title: Resistance of estrogen receptor function to BET bromodomain inhibition is mediated by transcriptional coactivator cooperativity

city: New York

first: Sicong

last: Zhang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: BRD4, a member of the BET family, can bind to ER binding sites and activate transcription of BETi-resistant genes, such as MYC, independently of bromodomains. Importantly, we uncover that the bromodomain-independent recruitment of BRD4 to enhancers relies on the Mediator complex, and that disruption of Mediator complex reduces BRD4's enhancer occupancy.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for BRD4 in MCF7 cells. DNase-seq in BRD4-dTAG cells. DNase-seq in BRD4-dTAG cells.


title: BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A (ChIP-seq)

status: Public on Jun 25 2024

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated co-dependency with SETD1A in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS) and induces transcriptional elongation defect along with the increasing of RNA polymerase II at TSS, but did not cause the reduction of H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and recruit SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for the transcriptional regulators and histone modifications in MOLM-13 leukemia cells

first: Takayuki

last: Hoshii


title: Transcriptomic profiling of the postnatal mouse cardiac conduction system

city: Ottawa

first: Kyoung-Han

last: Kim

state: Ontario

address: 40 Ruskin Street

country: Canada

institute: University of Ottawa Heart Institute

type: Expression profiling by high throughput sequencing

summary: The cardiac conduction system (CCS) comprises a network of highly specialized cells, including sinoatrial node, atrioventricular node, His bundle, bundle branches and Purkinje fibers. To uncover the transcriptomic landscape across the postnatal CCS and comparative profiling of different CCS components, we conducted scRNA-seq in purified postnatal CCS cells and spatial transcriptomic analysis in the postnatal CCS reporter mouse heart.

overall_design: The postnatal cardiac conduction cells were isolated from the CCS reporter (Cntn2-Cre;Rosa26tdTomato) mice, purified by FACS, labelled using MULTI-seq, and subjected to 10x Genomics scRNA-seq. Additionally, different regions of the CCS were captured through cryosectioning of the CCS reporter heart and subsequently analyzed using the NanoString GeoMX Digital Spatial Profiler (DSP). For GeoMx DSP: two ROIs were selected for the SA node (SAN), lower nodal bundle (LNB), His bundle (HIS), proximal left and right bundle branch (PLBB/PRBB), distal left and right bundle branch (DLBB/DRBB), and left and right Purkinje fibers (LPF/RPF). One ROI was collected for the compact AV node (cAVN). One ROI was collected ffor non-CCS regions adjacent to each CCS region, including the right atrial appendage (RAA), left endomyocardium (LENDO), left epimyocardium (LEPI), basal interventricular septum (IVS-Base), apical interventricular septum (IVS-Apex), and right ventricle (RV).

first: Yena

last: Oh


title: BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.

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

overall_design: Refer to individual Series


title: Transcriptomic change of ARDI1A mutant bladder cancer cell line treated with CPI-0209 or induced ARID1A expression

status: Public on Jun 26 2024

city: Cambridge

first: Patrick

last: Trojer

state: Massachusetts

address: 215 First Street, Suite 200

country: USA

institute: Constellation Pharmaceuticals

summary: Advanced bladder cancer remains a difficult cancer to treat, and for the majority of patients, current standard treatments ultimately prove ineffective.  These tumors frequently harbor mutations in the BAF complex subunit ARID1A, which has been reported to confer sensitivity to EZH2 inhibition in several tumor types.  Here we describe the generation of CPI-0209, a best-in-class, orally available EZH2 inhibitor.  We show that mutant bladder cancer lines harboring ARID1A loss of function (LOF) mutations are preferentially sensitive to inhibition of EZH2. Treatment with CPI-0209 not only elicits a significant monotherapeutic response in ARID1A mutant models, it also outperforms cisplatin and improves response in chemo-resistant models. These findings shine light on new therapeutic opportunities for patients with advanced urothelial carcinoma.

overall_design: HT1376-TetON control cells and a clonal HT1376-TetON-ARID1A cell line were induced with 50 ng/ml doxycycline for 24 hours and then treated for 4 days with DMSO or 250 nM CPI-0209.

first: Patricia

last: Keller

first: Elizabeth

last: Adams

first: Rentian

last: Wu


title: Gene expression profiling of hippocampal dentate gyrus in the central nervous system-specific Derlin-1 or Derlin-2 deficient mice

city: Miyazaki

first: Naoya

last: Murao

department: Medical Sciences

institute: University of Miyazaki

summary: To search gene expression change of dentate gyrus in the central nervous system-specific Derlin-1or Derlin-2 mice, we performed genome-wide DNA microarray analysis and compared the expression levels between Derlin-1 or 2 _control and Derlin-1 or 2_KO.

overall_design: Mice were sacrificed at 8-9 weeks of age by cervical dislocation and hippocampal dentate gyrus was dissected for DNA microarray analysis.

first: Hideki

last: Nishitoh


title: BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A (RNA-seq)

overall_design: RNA-sequencing (RNA-seq) in MOLM-13 leukemia cells


title: Small RNA-mediated genetic switches coordinate ALG-3/4 small RNA pathway function

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

summary: Coordination of gene regulatory networks is necessary for proper execution of cellular programs throughout development. RNA interference (RNAi) is an essential regulatory mechanism in all metazoans. Proper RNAi-mediated gene regulation requires coordination of several RNAi branches to ensure homeostasis. For example, in C. elegans, the Argonautes, ALG-3 and ALG-4, are expressed specifically during spermatogenesis (L4 stage) and bind small interfering RNAs (siRNAs) complementary to sperm-enriched genes. We find that alg-3 and alg-4 are regulated by siRNAs. Our work shows that gene switches are operated via these siRNAs to regulate the Argonautes’ expression in a temporal manner. This RNAi-to-RNAi regulatory cascade is essential for coordinating ALG-3/4 pathway function, particularly during heat stress, to provide thermotolerant sperm-based fertility. This work provides insight into one regulatory motif used to maintain RNAi homeostasis, across developmental stages, despite environmental stressors. As RNAi pathways are evolutionarily conserved, other species likely use similar regulatory architectures to maintain RNAi homeostasis.

overall_design: 8 mRNA-seq and 8 small RNA-seq libraries were generated and analyzed. Each genotype per condition were generated in duplicate.

middle: K


title: The influence of the transcription factor EB for BCR-induced gene expression in murine WEHI-231 B cells

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

summary: To investigate TFEB-dependent expression in BCR-stimulated and resting B cells, CRISPR/Cas9 knockout cell lines were established and subjected to RNA sequencing analysis

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental WEHI-231 B cells and their derivate TFEB knockout cell lines (TFEB KO #A-59 and #B-20) under different stimulation conditions, measured in duplicates

first: Matthias

last: Münchhalfen

first: Maren

last: Sitte


title: The influence of the transcription factor EB for BCR-induced gene expression in human Ramos B cells

overall_design: Comparative gene expression profiling analysis of RNA-seq data for parental Ramos B cells and their derivate TFEB knockout cell lines (TFEB KO #A-31 and #B-24) under different stimulation conditions, measured in duplicates


title: Profiling the transcriptomic changes in DTC upon germline ablation

city: Boston

first: Jiehui

last: Chen

state: MA

address: 320 Longwood Ave

institute: Boston Children’s Hospital

summary: DTC is the niche of GSCs in C. elegans. To pursue how DTC senses and responds to the loss of GSCs, we isolated DTCs from WT worms and glp-1 mutants (genetic germline ablation) and profiled their transcriptomes.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Distal Tip Cells (DTCs).

first: Yidong

last: Shen

first: Meng

last: Liu

first: Guizhong

last: Cui

first: Guangdun

last: Peng

first: Naihe

last: Jing


title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts (RNA-seq)

city: Madison

first: Jeffrey

last: Dilworth

state: Wisconsin

address: 1111 Highland Ave

institute: University of Wisconsin

summary: In human muscle, SMCHD1 mutations are associated with the onset of FSHD2, but the mechanism driving the disease onset remains unclear. A commonly accepted explanation is the loss of SMCHD1 binding to the D4Z4 locus activates the expression of DUX4 in FSHD2 muscle. In this study, we used human myoblasts having DUX4 non-permissive 4qB alleles as a model to study DUX4-independent functions of SMCHD1 on myoblast cell growth. Surprisingly, depletion of SMCHD1 in these cells resulted in a cell proliferation defect. Despite the absence of DUX4 target genes’ activation, these cells showed a repression of PAX7 target genes (a hallmark of FSHD) and similar changes in expression profile compared to FSHD myoblasts. Interestingly, downregulation of cell proliferation-related genes and dysregulation of fibroblasts-specific genes were observed in SMCHD1 knockdown myoblasts and FSHD2 myoblasts but not FSHD1 myoblasts. Additionally, we identified LAP2 as direct targets of SMCHD1. Depletion of LAP2 leads to cell proliferation defect similar to the effect after SMCHD1 knockdown. These data imply that DUX4 is not the only driver for the onset of FSHD, and SMCHD1 has DUX4-independent functions in muscle growth and development.

overall_design: Transcriptome profiling of proliferating human myoblast cell line WS234 (donor 15VBic) upon lentiviral transduction of non-silencing scramble shRNA or shRNA targeting SMCHD1

first: Matthew

last: Wong


title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts


title: SMCHD1 activates the expression of genes required for the expansion of human myoblasts  (ChIP-seq)

overall_design: SMCHD1 ChIP-seq in proliferating human myoblast cell line WS234 (donor 15VBic)


title: Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins

city: Gainesville

first: Lu

last: Li

state: Florida

address: 2033 Mowry Rd

institute: University of Florida

type: Non-coding RNA profiling by high throughput sequencing

summary: Binding of microRNAs (miRNA) to mRNAs normally results in post-transcriptional repression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (crosslinking, ligation, and sequencing of miRNA-target RNA hybrids) data, and identified numerous candidate TDMD triggers based on their ability to induce non-templated nucleotide addition at the miRNA 3 end. When overexpressed in HEK293T cells, nine highly conserved triggers induce degradation of corresponding miRNAs. Consistent with previous reports, both the TDMD base-pairing and surrounding sequences are important for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduce miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes an apoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated that they can functionally cooperate with the encoded proteins.

