

last: Munkley

state: Tyne & Wear

address: International Centre for Life

institute: Newcastle University

summary:
To identify signalling pathways altered by GALNT7 in prostate cancer cells, we established DU145 and CWR22Rv1 stable cell lines in which GALNT7 was overexpressed or knocked down, respectively.
We then performed differential gene expression and Gene Ontology analyses using data obtained from RNA-seq of the control and OE/KD cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Lenti-ORF negative control DU145 cells vs DU145 with GALNT7 overexpression, and shControl CWR22Rv1 cells vs CWR22Rv1 with GALNT7 KD.

first: Emma

last: Scott

first: Kirsty

last: Hodgson

first: Beatriz

last: Calle

first: Helen

last: Turner

first: Kathleen

last: Cheung

first: Abel

last: Bermudez

first: Fernando

last: Marques

first: Hayley

last: Pye

first: Edward

last: Yo

first: Khirul

last: Islam

first: Htoo

middle: Z

last: Oo

first: Urszula

last: McClurg

first: Laura

last: Wilson

first: Huw

last: Thomas

first: Fiona

middle: M

last: Frame

first: Margarita

last: Orozco-Moreno

first: Kayla

last: Bastian

first: Hector

last: Arredondo

first: Chloe

last: Roustan

first: Melissa

last: Gray

first: Lois

last: Kelly

first: Aaron

last: Tolson

first: Ellie

last: Mellor

first: Gerald

last: Hysenaj

first: Emily

last: Goode

first: Rebecca

last: Garnham

first: Adam

last: Duxfield

first: Susan

last: Heavey

last: Stopka-Farooqui

first: Aiman

last: Haider

first: Alex

last: Freeman

first: Saurabh

last: Singh

last: Johnston

first: Shonit

last: Punwani

first: Bridget

last: Knight

first: Paul

last: McCullagh

first: John

last: McGrath

first: Malcolm

last: Crundwell

first: Lorna

last: Harries

first: Denisa

last: Bogdan

first: Daniel

last: Westaby


title: GAGA-Associated Factor Fosters Loop Formation in the Drosophila Genome

city: Princeton

first: Michael

last: Levine

state: New Jersey

address: Icahn lab, Princeton University

institute: Princeton University

summary: The role of genome organization in the control of gene expression persists as a central mystery of modern biology. Most efforts have focused on the role of boundary elements and CTCF in the compartmentalization of the genome into a series of topological associating domains (TADs). These compartments have been suggested to enable long-range DNA-DNA associations via loop extrusion processes. However, there is emerging evidence for long-range focal contacts, whereby specific DNA sequences associated with promoters and distal enhancers interact to form chromatin loops. One such class of DNAs, tethering elements, binds GAGA-associated factor (GAF). Previous studies provided evidence that GAF possesses amyloid properties in vitro, enabling the formation of loops bridging separate DNA molecules. In this study we investigated the possibility that GAF also functions as a looping factor in Drosophila development. We employed a combination of Micro-C assays, proteasomal degradation, and genome editing to examine the impact of defined GAF mutants on genome topology. These studies suggest that the N-terminal POZ/BTB oligomerization domain is particularly important for long-range interactions of GAF bound to distant GAGA-rich tethering elements. By contrast, the C-terminal low complexity domain (poly Q) plays only a minor role in loop formation. The most striking effects of GAF mutants are observed for long-range promoter-promoter interactions that coordinate the activities of distant paralogous genes.

overall_design: Testing effect of GAF depletion or GAF mutants on chromatin structure, GAF binding to chromatin and gene expression in Drosophila

first: Li

last: Xiao

first: Tang

last: Xiaona

first: Bing

last: Xinyang

first: Catalano

last: Christopher

last: Taibo

first: Dolsten

last: Gabriel

first: Wu

last: Carl

first: Levine

last: Michael


title: Bulk transcriptome analysis of Myt1l mutant mouse neuron primary cultures.

city: Heidelberg

first: Bryce

last: Lim

address: In Neuenheimer Feld 280

institute: DKFZ

summary: We examined the effect of Myt1l deficiency in the neurons of mice. Homozygous Myt1l deficiency resulted in postnatal lethality, and mutant mice presented gene expression changes associated with developmental delays and resembled changes observed in autism spectrum disorder patients.

