title: Integrative Single-Cell Analysis of Gene Expression and Chromatin Accessibility Reveals CTCF as a Key Regulator of Stem Cell Differentiation and Lung Morphogenesis [multi-omics]

city: shenzhen

first: Jiang

last: Yamei

address: longfei

country: China

institute: The Chinese University of Hong Kong-Shenzhen

summary: The lungs develop into an intricate tree-like structure through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs that dictate embryonic lung development remain largely unclear. Here, we profile gene expression and chromatin accessibility in mouse embryonic lungs to generate a multi-omics atlas at single-cell resolution. By integrative analyses, we dissect 10 cell type-specific gene expression signatures and characterize177,990 cis-regulatory elements (CREs), 36,114 differential accessible chromatin regions (DARs), 27,628 gene-to-peak linkages, 632 highly regulated genes (HRGs), and their binding transcription factors (TFs). We also explore candidate regulators driving lung progenitor developmental trajectory and discover the important role of the AP-1 complex in mesenchymal differentiation. Based on this multi-modal dataset, we delineate gene regulatory networks (GRNs) across various cell types. Finally, using the Ctcf conditional knockout mouse model combined with multiple approaches, we reveal CTCF as a crucial regulator of Sox2+ progenitor specification and lung branching morphogenesis by reprogramming transcriptome and chromatin accessibility. Therefore, this study provides multi-omics resources and mechanistic insights for transcription regulation of lung morphogenesis.

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed multi-omics profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs using 10x Genomics paired snRNA-seq and snATAC-seq techniques.

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Kaijun

first: Xinna

last: Zhang

first: Hua

last: He

first: Miao

last: Yu

first: Xinhua

first: Xiaofang

last: Tang

first: Shenfei

last: Sun


title: Heat Shock Transcription Factors (HSFs) Mediate Multilayer Regulations of Heat-Induced Chromatin Dynamics in Plants [RNA-Seq]

status: Public on Nov 13 2025

city: Taipei

first: Lavakau

last: Thalimaraw

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plants and Microbial biology, Academia Sinica

type: Expression profiling by high throughput sequencing

summary: Eukaryotic organisms remodel chromatin landscapes to regulate gene expression in response to environmental stress. In plants, heat stress (HS) induces widespread chromatin changes, yet the role of early responsive Heat Shock Transcription Factors (HSFs) in chromatin remodeling and their evolutionary conservation remain unclear. Here, we use chromatin accessibility profiling and transcriptomics in Marchantia polymorpha hsf mutants to reveal HSFA1 as a key determinant in positioning cis-regulatory elements (CREs) for stress-induced gene activation. Comparative analysis suggests that this HSFA1-dependent chromatin remodeling mechanism is evolutionarily conserved across land plants. Multi-layered gene regulatory network (GRN) analysis further identifies MpWRKY10 and MpABI5B as HSF-independent regulators of HS responses, providing insights into parallel transcriptional subnetworks. We develop a cross-species and cross-condition machine learning framework that accurately predicts chromatin accessibility and gene expression, demonstrating a conserved regulatory logic of stress-responsive transcription. Our findings establish a scalable computational approach for decoding gene regulatory networks and provide a conceptual framework for how TFs coordinate chromatin architecture to drive stress adaptation in plants and other eukaryotes.

sample_organism:
Marchantia polymorpha
Arabidopsis thaliana

overall_design: RNA-seq profiling of Marchantia polymorpha Tak-1 and hsfa1/hsfb1 double mutant under 1 hour of 37℃ heat stress treatment or 22℃ control condition at Day7 of germmalings; RNA-seq profiling of Marchantia polymorpha Tak-1, hsfa1, hsfb1, and hsfa1/hsfb1 double mutant under 2 hours of 50µM ABA treatment or equal amount 20% EtOH (Mock) at Day7 of germmalings. RNA-seq profiling of Arabidopsis thaliana Col-0 and eTK mutant under 1 hour of 37℃ heat stress treatment at Day7 of seedlings.

first: Ming-Jen

last: Yen

first: Kuan-Hung

last: Lin

first: Hsiu-Ru

last: Yang

first: Kulaporn

last: Boonyaves

first: Chia-Yi

last: Cheng

first: Ting-Ying

last: Wu


title: Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [CLSY4_bisulfite_PCR]

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: UAS-GKVK Campus

country: India

institute: National Centre for Biological Sciences - TIFR

type: Methylation profiling by high throughput sequencing

summary: Knock down of CLSY4 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY4 in rice  endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the roles of CLSY4 in Endosperm

overall_design: We have performed targeted bisulfite sequencing to understand the methylation status of leaf upon CLSY4 and CLSY3 knockdown

first: Padubidri

middle: V

last: Shivaprasad

first: Pal

last: Avik Kumar


title: BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction

city: Baltimore

first: Jianfei

last: Qi

state: MD

address: 655W baltimore street

department: Biochemistry and Molecular Biology

country: USA

institute: University of Maryland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: BPTF, the scaffolding subunit of the nucleosome remodeling factor (NURF) complex, has been implicated in the progression of various malignancies. However, its role in prostate cancer (PCa) remains poorly understood. Here, we demonstrate that BPTF is upregulated in castration-resistant prostate cancer (CRPC) and promotes disease progression. RNA-seq revealed that BPTF primarily upregulates the expression of androgen receptor (AR) target genes. ChIP-seq showed that BPTF facilitates AR binding to enhancers and super-enhancers, while ATAC-seq demonstrated that BPTF increases chromatin accessibility to facilitate AR binding, partly via SMARCA1, a catalytic subunit of the NURF complex. Notably, BPTF/AR shared ChIP-seq peaks are highly enriched for FOXA1 motifs but only weakly enriched for AR motifs. We find that BPTF interacts with both FOXA1 and AR to form a protein complex in which FOXA1 recruits BPTF-AR to chromatin, while BPTF stabilizes the AR–FOXA1 interaction. Importantly, BPTF interacts with AR through its bromodomain, and a BPTF bromodomain inhibitor disrupts this interaction, leading to impaired AR signaling and suppressed PCa cell growth. In summary, our findings establish BPTF as a critical regulator of AR activity by promoting chromatin accessibility and stabilizing the AR–FOXA1 complex, highlighting BPTF as a potential therapeutic target in prostate cancer.

overall_design: Refer to individual Series


title: Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [CLSY4_small_RNA_sequencing]

type: Non-coding RNA profiling by high throughput sequencing

summary: Knock down of CLSY4 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY4 in rice  endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes .These analyses revealed the  roles of CLSY4 in Endosperm

overall_design: We have performed small RNA sequencing to understand the small RNA status of endosperm upon CLSY4 knockdown


title: Heat Shock Transcription Factors (HSFs) Mediate Multilayer Regulations of Heat-Induced Chromatin Dynamics in Plants [ATAC-Seq]

platform_organism:
Marchantia polymorpha
Arabidopsis thaliana

overall_design: ATAC-seq of Marchantia polymorpha Tak-1, hsfa1, hsfb1, and hsfa1/hsfb1 double mutant under 1 hour of 37℃ heat stress treatment or 22℃ control condition or 2 hours of 50µM ABA treatment or equal amount 20% EtOH (Mock) at Day7 of germmalings. ATAC-seq of Arabidopsis thaliana Col-0 and eTK mutant under 1 hour of 37℃ heat stress treatment or 22℃ control condition at Day7 of seedlings.


title: ATAC-seq of Chamaelirium luteum to determine the accessible chromatin regions

city: Seeland OT Gatersleben

first: Anne

last: Fiebig

address: Correnstraße 3

department: BIT

country: Germany

institute: IPK Gatersleben

summary: To determine the accessible chromatin regions of Chamaelirium luteum genome, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to generate the genome-wide chromatin accessibility profile.

overall_design: Chamaelirium luteum nuclei isolated from fresh leafs of  with two ATAC-seq replicates

first: Zihao

last: Zhu

first: Yi-Tzu

last: Kuo

first: Axel

last: Himmelbach

first: Nils

last: Stein

first: Andreas

last: Houben


title: Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [Bisulfite_sequencing]

summary: Knock down of CLSY4 in rice caused endosperm development defects. We investigated the molecular effects of loss of CLSY4 in rice  endosperm by profiling sRNA, targeted bisulfite PCR,whole genome bisulfite sequencing and mRNA transcriptomes. These analyses revealed the roles of CLSY4 in Endosperm.

overall_design: We have performed whole genome bisulfite sequencing to understand the methylation status of endosperm upon CLSY4 knockdown


title: CENH3-ChIP-seq of Chamaelirium luteum to determine the size and sequence composition of the large centromeres.

summary: To determine the size and sequence composition of the exceptionally large centromeres in the genome of monocentric Chamaelirium luteum, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. luteum and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chama satellite repeats (9.3%) in the C. luteum genome before immunoprecipitation.

overall_design: The CENH3-ChIP-Seq experiment was performed using a mixture of chromatin isolated from flower tissue of C. luteum and leaf tissue of Secale cereale inbred line Lo7. The normalized CENH-ChIP-Seq signal track of the average of read counts in ChIP over input in a genome-wide 1 kb windows.