overall_design: HEK 293T cells were transfected with plasmids encoding a GFP-reporter containing either a BCL2L11 or TRIM9 TDMD trigger in the 3'UTR. Total RNAs were extracted from transfected cells and subjected to Poly-A RNA sequencing and small RNA sequencing. This experiment was designed to assess the influence of TDMD triggers on miRNAs. TDMD stands for "target RNA directed microRNA degradation", in which extensive base-pairing between target RNA and miRNA leads to miRNA degradation. Here, we examine whether expression of TDMD triggers from BCL2L11 or TRIM9 could degrade their corresponding miRNAs ( miR-221/222 or miR-218, respectively). After transfection of plasmids expressing TDMD-triggers, HEK293T cell were lyszed by Trizol for total RNA extraction. Poly-A RNAs were selected by oligo-dT beads and 18-40nt RNAs were selected while constructing NEBNext small RNA seq library, and subjected to Illumina sequencing. Two biological replicateswere performed for each TDMD trigger.

first: Peike

last: Sheng

first: Mingyi

last: Xie


title: Activation of the PARIS immune complex by viral proteins results in host tRNA cleavage and can be overcome by viruses encoding non-cleavable tRNAs

status: Public on Jun 24 2024

city: Paris

first: Justine

middle: Rozenn

last: Groseille

address: 28 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Viruses compete with other viruses for limited cellular recourses, and some viruses deliver defense mechanisms that protect the host from competing genetic parasites. PARIS is a defense system, often encoded in viral genomes, that is composed of a 53 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB). Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex. We use cryo-EM to determine the structure of this complex which explains how six molecules of AriA assemble into a propeller-shaped scaffold that coordinates three subunits of AriB. ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving the host Lysine tRNA. Phage T5 can subvert PARIS immunity through expression of a non-cleavable tRNA variant. Collectively, these data explain how AriA functions as an ATP-dependent sensor that detects viral proteins and activates the AriB toxin. PARIS is one of an emerging set of immune systems that form macromolecular complexes for the recognition of foreign proteins, rather than foreign nucleic acids.

overall_design: to study  the chromosome organization in Paris conditoin we used HiC sample

first: David

last: Bikard

first: Blake

last: Wiedenheft

first: Artem

last: Isaev


title: Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon

city: Midlothian

first: Sarah

last: Salisbury

address: Easter Bush Campus

country: United Kingdom

institute: The Roslin Institute, University of Edinburgh

summary: Background:  Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.  Results: We characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.  Conclusions: Our results highlight the key role of keratinocytes in coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.

sample_organism:
Oncorhynchus kisutch
Salmo salar

platform_organism:
Oncorhynchus kisutch
Salmo salar

overall_design: Control and sea lice (Lepeophtheirus salmonis)-attached fin and skin tissue samples of Atlantic salmon (Salmo salar) and coho salmon (Oncorhynchus kisutch) were analyzed using snRNAseq.

middle: J

first: Rose

middle: R

last: Daniels

first: Sean

last: Monaghan

first: James

middle: E

last: Bron

first: Paula

last: Villamayor

first: Ophelie

last: Gervais

first: Mark

middle: D

last: Fast

first: Lene

last: Sveen

first: Ross

last: Houston

first: Nicholas

last: Robinson

first: Diego

last: Robledo


title: The Effect of Milk Fat Globule Membrane-Containing Protein Powder on C. elegans Gene Expression

city: Helsinki

first: Olli

last: Matilainen

address: Viikinkaari 9C

country: Finland

institute: University of Helsinki

summary: Milk-derived peptides and milk fat globule membrane (MFGM) have gained interest as health-promoting food ingredients. However, the mechanisms by which these nutraceuticals modulate the function of biological systems often remain unclear. We utilized Caenorhabditis elegans to elucidate how milk-derived Protein powders rich in MFGM, previously used in a clinical trial, affect the physiology of this model organism. Our results demonstrate that Protein powders do not affect lifespan but promote the fitness of the animals. Surprisingly, gene expression analysis revealed that Protein powders decrease the expression of genes functioning on innate immunity, which also translates into reduced survival on pathogenic bacteria. One of the innate immunity-associated genes showing reduced expression upon Protein powder supplementation is cpr-3, the homolog of human cathepsin B. Interestingly, knockdown of cpr-3 enhances fitness, but not in Protein powder-treated animals, suggesting that protein powders contribute to fitness by downregulating the expression of this gene. In summary, this research highlights the value of C. elegans in testing the biological activity of food supplements and nutraceuticals. Furthermore, this study should encourage investigations into whether milk-derived peptides and MFGM mediate their beneficial effects through the modulation of cathepsin B expression in humans.

overall_design: We compared the gene expression profiles of Protein powder 2- and control (H2O)-treated wild type C. elegans (N2)

first: Miina

last: Pitkänen


title: Trps1 targets Ccnd1 to regulate mouse Leydig cell proliferation

city: Fuzhou

first: sun

middle: jian

last: dong

address: 1 North Road, Xuefu

country: China

institute: Fujian medical university

summary: RNA-sequencing analysis was utilized to investigate the impact of Trps1 knockdown via siRNA on transcriptome profiling in mouse primary Leydig cells compared to the Negative siRNA

overall_design: Expression of Trps1 was downregulated via siTrps1. RNA-sequencing analysis was carried out to compare the transcriptome profiling between the siTrps1- and Negative siRNA-treated mouse primary Leydig cells under the same condition.

first: Jiandong

last: Sun

first: Shie

last: Wang


title: Transcriptome analysis of Derlin-1 knockdown neural stem cells

first: Naoya

last: Murao

summary: To search gene expression change of neural stem cells by Derlin-1 knockdown, we performed RNA-sequence analysis and compared the expression levels between control knockdown and Derlin-1 knockdown.

overall_design: Transcriptomic profiles of control and Derlin-1 knockdown neural stem cell at 2 days  post Bmp4 treatment were generated by deep sequencing, using Illumina Hiseq X.

first: Hodeki

last: Nishitoh


title: Time series study of ABA-treated Arabidopsis thaliana rosettes [Illumina TruSeq mRNA Sample Prep Kit]

city: Utrecht

first: Niels

last: Aerts

state: Utrecht

address: Padualaan 8

department: Biology

country: Netherlands

institute: Utrecht University

summary: The hormone abscisic acid (ABA) regulates many plant stress responses and plant development by activating a complex gene regulatory network. This time series experiment was designed to unravel the architecture and dynamics of the ABA gene regulatory network.

overall_design: Five week old Arabidopsis plants were treated with 0.05 mM ABA or a mock treatment by dipping. Per timepoint and treatment applied, six biological replicates were harvested consisting of a single leaf (the 6th leaf). Total RNA was extracted using the Qiagen RNeasy plant kit. Libraries were prepared from total RNA using the Illumina TruSeq mRNA Sample Prep Kit.

first: Richard

last: Hickman

first: Marcel

last: van Verk

first: Corné

last: Pieterse

first: Saskia

last: van Wees


title: Time series study of ABA-treated Arabidopsis thaliana rosettes [Illumina TruSeq mRNA Stranded Sample Prep Kit]

overall_design: Five week old Arabidopsis plants were treated with 0.05 mM ABA or a mock treatment by dipping. Per timepoint and treatment applied, six biological replicates were harvested consisting of a single leaf (the 6th leaf). Total RNA was extracted using the Qiagen RNeasy plant kit. Libraries were prepared from total RNA using the Illumina TruSeq mRNA Stranded Sample Prep Kit.


title: Mouse models to investigate in situ cell fate decisions induced by TP53 and other factors (CUT&RUN)

status: Public on Jun 28 2024

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: We developed triple-FLAG TRP53 knock-in mice for TRP53 pull-down and two TRP53 response reporter mice, knocking tdTomato or GFP into the Puma/Bbc3 or p21 gene loci, respectively. By crossing the reporter mice onto a TRP53-deficient background, we could show that these reporters reliably inform on TRP53-dependent and TRP53-independent initiation of the apoptotic as well as the cell cycle arrest/senescence programs in vitro and even in vivo.

overall_design: FLAG-TRP53 pulldown was used for CUT&RUN analysis to identify binding of TRP53 to its target genes. Murine dermal fibroblasts (MDFs) were generated from tails of 8-12 weeks-old mice from FLAG-Trp53 KI/KI, FLAG-Trp53 KI/+, and WT (negative control) genotypes and were treated for 6h in vitro with either Nutlin-3a or DMSO (vehicle control). Cell extracts were made and subjected to pulldown using an antibody against P53-FLAG antibody.

first: Pedro

middle: L

last: Baldoni


title: Time series study of ABA-treated Arabidopsis thaliana rosettes

overall_design: Refer to individual Series


title: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [GUIDE-seq]

city: Frederick

first: Thomas

last: Gonatopoulos-Pournatzis

address: 1050 Boyles Street

institute: NCI/NIH

summary: Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. Fitness-promoting exons are enriched in essential and highly expressed genes and frequently overlap protein domains and interaction interfaces. In contrast, fitness-suppressing exons that are enriched in low-expressed, non-essential genes and tend to overlap intrinsically disordered regions. In-depth mechanistic investigation of a screen hit, TAF5 alternative exon-8, reveals that its inclusion controls the assembly of the TFIID general transcription initiation complex regulating gene expression outputs. Collectively, by applying orthogonal exon perturbation screening strategies we have generated a resource of phenotypically important exons and uncovered mechanisms that control gene expression and cell fitness.

overall_design: The GUIDE-seq experiment was conducted according to a well-established protocol with minor adjustments, as detailed in a relevant publication (PMID: 34773119). Double-stranded dsODN was synthesized by annealing two modified oligonucleotides (PMID: 30654827). RPE1 cells, engineered to stably express both Cas9 and Cas12a nucleases, were transfected with dsODN and subsequently infected with viruses carrying various hgRNAs. Following puromycin selection, genomic DNA (gDNA) was isolated, sheared, and subjected to library preparation for high-throughput sequencing using NextSeq 1000/2000.

