title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis [CLIPseq]

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

institute: University of Toronto

summary: Alternative splicing (AS) is a critical regulatory layer, yet factors controlling networks of functionally coordinated splicing events during developmental transitions remain poorly understood. Here, we employ a multifaceted screening strategy to define factors that control dynamically regulated splicing events associated with neurogenesis. Among numerous previously unknown regulators, Rbm38 acts widely to negatively impact neural AS through Ptbp1-dependent and -independent mechanisms. Puf60, a ubiquitous splicing factor, is surprisingly found to promote neural splicing patterns. This activity is determined by a vertebrate-conserved, neural-differential exon that remodels Puf60 co-factor interactions. Ablation of this exon rewires distinct AS networks in embryonic stem cells and at multiple stages of neural Rbm38etc. Single-cell transcriptome analyses further reveal critical, multi-stage roles for Rbm38 and Puf60 isoforms in establishing neuronal identity. Our results thus reveal key new regulators of neurogenesis and establish how a single exon in a widely expressed splicing factor orchestrates temporal control over cell Rbm38etc.

overall_design: iCLIP-seq of Rbm38, Puf60 including exon 5, and Puf60 lacking exon 5, each in triplicate with size-matched input

first: Hong

last: Han

first: Andrew

last: Best

first: Nicholas

last: Mikolajewicz

first: Jack

last: Li

first: Jonathan

last: Roth

first: Fuad

last: Chowdhury

first: Federica

last: Mantica

first: Syed

last: Nabeel-Shah

first: Guillermo

last: Parada

first: Kevin

last: Brown

first: Dave

last: O'Hanlon

first: Jiarun

last: Wei

first: Yuxi

last: Yao

first: Abdelrahman

last: Zid

first: Emilia

last: Comsa

first: Mark

last: Jen

first: Jenney

last: Wang

first: Alessandro

last: Datti

first: Thomas

last: Gonatopoulos-Pournatzis

first: Robert

last: Weatheritt

last: Greenblatt

first: Jeffrey

first: Manuel

last: Irimia

first: Anne-Claude

last: Gingras

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Gene expression profiling of CD4 T cells in a mouse model of B-cell Lymphoma

status: Public on Jul 15 2022

city: Tampa

first: Rebecca

last: Hesterberg

address: 12902 Magnolia Dr.

country: USA

institute: Moffitt Cancer Center

type: Expression profiling by high throughput sequencing

summary: Early events mediated by cancer progression remain relative unknown. Here, we provide analysis of CD4 T cells derived from C57Bl/6 mice transplanted with Eu-Myc lymphoma cells at earlyand late  time points versus CD4 T cells derived from non-tumor-bearing control mice. Our data indicate that CD4 T-cell differentiation and fate is not provoked until late in tumor growth. These studies demonstrate when CD4 T-cell gene expression might change in the course of lymphoma progression.

overall_design: CD4 T cells were isolated from the spleens of Eu-Myc-bearing mice 7 days or 14 days after transplant (n=7,4 respectively). CD4 T cells were isolated from the spleens of non-tumor-bearing mice as a control (n=5). Transcriptome analysis was conducted

middle: S

first: John

middle: L

last: Cleveland


title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis [RNAseq_Puf60]

first: Ulrich

last: Braunschweig

country: Canada

summary: Alternative splicing (AS) is a critical regulatory layer, yet factors controlling networks of functionally coordinated splicing events during developmental transitions remain poorly understood. Here, we employ a multifaceted screening strategy to define factors that control dynamically regulated splicing events associated with neurogenesis. Among numerous previously unknown regulators, Rbm38 acts widely to negatively impact neural AS through Ptbp1-dependent and -independent mechanisms. Puf60, a ubiquitous splicing factor, is surprisingly found to promote neural splicing patterns. This activity is determined by a vertebrate-conserved, neural-differential exon that remodels Puf60 co-factor interactions. Ablation of this exon rewires distinct AS networks in embryonic stem cells and at multiple stages of neural differentiation. Single-cell transcriptome analyses further reveal critical, multi-stage roles for Rbm38 and Puf60 isoforms in establishing neuronal identity. Our results thus reveal key new regulators of neurogenesis and establish how a single exon in a widely expressed splicing factor orchestrates temporal control over cell differentiation.

overall_design: RNA-seq of N2A mouse neural cells upon control or Puf60 knockdown, the latter with or without rescue by knockdown-resistant Puf60 either with or without exon 5, in biological duplicate

first: Hong

last: Han

first: Andrew

last: Best

first: Nicholas

last: Mikolajewicz

first: Jack

last: Li

first: Jonathan

last: Roth

first: Fuad

last: Chowdhury

first: Federica

last: Mantica

first: Syed

last: Nabeel-Shah

first: Guillermo

last: Parada

first: Kevin

last: Brown

first: Dave

last: O'Hanlon

middle: A

middle: J

middle: F


title: Impacts of phosphatidylglycerol on plastid gene expression and light induction of nuclear photosynthetic genes

city: Hirosaki

first: Sho

last: Fujii

state: Aomori

address: Bunkyocho 3

department: Department of Biology, Faculty of Agriculture and Life Science

country: Japan

institute: Hirosaki University

summary: We report that phosphatidylglycerol (PG) biosynthesis in plastid is required for plastid gene expression mediated by plastid-encoded RNA polymerase and light-induced expression of nuclear-encoded photosynthesis-associated genes. A transcription factor GOLDEN-LIKE1 was also found to be involved in the downregulation of nuclear photosynthesis genes in responce to PG deficiency.

overall_design: Transcript levels in PG deificent mutant pgp1-2 and wild type were compared.

first: Koichi

last: Kobayashi

first: Ying-Chen

last: Lin

first: Yu-chi

last: Liu

first: Yuki

last: Nakamura

first: Hajime

last: Wada


title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis [RNAseq_neuroDiff]

first: Ulrich

last: Braunschweig

overall_design: RNA-seq of CGR8 mouse embryonic stem cells with mutations of the splicing factors Puf60 and Rbm38, and their parental wild type, as well as embryoid bodies and glutamatergic neurons differentiated from them, from two independent clones.

first: Hong

last: Han

first: Jiarun

last: Wei

first: Yuxi

last: Yao

first: Abdelrahman

last: Zid

first: Emilia

last: Comsa

first: Mark

last: Jen

first: Jenney

last: Wang

first: Alessandro

last: Datti

first: Thomas

last: Gonatopoulos-Pournatzis

first: Robert

last: Weatheritt

last: Greenblatt

first: Jeffrey

first: Manuel

last: Irimia

first: Anne-Claude

last: Gingras

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Expression data from Col-0 and mcu123 roots of 20-d-old seedlings grown in a sterile hydroponic system.

status: Public on Jul 18 2022

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

summary:
Ca2+ signaling is central to plant development, modulating gene expression to enable highly specific plant responses. While Ca2+-responsive proteins have been investigated intensely in plants, only few Ca2+ channels are known, and our understanding of how intracellular Ca2+ fluxes are facilitated remains limited. We obtained an Arabidopsis triple knockout mutant of homologues of the mammalian mitochondrial Ca2+ channel-forming MCU protein, in which mitochondrial Ca2+ uptake was severly perturbed in vivo in roots. To pinpoint the impact of the distrupted mitochondrial matrix free Ca2+ dynamcis, we performed transcriptome analysis in roots of an MCU triple knockout background (mcu123) and its corresponding wild type background (Col-0).
We devised a microarray-based analysis to investigate transcriptome differences  in roots of mcu123 triple knockout backgroudn and Col-0, without additional stimulation, and idenfitied distinct classes of differentially abundant transcripts.

overall_design: Two genetic backgrounds (Col-0 and mcu123) were used for RNA extraction in five replicates and hybridization of Affymetrix microarrays. Each replicate consists of pooled roots of 20-d-old seedlings grown in sterile hydroponics boxes (Phytatray II; Sigma-Aldrich, Darmstadt, Germany) filled with 150 mL half-strength Murashige and Skoog (MS) medium supplemented with 0.1% (w/v) sucrose and 0.05% (w/v) MES, pH 5.8 (KOH).

first: Cristina

last: Ruberti


title: Transcriptome analysis of Fusarium solani (NK-NH1) before and after  inhibition of volatile organic compounds produced by Xenorhabdus bovienii

city: Tianjin

first: Yu

address: Nankai University, Xuefu street, Nankai District

country: China

institute: Nankai University

summary: In order to study the inhibition mechanism of volatile organic compounds produced by Xenorhabdus bovienii on Fusarium solani (NK-NH1), we selected the inhibited and uninhibited Fusarium solani mycelia for transcriptome sequencing, and tried to find the corresponding inhibition mechanism at the gene level.

overall_design: We selected the inhibited and uninhibited Fusarium solani mycelia for transcriptome sequencing.

first: Fengyu

last: Zhang

first: Jiao

last: Pan

first: Kaixuan

last: Ma


title: Gene expression differences between Gata2cko and wt mouse midbrain

status: Public on Jul 14 2022

city: Helsinki

first: Kaia

last: Achim

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

summary:
Transcription factor Gata2 has been shown to regulate the development of the GABAergic neurons in the mouse midbrain. To gain information about the possible target genes of the Gata2 transcription factor, we used cDNA microarrays to compare gene expression in the embryonic day 12.5 (E12.5) wild-type and Gata2 mutant embryos. In this dataset, gene expression in control and Gata2cko dorsal and ventral midbrain tissues is reported.
The ventral_mb_mut_rep3 sample was identified as outlier in sample correlation analysis and excluded from the differential gene expression analysis. The samples 13-18 are part of the GEO dataset GSE89354:GSM2367121-GSM2367126.

overall_design: Dorsal midbrain and ventral midbrain regions of the neural tube were dissected from the E12.5 mouse embryos from the En1-cre, Gata2 flox/+ x Gata2 flox/flox crosses. Tissue pieces were frozen in liquid nitrogen. After genotyping, dissected samples were pooled according to genotype, combining 6 En1-cre, Gata2 flox/+ samples into one control pool, and 6 En1-cre, Gata2 flox/flox samples into one mutant pool. Separate sample pools were prepared from dorsal midbrain and ventral midbrain samples. RNA was extracted with TriZol, from 3 independent sample pools (biological replicates) per genotype. Extracted RNA was reverse transcribed and labelled according to standard Illumina protocols and hybridized on Illumina Mouse WG-6 Expression BeadChip arrays. For the comparison of gene expression, relicates were grouped according to genotype (control vs mutant).


title: Specific methylation marks in promoter regions are associated to the pathogenic process of Chronic Chagas disease Cardiomyopathy by modifying transcription factor binding patterns

city: Marseille

first: Pauline

last: Brochet

address: 13288 MARSEILLE cedex 09

country: France

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Transcriptome of miR-290-295 KO mESCs