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [CRISPRi]

city: San Francisco

first: Alexander

last: Marson

state: CA

address: 1650 Owens St.

institute: UCSF Gladstone Institutes

summary: FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. Tconv FOXP3 expression depended on a subset of Treg CREs and Tconv-selective positive (TcNS+) and negative (TcNS-) CREs. Combinatorial silencing of Tconv CREs revealed their epistatic logic. The CREs are occupied and regulated by TFs we identified as critical regulators of FOXP3. Finally, mutagenesis of murine TcNS- revealed that it is critical for restriction of FOXP3 expression to Tregs. We discover CRE and TF circuitry controlling FOXP3 expression and reveal evolution of mechanisms regulating a gene indispensable to immune homeostasis.

overall_design: Pooled CRISPR screens in human regulatory T cells (Tregs) and conventional T cells (Tconvs). The CRISPRi locus tiling library targets the FOXP3 locus. Tconv screens were conducted in 2 donors. Treg screens were conducted in 2 donors.

first: Jennifer

middle: M

last: Umhoefer

first: Maya

last: Arce

first: Sivakanthan

last: Kasinathan

first: Sean

last: Whalen

first: Rama

last: Dajani

first: Sanjana

last: Subramanya

first: Laine

last: Goudy

first: Julia

middle: A

last: Belk

first: Royce

last: Zhou

first: Minh

middle: T

last: N Pham

first: Wenxi

last: Zhang

first: Rosmely

last: Hernandez

first: Carinna

last: Tran

first: Nikhita

last: Kirthivasan

first: Jacob

middle: W

last: Freimer

first: Cody

last: Mowery

first: Vinh

last: Nguyen

first: Mineto

last: Ota

first: Benjamin

middle: G

last: Gowen

first: Dimitre

middle: R

last: Simeonov

first: Gemma

middle: L

last: Curie

first: Zhongmei

last: Li

first: Andy

middle: Y

last: Chen

middle: E

last: Corn

first: Howard

last: Chang

first: Qizhi

last: Tang

first: Luke

last: Gilbert

first: Ansuman

last: Satpathy

first: Katherine

middle: S

last: Pollard


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Sente

city: Rehovot

first: Miguel

middle: A.

last: Garcia-Campos

state: Center District

address: Herzl 234, Meyer Bldg., Room 1410

department: Molecular Genetics

country: Israel

institute: Weizmann Insitute of Science

summary: Over 170 modifications are deposited on RNA, across the tree of life. A major bottleneck to systematically dissecting RNA modifications has been the lack of methods allowing to acquire systematic, high-confidence maps of many RNA modifications and at scale. Here we have developed Pan-Mod-seq, which permits de-novo, sensitive and specific identification of 16 distinct modifications in dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 different species from all 3 domains of life, most of which sampled under highly variable chemical/physical/biological gradients, aiming to systematically explore the plasticity of rRNA modifications. While dynamically modified sites are relatively rare in mesophiles, we find that these are widespread in hyperthermophiles, where ~50% of identified modifications were induced with temperature. We focused on dissection of three key dynamically induced modifications: m5C, ac4C and Ψ. We uncover an m5C program encompassing dozens of targets across both rRNA subunits, all of which are dramatically induced with growth temperature in two of the sampled hyperthermophiles. In both cases m5C is introduced at a single consensus motif, via a single enzyme which is essential for growth at higher temperatures. ac4C in turn is dynamically induced among all three sampled hyperthermophiles at hundreds of sites, also at a single consensus motif. Remarkably, the methylation and acetylation overlap, and together form a tandemly modified temperature induced G-m5C-ac4C-G sequence motif.  Temperature-dependent induction of both enzymes can be recapitulated in vitro, establishing that it is an intrinsic property of the two enzymes rather than externally regulated. We obtain high-resolution cryoEM structures of ribosomes from WT strains at low and high temperatures and ones deleted of the methylating enzyme, and identify numerous mechanisms via which m5C confers structural stability. Finally, we also uncover a systematic induction in Ψ levels in T. kodakarensis, and reveal that it is largely coordinated by a single temperature-induced sRNA guiding pseudouridine formation at an unprecedented number of targets, whose loss results in growth deficiency at higher temperatures. Our findings offer a wide and systematic view of rRNA modification plasticity across representative species sampled from the tree of life, dissect the ability of different modifications to contribute to the stability of ribosomes at higher temperatures, and present a methodology allowing an unprecedented view on the the rRNA epitranscriptome in health and in disease.

overall_design: RNA-seq of total RNA from Salmonella enterica Typhimurium strain SL1344 grown at either combination of optical density at 600 nm and temperature: OD1.0/25°C, OD1.0/30°C, OD1.0/37°C, OD2.0/25°C, OD2.0/30°C, or OD2.0/37°C; under 17 different combinations of RTases and RNA library treatments, two replicates

first: Schraga

last: Schwartz

first: Joe

last: Georgeson

first: Ronit

last: Nir

first: Vinithra

last: Iyer

first: Anatoly

last: Kustanovich


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Tkoda

overall_design: RNA-seq of total RNA from Thermococcus kodakarensis strain KOD1 substrain TS559 grown at either temperature: 65C°, 75C°, 85C°, 95C°; under 18 different combinations of RTases and RNA library treatments; two replicates


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [CRISPRKO]

first: Alexander

last: Marson

overall_design: Pooled CRISPR screens in human regulatory T cells (Tregs) and conventional T cells (Tconvs). The CRISPR KO TF library targets transcription factors and select chromatin modifiers and immune genes of interest. Tconv screens were conducted in 3 donors. Treg screens were conducted in 2 donors.

first: Jennifer

last: Umhoefer

first: Maya

last: Arce

first: Sivakanthan

last: Kasinathan

first: Sean

last: Whalen

first: Rama

last: Dajani

first: Sanjana

last: Subramanya

first: Laine

last: Goudy

first: Julia

last: Belk

first: Royce

last: Zhou

first: Minh

last: N Pham

first: Wenxi

last: Zhang

first: Rosmely

last: Hernandez

first: Carinna

last: Tran

first: Nikhita

last: Kirthivasan

first: Jacob

last: Freimer

first: Cody

last: Mowery

first: Vinh

last: Nguyen

first: Mineto

last: Ota

last: Gowen


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry [human_Treg_ChIP-seq]

first: Alexander

last: Marson

summary: FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the FOXP3 locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. Tconv FOXP3 expression depended on a subset of Treg CREs and Tconv-selective positive (NS+) and negative (NS-) CREs. Combinatorial silencing of Tconv CREs revealed their epistatic logic. The CREs are occupied and regulated by TFs we identified as critical regulators of FOXP3. Finally, mutagenesis of murine NS- revealed that it is critical for restriction of FOXP3 expression to Tregs. We discover CRE and TF circuitry controlling FOXP3 expression and reveal cell and species-specific regulation of a gene indispensable to immune homeostasis.

overall_design: ChIP-seq in human T cells. ChIP-seq was conducted in using DSG/formaldehyde fixation.

first: Jennifer

last: Umhoefer

first: Maya

last: Arce

last: Kasinathan

first: Benjamin

first: Dimitre

last: Simeonov

first: Gemma

last: Curie

first: Zhongmei

last: Li

first: Andy

last: Chen

last: Corn

first: Howard

last: Chang

first: Qizhi

last: Tang

first: Luke

last: Gilbert

first: Ansuman

last: Satpathy

first: Katherine

last: Pollard


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Phalo

first: Miguel

last: Garcia-Campos

overall_design: RNA-seq of total RNA from Planococcus halocryophilus strain Or1 grown at either 10°C, 15°C, 25°C, or 30°C; under 18 different combinations of RTases and RNA library treatments; two replicates

first: Schraga

last: Schwartz

first: Joe

last: Georgeson

first: Ronit

last: Nir

first: Vinithra

last: Iyer

first: Anatoly

last: Kustanovich


title: FOXP3 Expression Depends on Cell-Type Specific Cis-Regulatory Element and Transcription Factor Circuitry

first: Alexander

last: Marson

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Loss of function of chromatin remodeler OsCLSY4 led to RdDM-mediated mis-expression of endosperm-specific genes effecting grain qualities [RNA-Seq]

first: Shivaprasad

last: Padubidri V.