first: M-S

last: Xiao

first: A

middle: P

last: Damodaran

first: B

last: Kumari

first: E

last: Dickson

first: K

last: Xing

first: T

last: On

first: N

last: Parab

first: H

last: King

last: Perez

first: W

middle: M

last: Guiblet

first: G

last: Duncan

first: R

last: Chari

last: Andresson

first: J

middle: A

last: Vidigal

last: Weatheritt

first: M

last: Aregger


title: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [RNA-seq]

last: Gonatopoulos-Pournatzis

state: MD

address: Building 560

institute: National Cancer Institute

summary: CRISPR-Cas technology has transformed functional genomics, yet understanding of how individual exons differentially shape cellular phenotypes remains limited. Here, we optimized and conducted massively parallel exon deletion and splice-site mutation screens in human cell lines to identify exons that regulate cellular fitness. Fitness-promoting exons are prevalent in essential and highly expressed genes and commonly overlap with protein domains and interaction interfaces. Conversely, fitness-suppressing exons are enriched in nonessential genes, exhibiting lower inclusion levels, and overlap with intrinsically disordered regions and disease-associated mutations. In-depth mechanistic investigation of the screen-hit TAF5 alternative exon-8 revealed that its inclusion is required for assembly of the TFIID general transcription initiation complex, thereby regulating global gene expression output. Collectively, our orthogonal exon perturbation screens established a comprehensive repository of phenotypically important exons and uncovered regulatory mechanisms governing cellular fitness and gene expression.

overall_design: RNA-Sequencing was performed in HEK293 Flp-in cells depleted from endogenous TAF5 with RNAi (non-targeting siRNAs were used as control) while expressing either full-length TAF5 (TAF5-FL) orthe TAF5 isoform lacking exon-8 (TAF5-∆E8)at endogenous levels using dox-inducible HEK293 Flp-In cell lines to systematically explore if TAF5 exon-8 regulates gene expression.

middle: S


title: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [ChIP-seq]

overall_design: ChIP-Sequencing for TBP and RNA pol II was performed in HEK293 Flp-in cells depleted from endogenous TAF5 with RNAi (non-targeting siRNAs were used as control) while expressing either full-length TAF5 (TAF5-FL) or the TAF5 isoform lacking exon-8 (TAF5-∆E8) at endogenous levels using dox-inducible HEK293 Flp-In cell lines to explore if TAF5 Exon-8 affects the occupancy of TBP and RNA Pol II.

last: Xiao


overall_design: Total RNA were extracted from HAP1 and RPE1 cells. RNAseq libraries were prepared with stranded poly(A) RNAseq kit and followed by sequencing on Illumina NovaSeq platform.

last: Damodaran


title: DNA damage primes hematopoietic stem cells for megakaryopoiesis

city: New York

first: Hans-Willem

last: Snoeck

address: 650 west 168th street

institute: Columbia University Irving Medical Centre

summary: Hematopoietic stem cells (HSCs) reside in the bone marrow (BM), can self-renew, and generate all blood cells. Most hematopoietic lineages arise through successive, increasingly lineage-committed progenitors. In contrast, megakaryocytes (MKs), hyperploid cells that generate platelets essential to hemostasis, can derive rapidly and directly from HSCs, subpopulations of which are primed for MK differentiation. The underlying mechanism is unknown however. Here we show that DNA damage and subsequent arrest in the G2 phase of the cell cycle rapidly induce MK commitment in HSCs, but not in progenitors, through an initially predominantly post-transcriptional mechanism. Cycling HSCs show extensive replication-induced DNA damage associated with uracil misincorporation in vivo and in vitro. Consistent with this notion, thymidine attenuated DNA damage, rescued HSC maintenance and reduced the generation of CD41+ MK-committed HSCs in vitro. Similarly, overexpression of the dUTP-scavenging enzyme, dUTPase, enhanced in vitro maintenance of HSCs. Replication stress-induced MK priming, at least in part caused by uracil misincorporation, is therefore a barrier to HSC maintenance and expansion. DNA damage-induced MK priming may allow rapid generation of a lineage essential to immediate organismal survival, while simultaneously removing damaged HSCs and potentially avoiding malignant transformation of self-renewing stem cells

overall_design: We performed scRNAseq of HSC cultured for 48hrs in RO-3066 or DMSO vehicle.

first: Corey

last: Garyn

first: Oriol

last: Bover

first: John

middle: W

last: Murray

first: Jing

last: Ma

first: Karen

last: Salas-Briceno

first: Susan

last: Ross


title: RNA polymerase stalling-derived genome instability underlies ribosomal antibiotic efficacy and resistance evolution

city: Beijing

first: Jintao

last: Liu

address: Haidian District

institute: Tsinghua University

summary: Bacteria often evolve antibiotic resistance through mutagenesis. However, the processes causing the mutagenesis have not been fully resolved. Here we found that a broad range of ribosome-targeting antibiotics caused mutations through an underexplored pathway. Focusing on the clinically important aminoglycoside gentamicin, we found that the translation inhibitor caused genome-wide premature stalling of RNA polymerase (RNAP) in a loci-dependent manner. Further analysis showed that the stalling was caused by disruption of transcription-translation coupling. Anti-intuitively, the stalled RNAPs subsequently induced lesions to the DNA via transcription-coupled repair. While most of the bacteria were killed by genotoxicity, a small subpopulation acquired mutations via SOS-induced mutagenesis. Given that these processes were triggered shortly after antibiotic addition, resistance rapidly emerged in the population. Our work revealed a new mechanism of action of ribosomal antibiotics, illustrates the importance of dissecting the complex interplay between multiple molecular processes in understanding antibiotic efficacy, and suggests new strategies for countering the development of resistance.

overall_design: To investigate the secondary effect of gentamicin treatment, which is transcription elongation chaos and mutagensis, we performed RNA-seq and 3' -end-seq to profile transcription dynamics and genome re-sequencing to identify mutations.

first: Yayun

last: Zheng

first: Ruochen

last: Chai

first: Tianmin

last: Wang

first: Zeqi

last: Xu

first: Yihui

last: He

first: Ping

last: Shen


title: CK2 phosphorylation of cap methyltransferase CMTR1 promotes RNAPII interaction

city: Potsdam

first: Radoslaw

last: Lukoszek

address: Karl-Liebknecht-Strasse 24-25

institute: University of Potsdam

summary: We investigated influence of CMTR1 phosphorylation by CK2 on RNA expression. In this experiment, we added wild-type and phosphorylation deficient mutant of CMTR1 and knocked out the endogenous CMTR1. We demonstrated that lack of phosphorylation of CMTR1 affects only small but specific group of genes.

overall_design: RNA sequencing of total RNA from mouse embroynic fibroblasts transduced with different variants of HA-tagged CMTR1 and treated with Cre recombinase to remove CMTR1 exon 3 flanked by loxP sites

first: Victoria

middle: H

last: Cowling


title: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness [CRISPR]

first: Thomas

last: Gonatopoulos-Pournatzis

sample_organism:
Homo sapiens
unidentified plasmid

platform_organism:
Homo sapiens
unidentified plasmid

overall_design: In brief, cells were infected with lentiviral CRISPR libraries, followed by proliferation-basd drop-out screening. Cell pellets were collected at the beginning and end time points, genomic DNA was extracted, hgRNA expression cassettes were amplified and sequencing libraries were prepared with custmorized protocols. The libraries were quantified and sequenced on Illumina sequencing platform.

first: M-S

last: Xiao

first: A

last: Damodaran

first: B

last: Kumari

first: E

last: Dickson

first: K

last: Xing

first: T

last: On

first: N

last: Parab

first: H

last: King

last: Perez

first: W

last: Guiblet

first: G

last: Duncan

first: R

last: Chari

last: Andresson

first: J

last: Vidigal

last: Weatheritt

first: M

last: Aregger


title: Divergent originations of parental DNA hydroxymethylation in human preimplantation embryos

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: DNA methylation and hydroxymethylation in human ES cells, and transcriptome and OTX2 bindings upon overexpression of OTX2.

overall_design: ACE-Seq and WGBS of human ES cells. CUT&Tag and RNA-seq of human ES cells (WT and OE OTX2)

first: Rui

last: Yan

first: Xin

last: Long


title: Genome-Scale Exon Perturbation Screens Uncover Critical Exons for Cell Fitness

first: Thomas

last: Gonatopoulos-Pournatzis

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


title: A hepatocyte-specific transcriptional program driven by Rela and Stat3 exacerbates experimental colitis in mice by modulating bile synthesis

status: Public on Jun 23 2024

city: New Delhi

first: Debasisa

last: Mohanty

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Imunology

summary: RelA and Stat3, often collaboratively, induce the synthesis of an array of factors,which orchestrate multiorgan crosstalk in health and diseases. RelA and Stat3 functions in theintestinal epithelial cells are known to tune colon inflammation. If their hepatic activity also impacts inflammation in the gut remains unclear. Here, we reveal that the combined deficiency of RelA and Stat3 specifically in hepatocytes ameliorates DSS-induced experimental colitis. Our transcriptomics analyses identified that they activated a hepatic gene program, which directed the expression of alternate bile synthesis pathway genes. Our metabolomics studies substantiated that an absence of RelA and Stat3 in hepatocytes led to a reduced accumulation of inflammatory bile acids, particularly chenodeoxycholic acid, not only in the liver but also in the gut. Indeed, knockout mice displayed a lessened expression of only in the liver but also in the gut. Indeed, knockout mice displayed a lessened expression of inflammatory cytokines and a diminished recruitment of inflammatory cells in the gut upon colitogenic insults; on the other hand, supplementing chenodeoxycholic acid was sufficient to restore the colitogenic sensitivity in these mice. In sum, we suggest that the engagement of inflammatory transcription factors in distant tissues promotes intestinal pathologies via metabolic wiring.