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

summary: In order to identify direct microRNA targets in mouse embryonic stem cells (mESCs), we knocked out microRNA effector genes, profiled their transcriptomes and integrated the data with additional published OMICs data sets. To validate the analysis, we generated miR-290-295 KO mutant cell lines, assessed the transcriptome profile and compared the observed misregulation to the predictions of the analysis.

overall_design: Transcriptome of miR-290-295 KO E14 mESCs were generated in biological duplicates using QuantSeq kit.

first: Moritz

last: Schäfer


title: Specific methylation marks in promoter regions are associated to the pathogenic process of Chronic Chagas disease Cardiomyopathy by modifying transcription factor binding patterns [methylation]

summary: Chagas disease, caused by Trypanosoma cruzi, is an endemic parasitical disease of Latin America, affecting 7 million people. Although most patients are asymptomatic, 30% develop complications, including Chronic Chagasic Cardiomyopathy (CCC), which ranges from moderate to severe stages depending on the cardiac ejection fraction. The pathogenic process remains poorly understood, although genetic and epigenetic factors have already been proposed. Based on bulk RNA-seq and EPIC methylation data, we investigated the genetic and epigenetic deregulations present in the moderate and severe stages of CCC. We identified 4 main biological processes associated with the pathology development, including immune response, ion transport, cardiac muscle processes and nervous system. An in-depth study of the transcription factors binding sites in the differentially methylated regions corroborated the importance of these processes. We also conducted a methylation study on blood to identify potential biomarkers for CCC. Our data revealed 198 differentially methylated positions (DMPs) that could serve as biomarkers of the disease, of which 61 are associated with disease severity.

overall_design: DNAs, extracted from whole tissue of 14 samples, were bisulfite converted and amplified with elongation of primers with EZ DNA methylation kit (ZymoResearch, Saint Marcel, France). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California). Blood (5 to 15 ml of blood) from 144 samples was  collected in EDTA tubes. Genomic DNA was isolated on a silica-membrane according to the manufacturer’s protocol (QIAamp DNA Blood Max Kit, Qiagen, Hilden, Germany). Amplified DNAs were fragmented and hybridized in beads (Infinium Human Methylation EPIC Bead Chip, Illumina, San Diego, California).

first: Chevillard

last: Christophe

first: Cunha-Neto

last: Edecio

first: Spinelli

last: Lionel

first: Brochet

last: Pauline


title: Transcriptomics profile of mouse dendritic cell subsets during epicutaneous allergen immunotherapy (EPIT)

status: Public on Jul 17 2022

city: Lyon

first: Marc

last: Vocanson

address: 21 avenue Tony Garnier

institute: CIRI - INSERM U1111

summary: Epicutaneous immunotherapy (EPIT) protocols have recently been developed to restore tolerance in patients with food allergy (FA). The mechanisms by which EPIT protocols promote desensitization rely on a profound immune deviation of pathogenic T and B cell responses. To date, little is known about the contribution of skin dendritic cells (skDCs) to T cell remodelling and EPIT efficacy. Our results emphasize that the acquisition of distinct phenotypic and functional specializations by skDCs during EPIT is at the cornerstone of the desensitization process.

overall_design: We capitalized on a preclinical model of FA to ovalbumin (OVA), in which allergic C57BL/6 mice were desensitized by 8 weekly 48h-applications of OVA-containing patches. The phenotype and functions of OVA+ skDCs were monitored throughout the course of EPIT by flow cytometry, single-cell RNA sequencing and in vitro DC-T-cell co-culture assays.

first: Léo

last: Laoubi


title: Activation of g-globin expression by hypoxia-inducible factor 1a [ATAC-Seq]

city: Memphis

first: Mitchell

last: Weiss

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Longstanding observations that fetal hemoglobin (HbF, a2g2) expression is reactivated in postnatal red blood cells (RBCs) during hypoxia or recovery from anemia remain unexplained. We identified the hypoxia inducible factor (HIF) signaling pathway as a direct regulator of HbF expression in a CRISPR/Cas9 genetic screen. In RBC precursors, depletion of the von Hippel–Lindau (VHL) E3 ligase stabilized its ubiquitination target HIF1a to induce g-globin gene transcription. Mechanistically, HIF1a-HIF1bheterodimers bound cognate DNA elements in BGLT3, a long-noncoding RNA gene located 2.7 kb downstream of the tandem g-globin genes. This was followed by recruitment of transcriptional activators, chromatin opening, and increased long-range interactions between the g-globin genes and their upstream enhancer. These effects were recapitulated by hypoxia or inhibition of prolyl hydroxylase domain (PHD) enzymes that target HIF1a for ubiquitination. Our findings link globin gene regulation with canonical hypoxia adaptation, elucidate a mechanism for HbF induction during stress erythropoiesis, and identify a novel therapeutic approach for β-hemoglobinopathies.

overall_design: ATAC-seq experiments were performed in HUDEP-2 cells or CD34+ HSPCs derived erythroblast cells treated with NT sgRNA and VHL sgRNA1 or 2

first: Ruopeng

last: Feng


title: Activation of g-globin expression by hypoxia-inducible factor 1a [CaptureC]

overall_design: Capture-C experiments were performed CD34+ HSPCs derived erythroblast cells treated with NT sgRNA or VHL sgRNA1


title: Diverse maturity-dependent and complementary anti-apoptotic brakes safeguard human iPSC-derived neurons from cell death [RNA-seq]

first: Philipp

last: Koch

state: Deutschland

institute: Hector Institute for Translational Brain Research

summary: In humans, most neurons are born during embryonic development and have to persist throughout the entire lifespan of an individual. Thus, human neurons have to develop elaborate survival strategies to protect against accidental cell death. We set out to decipher the developmental adaptations resulting in neuronal resilience. We demonstrate that, during the time course of maturation, human neurons install a complex and complementary anti-apoptotic signaling network. This includes i.) a downregulation of central proteins of the intrinsic apoptosis pathway including several caspases, ii.) a shift in the ratio of pro- and anti-apoptotic BCL-2 family proteins, and iii.) an elaborate regulatory network resulting in upregulation of the inhibitor of apoptosis protein (IAP) XIAP. Together, these adaptations strongly increase the threshold for apoptosis initiation when confronted with a wide range of cellular stressors. Our results highlight how human neurons are endowed with complex and redundant preemptive strategies to protect against stress and cell death.

overall_design: IPSCs were differentiated into forbrain neurons and samples were harvested as neural progenitors, day5, day25, day28 or day45 neurons.

first: Ruven

last: Wilkens

first: Anne

last: Hoffrichter

first: Malin

last: Schmidt


title: Single-cell Analysis of a High-grade Serous Ovarian Cancer Cell Line Reveals Transcriptomic Changes and Cell Subpopulations Sensitive to Epigenetic Combination Treatment

city: Bloomington

first: Kenneth

last: Nephew

state: IN

institute: Indiana University

summary: Ovarian cancer (OC) is a lethal gynecological malignancy with a five-year survival rate of only 46%. Development of resistance to platinum-based chemotherapy is a common cause of high mortality rates among OC patients. Tumor and transcriptomic heterogeneity are drivers of platinum resistance in OC. Platinum-based chemotherapy enriches for ovarian cancer stem cells (OCSCs) that are chemoresistant and contribute to disease recurrence and relapse. Studies examining the effect of different treatments on subpopulations of HGSOC cell lines are limited. Having previously demonstrated that combined treatment with an enhancer of zeste homolog 2 inhibitor (EZH2i) and a RAC1 GTPase inhibitor (RAC1i) inhibited survival of OCSCs, we investigated EZH2i and RAC1i combination effects on HGSOC heterogeneity using single cell RNA sequencing. We demonstrated that RAC1i reduced expression of stemness and early secretory marker genes, increased expression of an intermediate secretory marker gene and induced inflammatory gene expression. Importantly, RAC1i alone and in combination with EZH2i significantly reduced oxidative phosphorylation and upregulated Sirtuin signaling pathways. Altogether, we demonstrated that combining a RAC1i with an EZH2i promoted differentiation of subpopulations of HGSOC cells, supporting the future development of epigenetic drug combinations as therapeutic approaches in OC.

overall_design: Comparative gene expression profiling analysis of single-cell RNA-seq data for OVCAR3 cells, a representative HGSOC cell line, and treatments with combinations of two inhibitors, RAC and EZH2.

first: Tim

last: Lai

first: Shruthi

last: Sriramkumar

first: Tara

middle: X

last: Metcalfe

first: Xingyue

last: Zong

first: Fang

last: Fang

first: Heather

middle: M

last: O’Hagan

middle: P


title: Helminth-induced reprogramming of the stem cell niche inhibits type 2 immunity

city: Montreal

first: Irah

last: King

address: 1001 Decarie Blv

institute: McGill University


title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis [RNAseq_N2Akd]

first: Ulrich

last: Braunschweig

overall_design: RNA-seq of N2A mouse neural cells upon siRNA-mediated knockdown of splicing factors in biological duplicate, including non-targeting control in biological triplicate

first: Hong

last: Han

first: Andrew

last: Best

first: Nicholas

last: Mikolajewicz

first: Jack

last: Li

first: Jonathan

last: Roth

first: Fuad

last: Chowdhury

first: Federica

last: Mantica

first: Syed

last: Nabeel-Shah

first: Guillermo

last: Parada

first: Kevin

last: Brown

first: Dave

last: O'Hanlon

first: Jiarun

last: Wei

first: Yuxi

last: Yao

first: Abdelrahman

last: Zid

first: Emilia

last: Comsa

first: Mark

last: Jen

first: Jenney

last: Wang

first: Alessandro

last: Datti

first: Thomas

last: Gonatopoulos-Pournatzis

first: Robert

last: Weatheritt

last: Greenblatt

first: Jeffrey

first: Manuel

last: Irimia

first: Anne-Claude

last: Gingras

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Helminth-induced reprogramming of the stem cell niche inhibits type 2 immunity [scRNA-seq]

first: Irah

last: King

summary: Enteric helminths form intimate physical connections with the intestinal epithelium, yet their ability to directly alter epithelial stem cell fate has not been resolved. Here we demonstrate that infection of mice with the symbiotic parasite Heligmosomoides polygyrus bakeri (Hpb), reprograms the intestinal epithelium into a fetal-like state marked by the emergence of Clusterin-expressing revival stem cells (revSCs). Organoid-based studies using parasite-derived excretory/secretory products reveal that Hpb-mediated revSC generation occurs independent of host-derived immune signals and inhibits type 2 cytokine-driven differentiation of secretory epithelial lineages that promote their expulsion. Reciprocally, type 2 cytokine signals limit revSC differentiation and, consequently, Hpb fitness indicating that helminths compete with their host for control of the intestinal stem cell niche to promote continuation of their life cycle.