overall_design: Bulk RNA sequencing of Myt1l (+/+; WT) and Myt1l (+/-; HET) mouse cortical neuron primary cultures from P0 mice.

first: Bettina

last: Weigel

first: Jana

last: Tegethoff

first: Moritz

last: Mall


title: Bulk transcriptome analysis of conditional MYT1L-mutant ESC-derived human induced neurons following Wnt and/or Notch inhibitor treatment.

summary: We examined the effect of Wnt and/or Notch inhibition in the context of heterozygous MYT1L deficiency in human induced neurons. Increased expression of genes with MYT1L binding motifs and activation of non-neuronal genes were observed in human neurons along with deregulation of autism-associated risk genes upon depletion of MYT1L.

overall_design: Bulk RNA sequencing of Wnt and/or Notch inhibitor-treated MYT1L (+/flox) ESC-derived human induced neurons following cre-mediated depletion (+/-) compared to delta-cre transduced isogenic controls, 7 days after NGN2-mediated induced neurogenesis.


title: CUT&RUN analysis of MYT1L binding in mouse cortices across development.

summary: We examined MYT1L binding in the genome within cortices of mice during developement.

overall_design: CUT&RUN sequencing of WT mouse cortices at E18.5, P0, and adult (3-months-old).


title: Gene silencing dynamics are modulated by transiently active regulatory elements [PRO-seq]

first: Marit

last: Vermunt

overall_design: Precision Run On (PRO)-Sequencing at different time points of erythroid differentiation

first: Zhe

last: Zhang

first: Jing

last: Luan


title: Gene silencing dynamics are modulated by transiently active regulatory elements [ChIP-seq]


title: Gene silencing dynamics are modulated by transiently active regulatory elements


title: Gene silencing dynamics are modulated by transiently active regulatory elements [4C-seq]

overall_design: 4C-Sequencing at different time points of erythroid differentiation


title: scRNAseq of hepatic CD11b positive immune cells from uninjured control (Ctrl) and liver fibrosis resolved (RES) mice

city: Shinjuku-ku

first: Yohei

last: Mikami

state: Tokyo

address: Shinanomachi 35

institute: Keio University School of Medicine

summary: To explore key features associated with the resolution process in liver fibrosis, we here applied a previously reported murine liver fibrosis resolution model, in which wild-type mice were injected with carbon tetrachloride (CCl4) diluted in olive oil (1:9) intraperitoneally (0.6 μL/g body weight; Sigma) thrice per week for four weeks, and then observed without administration for 96 hours. We conformed that liver fibrosis was resolved in these mice (RES) after 96 hours from the last injection, along with upregulation of hepatic MMPs. Among CD45+ non-parenchymal cells, we noted that most MMPs were expressed by CD11b+ cells. To reveal the transcriptome profiling-based subtypes of CD45+ CD11b+ cells present during the liver fibrosis resolution, we performed scRNA-seq analysis. With corresponding cells from uninjured non-fibrotic wild-type mice as controls (Ctrl), a total of 7969 cells were clustered into 18 clusters based on the gene signatures. We revealed that a unique cluster of Ly6c2-low expressing CD11b+ macrophages (cluster Mac3) were enriched in livers resolved from CCl4-induced liver fibrosis. Comprehensive analysis of expression of known toll-like receptors in myeloid clusters demonstrated a unique upregulation of Tlr4 in Mac3. Moreover, only Ly6c2-low myeloid cells belonging to Mac 3 also demonstrated up-regulation of the expression of genes involved in extracellular matrix remodelling, post-phagocytosis, anti-inflammatory and antifibrotic pathways, and combined properties of both M1 and M2 features. Additionally, many of these genes highly expressed in Mac 3 were associated with the TLR4 pathway.

overall_design: mRNA profiles of liver non-parenchymal CD45+CD11b+ cells derived from Ctrl or RES mice.

first: Yuya

last: Hagihara

first: Rino

last: Ishihara

first: Yoichi

last: Takimoto

first: Po-sung

last: Chu

first: Takanori

last: Kanai


title: Systematic lineage tracing reveals clonal progenitors and long-term persistence of1 tumor-specific T cells during immune checkpoint blockade