overall_design: Liver were obtained from WT and relaΔhepstat3Δhep mice, either left untreated or treated with 2% DSS for 6 days. mRNA levels in all four group with 3 biological replicates were generated via next generation sequencing.

first: Rajesh

last: Gokhale

first: Soumen

last: Basak

first: Vinay

last: Nandicoori

first: Jyotsna

last: Singh

first: Priyadarshini

last: Sanyal


title: B cell activation gene signature in blood and liver of HBeAg+ immune active chronic hepatitis B patients

status: Public on Jun 22 2024

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

summary: In this study, we performed an unbiased characterization of total CD19+ B cells purified from peripheral blood of immune active chronic HBV patients and showed that HBV induced a B cell activation gene signature in blood but did not significantly induce interferon-stimulated genes (ISGs).

overall_design: We conducted RNA-seq on FACS purified peripheral blood CD19+ B cells of healthy controls (CTRL), chronic HBV and HCV patients. Patients that did not receive antiviral treatment with relatively high viral load and/or liver inflammation were selected for this study.

first: Zgjim

last: Osmani


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [PRO-seq]

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

summary: Analysis of chromatin marks, nascent transcription and mutational profiles at AID-target genes in human cell line and mouse

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: PRO-seq of human and murine cells in replicates

first: Ursula

last: Schoeberl

first: Johanna

last: Fitz

first: Kimon

last: Froussios

first: Renan

last: Valieris

first: Marina

last: Makharova

first: Iordanis

last: Ourailidis

first: Bernd

last: Bauer

first: Tobias

last: Neumann

first: Eva-Maria

last: Wiedemann

first: Marialaura

last: Mastrovito

first: Monika

last: Steininger

first: Adriana

last: Cantoran Garcia

first: Hugo

last: Mouquet

first: Israel

last: Tojal Da Silva

first: Rushad

last: Pavri


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [ATAC-seq]

overall_design: ATAC-seq of human Ramos B cell line to show DNA accessibility


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [ChIP-seq]

sample_organism:
Drosophila melanogaster
Homo sapiens

platform_organism:
Drosophila melanogaster
Homo sapiens

overall_design: ChIP-seq for H3K27Ac, H3K4me3, H3K36me3 in Ramos cells with S2 spike-ins


title: Evolutional heterochromatin condensation delineates chromocenter formation and retrotransposon constraint in plants

first: Weifeng

last: Zhang

address: Zhongguancun Street

summary: Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. However, it is a riddle why the presence of chromocenters is variable across species. Here, we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. The loss of intrinsically disordered regions (IDRs) in ADCP1 homologues during evolution has led to the absence of prominent chromocenter in various plant species, and introduction of IDR-containing ADCP1 with HMGA promotes heterochromatin condensation and retrotransposon silencing. Moreover, plants in the Cucurbitaceae group have evolved an IDR-containing chimera of ADCP1 and HMGA, which enables formation of chromocenters remarkably. Together, our work uncovers a coevolved mechanism of phase separation in packing heterochromatin and constraining retrotransposons.

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum
Nicotiana tabacum
Nicotiana benthamiana

overall_design:
1. Arabidopsis ChIP: ADCP1 ChIP were performed with GFP antibody using ADCP1-GFP tagged transgenic plants, HMGA ChIP were performed with mCherry antibody using mCherry-HMGA tagged transgenic plants, and Col-0 with no tag as control. H3K9me2 ChIP performed in Col-0 and H3 ChIP as control. 2. Tobacco ChIP: AtADCP1/NbADCP1/NbADCP1+Atlinkers ChIP were performed with GFP antibody using corresponding GFP tagged transgenic tobacco plants, and tobacco with no tag as control. H3K9me2 ChIP performed in tobacco with no tag. 3. Tomato ChIP: AtADCP1 ChIP were performed with GFP antibody using corresponding GFP tagged transgenic tomato plants, and tomato with no tag as control. H3K9me2 ChIP performed in tomato with no tag.
Arabidopsis ADCP1 ChIP were performed with GFP antibody using ADCP1-GFP tagged transgenic plants, and Col-0 with no tag as control. H3K9me2 ChIP performed in suvh456, and H3 ChIP as control.

first: Qianwen

last: Sun


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [PRO-cap]

first: Maximilian

last: von der Linde

platform_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: PRO-cap of human and murine cells in replicates

first: Ursula

last: Schoeberl


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks

overall_design: Refer to individual Series


title: Genetic diversity accelerates canine distemper virus adaptation to ferrets

status: Public on Jun 21 2024

city: Rochester

first: Christian

middle: Karl

last: Pfaller

state: MN

address: 200 First Street SW

department: Molecular Medicine

institute: Mayo Clinic

summary: RNA viruses adapt rapidly to new host environments by generating highly diverse genome sets, so-called “quasispecies”. Minor genetic variants promote their rapid adaptation allowing for emergence of drug-resistance or immune-escape mutants. Understanding these adaptation processes is highly relevant to assess the risk of cross-species transmission, and safety and efficacy of vaccines and antivirals. We hypothesized that genetic memory within a viral genome population facilitates rapid adaptation.

sample_organism:
Mustela putorius furo
Chlorocebus sabaeus
canine distemper virus

overall_design: We investigated the adaptation of the Morbillivirus canine distemper virus (CDV) to ferrets and compared an attenuated, Vero cell-adapted virus isolate (5804) with its recombinant derivative (r5804) over consecutive in vivo passages in ferrets. We performed RNA-seq analyses of infected organ homogenates and determined the mutant spectra within the CDV genome populations replicating in these tissues at each passage.

first: Oliver

last: Siering

first: Mareike

last: Langbein

first: Maike

last: Herrmann

first: Kevin

last: Wittwer

first: Bevan

last: Sawatsky

first: Veronika

last: von Messling


title: High-resolution transcriptional analysis of immunoglobulin variable regions reveals the absence of direct relationships between somatic hypermutation, nascent transcription and epigenetic marks [MutPE]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: MutPE-seq of human and murine cells in replicates

first: Johanna

last: Fitz

first: Kimon

last: Froussios

first: Renan

last: Valieris

first: Marina

last: Makharova

first: Iordanis

last: Ourailidis

first: Bernd

last: Bauer

first: Tobias

last: Neumann

first: Eva-Maria

last: Wiedemann

first: Marialaura

last: Mastrovito


title: Single-Cell Sequencing of IDH-Mutant Glioma

city: Chengdu

first: Yi

last: Wang

state: Please Select

address: 32 West Frist Ring Rd.,

institute: Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital

summary: Glioma, a prevalent and deadly brain tumor, is marked by significant cellular heterogeneity and metabolic alterations, yet the comprehensive cell-of-origin and metabolic landscape in high-grade (Glioblastoma Multiforme, WHO grade IV) and low-grade (Oligoastrocytoma, WHO grade II) gliomas remains elusive. In this study, we undertook single-cell transcriptome sequencing of these glioma grades to elucidate their cellular and metabolic distinctions. Following the identification of cell types, we compared metabolic pathway activities and gene expressions between high-grade and low-grade gliomas. The comprehensive analysis identified the most altered metabolic pathways (MCPs) and genes across all cell types, which were further validated against TCGA and CGGA datasets for their clinical significance.

overall_design: Our primary glioma samples were obtained from two untreated patients and analyzed using single-cell transcriptomics profiling

first: Zongze

last: He

first: Siyuan

last: Song


title: The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [DAP-Seq]

first: Teng

address: Yuanmingyuan West Road

institute: China agricultural university

summary:
Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear.
In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130.
In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA.
Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.

overall_design: Identification of genome-wide binding sites for downstream transcription factors of ZmNAC128 and ZmNAC130.


title: Haploinsufficiency in PTPN2 leads to early onset systemic autoimmunity from Evans syndrome to lupus

first: Quentin

last: Riller

address: 24 Boulevard du Montparnasse

institute: INSERM UMRS 1163, Imagine Institute

summary: An exome sequencing strategy employed to identify pathogenic variants in patients with pediatric-onset systemic lupus or Evans syndrome resulted in the discovery of six novel monoallelic mutations in PTPN2. PTPN2 is a phosphatase that acts as an essential negative regulator of the JAK/STAT pathways downstream of several cytokine pathways. All identified mutations led to a loss of PTPN2 regulatory function as evidenced by in vitro cytokine reporter and phosphatase assays, and by hyperproliferation of patients’ T cells stimulated with cytokines. Furthermore, patients exhibited high serum levels of various inflammatory cytokines, mimicking the profile observed in individuals with gain-of-function mutations in various STAT factors. Flow cytometry analysis of patients’ blood cells revealed typical alterations associated with autoimmunity, such as an expansion of CD11c+ B cells and follicular helper T cells, and all patients presented with anti-platelet or other autoantibodies. These findings further supported the notion that a loss of function in negative regulators of cytokine pathways can lead to a broad spectrum of autoimmune manifestations and that PTPN2 along with SOCS1 haploinsufficiency constitute a new group of monogenic autoimmune diseases that can benefit from targeted therapy.

overall_design:
The expanded T cells were starved of IL-2 for 24h, plated at cell concentration of 1.106 cells/ ml in Panserin medium only and then were left unstimulated or stimulated with IFN-a (104U/ml, Millipore, #IF007) or IL-2 (104U/ml) during 3h at 37°C. RNA was extracted using RNeasy Mini Kit (Qiagen) and quality was assessed using Fragment Analyzer (Agilent Technologies) with RNA Integrity Number >8 and 28S/18S ratio around 2. Messenger RNA was finally converted to complementary DNA by capture of poly-A+ RNA, amplified and sequenced to a depth of at least 50 million reads using the Illumina technology (Novaseq 6000 sequencer) at the Genomic Plateform of Imagine Institut.