overall_design: Small intestinal organoids from 1 mice were grown in ENR (control) medium or Hpb-CM, cell recovery target was 5000 cells

first: Danielle

last: Karo-Atar

first: Shaida

last: Ouladan

first: Tanvi

last: Javkar

first: Loick

last: Joumier

first: Macy

middle: K

last: Matheson

first: Sydney

last: Merritt

first: Susan

last: Westfall

first: Annie

last: Rochette

first: Maria

middle: E

last: Gentile

first: Ghislaine

last: Fontes

first: Gregory

last: Fonseca

first: Marc

last: Parisien

first: Luda

last: Diatchenko

first: Jakob

last: von Moltke

first: Mohan

last: Malleshaiah

first: Alex

last: Gregorieff


title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis [SPARseq]

first: Ulrich

last: Braunschweig

overall_design: Systematic Parallel Analysis of endogenous RNA regulation coupled to barcode Sequencing (SPAR-seq) of amplicons in 108 genes upon a total of 1536 knockdowns and controls in mouse N2A cells, in duplicate

first: Hong

last: Han

first: Andrew

last: Best

first: Nicholas

last: Mikolajewicz

first: Jack

last: Li

first: Jonathan

last: Roth

first: Fuad

last: Chowdhury

first: Federica

last: Mantica

first: Syed

last: Nabeel-Shah

first: Guillermo

last: Parada

first: Kevin

last: Brown

first: Dave

last: O'Hanlon

first: Jiarun

last: Wei

first: Yuxi

last: Yao

first: Abdelrahman

last: Zid

first: Emilia

last: Comsa

first: Mark

last: Jen

first: Jenney

last: Wang

first: Alessandro

last: Datti

first: Thomas

last: Gonatopoulos-Pournatzis

first: Robert

last: Weatheritt

last: Greenblatt

first: Jeffrey

first: Manuel

last: Irimia

first: Anne-Claude

last: Gingras

first: Jason

last: Moffat

first: Benjamin

last: Blencowe


title: Transcriptomes of miR-290-295 KO mESCs treated with siPOOLs for three different transcription factors and a negative control

first: Constance

last: Ciaudo

summary: In order to identify direct microRNA targets in mouse embryonic stem cells (mESCs), we generated miR-290-295 KO mutant cell lines, assessed their transcriptomes. We identified novel transcription factors (TF) as potential direct and functional targets of miR-290-295. To assess the role of these TFs, we rescued their expression in the miR-290-295 KO cell line using siPOOLs and profiled their transcriptomes.

overall_design: Transcriptomesof miR-290-295 KO E14 mESCs after siPOOL treatments for different Transcription Factors were generated in biological duplicates using QuantSeq kit.

first: Moritz

last: Schäfer


title: Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

city: Boston

first: Kevin

last: Dong

state: MASSACHUSETTS

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

type: Methylation profiling by high throughput sequencing

summary: Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in a locus or capture single-molecule dynamics. Here, we apply targeted nanopore sequencing to profile chromatin accessibility and DNA methylation on contiguous ~100-kb DNA molecules that span loci relevant to development, immunity and imprinting. We detect promoters, enhancers, insulators and transcription factor footprints on single molecules based on exogenous GpC methylation. We infer relationships among dynamic elements within immune loci, and order successive remodeling events during T cell stimulation. Finally, we phase primary sequence and regulatory elements across the H19/IGF2 locus, uncovering primate-specific features. These include a segmental duplication that stabilizes the imprinting control region and a noncanonical enhancer that drives biallelic IGF2 expression in specific contexts. Our study advances emerging strategies for phasing gene regulatory landscapes and reveals a mechanism that overrides IGF2 imprinting in human cells.

overall_design: targeted NOMe, RNA-seq and ATAC-seq were performed on cell lines and primary cells in resting or stimulated conditions.

first: Sofia

last: Battaglia

first: Jingyi

last: Wu

first: Zeyu

last: Chen

first: Bradley

last: Bernstein


title: Helminth-induced reprogramming of the stem cell niche inhibits type 2 immunity [Bulk RNA-seq]

first: Irah

last: King

overall_design: Small intestinal organoids from 2 mice were grown in ENR (control) medium or Hpb-CM

first: Danielle

last: Karo-Atar

first: Shaida

last: Ouladan

first: Tanvi

last: Javkar

first: Loick

last: Joumier

first: Macy

last: Matheson

first: Sydney

last: Merritt

first: Susan

last: Westfall

first: Annie

last: Rochette

first: Maria

last: Gentile

first: Ghislaine

last: Fontes

first: Gregory

last: Fonseca

first: Marc

last: Parisien

first: Luda

last: Diatchenko

first: Jakob

last: von Moltke

first: Mohan

last: Malleshaiah

first: Alex

last: Gregorieff


title: Orc1 and Kos3 ChIP-seq in Torulaspora delbrueckii

city: Buffalo

first: Laura

middle: N

last: Rusche

state: NY

address: 109 Cooke Hall, UB North/Amherst Campus

department: Biological Sciences

institute: State University of New York at Buffalo

summary: Chromatin Immunoprecipitation followed by high throughput sequencing to identify the location of Orc1 and Kos3 genomic enrichment.

overall_design: This data represents two technical replicates for each IP sample (Orc1-MYC and Kos3-V5) and two genomic input samples.

first: Haniam

last: Maria


title: Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells [ChiP-seq]

city: Bristol

first: Michael

middle: Paul

last: Greenwood

address: Whitson Street

department: Bristol Medical School / Translational Health Sciences

country: United Kingdom

institute: University of Bristol

summary: We have shown that the expression of the endoplasmic reticulum stress sensor Creb3l1 increases in magnocellular neurones (MCNs) in the rat hypothalamus in response to increased physiological demands for protein synthesis. Here we adopted a multiomic strategy to investigate specific roles of Creb3l1 in MCN homeostasis. We first performed chromatin immunoprecipitation followed by genome sequencing (ChIP-seq) to identify Creb3l1 genomic targets in the water deprived MCN enriched hypothalamic preparation. We then compared ChIP-seq gene targets with water deprived and Creb3l1 knockdown supraoptic nucleus RNA sequencing transcriptome datasets. This has provided an integrated signalling-gene regulation network for this transcription factor illuminating changes to cell pathways and function, an approach that has led us to understand the physiological changes that occur in MCNs to cope with excessive protein demands.

overall_design: This study was performed on samples collected from Sprague Dawley rats (n=9 pooled).  The hypothalamic supraoptic and paraventricular nucleus were collected by tissue punching from rats that underwent 72 hours of water deprivation. We performed Creb3l1 chromatin immunoprecipitation DNA-sequencing (ChIP-seq) in these magnocellular neurone (MCN) enriched hypothalamic samples to describe the Creb3l1 target transcriptome.

first: Benjamin

middle: T

last: Gillard

first: Mingkwan

first: David

last: Murphy


title: Transcriptomes of miR-290-295 KO mESCs treated with siPOOLs against the transcription factor Tfap4

first: Constance

last: Ciaudo

summary: In order to identify direct microRNA targets in mouse embryonic stem cells (mESCs), we knocked out microRNA effector genes, profiled their transcriptomes and integrated the data with additional published OMICs data sets. To validate the analysis, we generated miR-290-295 KO mutant cell lines, assessed the transcriptome profile and compared the observed misregulation to the predictions of the analysis. We identified the transcription factor Tfap4 as novel potential direct and functional target of miR-290-295. To assess the role of Tfap4, we rescued its expression in the miR-290-295 KO cell line using siPOOLs and profiled the transcriptome.

overall_design: Transcriptomes of WT mESCs and miR-290-295 KO E14 mESCs with and without siPOOL treatments for Tfap4 and a negative control were generated in biological duplicates using QuantSeq kit.  WT and miR-290-295_KO cells were prepared and sequenced together, as were all 4 siPOOL-treated samples.

first: Moritz

last: Schäfer


title: Systematic exploration of dynamic splicing networks reveals conserved multi-stage regulators of neurogenesis

first: Ulrich

last: Braunschweig

overall_design: Refer to individual Series


title: Activation of g-globin expression by hypoxia-inducible factor 1a [CUT&RUN]

first: Mitchell

last: Weiss

overall_design: CUT&RUN experiments were performed in HUDEP-2 cells or CD34+ HSPCs derived erythroblast cells treated with NT sgRNA or VHL sgRNA1, and base editor edited BGLT3 locus in VHLKO clones

first: Ruopeng

last: Feng


title: Activation of g-globin expression by hypoxia-inducible factor 1a [RNA-seq]

overall_design: RNA-seq experiments were performed in CD34+ HSPCs cells eletroporated with NT and VHL sgRNA1 RNP complex.


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_flyheads]

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

country: Israel

institute: Hebrew University Of Jerusalem, Migal

summary: Chromatin insulators are involved in transcription regulation and long-range chromatin contacts. In Drosophila the Boundary Element-Associated Factor Of 32kD (BEAF-32) binds to promoters of housekeeping genes and the boundaries of Topological Associated Domains (TAD) and is involved in the regulation of long-range targets by mechanisms that remain incompletely understood. Here we show that Relative-Of-WOC (ROW), which is part of the Heterochromatin Protein 1c (HP1c) complex, is essential for the long-range transcription regulation mediated by BEAF-32. We found that ROW physically interacts with the insulator complex proteins BEAF-32 and Chromator, as well as with HP1c, HP1b, and Without Children (WOC). Moreover, we found that ROW binds AT-rich sequences flanked by BEAF-32 motifs, which are located at promoters of housekeeping genes and in TAD boundaries. In agreement with these results, the genome distribution of ROW strongly correlated with BEAF-32 and WOC, but at a lower level with HP1c and HP1b. Knockdown of row resulted in downregulation of genes that are long-range targets of BEAF-32, are indirectly bound by BEAF-32 and ROW, and enriched with factors associated with RNA polymerase II pausing. These results suggest that ROW and BEAF-32 are involved in the recruitment of protein complexes required for transcription activation and long-range contacts between promoters of housekeeping and inducible genes.

overall_design: mRNA profiles of flies with knockdown of row or control flies in triplicates

first: Sebastian

last: Kadener

first: Sagiv

last: Shifman


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [RNA_seq_S2]

overall_design: mRNA profiles of S2 cells treated with RNAi to row/BEAF-32/both or non treated cells ( in triplicates)


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [ChIP_seq_S2]

overall_design: Binding profile of ROW and BEAF-32 in Drosophila S2 cells.


title: Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells [RNA-seq]

overall_design: This study was performed on samples collected from Sprague Dawley rats (n=5).  Adeno-associated viruses were injected unilaterally into the supraoptic nuclei of the hypothalamus.  The control virus was injected into the left supraoptic nucleus and the Creb3l1 knockdown virus into the right supraoptic nucleus of the same animal.  A 1 mm punch (Fine Scientific Tools, 18035-01) was used to collect SON samples from 100 μm coronal slices sectioned in a cryostat set at -20°C.  Total RNA was isolated from individual SONs (left and right) using phenol-chloroform phase separation method and Zymo Directzol RNA Miniprep kit.

last: Paterson


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [MNase_seq_flyheads]

overall_design: Nucleosomes profile in Drosophila fly heads (triplicate).