overall_design: We have performed RNA sequencing to understand transcriptomic status of endosperm upon CLSY4 knockdown

first: Padubidri

last: Shivaprasad

first: Pal

last: Avik Kumar


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Pfuri

overall_design: RNA-seq of total RNA from Pyrococcus furiosus strain VC1 grown at either 78°C, 95°C, or 102°C; under 18 different combinations of RTases and RNA library treatments; two replicates


title: Integrative Single-Cell Analysis of Gene Expression and Chromatin Accessibility Reveals CTCF as a Key Regulator of Stem Cell Differentiation and Lung Morphogenesis [scRNA-seq]

first: Jiang

last: Yamei

overall_design: To comprehensively study the heterogeneity and regulatory mechanisms of lung morphogenesis, we performed scRNA-seq profiling of nuclei extracted from embryonic day 12.5 (E12.5) lungs.

first: Yamei

last: Jiang

first: Fujing

last: Huang

first: Wei

last: Wei

first: Mathias

last: Hochgerner

first: Kaijun

last: Lin

first: Xinna

last: Zhang

first: Hua

last: He

first: Miao

last: Yu

first: Xinhua

first: Xiaofang

first: Shenfei

last: Sun


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Scere

first: Miguel

last: Garcia-Campos

overall_design: RNA-seq of total RNA from Saccharomyces cerevisiae strain SK1 under up to 18 different combinations of RTases and RNA library treatments, two batches, one replicate

first: Schraga

last: Schwartz

first: Joe

last: Georgeson

first: Ronit

last: Nir

first: Vinithra

first: Anatoly


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Sacid

overall_design: RNA-seq of total RNA from Sulfolobus acidocaldarius strain MW001 grown at either combination of pH and temperature pH2.5/75°C, pH3.5/75°C, pH5/75°C, pH3/55°C, pH3/85°C; under 17 different combinations of RTases and RNA library treatments, two replicates

last: Iyer

last: Kustanovich


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Paeru

overall_design: RNA-seq of total RNA from Pseudomonas aeruginosa strain PAO1; grown at either 25°C, 30°C, 37°C, 42°C; under 17 different combinations of RTases and RNA library treatments; two replicates


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Hvolc

overall_design: RNA-seq of total RNA from Haloferax volcanii strain H26 under 17 different combinations of RTases and RNA library treatments; grown at one of the following combinations of salinity and temperature: 1.4M_Salt/42°C, 4M_Salt/42°C, 2.4M_Salt/30°C, 2.4M_Salt/42°C, 2.4M_Salt/50°C; two replicates per condition


title: Expression data from pre-cancerous pancreatic tissue from a murine model of pancreatic ductal adenocarcinoma (PDAC) and control pancreas

city: Marseille

first: Ghislain

last: BIDAUT

address: 27 Bd Leï Roure

department: Bioinformatics

country: France

institute: Centre de Recherche en Cancérologie de Marseille

summary:
We used microarrays to detail the global gene expression signature of PDAC and to identify distinct up- and down-regulated transcripts in pre-cancerous pancreatic tissue compared to control pancreas.
We also established from this dataset the metabolic signature of pre-cancerous pancreas to define new metabolic therapeutic targets for PDAC.

overall_design: Pre-cancerous tissue wase removed at an early stage of transformation in 4-week-old mice with Mixed genetic background : B6CBAF1 x C57BL/6 x 129/Sv x FVB/n.

first: S

last: Vasseur

first: F

last: Guillaumond

first: G

last: Bidaut

last: Efthymiou


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Pabys

overall_design: RNA-seq of total RNA from Pyrodictium abyssi strain TAG11 grown at either 80 °C, 100 °C, or 102 °C; sequenced under 18 different combinations of RTases and RNA library treatments; two replicates


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Hsapi

overall_design: RNA-seq of total RNA from Homo sapiens HEK293T cells under up to 18 different combinations of RTases and library chemistries, two batches, one replicate each


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Tacid

overall_design: RNA-seq of total RNA from Thermoplasma acidophilum strain 122-1B2 grown at either pH1, pH2, or pH3, under 17 different combinations of RTases and RNA library treatments; two replicates


title: Age and cell type specific specific effects of histone variant H2BE in the brain [snRNA-seq]

city: Philadelphia

first: Sean

last: Louzon

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Transcription is regulated in part through histone proteins that complex with DNA and control access to genes. Histones can be replaced with variant forms that are particularly critical in the brain and accumulate throughout lifespan. Recently, we defined the first broadly expressed H2B variant, H2BE, and demonstrated that it regulates chromatin structure, neuronal transcription, and mouse behavior. However, the role of H2BE in other cell types and its role throughout lifespan remain unknown. Here, we discovered that H2BE is highly expressed in astrocytes as well as neurons and accumulates with age in both cell types. Using single-nucleus RNA-sequencing, we demonstrate that loss of H2BE robustly affects gene expression in both astrocytes and neurons, with divergent effects in young and aging brains. Interestingly, loss of H2BE in young brains causes similar gene expression changes as aging and some effects of aging are reversed with H2BE loss. Lastly, behavioral testing demonstrates that H2BE loss disrupts long-term memory but improves working memory in aging mice. Together, these data provide novel links between histone variants, aging-related gene expression changes in both astrocytes and neurons, and memory.

overall_design: Nuclei were isolated from cortices of 2-4 month old (young) and 18 month old (old) WT and H2BE-KO mice. Nuclei capture and library preparation were performed using single-nucleus Drop-seq (n=3 biological replicates per genotype for young and n=2 biological replicates per genotype for old)


title: Concerted Actions of FoxO1 and Pparα in hepatic gene expression and metabolic adaptation

city: NEW YORK

first: Domenico

last: Accili

state: NY

address: 1150 ST NICHOLAS AVENUE, RM238

department: Medicine

institute: Columbia University

summary: Several transcription factors regulate the fasting response in the liver. They include FoxO1 and 3, cAMP response element binding protein (CREB), CCAAT enhancer-binding proteins (CEBP α/ β), glucocorticoid receptor (GR), Pparα, FoxA2, HNF4α, and many others. Previous genome-wide chromatin occupancy studies demonstrated an unexpected overlap of FoxO1 and PPARα DNA binding sites at active intergenic and intron enhancers, where approximately half of FoxO1 sites are shared with PPARα. However, the functional significance of these findings remains unknown. To address this gap in knowledge, we performed molecular interaction analyses of these two transcription factors and generated a combined hepatocyte-specific ablation of the respective genes. We found a concerted regulation of genes involved in glucose metabolism, with additive effects on in vivo tests of glucose tolerance. The data reveal a heretofore unexplored functional relay of two critical transcriptional networks in liver metabolism.

overall_design: mRNA profiles of liver tissues from liver specific FoxO1 and/or PPARα knockout mice during 4h fasted. For constitutive liver-specific FoxO1 knockouts, we crossed FoxO1lox/lox or PPARα lox/lox and Albumin-cre transgenic mice. We also collected the samples after 3 weeks high-fat diet feeding.

first: Takumi

last: Kitamoto


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Ecoli

overall_design: RNA-seq of total RNA from Escherichia coli K-12 substrain MG1655 under 18 different combinations of RTases and RNA library treatments, one replicate


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Bsubt

overall_design: RNA-seq of total RNA from wildtype Bacillus subtilis strain 168 under 18 different combinations of RTases and RNA library treatments, one replicate.


title: RNA-seq analysis of YUMM1.7 mouse melanoma cells treated with ADAR1i-124 or 5-AZA-CdR to study their effects on RNA editing

first: Haoran

last: Zhang

state: Pennsylvania

address: 415 Curie Boulevard

summary: ADAR1i-124 is a small-molecule RNA editing inhibitor that can block the editase domain of ADAR1 and robustly suppress the A-to-I RNA editing on double-stranded RNAs (dsRNAs). 5-AZA-CdR is an FDA-approved DNA methyltransferase inhibitor (DNMTi) that can increase the transcription of transposable elements and thus induce more dsRNAs. To determine the efficacy of ADAR1i-124 and test whether it has overlapping targets or synergistic effects with 5-AZA-CdR, total RNA-seq analysis was performed on YUMM1.7 cells treated with 5-AZA-CdR (1 uM, 72 h), ADAR1i-124 (10 uM, 12 h) or combination of two treatments , using 0.1% DMSO as control. Immunoprecipitation (IP) with the J2 or Z22 antibodies was also adopted to enrich the dsRNA species and investigate how drugs affect the dsRNA forms and IP enrichment.