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cancer. Here, we report scRNA/TCR-seq analysis of 187,650 T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from 3 patients with lung cancer after immune checkpoint blockade (ICB). Regions with viable cancer cells were enriched for exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH). Tracking T cell clonotypes across tissues, combined with neoantigen specificity assays, revealed that TFH and tumor-specific exhausted CD8+ T cells could be clonally linked to TCF7+ SELL+ progenitors in tumor draining LNs, and progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells with proximity to the tumor microenvironment. Finally, longitudinal tracking of tumor-specific CD8+ and CD4+ T cell clones revealed persistence in the peripheral blood for years after ICB therapy.

overall_design: RNA single cell (scTCR/RNA-seq) and bulk sequencing of 32 samples from three patients undergoing immune checkpoint blockade therapy.

first: Joy

last: Pai

first: Andrew

last: Chow

first: Ansuman

middle: T

last: Satpathy

first: Matthew

middle: D

last: Hellmann


title: Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade [scTCR-seq]

city: Stanford

address: 240 Pasteur Drive

institute: Stanford University

overall_design: CD3+ T cells were sorted from tumor, adjacent normal, and lymph node regions of patients with lung cancer treated with anti-PD-1 therapy, and subjected to paired single-cell RNA- and TCR-sequencing on the 10x Genomics platform.

first: Jennifer

last: Sauter

first: Marissa

last: Mattar

first: Hira

last: Rizvi

first: Hyung

middle: J

last: Woo

first: Nisargbhai

last: Shah

first: Fathema

last: Uddin

first: Alvaro

last: Quintanal-Villalonga

first: Joseph

last: Chan

first: Parvathy

last: Manoj

first: Viola

last: Allaj

first: Marina

last: Baine

first: Jamie

last: Chaft

last: Plodkowski

first: Helen

last: Won

first: Daniel

last: Wells

first: Mark

last: Donoghue

first: Elisa

last: de Stanchina

first: Triparna

last: Sen

first: Jedd

last: Wolchok

first: Brian

last: Houck-Loomis

first: Taha

last: Merghoub

first: Charles

last: Rudin


title: Single-cell transcriptome analysis of Myt1l mutant mouse cortices at birth.

first: Bryce

last: Lim

summary: We examined the effect of Myt1l deficiency in the cortices of mice at birth on the single cell level. Homozygous Myt1l deficiency resulted in postnatal lethality, and mutant mice presented increased expression of non-neuronal genes in neurons.

overall_design: Single-cell RNA sequencing of Myt1l (+/+; WT), Myt1l (+/-; HET), and Myt1l (-/-; HOM) mouse cortices at birth.

first: Bettina

last: Weigel

first: Jana

last: Tegethoff

first: Moritz

last: Mall


title: Bulk transcriptome analysis of Myt1l mutant mouse cortices across development.

summary: We examined the effect of Myt1l deficiency in the cortices of mice during developement. Homozygous Myt1l deficiency resulted in postnatal lethality, and mutant mice presented gene expression changes associated with developmental delays and resembled changes observed in autism spectrum disorder patients.

overall_design: Bulk RNA sequencing of Myt1l (+/+; WT), Myt1l (+/-; HET), and Myt1l (-/-; HOM) mouse cortices at E18.5, P0, and of Myt1l (+/+; WT), Myt1l (+/-; HET) at P22, and adult (3-month-old).


title: Profiling active transcription in MDA-MB-231 cells using global run-on assays (GRO-seq)

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

summary: GRO-seq was performed to identify transcribed RNAs in MDA-MB-231 cells.

overall_design: Biological duplicates of MDA-MB-231 cells were analyzed for this experiment.

first: Lisa

last: Fish


title: MYT1L-deficiency and brain

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Bulk transcriptome analysis of conditional MYT1L-mutant ESC-derived human induced neurons.

summary: We examined the effect of heterozygous MYT1L deficiency in human induced neurons. Increased expression of genes with MYT1L binding motifs and activation of non-neuronal genes were observed in human neurons along with deregulation of autism-associated risk genes upon depletion of MYT1L.

overall_design: Bulk RNA sequencing of MYT1L (+/flox) ESC-derived human induced neurons upon cre-mediated depletion (+/-) compared to delta-cre transduced isogenic controls, 7 or 43 days after NGN2-mediated induced neurogenesis.