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes [ChIP_seq_flyheads]

overall_design: Binding profile of ROW (triplicate), HP1c (triplicate), HP1b (duplicate), WOC (triplicate), H3K4me3 (triplicate) and igG (duplicate) in Drosophila fly heads.


title: Elucidating oncogenic effects of androgen signaling in prostate tumorigenesis through aberrant activation of IGF1 and WNT signaling pathways [scRNA-Seq 2]

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

summary: Although a promotional role of the androgen receptor (AR) has been implicated in prostate tumorigenesis, the underlying mechanisms by which the AR, as a steroid-hormone receptor, induces prostatic oncogenesis still remain unknown. Conditional expression of the human AR transgene (hARtg) through Osr1 (old skipped related1) driven-Cre develops high-grade prostatic intraepithelial neoplasia (HGPIN) and adenocarcinomas in mice. Single-cell transcriptomic and genetic tracing analyses implicate the prostatic progenitor properties of prostatic Osr1-expressing cells through prostate development. Conditional expression of hARtg in Osr1-expressing basal epithelial cells elevates IGF1 signaling and initiates prostate oncogenesis and PIN formation.  Aberrant IGF1 signaling further cumulates Wnt/b-catenin activation in atypical PIN cells to promote tumor development.  Specific inhibition of Wnt signaling pathways significantly represses the growth of hARtg-positive prostate tumor cells in ex-vivo and xenograft models. These data elucidate a new and dynamic regulatory loop initiated by aberrant AR signaling altering IGF1 and Wnt signaling pathways in prostate oncogenesis and tumor development.

overall_design: Two sequencing datasets were analyzed containing prostatic intraepithelial neoplasia (PIN) and adenocarcinoma (PCa) tissues


title: Elucidating oncogenic effects of androgen signaling in prostate tumorigenesis through aberrant activation of IGF1 and WNT signaling pathways [ChIP-Seq]

overall_design: Two sequencing datasets were analyzed containing Input and hAR ChIP DNA from  prostatic intraepithelial neoplasia (PIN) tissues


title: Elucidating oncogenic effects of androgen signaling in prostate tumorigenesis through aberrant activation of IGF1 and WNT signaling pathways [scRNA-Seq 1]

overall_design: Three sequencing datasets were analyzed containing E18.5 male UGS and P14 & P35 prostate tissues


title: Elucidating oncogenic effects of androgen signaling in prostate tumorigenesis through aberrant activation of IGF1 and WNT signaling pathways [RNA-Seq]

overall_design: Two or Three replicates were included in each group.


title: Elucidating oncogenic effects of androgen signaling in prostate tumorigenesis through aberrant activation of IGF1 and WNT signaling pathways


title: The m6A methyltransferase Mettl3 deficiency attenuates hepatic stellate cell activation and liver fibrosis [m6A-RIP-seq]

status: Public on Jul 13 2022

city: Guangzhou

first: Yan

last: Xu

state: Guangdong

address: No. 600 Tianhe Road

institute: The Third Affiliated Hospital of Sun Yat-Sen University

summary: m6A-RIP sequencing of primary hepatic stellate cells (HSCs) isolated from Control and HSC-specific Mettl3-knockout (Mettl3 cKO) mouse liver tissues.

overall_design: Control and Mettl3 cKO mouse primary HSCs were isolated and cultured for 7 days in vitro for spontaneous activation.Total RNA was extracted for m6A-RIP sequencing. m6A peaks were analyzed and compared between Control and cKO HSCs.

first: Yanli

last: Li

first: Xinmei

last: Kang

first: Zhuowei

last: Zhou

first: Qi

last: Zhang


title: The m6A methyltransferase Mettl3 deficiency attenuates hepatic stellate cell activation and liver fibrosis [RNA-seq]

summary: RNA sequencing of LX2 cell line (a human hepatic stellate cell line). METTL3 overexpression or downreguation were achieved by lenti-virus transduction.

overall_design: Two shRNAs targeting human METTL3 (shMETTL3-1 and shMETTL3-2) or firefly luciferase (shLuc)  were cloned into pLKO.1 lentiviral vector (Addgene, 10878). shMETTL3 was used to achieve METTL3 knockdown, and shLuc was used as control. Lentivirus transfections were performed using polyethylenimine (PEI, Polysciences, 23966) according to the manufacturer's protocol. LX2 was infected with lentivirus-containing supernatants. Successfully infected cells were selected and prepared for futher RNA-seq.


title: The m6A methyltransferase Mettl3 deficiency attenuates hepatic stellate cell activation and liver fibrosis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Genome-wide reporter screen for transcriptional regulators of ribosome biogenesis genes and ribosomal protein genes

city: Würzburg

first: Elmar

last: Wolf

address: Am Hubland

department: Chair of Biochemistry and Molecular Biology

institute: University of Würzburg

summary: A genome-wide CRISPR/Cas9 knockout reporter screen was performed to identify transcriptional regulators of ribosomal biogenesis genes and ribosomal protein genes. The murine GeCKO v2 library provided by the Zhang lab was amplified and positive control sgRNAs targeting the reporters were spiked-in. NIH/3T3 cells (murine fibroblasts) harboring the "ribosome biogenesis" reporter Fbl-GFP (Fibrillarin promoter-driven enhanced GFP fused to the PEST domain of the murine ornithine decarboxylase) and the "ribosomal protein" reporter Rpl18-RFP (Rpl18 promoter-driven TurboRFP fused to the PEST domain of the murine ornithine decarboxylase) were transduced with the aforementioned library, selected and FACS-sorted six days after infection. The sorted conditions were i) low GFP, but middle to strong RFP expression (RiBi down); ii) low RFP, but middle to strong GFP expression (RP down); iii) low GFP and low RFP expression (Both down); iv) strong GFP and strong RFP expression (Both up). The same amount of cells that were used for sorting, were harvested as the "unsorted" condition to which all sorted samples were compared to. The plasmid library was also sequenced.

overall_design: Biological triplicates for "RiBi down", "RP down", "Both down", "Both up" and "Unsorted"; Control: "Unsorted"

first: Jessica

middle: D

last: Schwarz

first: Sören

last: Lukassen


title: 4sU-Seq of human U2OS cells upon acute RBM8A protein depletion

summary: The impact of acute RBM8A depletion on nascent transcription (using the auxin (IAA)-inducible degron system in conjunction with 4sU-sequencing) was investigated.

overall_design: Triplicates; conditions: RBM8A depletion (+IAA), no RBM8A depletion (-IAA; control), WT cells without tagged RBM8A (additional control)

first: Pranjali

last: Bhandare


title: RNA-Seq of murine NIH/3T3 cells upon Aldoa knockdown

summary: Aldoa knockdown (using a pool of 4 siRNAs) vs. non-targeting control knockdown (using a pool of 4 siRNAs) in murine NIH/3T3 cells (fibroblasts). Cells were harvested 48 hours after transfection.

overall_design: Triplicates; control: siCTR


title: RNA sequencing of liver and kidney tissues from mice treated with rapamycin during development

first: Anastasia

last: Shindyapina

state: MA

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

summary: RNA sequencing of mouse liver and kidney. UMHET pups were treated with diet containing encapsulated rapamycin or encapsulating material as a control from birth to 45 days of age, and tissues were collected at 2, 20-22 and 27-29 months of age from both males and females, and 3-5 samples per age, sex and treatment were sequenced.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice treated with rapamycin or control diet during postnatal development.

first: Vadim

last: Gladyshev


title: The chromatin factor ROW cooperates with BEAF-32 in regulating long-range genes

overall_design: Refer to individual Series


title: Collagenolysis dependent DDR1 signaling dictates pancreatic cancer outcome

city: La Jolla

first: Hua

last: Su

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly desmoplastic, aggressive cancer, frequently progressing and spreading by liver metastasis. Cancer-associated fibroblasts (CAF), extracellular matrix (ECM), and type I collagen (Col I) support or restrain PDAC progression and may impede blood supply and nutrient availability. The dichotomous role of the stroma in PDAC, and the mechanisms through which it influences patient survival and enables desmoplastic cancers to escape nutrient limitation remain poorly understood. Here we show that matrix metalloprotease (MMP)-cleaved or intact Col I (cCol I and iCol I, respectively) exert opposing effects on PDAC bioenergetics, macropinocytosis (MP), tumor growth and metastasis. While cCol I activates DDR1 (discoidin domain receptor-1)-NF-kB-p62-NRF2 signaling to promote PDAC growth, iCol I triggers DDR1 degradation and restrains PDAC growth. Patients whose tumors are iCol I enriched and DDR1 and NRF2 low have improved median survival compared to those with high cCol I, DDR1 and NRF2. Inhibition of DDR1-stimulated NF-kB or mitochondrial biogenesis blocked tumorigenesis in wildtype mice but not in mice expressing MMP-resistant Col I. The diverse effects of the tumor stroma on PDAC growth, metastasis, and patient survival are mediated through the Col I-DDR1-NF-kB-NRF2-mitochondrial biogenesis pathway, presenting new therapeutic opportunities.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for KPC960 (KPC) cells plated on WT ECM or MMP-resistant Col I (RR) ECM and incubated in low glucose (G) or low glutamine (Q) for 24 h.

first: Fei

last: Yang

first: Michael

last: Karin


title: Gliotransmission of D-serine promotes thirst-directed behaviors in Drosophila

city: Durham

first: Vincent

last: Croset

address: Stockton Road

department: Biosciences

institute: Durham University

summary: We used single-cell transcriptomics to address changes in gene expression across cell types in the brain of Drosophila melanogaster. Our results showed extensive gene regulation in glia and astrocytes. Among the regulated genes, astray (aay) encodes a phosphoserine phosphatase. We demonstrate that D-Serine produced by aay regulates thirst-directed behaviours by modulating glutamatergic neurotransmission.

overall_design: 4 different groups were studied: (1) water sated, (2) 6h water deprived, (3) 12 water deprived and (4) 12h water deprived followed by 45 minutes back on water. 2 replicates were obtained for each condition, with 24 Drosophila brains used for each sample.