overall_design: Total RNA-seq profiling of YUMM1.7 mouse melanoma cells treated with DMSO, ADAR1i-124_10uM_12h, 5-AZA-CdR_1uM_72h or two drug combination. Besides, the RNA pools were also enriched for dsRNA species by IP_J2 or IP_Z22 and then subjected to RIP-seq.

first: Moeko

last: Minakuchi

first: Qin

last: Li

first: Kazuko

last: Nishikura


title: Age and cell type specific specific effects of histone variant H2BE in the brain [Cut&Tag]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before collection for Cut&Tag-sequencing. (n = 3 biological replicates)


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - HsapiScere

first: Miguel

last: Garcia-Campos

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: RNA-seq of total RNA from Homo sapiens HEK293T cells and Saccharomyces cereveisiae SK1 cells, under 17 different combinations of RTases and RNA library treatments, two replicates

last: Schwartz


title: Age and cell type specific specific effects of histone variant H2BE in the brain [ATACSeq]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before collection for ATAC-sequencing. (n = 3 biological replicates merged)


title: The extracellular matrix drives guanylate production and protects pancreatic cancer cells from oxaliplatin-induced DNA damage.

summary: The excessive production of extracellular matrix (ECM) and the metabolic adaptations in pancreatic ductal adenocarcinoma (PDAC) contribute individually to enhanced chemoresistance, dramatic tumor progression and dismal patient survival. However, the ECM-driven metabolic alterations that promote chemoresistance in PDAC are less well described. Here, we use in-vitro-generated ECM bio-scaffolds that recapitulate cell-ECM interactions and induce broad metabolic alterations in PDAC cells. High-throughput integration of multi-omics datasets coupled with metabolic tracing showed that the ECM favors the accumulation of guanylates in PDAC cells and alleviation of oxaliplatin-induced DNA damage, thus supporting PDAC cell proliferation. This is controlled by the GMP-producing enzyme IMPDH, the expression of which was upregulated in resected PDAC tissue from patients who displayed low survival. We propose that targeting ECM-modulated metabolic processes in PDAC may be a more effective and safer approach, without the negative side effects of direct targeting of the ECM itself.

overall_design: RNAseq profiling of tumor cells isolated from a pancreatic ductal adenocarcinoma murine model when cultivated on the extracellular matrix of patient-derived cancer-associated fibroblasts compared to when grown on matrix-free tissue culture vessels.

first: Georgios

first: Eugénie

last: Lohmann

first: Sophie


title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome - Cther

overall_design: RNA-seq of total RNA from Acetivibrio thermocellum strain DSM1313 under 16 different combinations of RTases and RNA library treatments, grown at 50 °C and 60 °C, two replicates.

first: Schraga

first: Joe

last: Georgeson

first: Ronit

last: Nir

first: Vinithra

last: Iyer


title: Age and cell type specific specific effects of histone variant H2BE in the brain [RNASeq]

overall_design: Cortical astrocytes were isolated from WT P1 mouse pups. They were cultured for 7 days before RNA collection for sequencing. (n = 3 biological replicates)


title: Novel Homozygous FAT1 Mutation Causes glomerulotubular nephropathy in Asian adult

city: Shanghai

first: Aili

last: Cao

state: Shanghai

address: 600 Yishan Road

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary:
Introduction: Although sequence variants in FAT1 have been identified in patients with distinct renal disease, definitive proof of causality in human disease is meager.
Methods: A 35-year-old Chinese female with microscopic hematuria and proteinuria underwent a renal biopsy to identify the underlying cause. Whole-exome sequencing (WES) with homozygosity mapping revealed genetic factors, and patient-derived primary urinary epithelial cells confirmed the renal agenesis phenotype. RNA sequencing, immunofluorescence staining, and immunoblotting were used to explore the mechanisms involved.
Results: The patient, whose parents are cousins, exhibited a syndrome featuring ptosis, corneal dystrophy, macular degeneration and right feet syndactyly, with glomerulotubular nephropathy. A homozygous frameshift mutation in FAT1 (NM_005245: c.7444_7445delGT) was identified. Structural prediction, immunohistochemistry, and Western blot analyses confirmed that the mutation caused translational repression of FAT1. RNA-seq analysis revealed significant dysregulation of cell adhesion and the Rap1 signaling pathway. Immunofluorescence showed a marked loss of intercellular β-catenin junctions and cytoskeletal disruption in patient-derived primary urinary epithelial cells. Pull-down assays demonstrated that these effects were associated with a reduction in activated Rap1 levels.
Conclusion: This study presents compelling evidence that the homozygous FAT1 frameshift mutation (c.7444_7445delGT, p.Val2482fs) is causally associated with nephropathy and congenital anomalies. The mutation likely leads to the degradation of transcribed mRNA, which in turn impairs protein expression. These findings underscore the critical role of FAT1 in renal development and offer new insights into the molecular mechanisms underlying these conditions.

overall_design: Comparison of the transcriptional level differences of the  homozygous FAT1 frameshift mutation (c.7444_7445delGT, p.Val2482fs) to healthy control,with 3 replicates per group

first: Yang

last: Fei

first: Li

last: He

first: Meng

first: Qiong

last: Jiao

first: Qiye

last: Liu

first: Fujun

last: Lin

first: Wei

last: Wang

first: Niansong

first: Dongsheng

last: Chen


title: Age and cell type specific specific effects of histone variant H2BE in the brain [Intact_RNAseq]

first: Sean

last: Louzon

overall_design: Cortical nuclei were isolated from P0, P14, and P28 male mouse pups. Mice were heterozygous for the CAG-Sun1/sfGFP nuclear marker and NEX-cre. Cre-expressing cortical nuclei were isolated using isolation of nuclei tagged in specific cells type (INTACT) immunpurification method. (n = 4 biological replicates per age)


title: RNAs associated with ribosomes in aging synaptosomes

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: An important hallmark of aging is the loss of proteostasis, which can lead to the formation of protein aggregates and mitochondrial dysfunction in neurons. Although it is well known that protein synthesis is finely regulated in the brain, especially at synapses, where mRNAs are locally translated in activity-dependent manner, little is known as to the changes in the synaptic proteome and transcriptome during aging. Therefore, this work aims to elucidate the relationship between transcriptome and proteome at soma and synaptic level during aging. Proteomic and transcriptomic data analysis reveal that, in young animals, proteins and transcripts are correlated and synaptic regulation is driven by changes in the soma. During aging, there is a decoupling between transcripts and proteins and between somatic and synaptic compartments. Furthermore, soma-synapse gradient of ribosomal genes changes upon aging, i.e. ribosomal transcripts are less abundant and ribosomal proteins are more abundant in synaptic compartment of old mice with respect to younglings. Additionally, transcriptomics data highlight a difference in the splicing of certain synaptic mRNA with aging. Taken together, our data provide a valuable resource for the study of the aging synapse.

overall_design: 48 samples: age: 3w, 6m, 18m; conditions: 4 per age group (TH input/TH SC/SG input/SG SC); biol. Replicates per age group and condtion: 4

first: Cinzia

last: Caterino

first: Karol

last: Szafranski


title: Transcriptome analysis of synaptosomes in ageing

overall_design: 32 samples: age: 3w, 5m, 18m, 19m; conditions: 2 per age group (SG/TH); biol. Replicates per age group and condition: 4


title: SLAMF7 Defines Subsets of Human Effector CD8 T Cells.