title: Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loops

status: Public on Feb 13 2023

city: Edinburgh

first: Iain

last: Williamson

address: Crewe Road

department: Chromosomes and Gene Expression

institute: IGMM MRC Human Genetics Unit

summary: Polycomb-repressive complex 1 (PRC1) has a constraining influence on 3D genome organization, mediating localized and chromosome-wide clustering of target loci. Polycomb-bound regions form transcriptionally repressive chromatin domains independent of topologically associating domains (TADs). Several subunits of PRC1 have the capacity to form biomolecular condensates through liquid-liquid phase separation (LLPS) in vitro and when tagged and over-expressed in cells. Here, we use 1,6 hexandiol (1,6-HD), which disrupts liquid-like condensates, to examine the role of endogenous PRC1 biomolecular condensates on local and chromosome-wide clustering of PRC1-bound loci. Using imaging and chromatin immunoprecipitation combined with deep sequencing (ChIP-seq) analyses, we show that PRC1-mediated localized chromatin compaction and clustering of targeted genomic loci at megabase and tens of megabase scales can be reversibly disrupted by the addition and subsequent removal of 1,6-HD to mouse embryonic stem cells (mESCs). Decompaction and dispersal of polycomb domains and clusters cannot be solely attributable to the reduction of PRC1 binding following 1,6-HD treatment as the addition of 2,5-HD has similar effects despite this alcohol not perturbing PRC1-mediated clustering, at least at the sub-megabase and megabase scales. These results suggest that weak, hydrophobic interactions between PRC1 molecules characteristic of liquid condensates do have a role in polycomb-mediated genome organization.

overall_design: Calibrated ChIP sequencing of untreated, 2,5-HD, 1,6-HD and recovered mESCs

first: Shelagh

last: Boyle

first: Graeme

last: Grimes

first: Elias

last: Friman

first: Wendy

last: Bickmore


title: Altered GnRH neuron and ovarian innervation characterize reproductive dysfunction linked to the Fragile X messenger ribonucleoprotein (Fmr1) gene mutation

city: Riverside

first: Djurdjica

last: Coss

address: 900 University Ave

department: Biomedical Sciences

institute: UC Riverside

summary: Mutations in the Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene cause Fragile X Syndrome, the most common monogenic cause of intellectual disability. Mutations of FMR1 are also associated with reproductive disorders, such as early cessation of reproductive function in females. While progress has been made in understanding the mechanisms of mental impairment, causes of reproductive disorders are not clear. FMR1-associated reproductive disorders were studied exclusively from the endocrine perspective, while FMR1 role in neurons that control reproduction was addressed. Here, we demonstrate that similar to women with FMR1 mutations, female Fmr1 null mice stop reproducing early. However, young null females display larger litters, more corpora lutea in the ovaries, increased inhibin, progesterone, testosterone, and gonadotropin hormones in the circulation. Given elevated ovarian hormones, increase in gonadotropins is not due to the lack of ovarian feedback, and ovariectomy reveals both hypothalamic and ovarian contribution to elevated gonadotropins.  Increased vascularization of corpora lutea, higher sympathetic innervation of growing follicles in the ovaries of Fmr1 nulls, and higher numbers of synaptic GABAA receptors in GnRH neurons, which are excitatory for GnRH neurons, are also determined. Altered mRNA and protein levels of synaptic molecules in the hypothalamus are identified. Unmodified and ovariectomized Fmr1 nulls have increased LH pulse frequency, suggesting that Fmr1 nulls exhibit hyperactive GnRH neurons, regardless of ovarian feedback. These results reveal Fmr1 function in the regulation of GnRH neuron activity, and point to the role of GnRH neurons, in addition to the ovarian innervation, in the etiology of Fmr1-mediated reproductive disorders.

overall_design: In this study, (WT female, Fmr1 KO female) were analyzed for hypothalmic gene expression changes by Nanostring. Gene expression in 50 ng RNA per sample was analyzed using the Nanostring instrument, according to manufacturer’s instruction, with the nCounter Mouse Neuroinflammation Panel (770 genes, gene list available at the manufacturer’s website). Panel was customized with an addition of 30 custom probes for hypothalamic neuropeptides and their receptors.

first: Pedro

last: Villa


title: Comprehensive analyses of small RNAs associated with C. elegans argonautes