A1: Patient with the heterozygous mutation p.F403Lfs*25 in PTPN2
A2: Patient with the heterozygous mutation p.F403Lfs*25 in PTPN2
B1: Patient with the heterozygous mutation p.W98* in PTPN2
C1: Patient with the heterozygous mutation p.W289* in PTPN2
D1: Patient with the heterozygous mutation p.E24Mfs*20 in PTPN2
E1: Patient with the heterozygous mutation p.Y126N in PTPN2
F1: Patient with the heterozygous mutation p.C216S in PTPN2
HC1: Healthy donor, female 28 years old
HC2: Healthy donor, female, 35 years old
HC3: Healthy donor, male, 29 years old

first: Marie

last: Jeanpierre

first: Jade

last: Cognard

first: Maud

last: Tusseau

first: Linh-Chi

last: Bui

first: Jeremy

last: Berthelet

first: Audrey

last: Laurent

first: Etienne

last: Crickx

first: Marianna

last: Parlato

first: Marie-Claude

last: Stolzenberg

first: Felipe

last: Suarez

first: Guy

last: Leverger

first: Nathalie

last: Aladjidi

first: Sophie

last: Collardeau-Frachon

first: Christine

last: Pietrement

first: Marion

last: Malphettes

first: Antoine

last: Froissart

last: Bole

first: Nicolas

last: Cagnard

first: Fernando

last: Rodrigues-Lima

first: Thierry

last: Walzer

first: Frédéric

last: Rieux-Laucat

first: Alexandre

last: Belot

first: Anne-Laure

last: Mathieu


title: Antibiotics damage the colonic mucus barrier in a microbiota-independent manner

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St, P.O. Box 1589

department: The Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University


title: The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [ChIP-seq]

first: Teng

last: Song

overall_design: Identification of genome-wide binding sites for ZmNAC128 and ZmNAC130.


title: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Human KAS-ATAC-seq]

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

summary: Cis-regulatory elements (CREs) are pivotal in orchestrating gene expression throughout diverse biological systems. Accurate identification and in-depth characterization of functional CREs are crucial for decoding gene regulation network and dynamics during cellular processes. In this study, we developed a new KAS-seq (Opti-KAS-seq) procedure, with enhanced efficiency of capturing single-stranded DNA (ssDNA), broader genomic coverage, and adaptability to various sample types. By integrating the highly sensitive Opti-KAS-seq with ATAC-seq, we further introduce KAS-ATAC-seq, a new method that provides quantitative insights into transcriptional activity of CREs. A main advantage of KAS-ATAC-seq lies in its precise measurement of ssDNA levels within both proximal and distal ATAC-seq peaks. This feature is particularly adept at identifying ssDNA promoter and Single-Stranded Transcribing Enhancers (SSTEs). SSTEs are highly enriched with nascent RNA transcripts and specific transcription factors (TFs) binding sites that determine cellular identity. Moreover, KAS-ATAC-seq provides a detailed characterization and functional implications of various SSTE subtypes; KAS-ATAC-seq signals exhibit more robust correlation with enhancer activities when compared with ATAC-seq data and active histone mark profiles. Our analysis of promoters and SSTEs during mouse neural differentiation demonstrates that KAS-ATAC-seq can effectively identify immediate-early activated CREs in response to RA treatment. We further discovered that ETS TFs and YY1 are critical in initiating early neural differentiation from mESCs to NPCs. Our findings indicate that KAS-ATAC-seq provides more precise annotation of functional CREs in transcription. Future applications of KAS-ATAC-seq would help elucidate the intricate dynamics of gene regulation in diverse biological processes and biomedical applications.

overall_design: We developed a new KAS-seq procedure, Opti-KAS-seq, with enhanced efficiency of capturing single-stranded DNA (ssDNA), broader genomic coverage, and adaptability to various sample types. We further KAS-ATAC-seq, a new method that provides quantitative insights into transcriptional activity of CREs.

first: Chuan

last: He

first: Yun

last: Gao

first: Tong

last: Wu


title: The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm [RNA-Seq]

overall_design: Identification of differentially expressed genes of zmnac128, zmnac130 and zmnac128/130 during maize endosperm


title: Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development  [ATAC-seq]

first: Moritz

last: Gaidt

address: Campus-Vienna-Biocenter 1

institute: IMP

summary: Early B-lymphopoiesis depends on E2A, Ebf1, Pax5 and Ikaros family members. Here, we used acute protein degradation in vivo to identify direct target genes of these transcription factors in pro-B, small pre-B and immature B-cells. E2A, Ebf1 and Pax5 predominantly function as transcriptional activators by inducing open chromatin at their target genes, have largely unique functions and maintain cell viability in vivo by activating Bcl2l1. Ikaros and Aiolos cooperatively control early B-cell development and act as dedicated repressors to suppress open chromatin at their target genes. The surrogate light-chain genes Igll1 and Vpreb1 are directly activated by Ebf1 and Pax5 in pro-B cells and directly repressed by Ikaros and Aiolos in small pre-B cells. Pax5 and E2A contribute to V(D)J recombination by activating Rag1, Rag2, Dntt, Irf4 and Irf8. Like Pax5, Ebf1 also represses the cohesin-release factor gene Wapl to mediate prolonged loop extrusion across the Igh locus. In summary, in vivo protein degradation has provided unprecedented insight into the control of early B-lymphopoiesis by five transcription factors.

overall_design: ATAC-seq: Peak calling and read signal comparison between control and 5-Ph-IAA treated pro-B, pre-B and immature B cells of the same genotype. Two replicas each.

first: Anna

last: Fedl

first: Hiromi

last: Tagoh

first: Sarah

last: Gruenbacher

first: Qiong

last: Sun

first: Kimon

last: Froussios

first: Markus

last: Jaritz

first: Meinrad

last: Busslinger

first: Tanja

last: Schwickert

first: Robyn

last: Schenk


title: Concentration-response transcriptomic changes induced by silver nanoparticles (AgNPs) in hepatocytes derived from human induced pluripotent stem cells (iPSCs)

city: Laurel

first: Xiugong

address: 8301 Muirkirk Rd

department: HFP/OLOAS/OCT/DT

institute: US FDA

summary: Transcriptomic changes in iPSC-derived hepatocytes after exposure to varying concentrations of AgNPs (0.01-25 μg/ml) for 24 h.

overall_design: The experiment was conducted in two batches with the fist batch (batch 1) covering a higher concentration range (0, 5.0, 10, 20, and 25 µg/ml) and the second batch (batch 2) covering a lower concentration range (0, 0.01, 0.05, 0.1, 0.5, 1.0, and 5.0 µg/ml). Three replicates were included for each concentration.


title: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Mouse KAS-seq]


title: Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development  [RNA-seq]

overall_design: total RNA-seq: Comparative gene expression analysis of rRNA depleted, total RNA-seq of untreated control and 5-Ph-IAA treated pro-B, pre-B and immature B cells of the same genotype. Two replicas each.


title: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Mouse KAS-ATAC-seq]


title: Nonviral CRISPR/Cas9 Mutagenesis for Streamlined Generation of Mouse Lung Cancer Models

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

summary: Functional analysis in mouse models is necessary to establish the involvement of a set of genetic variations in tumor development. Many lung cancer models have been developed using genetic techniques to create gain- or loss-of-function alleles in genes involved in tumorigenesis; however, because of their labor- and time-intensive nature, these models are not suitable for quick and flexible hypothesis testing. Here we introduce a lung mutagenesis platform that utilizes CRISPR/Cas9 RNPs delivered via cationic polymers. This approach allows for the simultaneous inactivation of multiple genes. We validate the effectiveness of this system by targeting a group of tumor suppressor genes, specifically Rb1, Rbl1, Pten, and Trp53. chosen for their potential to cause lung tumors. This polymer-based delivery platform enables the modeling of lung tumorigenesis independently of the genetic background, simplifying and expediting the process without the need for modifying the mouse germline or creating custom viral vectors.

overall_design: RNA-seq data from mouse tumors, and normal lung from mice.

first: Mirentxu

last: Santos


title: Transcriptional function of E2A, Ebf1, Pax5, Ikaros and Aiolos analyzed by in vivo acute protein degradation in early B cell development [CUT&RUN]

overall_design: Cut & Run: Peak calling and read signal comparison. Two replicas each.


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_SW1783

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine


title: Sodium chloride in the tumor microenvironment enhances T cell metabolic fitness and cytotoxicity

city: Jena

first: Christina

last: Zielinski

address: Beutenbergstrasse 11a

department: Department of Infection Immunology, Leibniz Institute for Natural Product Research and Infection Biology

institute: Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute

summary: The efficacy of antitumor immunity is associated with the metabolic state of cytotoxic T cells, which is highly amenable to perturbation by the tumor microenvironment. It is therefore of tremendous interest to bypass immunosuppressive signaling in the tumor microenvironment and to identify factors that augment T cell immunometabolism, cytotoxic effector functions and eventually tumor killing. Whether ionic signals serve as aberrant immune signals and influence the adaptive human antitumor immune response is still largely unexplored. We demonstrate a significant enrichment of sodium in solid tumors of breast cancer patients, which leaves a transcriptomic imprint on intratumoral immune cells. Sodium chloride (NaCl) enhanced the activation state and effector functions of human CD8+ memory T cells. These functional alterations were associated with improved metabolic fitness, in particular with an increase in glycolysis and oxidative phosphorylation and overall nutrient uptake. These NaCl-induced effects translated into increased tumor cell killing in vitro and in a tumor mouse model in vivo. We therefore propose NaCl as a positive regulator of acute antitumor immunity, which could be harnessed for ex vivo conditioning of adoptively transferred T cells in the future.

overall_design: For scRNA-seq, a library of human CD8+CD45RA–CD45RO+ cells that were stimulated with anti-CD3 and anti-CD28 monoclonal antibodies for 3 days in high and low NaCl conditions was constructed with Chromium Next GEM Single Cell 5′ Reagents v.2 (Dual Index) (10x Genomics, Inc.). The library was sequenced on an Illumina NovaSeq 6000 Sequencing System (Flow Cell Type S4) according to the manufacturer’s instructions, with 150-bp, paired-end, dual-indexing sequencing (sequencing depth: 20,000 read pairs per cell).