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Long-term control of viral replication relies on the efficient differentiation of memory T cells into effector T cells during secondary immune responses. Recent findings have identified T cell precursors for both memory and exhausted T cells, suggesting the existence of progenitor-like effector T cells. These cells can persist without antigenic challenge but expand and acquire effector functions upon recall immune responses. In this study, we demonstrate that the combination of SLAMF7 with either CD27 or TCF-1 effectively identifies progenitor-like effector CD8 T cells, while SLAMF7 with GPR56 and TOX defines effector CD8 T cells. These markers allow for the clear segregation of these distinct cell subsets. SLAMF7+ CD8T cells are dynamically modulated during viral infections, including HIV, HCV, CMV, and SARS-CoV-2, as well as during aging. We further characterize the SLAMF7 signature at both phenotypic and transcriptional levels. Notably, during aging, the SLAMF7 pathway becomes dysregulated, resulting in persistent phosphorylation of STAT1. Additionally, SLAMF7 ligation in the presence of IL-15 induces TCF-1 expression, which promotes the homeostatic proliferation of progenitor-like effector CD8 T cells.

overall_design: To investigate transcriptional signature of virus-specific T cells during aging. Human CMV- and EBV-specific CD8 T cells restricted by different HLA were isolated by flow cytometry.

first: Hassen

last: Kared

first: Crystal

last: Tan

first: Vipin

last: Narang

first: Anis

last: Larbi


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [VCD_Cycle7]

city: Sha Tin

first: Jacquelyne

last: Sun

state: New Territories

address: Room 612A, Mong Man Wai Building,

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Sex-biased differences in Alzheimer’s disease (AD) are well documented, but the mechanisms underlying increased vulnerability in postmenopausal women remain unclear. This study aimed to model the effects of perimenopausal hormonal fluctuations on AD pathophysiology. Using a VCD-induced accelerated ovarian failure model in young female C57BL/6J and 3xTg mice, we simulated a perimenopausal state with hormonal changes characterized by elevated oestradiol levels and reduced progesterone levels. Supporting human brain transcriptomic and metabolomic data from the ROSMAP study revealed that impaired oestrogen-related receptor alpha (ERRα) function was a key driver of female sex-biased vulnerability. In female mice, progesterone-guided oestrogen receptor signalling maintained ERRα activity by regulating neuronal cholesterol homeostasis and the TCA cycle. Hormonal imbalances disrupted this mechanism, triggering an aspartate-driven “minicycle,” which increased glutamate release, neuronal excitability, ATP depletion, and energy crisis susceptibility. This study demonstrates how perimenopausal hormonal imbalances exacerbate AD risk via ERRα dysfunction, linking neuronal cholesterol and energy homeostasis to disease vulnerability.

overall_design: To investigate the effect of peripheral loss in estradiol to progesterone balance, whole cerebral cortex tissues harvested from animals treated with or without 4-vinylcyclohexene diepoxide (VCD) were harvested for bulk transcriptomics analysis

first: Kim Hei-Man

last: CHOW


title: single-nucleus transcriptomic analysis of cortical tissue from control and Dot1l HET 10 week old mice.

first: Marissa

last: Maroni

summary: We aimed to understand the transcriptional impact of monoallelic loss of DOT1L in cortical nuclei from 10 week old mice.

overall_design: Control and DOT1L HET cortical nuclei were isolated from 10-week-old mice. DOT1L HET mice were heterozygous for floxed DOT1L and both Controls and DOT1L HET were heterozygous for CMV-cre (Strain #:006054). Cortical nuclei were isolated and prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression reagents. (n = 6 biological replicates combined per sample/genotype, 3 male mice and 3 female mice)

middle: J


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [VCD_Cycle14]


title: Senataxin Promotes RNA Polymerase II Elongation [DRBrelease_TTseq]

city: Copenhagen

first: Zhong

last: Han

address: Blegdamsvej 3B

department: ICMM, Institut for Cellulær og Molekylær Medicin

country: Denmark

institute: University of Copenhagen

summary: Senataxin (SETX) is recognized as a critical regulator of RNA Polymerase II (RNAPII) transcription and plays a pivotal role in maintaining genomic stability. Despite its importance, the direct in vivo functions of SETX remain inadequately characterized. Employing the degradation tag (dTAG) system for acute protein depletion, we demonstrate that SETX does not influence transcription termination but significantly enhances RNAPII elongation. Through in vitro reconstitution assays, we show that SETX actively drives RNAPII forward across complex transcriptional landscapes, akin to the way bacterial ribosomes mitigate transcriptional pauses. In vivo analyses further reveal an accumulation of pausing RNAPII at early transcription stages and a corresponding increase in R-loop formation at these sites following SETX depletion. These insights not only redefine our understanding of SETX's role in transcriptional regulation but also highlight its potential as a therapeutic target in disorders linked to transcriptional dysregulation.

overall_design: Determination of RNAPII elongation speed by DRBrelease_TTseq under DMSO vs dTAGV1

first: Jesper

middle: Q

last: Svejstrup


title: Senataxin Promotes RNA Polymerase II Elongation [RChIPseq]

overall_design: Determination of R-loop accumulation by RChIPseq  under DMSO vs dTAGV1 treatment (4h)


title: Cell surface ribonucleoproteins cluster with heparan sulfate to regulate growth factor signaling

city: Boston

first: Ryan

last: Flynn

address: 1 Blackfan St

institute: Harvard University

summary: Receptor-ligand interactions govern a wide array of biological pathways, facilitating a cell’s ability to interrogate and integrate information from the extracellular space. Here, we identify heparan sulfate proteoglycans (HSPGs) as a major organizational mechanism of glycoRNA and cell surface RNA binding proteins (csRBPs). If growth factors, which use HSPGs to bind the cell surface, interact with RNA is not well understood. Here we use biochemical pulldowns of VEGF-A165 coupled to RNA-seq to determine if and which RNAs are selectively isolated with this growth factor in vitro.

overall_design: Small RNA fractions (generally less than 200 nucleotides) were biochemically isolated from HUVEC cells. This RNA served as input material for RNA-seq libraries as well as to perform a biochemical enrichment with anti-VEGF-A antibodies with or without the addition of VEGF-A165. After incubation with the small RNA from HUVEC cells, enriched RNAs bound to the antibody or antibody-VEGF-A165 complex were purified and RNA-seq libraries generated from the resulting RNA.

first: Peiyuan

last: Chai

first: Petar

last: Hristov

first: Christopher

last: Watkins

first: Ruiqi

last: Ge


title: Genome structure in single nucleoli by sequencing of laser capture nucleolar microdissection (ActD_RNAseq)

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

summary: The three-dimensional architecture of the eukaryotic genome is a critical determinant in the regulation of gene expression programs. Repressive chromatin regions are localized either at the nuclear lamina or the nucleolus. While the role of the nuclear lamina in genome organization has been widely studied, the role of the nucleolus has only recently come under investigation. Here, we present a new method called nucleolus architecture mapping (NAM) for identifying nucleolus-associated genomic domains (NADs) at a single nucleolus resolution. NAM combines laser capture microdissection and DNA sequencing. We applied NAM to embryonic stem cells (ESCs) and neural progenitor cells and observed a distinct pattern of nucleolus-to-nucleolus heterogeneity for NADs. NAM not only identified characteristic features of NADs, such as high levels of H3K9me2, depletion of H3K27me3, low active histone marks, and repressed gene expression but also revealed that the genomic domains seen in cell population studies to contact both nucleoli and nuclear lamina (NAD/LAD regions) can contact the nucleolus in one cell and the NL in another cell, but rarely both nucleolus and NL in the same cell. Additionally, we found that ribosomal protein (RP) genes are frequently associated with the nucleolus, suggesting a potential direct crosstalk between the nucleolus and the regulation of RP genes, and hence ribosome biogenesis. We also performed NAM upon perturbation of the nucleolus structure by inhibiting PolI transcription with Actinomycin D. This showed a loss of mostly NADs from the nucleolus other than the chromosomes containing rRNA genes, demonstrating that nucleolar integrity is required for genomic contacts with the nucleoli. Additionally, NAM applied to hybrid ESCs demonstrates a predominantly monoallelic distribution of NADs in single cells. We identify parental-specific NADs exhibiting a non-uniform distribution across different chromosomes. Our findings underscore NAM as an invaluable tool for investigating nucleolar organization in individual cells and, potentially, genome organization in other large phase-separated organelles in the future.

overall_design: NoLM-seq, ChIP-seq and RNA-seq in E14 ESCs, ActinomycinD treated ESCs, NPCs and F123 hybrid mESCs

first: Kaivalya

last: Walavalkar


title: Senataxin Promotes RNA Polymerase II Elongation [PROseq]

overall_design: Determination of RNAPII position by PROseq under DMSO vs dTAGV1 treatment (4h)


title: CRISPRa-mediated entanglement of the Dux-MERVL axis

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Transposable elements (TEs) provide sequences that are powerful cis-regulatory drivers of gene expression programmes. This is particularly apparent during early development when many TEs become de-repressed. MERVL elements are highly yet transiently upregulated in mouse totipotent 2-cell (2C) embryos during major zygotic genome activation (ZGA), and in 2C-like cells in vitro. One of the most powerful activators of MERVL is the pioneer transcription factor, Dux. However, apparent differences lie in the requirement for Dux versus MERVL activation in development, for unclear reasons. Moreover, sustained Dux activation causes cell toxicity in multiple cell types, which may or may not be linked to MERVL activation. Using a CRISPR-activation, 2C-GFP reporter system, we have unpicked the relative role of Dux and MERVL in ZGA, totipotent-like characteristics and cell toxicity. We find that direct MERVL activation comprises only a portion of the Dux-dependent transcriptome, and which is sufficient for some – but not all – totipotency features. Conversely, Dux-induced pathology is independent of MERVL activation and involves induction of the pro-apoptotic factor, Noxa. Our study highlights the complexity of the Dux-MERVL transcriptional network and uncovers a new player in Dux-driven pathology.