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

summary:
To genome-widely investigate functions of C. elegans argonautes (AGOs), we applied CRISPR/Cas9 technology to introduce an in-frame GFP::FLAG multiplex tag into the endogenous locus of C. elegans AGOs and performed RNA immunoprecipitation (IP) with anti-GFP or anti-FLAG antibody, followed by unique molecular identifier (UMI)-mediated cDNA library constructions and subjected to high-throughput sequencing.
We obtained targets of C. elegans AGOs analyzed from small RNA reads of input and 19 AGO IP samples.

overall_design: Comprehensive analyses of C. elegans argonaute targets

first: Lei

last: Liu

first: Jingxin

last: Li


title: Single-nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild-type and nr5a2 mutant zebrafish embryos

city: Los Angeles

first: Gage

last: Crump

address: 1425 San Pablo Street, BCC 403 Crump Lab

institute: Stem Cell Department at USC

summary: The functional jaw is composed of multiple connective tissues including skeletal components (bone, cartilage, and teeth), tendon, ligament, and musculature. Cranial neural crest-derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved, we profile multi-omic chromatin accessibility (snATACseq) and transcriptome (snRNAseq) of jaw mesenchyme at single-cell resolution from the developing zebrafish jaw.

overall_design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw, we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single-cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.

first: Crump

last: Gage

first: Chen

last: Hung-Jhen


title: Global change of RNA expression upon silencing TET1 in PDX2 B-ALL cells; Landscapes of TET1 and STAT5B binding on DNA across the entire genome in PDX2 B-ALL cells

city: Monrovia

first: Jianjun

last: Chen

department: Systems Biology

institute: Beckman Research Institute of City of Hope


title: Genome-wide chromatin profiles of PBRM1 Drug treatment [ChIP-Seq]

city: Singapore

first: Xiaosai

last: Yao

address: 60 Biopolis Street, Genome, #02-01

institute: Genome Institute of Singapore

summary: PBRM1 encodes an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney cancer. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been well examined. Here we show that in VHL-deficient renal tumors, PBRM1 deficiency results in aberrant PBAF complexes that localize to de novo genomic loci and activate the pro-tumorigenic NF-κB pathway. PBRM1-deficient PBAF complexes, despite retaining the association between SMARCA4 and ARID2, have loosely tethered BRD7 and redistribute from promoter proximal regions to distal enhancers containing NF-κB motifs. Subsequently, PBRM1-deficient cells display heightened NF-κB activity in multiple models and clinical samples. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib reverses NF-κB activation by reducing RELA occupancy and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes.

overall_design: ChIP-seq of parental and PBRM1-deficient 786-O cells treated with SMARCA4 ATPase inhibitor BRM014 and bortezomib

first: Bin

last: Teh


city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: In oroder to understand the maturation process of pre-HSCs to HSC, we conducted scRNA-seq using E11.5pre-HSCs and E12.5&E14.5 LT_HSC populations. Pseudotime analysis and velocity analysis show the progression of pre-HSC to mature HSCs and also divergent point of lineage trajectory.

overall_design: Characterization of E11.5 pre-HSCs and E12.5 & E14.5 HSCs to understand their transition using scRNA-seq. Each cell was single cell sorted into 96 well plate (1 cell/well) and RNA was extracted and converted into cDNA using SAMRT-Seq Single cell kit (Takara)

first: Momoko

last: Yoshimoto

first: Michihiro

last: Kobayashi

first: Jiqian

last: Wu

first: Hichao


title: Master regulators of oxidative stress associated genes improves stress adaptation in rice

city: Bangalore

first: Vidya

last: Niranjan

address: Mysuru Road, Kengeri

country: India

institute: R V College of Engineering

summary:
Microarray data of contrasting genotypes were performed between control and stress conditions.