first: Dominik

last: Soll

first: Chang-Feng

last: Chu

first: Shan

first: Veronika

last: Lutz

first: Mahima

last: Arunkumar

first: Mariam

last: Gachechiladze

first: Sascha

last: Schäuble

first: Maha

last: Alissa-Alkhalaf

first: Trang

last: Nguyen

first: Michelle-Amirah

last: Khalil

first: Ignacio

last: Garcia-Ribelles

first: Michael

last: Müller

first: Katrin

last: Buder

first: Bernard

last: Michalke

first: Gianni

last: Panagiotou

first: Kai

last: Ziegler-Martin

first: Pascal

last: Benz

first: Philipp

last: Schatzlmaier

first: Karsten

last: Hiller

first: Hannes

last: Stockinger

first: Maik

last: Luu

first: Kilian

last: Schober

first: Carolin

last: Moosmann

first: Wolfgang

last: Schamel

first: Magdalena

last: Huber

first: Chrisritna


title: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq [Human KAS-seq]

first: Ruitu

last: Lyu

first: Chuan

last: He

first: Yun

last: Gao

first: Tong

last: Wu


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_HT29

first: Musun

last: Park


title: Sodium chloride in the tumor microenvironment enhances T cell metabolic fitness and tumor killing

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: To gain mechanistic insight into the effect of NaCl on CD8+ T cells, we explored the specific impact of NaCl on the bulk transcriptome of human memory CD8+ T cells.

overall_design: For comparative gene expression profiling analysis of bulk RNA-seq data, CD8+ memory T cells were isolated ex vivo and stimulated for 48 h with anti-CD3 and anti-CD28 mAbs for a total culture time of 5 days in the presence of low and high NaCl concentrations.

first: Dominik

last: Soll

first: Chang-Feng

last: Chu

first: Shan

last: Sun

first: Veronika

last: Lutz

first: Mahima

last: Arunkumar

first: Mariam

last: Gachechiladze

first: Maha

last: Alissa-Alkhalaf

first: Trang

last: Nguyen

first: Michelle-Amirah

last: Khalil

first: Ignacio

last: Garcia-Ribelles

first: Michael

last: Mueller

first: Katrin

last: Buder

first: Bernhard

last: Michalke

first: Gianni

first: Christina

last: Zielinski


title: Profiling of Sarcomas from Archival Tissues

first: Karan

last: Luthria

state: New York

address: 650 W 168th Street

department: Medicine

institute: Columbia University Vagelos College of Physicians and Surgeons


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_A549

first: Musun

last: Park


title: Profiling of Sarcomas from Archival Tissues [snRNA-Seq]

summary: We performed single nuclei RNA-sequencing (snRNA-seq) with matched T cell receptor sequencing (TCR-seq), and pool matched low pass whole genome sequencing (WGS) of eight specimens from six patients, encompassing four undifferentiated polymorphic sarcomas (UPS)  and four intimal sarcomas (INS), and paired specimens from two patients (one UPS and INS each) treated with immune checkpoint blockade (ICB).

overall_design:
Pool matched lp-WGS was performed in addtion to single-nuclei RNA which involved 75,716 cell transcriptomes and  an average of 9465 cell transcriptomes per specimen. Together, this data served to improve the identification of the malignant and non-malignant cell compartments within the 8 collected samples of frozen sarcoma tissue.

Submitter states that missing raw data are being made available for controlled access in dbGaP.

first: Benjamin

last: Izar

first: Blake

last: Caldwell


title: Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

summary: The loading and activation of the replicative helicase MCM2-7 are key events during the G1-S phase transition.In budding yeast, the origin recognition complex (ORC) binds to the conserved DNA elements A and B1 of the autonomously replicating sequence (ARS).This is followed by the consecutive loading of two MCM2-7 hetero-hexamers into a MCM2-7 double-hexamer(DH).In S-phase the MCM2-7DH is activated, resulting in two Cdc45-MCM-GINS(CMG) helicases that bidirectionally unwind DNA ahead of the replication fork.Here,we show that MCM2-7 helicase loading across the B1 element displaces ORC fromo rigins.This allows ORC binding and helicase loading at lower affinity binding sites and origins throughout the genome.Furthermore, we mapped the sites of initial DNA unwinding genome-wide and show that these sites appear near the N-terminal domains of the MCM2-7 double-hexamer in proximity of the B1 element.Finally, employing a chemical-biology approach, we establish that during helicase activation the Mcm2/5 interface acts as the DNA exit gate for single-stranded-DNA extrusion.Our work identifies that helicase loading follows a distributive mechanism, allowing for equal MCM2-7 loading across the genome and surprisingly finds that DNA unwinding initiates from the helicase N-terminal interface in proximity to the ARS B1 element.

overall_design: ChIP-seq analysis of wt yeast cells, cdc6-1 and cdc46-1 mutants arrested in G2- and G1-phase to monitor pre-RC formation

first: L

last: Reuter

first: Sanjay

last: Khadayate

first: Mohammed

last: Karimi

first: Christian

last: Speck

first: Audrey

last: Mossler

first: Korbinian

last: Liebl


title: RNA sequencing data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

summary: Single eng 3' RNA sequencing of primary CAF isolated from fresh ex vivo GCT patient tissue. Purity of CAF populations were verified by qPCR analysis of common CAF, GCT, endothelial and epithelial markers. 14 different CAF cultures from distinct GCT subtypes (seminoma(SE), non-seminoma(NS)) and 5 non-malignant fibroblast cultures were analyzed.

overall_design: RNA sequencing of 6 SE-derived CAF (SE-CAF), 3 embryonal carcinoma-derived CAF (EC-CAF), 3 teratoma-derived CAF (TE-CAF), 2 Mix-CAF derived from mixed subtypes (SE and NS), and 5 non-malignant fibroblasts (nF).


title: Profiling of Sarcomas from Archival Tissues [lp-WGS]


title: Spatially resolved transcriptome of brain white matter brain lesions of a patient with progressive multiple sclerosis

city: Odense

first: Anne

last: Hartebrodt

address: Campusvej 55

country: Denmark

institute: University of Southern Denmark

summary: Different lesion types were microdissected out from snap-frozen white matter and placed on visium slides. Optimization of RNA release and visualization with Nikon Ecclipse Ti2 were followed by barcoded recover, library preparation and sequencing.

overall_design: spatial transcriptomics

first: Maria

last: Elkjaer


title: Gene expression profiling at single nucleus level of microdissected white matter tissue samples of patients with progressive multiple sclerosis and non-neurological disease controls

summary: Different lesion types were microdissected out from snap-frozen white matter tissue. Brain nuclei were fluorescence-activated nuclear sorted. Gel beads-in-emulsion was generated, barcoded, reverse transcribed followed by library construction and sequencing.

overall_design: snRNA-Seq


title: DNA accessibility profiling at the single nucleus level of post mortem white matter brain tissue of patients with progressive multiple sclerosis and non-neurological disease controls

summary: Different lesion types were microdissected out from snap-frozen white matter. Brain nuclei were fluorescence-activated nuclear sorted and treated with Transposase Tn5. Gel beads-in-emulsion was generated, barcoded  followed by library construction and sequencing.

overall_design: snATAC-Seq


title: Cellular spermine targets JAK1 to restrain cytokine-mediated autoimmunity (Human)

city: Tianjin

first: Henan

last: XU

address: No.94 Weijin Road

department: immunology

institute: Nankai University

summary: Whole blood samples from SLE patients were collected and PBMCs were isolated using Ficoll-PaqueTM PLUS reagent according to the manufacturer’s protocol. The fresh isolated PBMCs from SLE individuals  were treated with DMSO or spermine for 3h,  PBMCs from healthy control were used as control, then samples were harvested and lysated with Trizol reagend for RNA-sequencing analysis.

overall_design: Gene Set Enrichment Analysis (GSEA) and interferon alpha or IL-6 response genes profiling of PBMCs from SLE patient treated with spmermine or DMSO, PBMCs from healthy control were used as control.

last: Xu

first: Xiao

last: Zhang


title: Cellular spermine targets JAK1 to restrain cytokine-mediated autoimmunity (Mouse)

summary: Combining metabolomics analyses with an IFN-stimulated response elements reporter system, we identify spermine as a cellular metabolite brake for JAK1 signaling. Spermine directly binds to FERM and SH2 domains of JAK1 to impair IFNAR2-JAK1 interaction. Spermine suppresses JAK1 phosphorylation triggered by types I and II cytokines, including IFN-I/II, IL-2, and IL-6. Spermine treatment attenuates autoimmune pathogenesis in a SLE murine model and reduces IFN-I signaling in monocytes from SLE patients, which have reduced spermine levels.

overall_design: 7 weeks old female Ifnar1+/+ or Ifnar1-/- mice were pretreated with spermine or PBS for 3days, then injected with pristane (Sigma-Aldrich) to induce SLE as described. Blood was collected from posterior orbital venous plexus to isolate mRNA for RNA-sequencing.


title: Illumina Infinium MethylationEPIC BeadChip (850k) data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue

type: Methylation profiling by genome tiling array

summary: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of primary CAF isolated from fresh ex vivo GCT patient tissue. Purity of CAF populations were verified by qPCR analysis of common CAF, GCT, endothelial and epithelial markers. 14 different CAF cultures from distinct GCT subtypes (seminoma(SE), non-seminoma(NS)) and 5 non-malignant fibroblast cultures were analyzed.

overall_design: Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of 6 SE-derived CAF (SE-CAF), 3 embryonal carcinoma-derived CAF (EC-CAF), 3 teratoma-derived CAF (TE-CAF), 2 Mix-CAF derived from mixed subtypes (SE and NS), and 5 non-malignant fibroblasts (nF).


title: Digital transformation of herbal medicine: Conversion to biological entity data using tonifying herbal medicine-induced transcriptome sequencing_Tonifying_HepG2