overall_design: Mouse E14 ESCs grown in serum/LIF conditions on 0.2% gelatin were transfected with control sgRNAs (sgGAL4), MERVL sgRNAs or Dux sgRNAs, then 48h samples sorted by 2C-GFP fluorescence and 2C-GFP positive and negative samples analysed by RNA-seq. Samples from 3 independent experiments are included.

first: Paul

last: Chamas

first: Michelle

last: Percharde

first: George

last: Young


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [VCD+P4_Cycle14]


title: Transcriptomic analysis of a zebrafish model of heart failure induced by isoproterenol

city: Albacete

first: Aaron

last: Garcia-Blazquez

address: C/ Almansa 14

department: Facultad de Medicina de Albacete

country: Spain

institute: Universidad de Castilla-La Mancha

summary: Heart failure is a complex cardiac disorder characterized by ventricular dilation and disruption of the cardiac performance. After a cardiac injury, such as a myocardial infarction, the activation of sympathetic and adrenergic  systems attempts to maintain cardiac output. However, sustained elevation of circulating catecholamines triggers maladaptive changes in the heart that eventually lead to heart failure. Chronic isoproterenol treatment is a well established approach to mimic the development of heart failure in animal models to study pathophysiological mechanisms.

overall_design: Here, we induced heart failure in zebrafish by exposing larvae from 3 to 14 days post-fertilization (dpf) to isoproterenol and performed comparative gene expression profiling analysis by RNA-seq of zebrafish hearts after isoproterenol treatment.

first: Manuel

last: Vicente

first: Aarón

last: García-Blázquez

first: Antonio

last: Martínez-Sielva

first: Jussep

last: Salgado-Almario

first: Beatriz

last: Domingo

first: Juan

last: Llopis


title: Dual Host-Pathogen RNA-Seq Aphanius dispar and Candida auris Yolk Sac Microinjection

city: Exeter

first: Rhys

last: Farrer

state: Devon

address: Stocker Road

department: MRC Center for Medical Mycology

institute: University of Exeter

summary: Candida auris is an emerging infectious agent and WHO critical priority fungal pathogen. Rising pan-resistance, massive nosocomial outbreaks and diagnostic challenges complicate clinical treatment, with an associated human mortality rate of 45%. Importantly, in vivo gene expression of C. auris during infection has not been described to date. We developed the novel thermotolerant teleost fish embryo yolk-sac microinjection model of Aphanius dispar (Arabian Killifish, AK) for infection by each of the five major C. auris clades. This model enabled dual host-pathogen RNA-seq at 24 and 48 hours post injection (HPI) at mammalian temperature (37 °C), which has not been reported in other teleost fish models. Host gene expression indicated features of nutritional and innate immune responses, including haem-oxygenase and C-type lectin receptor expression. We identified an in vivo transcriptome signature common to all five clades of C. auris compared to in vitro expression that was highly enriched for putative xenosiderophore transmembrane transporters. We describe the seventeen-member xenosiderophore transport candidate family in terms of diverse in-host patterns of expression and cross-kingdom functional prediction. We discovered that only the basal clade V isolate formed filaments in vivo, corresponding with Candida-typical and atypical hypha-formation genetic signals, such as the novel adhesin SCF1. Furthermore, clades that were more virulent (I or IV vs II or III) were strongly characterised by upregulation of the majority of genes at the mating-type locus (MTL), including non-mating genes, consistent with a role for the MTL in C. auris pathogenicity. We hypothesise that both xenosiderophore transport genes and the MTL may play critical roles in C. auris virulence, and are urgent targets for potential therapy.

sample_organism:
Candidozyma auris
blank sample
Aphanius dispar

overall_design: AK embryos without injection (negative control, "None"), with sham injection only ("Water"), or injected with Candida auris (clade I, II, III, IV or V). After microinjection at 3 days post fertilisation, RNA was extracted at 24 or 48 hours post injection (HPI). Samples labelled "ypd" contain only C. auris. All samples are in technical triplicate, except embryos without injection.

first: Hugh

last: Gifford

first: Nicolas

last: Helmstetter

first: Tina

last: Bedekovic

first: Jack

last: Gregory

first: Qinxi

last: Ma

first: Mark

last: Ramsdale

first: Alex

last: Brand

first: Duncan

last: Wilson

first: Johanna

last: Rhodes

first: Tetsu

last: Kudoh


title: TOP2B cooperates with ATRX to resolve G-quadruplexes and maintain replication fork stability in glioma

first: Chunlong

last: Zhong

address: 150 Jimo Road

department: Department of Neurosurgery

institute: Shanghai East Hospital, School of Medicine, Tongji University

summary: ATRX is a chromatin remodeling protein that maintains genomic stability by resolving G-quadruplex (G4) DNA structure. However, the details of resolving G4 by ATRX remain unclear. Here, we unveil that TOP2B and ATRX collaborate to maintain genomic stability by regulating G4. ATRX deficiency causes the accumulation of G4 and increases cells’ reliance on TOP2B to resolve G4 structures and maintain replication fork stability. CX-5461, as a TOP2B poison, stabilizes G4 by trapping TOP2B on DNA as well as inhibiting the formation of the ATRX-TOP2B complex and its recruitment to G4 sites. CX-5461 treatment resulted in the entrapment of TOP2B and the subsequent hyperaccumulation of G4 in ATRX-deficient glioma cells, ultimately leading to genomic instability and cell death. Furthermore, we found that YTHDF3 promotes ATRX protein synthesis through m6A modification. Our findings suggest that targeting TOP2B with CX-5461 has therapeutic potential for ATRX-deficient gliomas, offering a promising direction for future treatment strategies.

overall_design: To investigate the cooperative function of ATRX/TOP2B complex in the DNA replication and DNA damage response, we established U87MG cell lines in which each target gene has been knocked down by siRNA.

first: Ying

last: Pang

first: Meng

last: Cheng

first: Rui

last: Wang

first: Xu

last: Chen


title: Investigate the functions of HUSH complex in embryonic stem cells

city: Nanjing

first: Bowen

address: 12 Xue-fu Road, Pukou District

institute: Nanjing University

summary: Purpose: The goals of this study are to compare control and HUSH complex core subunits-deficient embryonic stem cells transcriptome profiling (RNA-seq) to evaluate the target genes regulated by HUSH.

overall_design: mRNA profiles of WT and MPP8/Tasor/Pphln1-null embryonic stem cells were generated by deep sequencing, in triplicate, using Illumina Novaseq6000.

first: Jinzhong

last: Qin


title: In vitro neuronal RNA-sequencing, in vivo cortical single nucleus RNA-sequencing, in vivo cortical ChIP-sequencing of H3K79me2 in models of DOT1L loss

first: Marissa

last: Maroni

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

overall_design: Refer to individual Series


title: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics

city: Los Angeles

first: Colette

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

summary: Arabidopsis MBD5, MBD6, and MBD7 are CG-specific methyl-readers with opposite functions: MBD5 and MBD6 (MBD5/6) repress methylated loci in pollen vegetative nuclei (VN), while MBD7 prevents transgene silencing, possibly by promoting DNA demethylation. Here we show that loss of MBD7 rescues transcriptional defects at a large subset of MBD5/6-bound loci. Using simultaneous profiling of DNA methylation and transcription in single pollen nuclei, we found that MBD5/6-bound loci that are actively demethylated in immature VN lose additional methylation in mbd5/6, prior to transcriptional derepression. A subset of these loci is also bound by MBD7, correlating with demethylation and transcriptional derepression in mbd5/6 that are both reversed by loss of MBD7. Conversely, ectopically recruiting the MBD7 complex to MBD5/6 targets causes partial demethylation and upregulation. We propose that MBD5/6 maintain silencing in VN in part by preventing the MBD7 complex from enhancing the active demethylation that occurs during VN maturation.

overall_design: To investigate rescue of the mbd5/6 demethylation phenotype in pollen by mbd7.