Please cite the following work, if you are using the data

Sujitha, D., Kumar, H.G.J., Thapliayal, G. et al. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.). Plant Biotechnol Rep (2023). https://doi.org/10.1007/s11816-023-00819-8

overall_design: Based on stress responses AC39020 (Hightype) and BPT5204 (Lowtype) were selected for microarray analysis

first: D

last: Sujitha

first: Jalendra

last: Kumar

first: Garima

last: Thapliayal

first: Vanitha

middle: P

last: A

first: Akshay

last: Uttarkar

first: Mahesh

last: Patil

first: Rajashekar

last: Reddy

first: Usha

last: Rayalcheruvu

first: Geetha

last: Govind

first: Ramu

middle: S

last: Vemanna


title: Global change of RNA expression upon silencing TET1 in PDX2 B-ALL cells

first: Jianjun

last: Chen

summary: Here we report that TET1 has a critical role in B-ALL development. TET1-depleted cells delayed the onset of B-ALL. To investigate the mechanisms, we first generate the patient-derived xenograft cells (PDX2) and transduce with inducible-Cas9 and sgRNA targeting TET1. After treatment with doxycycline, we observe the expression of Cas9 and a depletion of TET1 protein. By using the high throughput sequencing RNA-seq, we check the potential targets of TET1 in B-ALL cells. Finally, we validate that CD72 and JCHAIN are two essential targets of TET1 signaling in B-ALL cells.

overall_design: Collect the PDX2-sgNS and PDX2-sgTET1 cells after treatment with doxycylcine for 6 days, and extract total RNA. Use 10 µg for next library preparation and sequencing.

first: Zhenhua

first: Keren

last: Zhou

first: Xiaolan

last: Deng


title: Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade [scRNA-seq]

first: Ansuman

last: Satpathy

first: Joy

last: Pai

first: Andrew

last: Chow

first: Jennifer

last: Sauter

first: Marissa

last: Mattar

first: Hira

last: Rizvi

first: Hyung

last: Woo

first: Nisargbhai

last: Shah

first: Fathema

last: Uddin

first: Alvaro

last: Quintanal-Villalonga

first: Joseph

last: Chan

first: Parvathy

last: Manoj

first: Viola

last: Allaj

first: Marina

last: Baine

first: Jamie

last: Chaft

last: Plodkowski

first: Helen

last: Won

first: Daniel

last: Wells

first: Mark

last: Donoghue

first: Elisa

last: de Stanchina

first: Triparna

last: Sen

first: Jedd

last: Wolchok

first: Brian

last: Houck-Loomis

first: Taha

last: Merghoub

first: Charles

last: Rudin

first: Matthew

last: Hellmann


title: Systematic lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade

first: Ansuman

last: Satpathy


title: Landscapes of TET1 and STAT5B binding on DNA across the entire genome in PDX2 B-ALL cells

first: Jianjun

last: Chen

summary: Here we report both TET1-WT and catalytically dead mutant TET1 (TET1-MUT) directly interact with STAT5B in PDX2 B-ALL cells. To study the landscape of TET1 and STAT5B binding in whole genomic DNA and test if the STAT5B binding signal is affected by TET1, we conduct the ChIP-seq assay with flag antibody (TET1-WT, TET1-MUT) and STAT5B antibody (sgNS or sgTET1) respectively. The results showed that TET1 bound peaks overlap with STAT5B very well and the tag density of STAT5B on target genes decreases in TET1-impeded cells. We conclude that TET1 recruit STAT5B to the promoters of its target genes and further promote the target genes’ transcriptions.

overall_design: We generate the stable PDX2 cells with forced expression of flag-tagged TET1-CD-WT and TET1-CD-MUT. Meanwhile we also conduct the ChIP in wild type or TET1 knockout PDX2 cells(sgNS and sgTET1).

first: Zhenhua

first: Keren

last: Zhou

first: Xiaolan

last: Deng


title: Genome-wide chromatin profiles of PBRM1 Drug treatment [RNA-Seq]

first: Xiaosai

last: Yao

overall_design: RNA-seq of parental and PBRM1-deficient 786-O cells treated with SMARCA4 ATPase inhibitor BRM014 and bortezomib

first: Bin

last: Teh


title: Autophagy-overactivated composite microbe engineered from oncolytic adenoviruses for the cascade enhancement of cancer immunotherapy

status: Public on Feb 12 2023

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

summary: Cell derived xenografts treated with OMVs@P2O-Ads or PBS were collected and then the total RNA was isolated. After removal of the remaining genomic DNA,  mRNA was purified from total RNA using polyT and then fragmented with 10× RNA fragmentation buffer and the RNA-seq library was constructed using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit and was sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for OMVs@P2O-Ads treated cell derived xenograft and PBS treated cell derived xenograft