first: Devika

last: Agarwal

first: Christoph

last: Treiber

first: Scott

last: Waddell


title: Androgens Alleviate Allergic Airway Inflammation by Suppressing Cytokine Production of Th2 Cells

city: Kyoto

first: Koichi

last: Ikuta

state: Kyoto

address: 53 Shogoin-Kawaharamacho, Sakyo-ku

department: Department of Virus Research

institute: Institute for Frontier Life and Medical Sciences, Kyoto University

summary: This study reveraled that androgen signaling suppresses differentiation and cytokine production of Th2 cells by inducing DUSP-2, explaining, in part, the sex bias of asthma after adolescence.

overall_design: Transcriptional profiling of Th2 differentiated cells with DHT from AR-flox/y (WT) and CD4-Cre; AR-flox/y mice

first: Aki

last: Ejima


title: Functional analysis of Vsx2 super-enhancer reveals an autoregulatory network governing Vsx2 expression during retinogenesis [ChIP-seq_mouse]

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: The roles of retinal cis-regulatory landscape in controlling the expression of gene regulatory networks important for retinogenesis remain poorly understood. Vsx2 is a transcription factor essential for retinal proliferation and bipolar cell differentiation but the molecular mechanisms underlying its developmental roles are unclear. Here, we profiled VSX2 genomic occupancy during mouse retinogenesis,  revealing extensive retinal gene regulatory networks associated with Vsx2 during development. We defined an autoregulatory loop in which VSX2 binds and transactivates its own enhancer in association with the transcription factor PAX6 . The Vsx2 regulatory landscape contains elements that are required for Vsx2 expression, retinal proliferation and proper cell type differentiation. We further show that retinae in which the Vsx2 enhancer landscape has been largely deleted suffer a bias toward photoreceptor production. Genomic data indicate that VSX2 occupies cis-regulatory elements nearby genes associated with photoreceptor differentiation and homeostasis in mouse and human retinae, including  a conserved region nearby the rod-specifying factor Prdm1. We provide evidence that VSX2 associates with OTX2 and can act to suppress OTX2-dependent enhancer transactivation of Prdm1 enhancer.  Taken together, our analyses illuminate important mechanistic insights on how VSX2 is engaged with gene regulatory networks that are essential for retinal proliferation and cell fate acquisition.

overall_design: ChIP-seq expriments on VSX2-E14.5 (two replicates) and VSX2-Adult mouse (two replicates) with their corresponding input

first: Fuyun

last: Bian

first: Marwa

last: Daghsni

first: Fangfang

last: Lu

first: Silvia

first: Jeffrey

last: Gross

first: Issam

last: Aldiri


title: Apyrase-mediated amplification of secretory IgA promotes intestinal homeostasis

city: Bellinzona

first: Fabio

last: Grassi

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine

summary: Morphogenesis of epithelial tissues relies on the precise developmental control of cell polarity and architecture. In the early Drosophila embryo, the primarSecretory IgA (SIgA) interaction with commensal bacteria regulates the composition and function of the microbiota, contributing to gut ecosystem homeostasis. However, mechanisms regulating the reciprocal control of microbiota and SIgA are not defined. Bacteria-derived ATP limits T follicular helper (Tfh) cells activity in the Peyer’s patches (Pps) of the small intestine via the P2X7 receptor and thereby SIgA generation. Here we show that inhibition of bacteria derived ATP signaling by delivery of the ATP-degrading enzyme apyrase to the intestine results in the amplification of the SIgA repertoire. The enhanced breadth of SIgA in mice colonized with apyrase-releasing E. Coli conditioned topographical distribution of bacteria and expression of genes involved in metabolic versus immune functions in the intestinal epithelium. SIgA mediated conditioning of bacteria and enterocyte function was also reflected by selective differences in nutrients absorption in mice colonized with apyrase expressing bacteria. Hydrolysis of bacteria derived ATP was particularly helpful in restoring intestinal homeostasis via SIgA in antibiotics induced dysbiosis. Administration of apyrase expressing bacteria attenuated intestinal barrier impairment, glucose metabolism perturbation and susceptibility to infection by enteric pathogens induced by antibiotic treatments. Therefore, microbiota derived ATP regulates SIgA, and amplification of SIgA response by apyrase can be leveraged to restore intestinal fitness in dysbiotic conditions.y epithelium forms during cellularisation, following a tightly controlled genetic programme where specific sets of genes are up-regulated. Some of them, for instance, control membrane invagination between the nuclei anchored at the apical surface of the syncytium.

overall_design: We performed genome-wide expression profiling of small intestinal epithelium from GF mice colonized with E. colipApyr or E. colipBAD28. To evaluate the effect of bacteria-derived eATP on the epithelial transcriptional activity independently of SIgA coating of E. Coli, we performed the same analysis in epithelial cells isolated from gnotobiotic E. colipApyr or E. colipBAD28 C57BL/6 Igh-J-/- mice, which carry a deletion in the J segment of the Ig heavy chain locus and therefore are devoid of immunoglobulins.

first: Lisa

last: Peruzza

first: Francesco

last: Strati


title: Functional analysis of Vsx2 super-enhancer reveals an autoregulatory network governing Vsx2 expression during retinogenesis [RNA-seq_mouse]

overall_design: RNA-seq on mouse VSX2 SE WT at E14.5 (three replicates), VSX2 SE KO at E14.5 (three replicates), VSX2 EN1 WT at E14.5 (four replicates) and VSX2 EN1 KO at E14.5 (four replicates).


title: Single-Cell Analyses Reveal Early Thymic Progenitors and Pre-B Cells in the Zebrafish

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ~70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B and T cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.

overall_design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations, a total of 7 adult zebrafish (3-5 months post-fertilization) and 21 juvenile zebrafish (4 weeks post-fertilization) were studied. More specifically, kidney marrows only were dissected from 3 adult GESTALT zebrafish, paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish, and thymi only were dissected from 2 adult Tg(lck:eGFP) zebrafish. Thymi only were dissected and pooled from 21 juvenile Tg(lck:eGFP) zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation, filtering, and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics (lymphoid and progenitor fraction; granulocyte fraction) were collected in preparation for 10x single-cell RNA sequencing. A single 10x lane was used for each adult sample, whereas 4 lanes were used for the juvenile thymi to obtain 4 technical replicates.

first: Sara

last: Rubin

first: Chloé

last: Baron

first: Alexandra

last: Corbin

first: Song

last: Yang

middle: I


title: Functional analysis of Vsx2 super-enhancer reveals an autoregulatory network governing Vsx2 expression during retinogenesis [ChIP-seq_human]

overall_design: ChIP-seq expriments on VSX2-Adult human sample (two replicates) with its corresponding input


title: Single cell RNA sequencing of mesenteric lymph node dendritic cells in segmented filamentous bacteria(SFB)-colonized C57BL/6 mice

city: Columbus

first: Soo

last: Ngoi

state: OH

address: 460 W 12th Ave

department: Internal Medicine Hematology

institute: OSU

summary:
Purpose: The goal of this study is to identify gut dendritic cells that induces CD4 Th17 cells that play an critical role in mucosal immunity
Methods: C57BL/6 mice were orally gavaged with fecal material derived from SFB-positive donor mice. Five days post oral gavage, mesenteric lymph nodes were harvested and dendritic cells were FACS-sorted. cDNA library from migratory dendritic cells (MHCII-highCD11c+) and resident dendritic cells (MHCII+CD11c-high) were generated using Chromium Single Cell 3' Library v2 Kit (10x Genomics). RNA sequencing was performed using NovaSeq S4 flow cell (Illumina). Data was processed using the Cell Ranger software (10x Genomics) followed by analysis using the R-based package Seurat.
Results: Gut colonization with SFB increased the migration of type 2 but not type 1 dendritic cells to the mesenteric lymph nodes. Based on transcriptomic profiles, migratory type 2 dendritic cells consist of 2 major cell clusters (Cd40-Ccl22 and Cd1d1-Tnfrsf4-enriched cells). The Th17 response inducing cytokine IL-6 co-localized with the Cd40-Ccl22-expressing cells.
Conclusion: Our study represents the first to carefully characterize the mucosal dendritic cells at steady state and during acute CD4 Th17 response. Transcriptomic profiling enabled the subsetting of dendritic cells based on functional markers (such as cytokines and chemokines) that are otherwise difficult to measure at the protein level. These results provide a focused look at mucosal dendritic cells and their roles in dictating different T cell responses.

overall_design: Examination of gut migratory dendritic cells and lymph node resident dendritic cells in naïve and SFB-colonized mice.

first: Bei


title: Functional analysis of Vsx2 super-enhancer reveals an autoregulatory network governing Vsx2 expression during retinogenesis

first: Shuchang


title: Histone methylation profiles of H3K4me3, H3K9me3, H3K36me3, H4K20me3, and RIOX2 in WT and mdig/mina53 KO MDA-MB 231 breast cancer cells

status: Public on Jul 12 2022

city: Stony Brook

first: Fei

last: Chen

state: New York

address: Lauterbur Drive Stony Brook, NY 11794

institute: Stony Brook Cancer Center

summary: The mineral dust-induced gene (mdig, also called as MINA or RIOX2) is overexpressed in breast cancer and its high expression correlates with poor overall survival of the patients. Our  studies suggested its role in cell motility, invasion and in the demethylation of DNA and histone proteins. Here we studied the global histone methylation profiles of human triple negative breast cancer cells MDA-MB-231 that were knocked out for mdig via CRISPR-Cas 9 gene editing. Altered histone methylation profiles impacted the transcriptional status of key genes implicated in cell growth, motility, invasion and cancer.

overall_design: Examination of 5 different histone modifications in WT and mdig KO MDA-MB 231 cells.

first: Chitra

last: Thakur

first: Qian

last: Zhang


title: Activation of g-globin expression by hypoxia-inducible factor 1a

city: Memphis

first: Mitchell

last: Weiss

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital


title: Epigenome analysis of monocytes and derived nurse-like cells from chronic lymphocytic leukemia patients, along with healthy-donor controls

first: Jonathan

last: Butchar

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

summary:
Monocytes and matching culture-derived nurse-like cells were compared using Illumina's EPIC/850k arrays
Monocytes isolated using MACS and NLCs isolated using cytometry sorting as CD14+/CD19-

overall_design: Bisulphite-converted DNA was hybridized to Illumina EPIC/850k chips.