first: Lucia

last: Ichino

first: Brandon

last: Boone

first: Tyler

last: Buckley

first: Jaewon

last: Yun

first: Kevin

last: Abuhanna

first: Yi

last: Zhang

first: Noah

last: Behrendt

first: SuMay

last: Soe

first: Chongyuan

last: Luo

first: Steven

last: Jacobsen


title: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics [ChIP-Seq]

summary: Arabidopsis MBD5, MBD6, and MBD7 are CG-specific methyl-readers with opposite functions: MBD5 and MBD6 (MBD5/6) repress methylated loci in pollen vegetative nuclei (VN), while MBD7 prevents transgene silencing, possibly by promoting DNA demethylation. Here we show that loss of MBD7 rescues transcriptional defects at a large subset of MBD5/6-bound loci. Using simultaneous profiling of DNA methylation and transcription in single pollen nuclei, we found that MBD5/6-bound loci that are actively demethylated in the early post-mitotic VN lose additional methylation in mbd5/6, prior to transcriptional derepression. A subset of these loci is also bound by MBD7, correlating with demethylation and transcriptional derepression in mbd5/6 that are both reversed by loss of MBD7. Conversely, ectopically recruiting the MBD7 complex to MBD5/6 targets causes partial demethylation and upregulation. We propose that MBD5/6 maintain silencing in VN in part by preventing the MBD7 complex from enhancing the active demethylation that occurs during VN maturation.

overall_design: The goal of these ChIP-seq experiments was to determine the normal localization of MBD6 and MBD7 in inflorescence tissue, and to see if MBD7 localization is affected by loss of mbd5 and mbd6.

first: Su May Lei


title: RNA-seq analysis of Luciferase control-infected and DOT1L shRNA-infected primary cortical neurons.

summary: We aimed to understand the transcriptional impact of partial loss of DOT1L in primary neurons from mice.

overall_design: WT primary cortical neurons were isolated from E16.5 mice and cultured for 14 DIV total. Control luciferase shRNA and DOT1L shRNA were used to infect WT primary cortical neurons at 9 DIV  (n = 3 biological replicates per genotype).


title: Integrative RNA-seq and CLIP-seq analysis reveals hnRNP-F regulation of the TNFα/NFκB signaling in high glucose conditions

city: Wu Han

first: LAN

last: WANG

state: Hubei

address: 湖北省武汉市武昌区湖北中医药大学昙华林校区昙华林188号

institute: Hubei University of Chinese Medicin

summary: Using RNA-seq and ChIP-seq we found that we found that hnRNP-F may bind to lncRNA SNHG1 to negatively regulate the transcription of genes involved in the TNFα/NFκB signaling pathway in diabetic nephropathy. Our study suggests that hnRNP-F may play a role in diabetic nephropathy by regulating the differential expression and variable splicing of diabetic nephropathy-associated genes, especially those related to inflammatory response.

overall_design: In this study, hnRNP-F was overexpressed in human renal proximal tubular epithelial (HK-2) cells cultured in high glucose conditions, while an empty vector was transfected into HK-2 cells as a control group (NC). RNA-seq was utilized to generate transcriptome data following hnRNP-F overexpression, allowing for the analysis of differential gene expression and alternative splicing events influenced by hnRNP-F overexpression. We also downloaded the CLIP-seq data of hnRNP-F in human 293T cells from GEO database. Through integrative analysis of RNA-seq and CLIP-seq, we tried to identified a set of potential direct targets of hnRNP-F in cells.

first: Lan

first: Huimeng

last: Li

first: Xiaoqin

first: Xinyuan

last: Guo


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (murine subset)

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

summary: Embryonal brain tumors (EBTs), arising during early brain development, present significant challenges in understanding pathogenesis and developing treatments. This study explores the efficacy of forebrain organoid models in replicating the complexities of the EBT microenvironment. We established an EBT-forebrain-organoid (EBT-FBO) model, incorporating embryonal tumor with multilayered rosettes (ETMR) and atypical teratoid and rhabdoid tumor (ATRT), using a scalable liquid-handling-assisted coaggregation method. Comprehensive characterization, including wholemount immunostaining, immunohistochemistry, single-cell RNA sequencing, integration with existing datasets, and automated cell-type-specific drug screening, validated the EBT-FBO model. EBT-FBOs closely mimicked mid-gestational fetal brain environments, with EBTs reflecting intratumoral heterogeneity at both histological and transcriptomic levels. Drug screening on ETMR-FBOs identified promising treatment options, including anthracyclins and Triptolide, which demonstrated anti-tumoral effects with minimal neurotoxicity. Scalable EBT-FBO models that resemble immature neuronal microenvironments similar to ETMR or ATRT mark significant progress towards targeted therapy and personalized precision medicine that requires recapitulation of individual tumor heterogeneities.

relation:
Reanalysis of: GSM7024927
Reanalysis of: GSM7024928
Reanalysis of: GSM7024921
Reanalysis of: GSM7024922
Reanalysis of: GSM7024923
SubSeries of: GSE270073

overall_design:
scRNA-seq (10xGenomics) of fresh samples: tumor cell lines (n = 2) and ETMR tumor data, murine (n = 3).
Sample(s) moved from GSE224474.

first: Nicole

middle: C

last: Riedel

first: Flavia

last: de Faria

first: Paula

last: Aust

first: Lea

last: Atendorf

last: Göbel

first: Archana

last: Verma

first: Annika

last: Ballast

first: Ivan

last: Bedhzov

first: Rajanya

last: Roy

first: Daniel

last: Münter

first: Thomas

middle: K

last: Albert

first: Claudia

last: Rössig

first: Pascal

last: Johann

first: Barbara

last: von Zezschwitz

first: Sarah

last: Sandmann-Varghese

first: Julian

last: Varghese

first: Hans

last: Schöler

first: Christian

last: Thomas

first: Ulrich

last: Schüller

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: Single-cell profiling identifies a specific RPE subset undergoing senescence

city: Guangzhou

first: Tian

last: Zhou

state: Guangdong

address: NO.7 Jinsui Road

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center

summary: To elucidate the classification and function of RPE subsets in the degenerative retina, we used single-cell RNA sequencing on isolated murine RPE-choroidal complex. We identified a novel subpopulation of RPE named R1, which highly expressed IL-6R and senescent marker genes.

overall_design: Single cell profiling of RPE choroidal cells derived from PBS or NaIO3 treated mice, using 10X genomic platform.

first: Ziqi

last: Yang

first: Biyan

last: Ni

first: Hong

first: Yang

first: Huiyi

last: Xu

first: Xiaojing

last: Lin

first: Shiya

first: Wei

last: Yi

first: Chang

last: He

first: Xialin

last: Liu


title: Senataxin Promotes RNA Polymerase II Elongation [TTseq]

first: Zhong

last: Han

overall_design: Determination of nascent RNA synthesis by TT-seq under DMSO vs dTAGV1 treatment (4h)

first: Jesper

last: Svejstrup


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human subset)

first: Carolin

last: Walter

relation:
Reanalysis of: GSM7024916
SubSeries of: GSE270073

overall_design:
scRNA-seq (10xGenomics) of fresh samples: ETMR tumor data, human (n = 1).
Sample(s) moved from GSE224473.

first: Nicole

last: Riedel

first: Flavia

last: de Faria

first: Paula

last: Aust

first: Lea

last: Atendorf

last: Göbel

first: Archana

last: Verma

first: Annika

last: Ballast

first: Ivan

last: Bedhzov

first: Rajanya

last: Roy

first: Daniel

last: Münter

first: Thomas

last: Albert

first: Claudia

last: Rössig

first: Pascal

last: Johann

first: Barbara

last: von Zezschwitz

first: Sarah

last: Sandmann-Varghese

first: Julian

first: Hans

first: Christian


title: Peroxisomal integrity in myeloid cells is required for myelin debris clearance and remyelination

city: Houston

first: Jian

last: Hu

state: TX

address: 1881 East Rd, South Campus Research Building 3

department: Cancer Biology

institute: University of Texas MD Anderson Cancer Center

summary: During demyelination myeloid cells remove myelin debris and promote remyelination. Dysfunctional myeloid cells are associated with peroxisomal leukodystrophies, yet the role of peroxisomes in myeloid cells responding to demyelination remains unknown. The impact of dysfunctional peroxisomes in demyelination-responding myeloid cells was interrogated in Abcd1 and Pex5 knockout mice using the cuprizone model for myelin damage. Abcd1 loss did not affect the demyelination response in myeloid cells, however, Pex5 deficiency impaired remyelination and significantly undermined myelin debris clearance. Molecular analysis in Pex5 depleted macrophages revealed repressed APOE activity and attenuated expression of the sterol exporter pathway integral to myelin debris metabolism, which was associated with an aggravated foamy macrophage phenotype in myelin engulfing myeloid cells. In summary, we report a critical contribution of peroxisomes to myelin debris clearance, myelin lipid processing, and pro-remyelinating properties in myeloid cells.