first: Bingwu

last: Li

first: Wanxu

last: Huang


title: The role of p53 in pancreatic cancer suppression

city: Saarbrücken

first: Fabian

last: Müller

address: Campus A 2.4

institute: Saarland University

summary: The occurrence of TP53 mutations in late-stage PanINs has led to the idea that p53 acts to suppress malignant transformation of PanINs to PDAC. However, the cellular basis for p53 action during PDAC development has not been explored in detail. Here, we leverage a hyperactive p53 variant – p5353,54 – which we previously showed is a more robust PDAC suppressor than wild-type p53, to elucidate how p53 acts at the cellular level to dampen PDAC development. We find that p5353,54 both limits ADM accumulation and suppresses PanIN cell proliferation and does so more effectively than wild-type p53. We find further that p53 enhances chromatin accessibility at sites controlled by acinar cell identity transcription factors. These findings reveal that p53 acts at multiple stages to suppress PDAC, both by limiting metaplastic transformation of acini and by dampening KRAS signaling in PanINs, thus providing key new understanding of p53 function in PDAC.

overall_design: The pancreas from KrasLSL-G12D/+;Ptf1a-Cre;Trp53+/+ (n=3) and KrasLSL-G12D/+;Ptf1a-Cre;Trp53fl/fl (n=4) mice at ~3 and 1 months of age, respectively, were dissociated, and acinar cells were sorted using a surface marker for acinar cell identity (CD49F), as well as markers to exclude ductal-like cells (CD133), erythroid (TER-119) and immune cells (CD45).

first: Stephano

last: Mello

first: Sarah

middle: K

last: Denny

first: William

last: Greenleaf

first: Laura

last: Attardi


title: Intron dynamics reveal principles of gene regulation during the maternal-to-zygotic transition

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: The maternal-to-zygotic transition (MZT) is a conserved embryonic process in animals where developmental control shifts from the maternal to zygotic genome. A key step in this transition is zygotic transcription, and deciphering the MZT requires classifying newly transcribed genes. However, due to current technological limitations, this starting point remains a challenge for studying many species. Here we present an alternative approach that characterizes transcriptome changes based solely on RNA-seq data. By combining intron-mapping reads and transcript-level quantification, we characterized transcriptome dynamics during the Drosophila melanogaster MZT. Our approach provides an accessible platform to investigate transcriptome dynamics that can be applied to the MZT in non-model organisms. In addition to classifying zygotically transcribed genes, our analysis revealed that over 300 genes express different maternal and zygotic transcript isoforms due to alternative splicing, polyadenylation, and promoter usage. The vast majority of these zygotic isoforms have the potential to be subject to different regulatory control, and over two-thirds encode different proteins. Thus, our analysis reveals an additional layer of regulation during the MZT, where new zygotic transcripts can generate additional proteome diversity.

overall_design: Nanopore Direct RNA sequencing of drosophila embryos pre and post zygotic genome activation.

first: Jesslyn

last: Henrikson

first: Olivia

last: Rissland


title: Warm temperature-triggered developmental reprogramming requires VIL1-mediated, genome-wide H3K27me3 accumulation in Arabidopsis

city: Austin

first: Sibum

last: Sung

institute: University of Texas at Austin

summary: Through RNA-seq and ChIP-seq we show that VIL1 mediates warm ambient temperature responses.

overall_design: We grew Col-0 (WT) and vil1-1 mutant at two different temperatures (22C and 27C) and compared the transcriptome. RNA-seq analysis shows that vil1 fails to downregulate high ambient temperature suppressed genes. H3K27me3 ChIP-seq showed high temperature-mediated accumulation of H3K27me3 compromised in vil1. We also found that vil1 suppresses constitutive thermo-morphogenic transcriptome of arp6. RNA-seq analysis revealed that constitutive heat responsive transcriptome of arp6 reverted back to the wild-type levels in arp6vil1. This observation suggests an antagonistic relationship between VIL1 and ARP6. H2A.Z ChIP-seq showed that unlike wild type, vil1 fails to evict H2A.Z at high ambient temperature from high temperature responsive genes.

first: Junghyun

last: Kim

first: Yogendra

last: Bordiya

first: Bo

last: Zhao