first: Christopher

middle: C

last: Oakes


title: Next Generation Sequencing of Mislocalized POPEYE Enables Quantitative Analysis of Arabidopsis Root Transcriptomes in Iron Deficient Conditions

city: Raleigh

first: Terri

last: Long

state: NC

department: Plant & Microbial Biology

institute: North Carolina State University

summary:
Purpose: Identify differences in the trascriptional landscape of Arabidopsis roots under iron deficiency stress where POPEYE, a non cell autonomous iron responsive transcription factor, is localized to specific cell files.
Method: RNA-Seq was performed on 7 day old roots (4d +Fe then transferred for 3d - Fe) of cell specific localization lines (WT;+ iron, WT,  pye-1, PPL, SHR23, PEP45, WER13, WER65) - triplicates. RNA was extracted using RNAeasy Plant RNA Purification Kit (Qiagen). cDNA synthesis and amplification were performed using the NEBNext® Poly(A) mRNA Magnetic Isolation Module followed by the NEBNext® Ultra™ II Directional RNA Library Prep and NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) and sequenced using an Illumina HiSeq 2500 sequencing machine, with 125bp single end reads. Adapters and low quality reads were filtered out using fastQC and fastq-mcf. Clean reads were mapped against the TAIR 10 reference genome using the tophat2. RPKM were acquired using RSubread, followed by edgeR to identify differentially expressed genes (DEGs), using a maximum false discovery rate (FDR) of 0.05 and minimum log fold change threshold of 0.75.
Results: We identified 4414 DEGs between WT (+iron) and WT (-iron). WT minus was used as the baseline to compare transcriptome landscape between cell specific localization lines. Compared to WT minus iron, pye-1 had 3878 DEGs, SHR23 had 3697 DEGs, PEP45 had 3678 DEGs, WER13 had 4696 DEGs, and WER65 had 3920 DEGs.
Conclusion: Transcriptomic profiles indicated that localization of PYE to the vasculature and endodermis (SHR23;V-EN) increased genes involved in metal aquisition, while localization expanded to the cortex (PEP45;C-EN-V) helps regulate overall iron bioavailability, and the expression of genes associated with various aspects of photosynthesis and carbon metabolism.

overall_design: RNA-Seq of 7 day old roots (4d +Fe then transferred for 3d - Fe) of cell specific localization lines (WT;+ iron, WT,  pye-1, PPL, SHR23, PEP45, WER13, WER65) triplicates

first: DurreShahwar

last: Muhammad


title: Transcription factor Creb3l1 maintains proteostasis in neuroendocrine cells

first: Michael

last: Greenwood

institute: University of Bristol


title: Identification of genes regulated by Bcl11b

status: Public on Jul 11 2022

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

institute: CRCL

summary: Gain and loss of function approaches for Bcl11b were used to identify the gene regulatory network regulated by this transcription factor in MEF

overall_design: Comparison of transcriptomes of control MEF or MEF infected with Bcl11b shRNA or overexpressing plasmids particles

first: Aurélia

last: Huyghe

first: Giacomo

last: Furlan


title: Interactome of Aiolos/Ikaros Reveals Combination Rationale of Cereblon Modulators with HDAC Inhibitors in DLBCL

city: Summit

first: Rida

last: Khan

state: NJ

address: 556 Morris Ave

department: Knowledge Science Research, IPS

institute: Bristol-Myers Squibb

summary:
Purpose: Cereblon (CRBN), a substrate receptor of the E3 ubiquitin ligase complex CRL4CRBN, is the target of the small molecules lenalidomide (Len) and avadomide (Ava). Upon binding of the drugs, Aiolos and Ikaros are recruited to the E3 ligase, ubiquitylated and subsequently degraded. In DLBCL cells, Aiolos and Ikaros are direct transcriptional repressors of interferon stimulated genes (ISG) and degradation of these substrates results in increased ISG protein levels resulting in decreased proliferation and apoptosis. Herein, we aimed to uncover the mechanism(s) Aiolos and Ikaros use to repress ISG transcription and provide a mechanistic rationale for a combination strategy enhance cell autonomous activites of CELMoDs.
Results: We describe that in DLBCL, the repression of ISG transcription is accomplished in part through recruitment of large transcriptional complexes such as the nucleosome remodeling and deacetylase (NuRD) which modify the chromatin landscape of these promoters. A rational combination approach of Ava with a specific HDAC inhibitor leads to a significant increase in ISG transcription compared to either single agent, and synergistic antiproliferative activity in DLBCL cell lines.
Conclusion: Our results provide a novel role for lineage factors Aiolos and Ikaros in DLBCL as well as further insight into the mechanism(s) of Aiolos and Ikaros mediated transcriptional repression and unique therapeutic combination strategies.

overall_design: For the RNAseq experiment: 4 DLBCL cell lines were treated with either DMSO, Lenalidomide or CC-122

first: Patrick

last: Hagner

first: Martino

last: Colombo


title: Mechanical checkpoint regulates monocyte differentiation in fibrotic niches.

city: Cambridge

first: David

last: Mooney

address: 58 Oxford Street

institute: Harvard University

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

sample_organism:
Homo sapiens
Mus

platform_organism:
Homo sapiens
Mus


title: Turning coldspots into hotspots: targeted recruitment of axis protein Hop1 stimulates meiotic recombination in Saccharomyces cerevisiae

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

summary: The DNA double strand breaks (DSBs) that initiate meiotic recombination are formed in the context of the meiotic chromosome axis, which in budding yeast contains a meiosis-specific cohesin isoform and the meiosis-specific proteins Hop1 and Red1. Hop1 and Red are important for DSB formation; DSB levels are reduced in their absence and their levels, which vary along the lengths of chromosomes, are positively correlated with DSB levels. How axis protein levels influence DSB formation and recombination remains unclear. To address this question, we developed a novel approach that uses a bacterial ParB-parS partition system to recruit axis proteins at high levels to inserts at recombination coldspots where Hop1 and Red1 levels are normally low. Recruiting Hop1 markedly increased DSBs and homologous recombination at target loci, to levels equivalent to those observed at endogenous recombination hotspots. This local increase in DSBs did not require Red1 or the meiosis-specific cohesin component Rec8, indicating that, of the axis proteins, Hop1 is sufficient to promote DSB formation. However, while most crossovers at endogenous recombination hotspots are formed by the meiosis-specific MutLγ resolvase, only a small fraction of crossovers that formed at an insert locus required MutLγ, regardless of whether or not Hop1 was recruited to that locus. Thus, while local Hop1 levels determine local DSB levels, the recombination pathways that repair these breaks can be determined by other factors, raising the intriguing possibility that different recombination pathways operate in different parts of the genome.

overall_design: calibrated ChIP-seq

first: Anura

last: Shodhan

first: Martin

last: Xaver

last: Wheeler

last: Lichten


title: Viscoelastic properties of ECM differentially regulate monocyte patterns of gene expression

summary: Myelofibrosis (MF) is a progressive, bone marrow (BM) malignancy associated with monocytosis, and is believed to promote the pathological remodelling of the extracellular matrix. Here, we show that the mechanical properties of MF, namely the liquid-to-solid properties (viscoelasticity) of BM, contribute to aberrant differentiation of monocytes. Human monocytes cultured in stiff, elastic hydrogels show pro-inflammatory polarization and differentiation towards dendritic cells, as opposed to those cultured in a viscoelastic matrix.

overall_design: Human primary monocytes were encapsulated in artificial fibrotic matrix hydrogels for 3 days in soft vs. stiff and viscous vs. elastic conditions to test the effects of mechanical cues on gene transcription of monocytes by a custom nanoString panel of myeloid markers

first: Kyle

middle: H

last: Vining


title: Co-Profiling of Chromatin Occupancy and RNAs in single cells

first: Keji

last: Zhao

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

summary: Elucidating the relationship between cellular heterogeneity in epigenome and gene expression is critical to understand the underlying cellular states and functions. Jointly profiling chromatin occupancy and RNA at the single level is needed for this purpose, which is however not available currently. Therefore, we developed Single-cell co-profiling of chromatin occupancy and RNAs sequencing (scPCOR-seq) for simultaneously profiling genome-wide gene expression and TF/histone bindings in the same cell. By applying scPCOR-seq to human H1 and 293T cells, scPCOR-seq can successfully detect gene expression and PolII bindings in the same cell at the single cell level and identify cell type specific Cis-regulatory elements (CRE). We observed that the cellular variation in PolII bindings is strongly correlated with that in gene expression, which is affected by the location of polII bindings. This suggests that a new mechanism for the source of cellular heterogeneity in gene expression. Overall, our work provides a promising approach to understand the relationships among different omics layers.

overall_design: Jointly Profiling genome-wide PolII binding and gene expression with multiplex indexing tecnique at the single cell level

first: Lixia

last: Pan

first: Wai

last: Ku

first: Qingsong

last: Tang


title: The nuclear receptor TLX (NR2E1) inhibits growth and progression of triple-negative breast cancer

city: Urbana

first: Erik

middle: Russell

last: Nelson

state: IL

address: 407 South Goodwin Ave

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana-Champaign

summary: Development of targeted therapies will be a critical step towards reducing the mortality associated with triple-negative breast cancer (TNBC). To achieve this, we searched for targets that met three criteria: (1) pharmacologically targetable, (2) expressed in TNBC, and (3) expression is prognostic in TNBC patients. Since nuclear receptors have a well-defined ligand-binding domain and are thus highly amenable to small-molecule intervention, we focused on this class of protein. Our analysis identified TLX (NR2E1) as a candidate. RNA-Seq analysis revealed that TLX reduced the expression of genes implicated in the pro-proliferative KRAS signaling pathway as well as epithelial-mesenchymal transition (EMT), a cellular program known to drive metastatic progression. Indeed, TLX overexpression significantly decreased cell proliferation, migration and invasion, and robustly decreased the metastatic capacity of TNBC cells in murine models. Taken together, our work indicates that TLX retards the progression of TNBC. Several ligands have been shown to regulate the transcriptional activity of TLX, providing a framework for the future development of this receptor for therapeutic intervention.

overall_design: Overall 9 samples were analyzed from MDA-MB-231 cells. 3 replicates of control cells treated with control siRNA (CTL + siCTL). 3 replicates of TLX overexpressing cells treated with control siRNA (TLX+siCTL). 3 replicates of TLX overexpressing cells treated with an siRNA against TLX (TLX+siTLX)

first: Adam

last: Nelczyk

first: Liqian

last: Ma

first: Hashni

last: Gamage

last: McHenry

first: Madeline

last: Henn

first: Mohammed

last: Kadiri

first: Yu

last: Wang

first: Anasuya

last: Gupta

first: Natalia

last: Krawczynska

first: Shruti

last: Bendre

first: Sisi

last: He

first: Sayyed

last: Shahoei

first: Shih-Hsuan

last: Hsiao

first: Tareq

last: Saleh

first: Valerie

last: Carpenter

last: Gewirtz

last: Spinella

middle: R


title: RNA-seq analysis of Jak2-V617F monocytes in elastic versus viscous fibrotic matrix

first: David

last: Mooney

overall_design: Bone marrow-derived monocytes were isolated from control mice (Vav-iCre) and a knock-in murine model of MPN harboring an endogenous Jak2-V617F49 mutation (Jak2-V617F-Vav-iCre). Similar to studies with human cells, monocytes were encapsulated in viscous, stiff and elastic, stiff artificial ECM to determine the impact of elasticity.