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

overall_design: Refer to individual Series


title: Cellular spermine targets JAK1 to restrain cytokine-mediated autoimmunity

overall_design: Gene Set Enrichment Analysis (GSEA) and interferon alpha response genes profiling of PBMCs from SLE patient, with high or low spermine content.


title: Profiling of Sarcomas from Archival Tissues [TCR-Seq]

city: New York

last: Luthria


title: Mechanisms of MCM2-7 loading and initial DNA melting at near base-pair resolution [MCM4 & ORC2 ChIP-exo]

summary: The loading and activation of the replicative helicase MCM2-7 are key events during the G1-S phase transition. In budding yeast, the origin recognition complex (ORC) binds to the conserved DNA elements A and B1 of the autonomously replicating sequence (ARS). This is followed by the consecutive loading of two MCM2-7 hetero-hexamers into a MCM2-7 double-hexamer (DH). In S-phase the MCM2-7 DH is activated, resulting in two Cdc45-MCM-GINS (CMG) helicases that bidirectionally unwind DNA ahead of the replication fork. Here, we show that MCM2-7 helicase loading across the B1 element displaces ORC from origins. This allows ORC binding and helicase loading at lower affinity binding sites and origins throughout the genome. Furthermore, we mapped the sites of initial DNA unwinding genome-wide and show that these sites appear near the N-terminal domains of the MCM2-7 double-hexamer in proximity of the B1 element. Finally, employing a chemical-biology approach, we establish that during helicase activation the Mcm2/5 interface acts as the DNA exit gate for single-stranded-DNA extrusion. Our work identifies that helicase loading follows a distributive mechanism, allowing for equal MCM2-7 loading across the genome and surprisingly finds that DNA unwinding initiates from the helicase N-terminal interface in proximity to the ARS B1 element.

overall_design: ChIP-Exo 5.0 analysis of Mcm4 and Orc2 from cells arrested in G1 or G2


title: Shared features of blastula and neural crest stem cells evolved at the base of vertebrates

city: Evanston

first: Joshua

middle: Ryan

last: York

state: Illinois

address: 2205 Tech Dr

department: Molecular Biosciences

institute: Northwestern University

summary: We address the evolutionary origins of vertebrate pluripotency by comparing the development of neural crest and blastula stem cells using representatives from both jawed (Xenopus) and jawless (lamprey) vertebrates.

sample_organism:
Petromyzon marinus
Xenopus laevis

platform_organism:
Petromyzon marinus
Xenopus laevis

overall_design: We performed gene expression profiling of blastula stem cells and neural crest cells using RNA-Seq

first: Carole

last: LaBonne


title: Retinoic acid induces human gastruloids with posterior embryo-like structures

status: Public on Jun 20 2024

city: Seattle

first: Nobuhiko

last: Hamazaki

state: Washington

address: Foege Building S-210 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Gastruloids are a powerful in vitro model of early human development. However, although elongated and composed of all three germ layers, human gastruloids do not morphologically resemble post-implantation human embryos. Here we show that an early pulse of retinoic acid (RA), together with later Matrigel, robustly induces human gastruloids with posterior embryo-like morphological structures, including a neural tube flanked by segmented somites, and diverse cell types including neural crest, neural progenitors, renal progenitors, and myocytes. Through in silico staging based on single-cell RNA-seq (scRNA-seq), we find that human RA-gastruloids progress further than other human or mouse embryo models, aligning to E9.5 mouse and CS11 cynomolgus monkey embryos. We leverage chemical and genetic perturbations of RA-gastruloids to confirm that WNT and BMP signalling regulate somite formation and neural tube length in the human context, while transcription factors TBX6 and PAX3 underpin presomitic mesoderm and neural crest, respectively. Looking forward, RA-gastruloids are a robust, scalable model for decoding early human embryogenesis.

overall_design: Single-cell RNA-seq of human gastruloids and RA gastruloids

first: Wei

last: Yang

first: Connor

last: Kubo

first: Chengxiang

last: Qiu

first: Beth

middle: K

last: Martin

first: Riddhiman

last: Garge

first: Samuel

middle: G

last: Regalado

first: Eva

last: Nichols

first: Choli

last: Lee

first: Riza

last: Daza

last: Srivatsan

first: Jay

last: Shendure


title: Cellular spermine controls autoinflammation by targeting JAK1 to restrain cytokine response

last: XU

summary: Using an unbiased metabolomics approach and a IFN-stimulated response elements (ISRE) reporter screening system, we have identified the cellular metabolite spermine as an endogenous brake restraining IFN-I signaling and autoinflammation. Cellular spermine concentration decrease upon stimulations with IFN-I, IL-2, and IL-6. Spermine suppresses phosphorylation of JAK1 in macrophages responding to IFN-I, T cells responding to IL-2, and fibroblasts responding to IL-6. Mechanistically, spermine binds directly to the N-terminal domains of JAK1, resulting in impaired IFNAR2-JAK1 interaction required for initiating downstream signaling and, subsequently, restrained IFN-I effector response. Moreover, spermine attenuates SLE progression in an SLE murine model and reduces IFN-I signaling in PBMCs from SLE patients.

overall_design: Interferon-stimulated genes (ISGs) profiling of bone marrow derived macrophages treated with DMSO or spermine, and stimulated with IFN-β.

first: X

last: Henan


title: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

first: Ruitu

last: Lyu


title: RNA Sequencing of murine MPNST Tumors

status: Public on Jun 19 2024

city: Columbus

first: Katherine

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

institute: Nationwide Children's Hospital

summary: We utilized three murine MPNST cell lines. 67C-4 and #5NPCIS cell lines are derived from spontaneously arising tumors in mice mutated for NF1 and p53 (so-called NP-cis mice; PMID: 12154062). SN4-4 cells originated from MPNST tumors induced by injecting adenovirus containing Cas9 and guide RNA for Nf1 and p53 into the sciatic nerves, resulting in NF1/p53-null MPNST (PMID: 32456131). We implanted  5 x 10^6 murine MPNST cells, subcutaneously, into the flanks of 6-8 weeks old gender-matched C57BL/6 mice (for 67C-4 and #5NPCIS) and BALB/c mice (for SN4-4 mice) to generate MPNST tumors. All mice were procured from Envigo. Upon reaching a size of 300-500 mm3, the mice were euthanized to harvest the tumors, which were subsequently flash frozen using liquid nitrogen and processed for RNA sequencing.

overall_design: Gene Expression Analysis of murine Malignant Peripheral Nerve Sheath Tumors (MPNST)

first: Siddhi

middle: N

last: Paudel

first: Elizabeth

last: Garfinkle


title: Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

city: Ann Arbor

first: Gabriel

last: Vasconcelos Pereira

state: Michigan

address: 1150 W. Medical Center Dr.

institute: University of Michigan

summary: Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and b1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD.

overall_design: Ruminococcus torques VIII-239 was grown in 3 biological replicate cultures to mid-log phase under anaerobic conditions at 37ºC on YCFA medium containing either glucose or mucin O-glycans. RNA was isolated and rRNA depleted. RNA-seq analysis was performed to identify differentially regulated genes on these substrates.

first: Sadie

last: Schaus

last: Pereira

first: Eric

last: Martens


title: Noncanonical Formation of SNX5 Gene-Derived Circular RNA Regulates Cancer Growth

city: Taoyuan

first: Yi-Tung

last: Chen

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary:
To investgate the funcitonal role of STAU1 on the formation of circSNX5.
We performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells (replicate)

overall_design: Differentiated gene expression profiling analysis of RNA-seq data for Ctrl and shcSNX5 SAS cells

first: Chia-Hua

last: Kan


title: Sequence diversity of apidaecin-like peptides arresting the terminating ribosome

status: Public on Jun 18 2024

first: Alexander

last: Mankin

address: 900 S. Ashland Ave, Rm. 3052,

department: College of Pharmacy

institute: University of Illinois at Chicago

summary: The Proline-rich Antimicrobial Peptide (PrAMP) apidaecin (Api) inhibits translation by binding in the ribosomal nascent peptide exit tunnel, trapping release factors RF1 or RF2, and arresting ribosomes at stop codons. To explore the extent of sequence variations of the native 18-amino acid Api that allows it to preserve its activity, we screened a library of synthetic mutant Api genes expressed in bacterial cells, resulting in nearly 350,000 peptide variants with multiple substitutions. By applying orthogonal negative and positive selection strategies, we identified a number of multi-substituted Api variants capable of arresting ribosomes at stop codons. Our findings underscore the critical contribution of specific amino acid residues of the peptide for its on-target function while significantly expanding the variety of PrAMPs acting on the terminating ribosome. Additionally, some of the tested synthesized multi-substituted Api variants exhibit improved antibacterial activity compared to that of the wild type PrAMP and may constitute the starting point to develop clinically useful antimicrobials.

overall_design: We used deep mutational analysis combined with orthogonal selection strategies to identify multi-substituted variants of the antibacterial peptide apidaecin (Api) that preserve the ability of binding to the ribosome and inhibit translation termination.

first: Weiping

last: Huang

first: Chetana

last: Baliga

first: Nora

last: Vázquez-Laslop


overall_design: Differentiated gene expression profiling analysis of RNA-seq data for Ctrl and shSTAU1 SAS cells


title: Directed differentiation of pancreatic δ cells from human pluripotent stem cells

city: Guangzhou

first: LIHUA

last: CHEN

state: Guangdong

address: Guangzhou International Bioland

institute: Guangzhou Laboratory

summary: Human pancreatic δ cells maintain the balance of pancreatic hormones and loss of δ cells or disruption of somatostatin release is associated with diabetes. Despite their important role, human δ cells are scarce (~5% within the islets), limiting physiological studies and drug discovery targeting δ cells. To date, no directed δ-cell differentiation method has been established. In this study, we established a link between fibroblast growth factor (FGF) signaling pathways and pancreatic δ-cell lineage specification. FGF7 helped maintain a pancreatic endoderm/progenitor state with higher expression levels of PDX1 and CHGA, whereas FGF2 biased cells towards the pancreatic δ-cell lineage by inducing the expression of SST and the δ-cell specific transcription factor HHEX, via FGF receptor 1(FGFR1). We developed a differentiation method to generate δ cells from human stem cells by combining FGF2 with FGF7, which synergistically directs pancreatic lineage differentiation and modulates the expression of transcription factors and SST activators during endoderm/endocrine precursor induction. These δ cells display mature RNA profiles and fine secretory granules, secrete somatostatin in response to various stimuli, and suppress insulin secretion from in vitro co-cultured b cells and mouse b cells upon transplantation. The generation of somatostatin-secreting pancreatic δ cells from human stem cells in vitro would provide an unprecedented cell source for drug discovery and cell transplantation studies in diabetes.

overall_design: H1 ES cells were differentiated into delta cell-containing islet organoids. The Islet organoids  were collected at S7D14 and analysed by scRNA-seq.

first: Huisheng

last: Liu

first: Lihua

first: Tingran

last: Zhang

first: Nannan

last: Wang


title: Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (WGBS aerial)

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

summary: Genomic imprinting, an epigenetic phenomenon leading to parent-of-origin-specific gene expression, has independently evolved in the endosperm of flowering plants and the placenta of mammals—tissues crucial for nurturing embryos. While transposable elements (TEs) frequently colocalize with imprinted genes and are implicated in imprinting establishment, direct investigations of the impact of de novo TE transposition on genomic imprinting remain scarce. In this study, we explored the effects of chemically induced transposition of the Copia element ONSEN on genomic imprinting in Arabidopsis thaliana. Through the combination of chemical TE mobilization and doubled haploid induction, we generated a line with 40 new ONSEN copies. Our findings reveal a preferential targeting of maternally expressed genes (MEGs) for transposition, aligning with the colocalization of H2A.Z and H3K27me3 in MEGs—both previously identified as promoters of ONSEN insertions. Additionally, we demonstrate that chemically-induced DNA hypomethylation induces global transcriptional deregulation in the endosperm, leading to the breakdown of MEG imprinting. This study provides insights into the consequences of chemically induced TE remobilization in the endosperm, underscoring the need for cautious interpretation of the connection between TEs and genomic imprinting.

overall_design: RNAseq, WGBS and CUT&Tag datasets were obtained from INTACT purified endosperm nuclei from Col × Ler (L) reciprocal crosses at 4 days after pollination (DAP).  WGBS and CUT&Tag were generated in duplicates using the INTACT line (referred as C) or TEmob (T3, referred as Cm) genetic background in recirpocal crosses with Ler (L). RNAseq libraries were generated in triplicates from TEmob (Cm) x Ler (L) reciprocal crosses.

first: Gerardo

last: del Toro de Leon

first: Joram

last: van Boven

first: Jiao

last: Wen-Biao

first: Korbinian

last: Schneeberger

first: Claudia

last: Köhler


title: Epigenetic and transcriptional consequences of chemically induced transposon mobilization in the endosperm (RNA-Seq)


title: STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia [ATAC-Seq]

city: Regensburg

last: Fischer

address: Franz-Josef-Strauß-Allee 11

institute: Leibniz Institute for Immunotherapy

summary: Cohesin shapes the chromatin architecture, including enhancer-promoter interactions. Its components, especially STAG2 but not its paralogue STAG1, are frequently mutated in myeloid malignancies. To elucidate the underlying mechanisms of leukemogenesis, we comprehensively characterized genetic, epigenetic, transcriptional, and chromatin conformational changes in acute myeloid leukemia (AML) patient samples. Specific loci displayed altered cohesin occupancy, gene expression and local chromatin activation which were not compensated by STAG1. These changes could be linked to disrupted spatial chromatin looping in cohesin-mutated AMLs. We performed complementary depletion of STAG2 or STAG1 in primary human hematopoietic progenitors (HSPCs). We detected effects overlapping STAG2-mutant AML-specific changes following STAG2 knockdown, not invoked by depletion of STAG1. STAG2-deficient HSPCs displayed impaired differentiation capacity and maintained HSPC-like gene expression. This work establishes STAG2 as a key regulator of chromatin contacts, gene expression and differentiation in the hematopoietic system and identifies candidate target genes that may be implicated in human leukemogenesis.

overall_design:
To determine the impact of Cohesin subunit loss on chromatin accessibility, we performed ATAC-seq on STAG2-mutant, RAD21-mutant and cohesin wildtype AML patients samples. In parallel we conducted ATAC-seq using primary CD34+ cord-blood derived HSPC cultures of independent donors electroporated with siRNAs for knockdown targeting either STAG2, STAG1, RAD21 or STAG2+STAG1. As controls a non-targeting (luciferase-specific) control siRNA (siCtrl) or mock-electroporated (Mock) samples were used.

***************************************************************
Due to patient privacy concerns, raw sequencing data of adult AML patients is deposited in the European Genome Archive (EGA) under study number EGAS00001007405. Due to special legal and ethical privacy concerns regarding newborns, raw sequencing data of cord blood HSPC samples cannot be deposited in any online repository.
***************************************************************

first: Margit

last: Nuetzel

first: Edith

last: Reuschl

first: Michael

last: Rehli

first: Ruud

last: Delwel

last: Gebhard


title: TFAM deficiency promotes mitochondrial dysfunction to drive inflammation in the corneas of dry eye disease through mtDNA stress-mediated AIM2 inflammasome activation

city: Beijing

first: yaqiong

last: li

address: youanmenwai

institute: Capital Medical University

summary: Background & Aims Mitochondrial dysfunction and mtDNA stress-mediated inflammasome activation play critical roles in the pathogenesis of dry eye disease (DED). Mitochondrial transcription factor A (TFAM) is essential for regulating mtDNA stability and mitochondrial homeostasis. However, the mechanism underling TFAM to infuence DED progression is largely unknown. As a cytosolic DNA sensor, absent in melanoma 2 (AIM2) may contribute to the development of DED. Therefore, we aimed to explore whether the role of TFAM is associated with AIM2 inflammasome activation in DED. Methods The changes in inflammation, mitochondrial function, mtDNA homeostasis and TFAM expression were analyzed in the corneas of DED mice in vivo and in HCECs under oxidative stress in vitro. The effects of TFAM knockout on mtDNA homeostasis, mitochondrial respiration and cytokine release were also investigated in HCECs. The mechanism was analyzed by RNA sequencing in the corneas of DED mice, which was further verified by the HCECs with TFAM depletion. Results We found that the corneas of DED mice and HCECs under oxidative stress exhibited inflammation, mitochondrial damage and mtDNA maintenance disruption , which were highly associated with significantly reduced TFAM protein levels. Furthermore, we demonstrated that silencing of TFAM in HCECs suppressed mitochondrial respiratory capacity, induced mtDNA released into the cytosol and triggered cytokine release. Mechanistically, cytosolic mtDNA accumulation caused by TFAM depletion activated the AIM2 inflammasome and facilitated inflammation, thereby driving DED progression. Conclusions Our findings elucidate that TFAM deficiency induces mitochondrial dysfunction and cytosolic mtDNA stress, which subsequently activates the AIM2 inflammasome, triggers inflammatory responses and promotes DED progression. TFAM pathway may provide a novel therapeutic strategy for DED.

overall_design: The global gene expression of cornea in dry eye disease mice and control mice was analyzed and compared (n=4).

first: Yaqiong

last: Li

first: Ying

last: Jie


title: STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia [DNAInputSeq]

first: Alexander

overall_design:
We performed low pass whole genome DNAseq on all AML patients samples used for chromatin assays in the study to determine copy number variations used for the normalization of associated ChIP-seq data sets.

***************************************************************
Due to patient privacy concerns, raw sequencing data of adult AML patients is deposited in the European Genome Archive (EGA) under study number EGAS00001007405. Due to special legal and ethical privacy concerns regarding newborns, raw sequencing data of cord blood HSPC samples cannot be deposited in any online repository.
***************************************************************

first: Ute

last: Ackermann

first: Stanley

last: van Herk


title: STAG2 Mutations Reshape the Cohesin-Structured Spatial Chromatin Architecture to Drive Gene Regulation in Acute myeloid Leukemia [scRNA-Seq]

overall_design:
To determine the impact of stable genomic STAG2 deletion on the cellular differentiation stages of hematopoietic cells, we performed RNA-seq on primary CD34+ cord-blood derived HSPC cultures of independent donors electroporated with sgRNA Cas9 ribonucleoprotein complexes targeting the STAG2 gene (SA2KO). As controls, cells were transfected with a non-targeting guide RNA (NC) Cas9 complex. SA2KO and NC cells of the same donor were stained with two different DNA-barcoded Hashtag antibodies and pooled for 10X GENOMICS single cell transcriptomic library generation.

***************************************************************
Due to patient privacy concerns, raw sequencing data of adult AML patients is deposited in the European Genome Archive (EGA) under study number EGAS00001007405. Due to special legal and ethical privacy concerns regarding newborns, raw sequencing data of cord blood HSPC samples cannot be deposited in any online repository.
***************************************************************

first: Hanna

last: Stanewski

first: Strieder

last: Nicholas

first: Inmaculada

last: Hernández-López


title: A single cell altas of mouse embryonic diapause and peri-implantation development

city: Muenster

first: Hyun-Woo

last: Jeong

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: Here, we molecularly defined embryonic diapause at single-cell resolution, revealing hidden transcriptional dynamics while seemingly the embryo resides in a state of suspended animation. Alongside, we found that the dormant pluripotent cells are “aware” of their microenvironment which sustains their viability via Yap-mediated mechanotransduction.

overall_design: Approximately 200~250 blastocysts from each developmental stage – E4.5, EDG7.5, EDG9.5 and Reactivated and 50 embryos from E5.5 stage were collected and analyzed using sc-RNA seq.

first: Rui

last: Chen

last: Fan

first: Fei

first: Niraimathi

last: Govindasamy

first: Martin

last: Stehling

first: Ralf

last: Adams

first: Ivan

last: Bedzhov