first: Kyle

last: Vining

first: Kwasi

last: Adu-Berchie

first: Anna

last: Marneth


title: GI is a repressor of ABA transcriptional responses and sensitivity in Arabidopsis

city: Milan

first: Matteo

last: Chiara

address: via celoria 26

country: Italy

institute: University of Milan

summary: Transcriptional reprogramming plays a key role in drought stress responses, preceding the onset of morphological and physiological adaptations. The best characterised signal regulating gene expression in response to drought is the phytohormone abscisic acid (ABA). ABA-regulated gene expression, biosynthesis and signalling are highly organised in a diurnal cycle, so that ABA-regulated physiological traits occur at the appropriate time of the day. The mechanisms that underpin such diel oscillations in ABA signals are poorly characterised.  Here we uncover GIGANTEA (GI) as a key gate keeper of ABA-regulated transcriptional  and physiological responses. Time-resolved RNAseq under different irrigation scenarios indicate that gi mutants produce an exaggerated ABA response at midday, despite accumulating wild-type levels ABA. The direct comparison with ABA-deficient mutants confirms the role of GI in controlling ABA-regulated genes and enabled us to distinguish a phase of high ABA sensitivity at dawn, characterized by low GI accumulation.

overall_design: Analysis of RNAsequencing data in different irrigation conditions and genetic backgrounds

first: Beata

last: Siemiatkowska

first: Lucio

last: Conti


title: Endothelial progenitor migration and differentiation is regulated by distinct transcriptional effectors of Cloche/Npas4l

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: Embryonic cells including endothelial progenitors undergo extensive migration and differentiation events; however, whether and how these processes are interrelated remains unclear.  The transcription factor Npas4l is necessary for endothelial specification in zebrafish by inducing the expression of the transcription factor genes etsrp, tal1 and lmo2.  We generated a knock-in reporter in the npas4l locus to visualize endothelial progenitors and their derivatives in wild-type and mutant embryos.  We find that in npas4l mutants, npas4l reporter expressing cells do not migrate to the midline and instead contribute to skeletal muscle and pronephric tubules.  Investigating the Npas4l transcriptional effectors, we find that npas4l reporter expressing cells in tal1 mutants fail to migrate while those in etsrp mutants migrate but fail to differentiate.  In lmo2 mutants, npas4l reporter expressing cells migrate and differentiate, but many express pronephric tubule markers.  Altogether, these data reveal the complex regulation of endothelial progenitor migration, differentiation and fate restriction.

overall_design: Comparison of npas4l reporter positive cells from heterozygous and homozygous npas4l mutant embryos using single cell RNAseq on sorted cells.

first: Kenny

last: Mattonet

last: Guenther

first: Ingo

last: Ebersberger

first: Sven

last: Reischauer

first: Didier

middle: Y

last: Stainier


title: Longitudinal inflammatory gene expression associated with advanced myelofibrosis

summary: Myelofibrosis (MF) is a progressive, bone marrow (BM) malignancy associated with monocytosis, and is believed to promote the pathological remodelling of the extracellular matrix. Here, we show that the pathologic grading of MF was associated with inflammatory gene expression in primary patient samples.

overall_design: The pathology archives at Brigham & Women’s Hospital (BWH) and Massachusetts General Hospital (MGH) was queried to identify patients with myelofibrosis on bone marrow biopsy obtained between 2005 and 2016. Patients diagnosed with myelodysplastic syndrome/MPN overlap disease and those who had progressed to acute leukemia, received treatment with chemotherapeutic agents for prior cancer diagnoses, or had undergone stem cell transplantation were excluded. Histologic review and fibrosis grading were performed by W.W., R.P.H. and O.P. based on consensus, using the 2016 WHO Revised Classification of Myeloid Neoplasms. The study was conducted in accordance with the principles set forth by the Declaration of Helsinki and the requirement for informed consent was waived by the institutional review board. This dataset is an example of data from one patient who progressed from grade 2 to grade 3 myelofibrosis from 2013 to 2016. A separate shared dataset shows single timepoint data from the cohort of patients.

first: Waihay

middle: J

last: Wong


title: A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites

city: Helsinki

first: Paivi

last: Pihlajamaa

address: Haartmaninkatu 8

institute: University of Helsinki

summary: Many biological processes are controlled by master regulators that activate complex downstream transcriptional and/or posttranslational networks. These networks have been hard to dissect using reverse genetics because of the difficulty of mutating large numbers of binding motifs or phosphorylation sites at different chromosomal loci. Here, we use a novel competitive genome editing (CGE) assay for dissecting the transcriptional network downstream of the master regulatory oncogene MYC. The CGE method is based on precision genome editing using template libraries that either reconstitute the original feature or introduce an altered sequence. Both types of libraries also introduce sequence tags, generating a large number of replicate lineages and enabling direct comparison between cells that carry original and mutant features. By using precision editing and by comparing two populations of edited cells, the CGE method overcomes the two main limitations of CRISPR/Cas9-technology in analyzing the effect of genotype on phenotype: the difficulty of cutting DNA exactly at the intended site, and the decreased cell proliferation caused by the DNA cuts themselves. Importantly, it provides a powerful method for studying subtle effects elicited by mutation of individual transcription factor binding sites. We show here that E-box mutations at several MYC target gene promoters resulted in reduced cellular fitness, demonstrating a direct correlation between MYC-regulated cellular processes and MYC binding, and identifying important transcriptional targets responsible for its functions.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor MYC and the histone modification H3K27ac in HAP1 cells.

first: Päivi

first: Otto

last: Kauko

first: Biswajyoti

last: Sahu

first: Teemu

last: Kivioja

first: Jussi

last: Taipale


title: Adrenomedullin2  stimulates progression of thyroid cancer in mice under nutrient excess conditions

status: Public on Jul 10 2022

city: Daejeon

first: Jung Tae

last: Kim

address: 282 Munhwaro

department: School of Medicine

country: South Korea

institute: Chungnam National University

summary: Thyroid cancer is associated with genetic alterations, e.g., BRAFV600E, which may cause carcinomatous changes in hormone-secreting epithelial cells. Epidemiological studies have shown that overnutrition is related to the development and progression of cancer. In this study, we attempted to identify the cell non-autonomous factor responsible for the progression of BRAFV600E thyroid cancer under overnutrition conditions. We developed a mouse model for inducible thyrocyte-specific activation of BRAFV600E, which showed features similar to those of human papillary thyroid cancer. LSL-BrafV600E;TgCreERT2 showed thyroid tumour development in the entire thyroid, and the tumour showed more abnormal cellular features with mitochondrial abnormalities in mice fed a high-fat diet (HFD). Transcriptomics revealed that adrenomedullin2 (ADM2) was increased in LSL-BrafV600E;TgCreERT2 mice fed HFD. ADM2 was upregulated on addition of a mitochondrial complex I inhibitor or palmitic acid with integrated stress response (ISR) in cancer cells. ADM2 stimulated protein kinase A (PKA) and extracellular signal-regulated kinase (ERK) in vitro. The knockdown of ADM2 suppressed the proliferation and migration of thyroid cancer cells. We searched The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases and found that increased ADM2 expression was associated with ISR and poor overall survival. Consistently, upregulated ADM2 expression in tumour cells and circulating ADM2 molecules were associated with aggressive clinicopathological parameters, including body mass index, in thyroid cancer patients. Collectively, we identified that ADM2 is released from cancer cells under mitochondrial stress resulting from overnutrition and acts as a secretory factor determining the progressive properties of thyroid cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for thyroid from LSL-BrafV600E;TgCreERT2 mice fed chow diet and high fat diet for 12 weeks

first: Jung

first: Yea

last: Kang

first: Bon

middle: S

last: Koo

first: Minho

last: Shong


title: Synonymous codon massive reporter library in zebrafish embryos

status: Public on Jul 09 2022

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

summary: Messenger RNA (mRNA) stability substantially impacts steady-state gene expression levels in a cell. mRNA stability is strongly affected by codon composition in a translation-dependent manner across species, through a mechanism termed codon optimality. We have developed iCodon (www.iCodon.org), an algorithm for customizing mRNA expression through the introduction of synonymous codon substitutions into the coding sequence. iCodon is optimized for four vertebrate transcriptomes: mouse, human, frog, and fish. Users can predict the mRNA stability of any coding sequence based on its codon composition and subsequently generate more stable (optimized) or unstable (deoptimized) variants encoding for the same protein. Further, we show that codon optimality predictions correlate with both mRNA stability using a massive reporter library and expression levels using fluorescent reporters and analysis of endogenous gene expression in zebrafish embryos and/or human cells. Therefore, iCodon will benefit basic biological research, as well as a wide range of applications for biotechnology and biomedicine.

overall_design: We designed a library of 1,600 sequences containing 100 different 100 amino acid long coding sequences capturing the average composition of the zebrafish proteome, with 10 variants each designed using iCodon to have 5 bins of increasing predicted stability with 2 sequences in each bin. The groups were referred as iCodon 1, iCodon 2, iCodon 3, iCodon 4, and iCodon 5, from less to more stable mRNA predictions. Additionally, 5 synonymous sequences were designed using 5 independent iterations of IDT’s codon optimization tool and 1 synonymous sequence using Genewiz’s codon optimization tool as this method returned the exact same sequences in each independent run. These sequences were cloned downstream of 11 fixed codons to control for similar translation initiation and the reporters contain constant 5’ and 3’ UTR sequences. 1395 of the 1600 designed sequences were ordered, in vitro synthetized mRNA was injected into 1-cell stage zebrafish embryos, and the mRNA decay after 2, 5, and 8 hours post injection was calculated by targeted RNA-sequencing.

first: A

middle: A

last: Bazzini

first: S

middle: G

last: Medina

first: M

last: Diez


title: Ribotag-based Next Generation Sequencing of tumor-associated astrocytes

city: Tel Aviv

first: Lior

last: Mayo

state: Israel

address: Britannia Bldg. Room 204, Tel Aviv univeristy

institute: Tel Aviv Unoversity

summary: GfapCRE:Rpl22HA mice were intracranially implanted with GL261 glioma cells (GBM) or injected with PBS (sham). Seventeen days later, RNA was retrieved from mouse brain extract (input) by anti-HA immunoprecipitation

overall_design: 4 samples of ribotag-isolated RNA of astrcoytes from sham control; 4 samples of ribotag-isolated RNA of Tumor-associcated astrcoytes

first: Mayo

last: Lior


title: RNA-sequencing of DMSO or Ginsenoside Rb1-treated Rat BMSCs

city: Shanghai

first: Hongmeng

last: Yu

address: No.83, Fenyang Road

department: Department of Otolaryngology

institute: Eye & ENT Hospital, Fudan University

summary: RNA sequencing for 6 samples..

overall_design: Examing DMSO or Ginsenoside Rb1-treated Rat BMSCs, each with 3 replicates


title: CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (ChIP-seq)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

institute: Ludwig-Maximilians-Universität München

summary: Pre-mRNA splicing is a highly regulated process catalyzing intron excision by spliceosome. Spliceosome activation is a major control step requiring dramatic protein and RNA rearrangements leading to a catalytically active complex. Prior research has linked hyperphosphorylation of SF3B1, a subunit of U2 snRNP, with spliceosome activation and catalytically active spliceosome, rendering a relevant kinase a key player for pre-mRNA splicing. Here we use OTS964, the first potent inhibitor of cyclin-dependent kinase 11 (CDK11), to show rapid and selective dephosphorylation of SF3B1 on threonines required for spliceosome activation. CDK11 associates with SF3B1 and its inhibition causes massive intron retention, block in precatalytic spliceosome complex B to activated spliceosome complex Bact transition and accumulation of non-functional spliceosomes on pre-mRNA and chromatin. These studies reveal crucial regulatory role of CDK11 in human pre-mRNA splicing and define the compound OTS964 as a quality chemical biology probe for CDK11.

overall_design: Examination of RNA-seq, 4SU-seq, SF3B1 iCLIP, U2AF65 iCLIP,AQR iCLIP,P-Ser2 ChI, P-Ser5 ChIP, P-Ser7 ChIP, and RNAPolII ChIP in the presence or absence of OTS964 inhibitor on HCT116 cells

first: Milan

last: Hluchy

first: Pavla

last: Gajduskova

first: Igor

last: Ruiz de Los Mozos

first: Michal

last: Rajecky

first: Michael

last: Kluge

first: Benedict-Tilman

last: Berger

first: Zuzana

last: Slaba

first: Katerina

last: Hanakova

first: Elena

last: Weiß

first: Stefan

last: Knapp

first: Zbynek

last: Zdrahal

first: Kamil

last: Paruch

first: Dalibor

last: Blazek


title: Ets21C sustains a pro-regenerative transcriptional program in blastema cells of Drosophila imaginal discs

city: Berkeley

first: Iswar

middle: Krishna

last: Hariharan

address: Weill Hall

department: Molecular & Cell Biology

institute: University of California, Berkeley

summary: An important unanswered question in regenerative biology is to what extent regeneration is accomplished by the reactivation of gene regulatory networks used during development versus the activation of regeneration-specific transcriptional programs. Following damage, Drosophila imaginal discs, the larval precursors of adult structures, can regenerate missing portions by localized proliferation of damage-adjacent tissue. Using single-cell transcriptomics in regenerating wing discs, we have obtained a comprehensive view of the transcriptome of regenerating discs and identified two regeneration-specific cell populations within the blastema, Blastema1 and Blastema2. Collectively, these cells upregulate multiple genes encoding secreted proteins that promote regeneration including Pvf1, upd3, asperous, Mmp1, and the maturation delaying factor Ilp8. Expression of the transcription factor Ets21C is restricted to this regenerative secretory zone; it is not expressed in undamaged discs. Ets21C expression is activated by the JNK/AP-1 pathway, and it can function in a type 1 coherent feedforward loop with AP-1 to sustain expression of downstream genes. Without Ets21C function, the blastema cells fail to maintain the expression of a number of genes, which leads to premature differentiation and severely compromised regeneration. As Ets21C is dispensable for normal development, these observations indicate that Ets21C orchestrates a regeneration-specific gene regulatory network. We have also identified cells resembling both Blastema1 and Blastema2 in scribble tumorous discs. They express the Ets21C-dependent gene regulatory network, and eliminating Ets21C function reduces tumorous growth. Thus, mechanisms that function during regeneration can be co-opted by tumors to promote aberrant growth.

overall_design: Cells were dissociated from regenerating Drosophila melanogaster wing-imaginal discs, barcoded using the 10x Chromium single-cell RNA sequencing platform, and sequenced on an Illumina NovaSeq. Prior to dissection, flies were raised at 18 degrees Celsius, shifted on day 7 to 30 degrees Celsius to induce tissue damage, and then returned to 18 degrees to allow for tissue regeneration. Discs were collected 24 hours into the regeneration period. FACS was employed to remove doublets and dead cells from the samples. The second replicate (24R2) included a fluorescent marker of wing disc myoblasts (Him-GFP); these myoblasts were sorted out during FACS, allowing for better isolation of cells from the regenerating disc epithelium.

first: Melanie

last: Worley

first: Nicholas

last: Everetts

first: Riku

last: Yasutomi

first: Rebecca

last: Chang

first: Shrey

last: Saretha

first: Nir

last: Yosef


title: Mesenchymal-epithelial interaction guides development of stomach and intestine in mouse embryos

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

summary: After gut tube patterning in early embryos, the cellular and molecular changes of developing stomach and intestine remain largely unknown. Here, combining single-cell RNA-sequencing and spatial RNA-sequencing, we constructed a spatiotemporal transcriptomic landscape of the mouse stomach and intestine during embryonic day E9.5-E15.5. We observed regionalization and heterogeneity of both the epithelium and mesenchyme in the gastrointestinal (GI) tract at E9.5 and dynamic cell evolution afterwards. The spatiotemporal distributions of cell clusters and the epithelium-mesenchyme interactions indicate a coordinated development of the epithelium and mesenchyme. The cell evolution and signaling events regulate the stomach regionalization and intestine segmentation. Using the gut tube-derived organoids, we found that the cell fate of the foregut and hindgut could be switched by the regional niche factors. Together, this work demonstrates the important function of the epithelium-mesenchyme interactions in early GI tract development, laying a foundation for further dissection of the mechanisms governing this process.

overall_design: Constructing single cell atlas of mouse embyro stomach and intestine during E9.5-E15.5.

first: Ye-Guang

first: Lianzheng

last: Zhao

first: Wanlu

last: Song


title: Effect of tubular IKKb deletion in acute ischemic kidney injury

city: Kiel

first: Eileen

last: Dahlke

state: Schleswig-Holstein

address: Otto-Hahn-Platz 8

department: Anatomisches Institut

institute: Christian-Albrechts-Universität Kiel

summary: To establish the role of Ikkb during acute kidney injury, we use a mouse line with a specific deletion of Ikkb in the renal tubular system and exposed them to ischemia/reperfusion. Sample collection were done 2 days and 14 days after ischemia/reperfusion.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of control mice and tubular Ikkb-deletion mice at three time points (baseline, d2 and d14).

first: Toni

last: Engmann

first: Robert

last: Häsler

first: Franziska

last: Theilig


title: CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (iCLIP)

first: Caroline

last: Friedel

first: Milan

last: Hluchy

first: Pavla

last: Gajduskova

first: Igor

last: Ruiz de Los Mozos

first: Michal

last: Rajecky

first: Michael

last: Kluge

first: Benedict-Tilman

last: Berger

first: Zuzana

last: Slaba

first: Katerina

last: Hanakova

first: Elena

last: Weiß

first: Stefan

last: Knapp

first: Zbynek

last: Zdrahal

first: Kamil


title: Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC

status: Public on Jul 08 2022

city: Orange

first: Matthew

last: Simon

state: CT

address: West Campus, 100 West Campus Drive, Ste MIC312A

department: MBB

institute: Yale University

summary: The RNA decapping scavenger, DcpS, has recently been identified as a dependency in acute myeloid leukemia.   The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by modulation of DcpS. Considering this strong dependence of AML cell lines on DcpS, we wanted to explore PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, the first PROTAC capable of degrading an mRNA-decapping enzyme. JCS-1 non-covalently binds DcpS with an RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 will serve as a chemical biology tool to interrogate DcpS function in different cellular contexts and may be an applicable strategy for the treatment of AML and other DcpS-dependent genetic disorders.

overall_design: RNA isolated from MOLM-14 cells treated with JCS-1, JCS-2, or RG3039 for 6 hours, and +/- s4U was subjected to oxidative-nucleophilic-aromatic-substitution chemistry. Sequencing libraries were prepared from all RNA

first: Jake

last: Swartzel

last: Bond

first: Andreas

last: Pintado-Urbanc

first: Mehana

last: Daftary

first: Mackenzie

last: Krone

first: Todd

last: Douglas

first: Evan

last: Carder

first: Joshua

last: Zimmer

first: Takahiro

last: Maeda

first: Craig

last: Crews


title: CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (4sU-seq)

first: Caroline

last: Friedel

first: Milan

last: Hluchy

first: Pavla

last: Gajduskova

first: Igor

last: Ruiz de Los Mozos

first: Michal

last: Rajecky

first: Michael

last: Kluge

first: Benedict-Tilman

last: Berger

last: Paruch

first: Dalibor

last: Blazek


title: Enhancing GAT-3 in thalamic astrocytes promotes resilience to brain injury in rodents

city: San Francisco

first: Ilia

middle: D.

last: Vainchtein

state: California

address: 1550 4th street

department: Psychiatry

institute: UCSF

summary: Thalamic inflammation mediates enhanced seizure risk and altered cognition-related cortical states through astrocytic GAT-3 in mice.

overall_design: RNA-sequencing data from ipsilateral (eGFP-pos and eGFP-neg) and contralateral (eGFP-neg) VB thalamic astrocytes three weeks after unilateral injection of AAV2/5-Gfa104-eGFP in VB thalamus in mice.

first: Frances

last: Cho

first: Jeanne

last: Paz

first: Anna

middle: V

last: Molofsky


title: Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [RNA-seq]

city: Napoli

first: Pietro

last: Zoppoli

state: Napoli

address: via S.Pansini,5

department: DMMBM

institute: Università degli Studi di Napoli Federico II

summary: Hmga2 KO pluripotent stem cells fail to develop into epiblast-like stem cells (EpiLCs). By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in stabilized epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. As nuclear lamina is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of HiC data in wt and Hmga2 KO cells allowed us to observe that inter-TAD interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hmga2 wt and KO PSCs induced to differentiate into EpiLCs.

first: Tommaso

last: Russo


title: CDK11 phosphorylates SF3B1 and is essential for constitutive splicing (RNA-seq)

first: Zuzana

last: Slaba

first: Katerina

last: Hanakova

first: Elena

last: Weiß

first: Stefan

last: Knapp

first: Zbynek

last: Zdrahal

first: Kamil


title: Hmga2 protein loss alters nuclear envelope and affects 3D chromatin structure upon the induction of pluripotent stem cell commitment [HiC]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hmga2 wt and KO PSCs induced to differentiate into EpiLCs. Genome binding/occupancy profiling of Hmga2 in EpiLCs by high throughput sequencing.  High-throughput chromatin conformation capture sequencing (HiC-seq) of Hmga2 wt and KO PSCs induced to differentiate into EpiLCs.

first: Andrea

middle: M

last: Chieriello