overall_design: Adult mice (8 to 12-weeks, all males) received 100 uL of tamoxifen (20 mg/mL dissolved in corn oil) via intraperitoneal injection daily for five consecutive days. 1 week post injection, mice were fed 0.2% cuprizone diet  (CPZ) or standard chow (baseline) for 6 weeks. After 6 weeks, the mice were perfused with PBS transcardially and the brain was excised and flash frozen in liquid nitrogen. Frozen brain, including corpus callosum, was homogenized to release nuclei, which were stained with DAPI and PI to enable fluorescence-activated nuclei sorting. Purified nuclei were used to generate 10X v3.1 dual index libraries for single nuclei RNA sequencing.

first: Joseph

last: Barnes-Vélez


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human organoids subset 3)

first: Carolin

last: Walter

relation:
Reanalysis of: GSM7024931
SubSeries of: GSE270073

overall_design:
scRNA-seq (10xGenomics) of fresh samples: forebrain organoids (n=1).
Sample(s) moved from GSE224475.  For sample "Forebrain-Organoid D30", there are new additional processed data (KK21-H-164_pureHuman_*).

first: Nicole

last: Riedel

first: Flavia

first: Paula

last: Varghese

last: Schöler

last: Thomas

first: Ulrich

last: Schüller

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human+murine organoids subset)

relation:
Reanalysis of: GSM7024932
Reanalysis of: GSM7024934
Reanalysis of: GSM7024936
Reanalysis of: GSM7024939
SubSeries of: GSE270073

overall_design:
scRNA-seq (10xGenomics) of fresh samples: forebrain organoids harboring tumor cell lines (n=4).
Sample(s) moved from GSE224475.

last: de Faria

last: Aust

first: Lea

last: Atendorf

last: Göbel

first: Archana

last: Verma

first: Annika

last: Ballast

first: Ivan

last: Bedhzov

first: Rajanya

last: Roy

first: Daniel

first: Thomas


title: The exit of naïve pluripotency contains a metabolism-induced checkpoint for telomere homeostasis [RNA-seq]

first: Veronique

last: Azuara

state: London

address: Institute of Reproductive and Developmental Biology, Hammersmith Hospital Campus

department: Metabolism, Digestion and Reproduction

institute: Imperial College London

summary: During peri-implantation development, the pluripotent tissue of the early embryo undergoes profound cellular and biochemical reprogramming. These transformations are essential for subsequent development, yet how they are coordinated with the preservation of genome integrity remains poorly understood. Here, we uncover a telomere length checkpoint that is elicited by metabolic remodeling as mouse embryonic stem cells (ESCs) transition from the naïve to formative pluripotent state. We show that the exit of naïve pluripotency is marked by accelerated mitochondrial respiration and de novo lipogenesis, fueling lipid droplet accumulation required for tissue remodeling. Unexpectedly, these acute metabolic shifts trigger transient telomere shortening and activate ZSCAN4, a pluripotency-associated regulator of telomeres, followed by telomere re-elongation as cells adopt a more glycolytic metabolic profile. Our findings reveal a feedback mechanism in which metabolism-induced telomere stress engages ZSCAN4 as a protective response, thereby linking metabolic state to telomere homeostasis during early developmental progression.

overall_design: Clones exhibiting varied lipid droplet sizes were isolated from bulk E14 mouse ESCs grown in routine FBS/LIF conditions. These were then passaged and expanded in the same culture conditions. RNA was then extracted from nine clones and sequenced to compare gene expression profiles.

first: Roshni

last: de Souza


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human organoids subset 2)

last: Walter

relation:
Reanalysis of: GSM7024953
Reanalysis of: GSM7024955
Reanalysis of: GSM7024958
Reanalysis of: GSM7024952
Reanalysis of: GSM7024954
Reanalysis of: GSM7024960
SubSeries of: GSE270073

overall_design:
scRNA-seq (10xGenomics) of fresh samples: forebrain organoids (n=6).
Sample(s) moved from GSE224476.

last: Riedel

last: Münter

last: Albert

first: Claudia

last: Rössig

first: Pascal

last: Johann

first: Barbara

last: von Zezschwitz

first: Sarah

last: Sandmann-Varghese

first: Julian

first: Hans

first: Christian


title: In vivo intratumoral Heterogeneity in a dish: Scalable Forebrain Organoid Models of Embryonal Brain Tumors for High-Throughput Personalized Drug Discovery (human organoids+cell lines subset 1)

first: Carolin

overall_design: scRNA-seq (10xGenomics) of fresh samples: 1) forebrain organoids harboring (n = 12) and non-harboring (n = 12) tumor cell lines, 2) tumor cell lines (n = 6), and 3) ETMR tumor data from human (n = 1) and murine (n = 3)

first: Nicole

first: Flavia

last: de Faria

first: Paula

last: Aust

last: Varghese

last: Schöler

last: Thomas

first: Ulrich

last: Schüller

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: Single-nucleus methylcytosine and transcriptome sequencing in pollen reveals antagonism between MBD5/6 and MBD7 in transcriptional regulation [RNA-seq]

first: Colette

last: Picard

summary: MBD5, MBD6, and MBD7 are CG-specific methyl-readers with opposite functions: MBD5 and MBD6 (MBD5/6) redundantly repress methylated loci in pollen vegetative nuclei (VN), while MBD7 prevents transgene silencing, possibly by promoting DNA demethylation. Here we show that transcriptional derepression in mbd5/6 pollen is rescued by loss of MBD7, suggesting that MBD5/6 counteract MBD7 activity. By simultaneously profiling DNA methylation and gene expression in single pollen nuclei, we found that CG methylation is lost at MBD5/6 targets specifically in the early post-mitotic VN of mbd5/6. This loss precedes mbd5/6 transcriptional derepression and is largely restored in mbd5/6/7 triple mutants. Altering MBD6 to recruit the MBD7 complex instead of its normal interactors caused demethylation and upregulation of MBD5/6 targets, turning MBD6 from a repressor into an activator. We propose that in VN, where chromatin is decondensed, MBD5/6 are required to protect accessible DNA from demethylation and derepression by the MBD7 complex.

overall_design: For libraries 1 and 2, to investigate the rescue of the mbd5/6 gene/TE derepression phenotype by mbd7 in pollen. For library 3, to test the effect of swapping the stkyC domain of MBD6 with the one of MBD7 on gene/TE expression in pollen.

first: Lucia

last: Ichino

first: Brandon

last: Boone

first: Tyler

last: Buckley

first: Jaewon

last: Yun

first: Kevin

last: Abuhanna

first: Yi

last: Zhang

first: Noah

last: Behrendt

first: Chongyuan

last: Luo

first: Steven

last: Jacobsen


title: Genome structure in single nucleoli by sequencing of laser capture nucleolar microdissection (NoLMseq)

first: Raffaella

last: Santoro

overall_design: NoLM-seq, ChIP-seq and RNA-seq in E14 ESCs, ActinomycinD treated ESCs, NPCs and F123 hybrid mESCs

first: Kaivalya

last: Walavalkar


title: Transcriptome analysis and ribosome footprints in engineered chromosome 3 and chromosome 8 isogenic aneuploidy cell model.

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

institute: Yale University

summary: We analyzed two isogenic aneuploidy models. The first model is the chromosome 3 isogenic aneuploidy model, which includes three cell types: chromosome 3 WT, 3q gain, and 3p loss. By comparing with chromosome3 WT, we evaluated the overall transcript expression changes in 3q gain and 3p loss cells. Additionally, by comparing with chromosome3 WT, we assessed the changes in ribosome-protected fragments in 3p loss cells. The second model is the chromosome 8 isogenic aneuploidy model, which includes two cell types: chromosome 8 WT and 8p loss. By comparing with chromosome 8 WT, we evaluated the overall transcript expression changes in 8p loss cells.

overall_design: mRNA expression was quantified in chromosome 3 WT, 3q gain, and 3p loss cells, with three biological replicates for each genotype. Additionally, ribosome-protected fragments were quantified in chromosome 3 WT and 3p loss cells, also with three biological replicates. Furthermore, mRNA expression was measured in chromosome 8 WT and 8p loss cells with three biological replicates.

last: Di

first: Alison

last: Taylor

first: Yansheng

last: Liu


title: Genome structure in single nucleoli by sequencing of laser capture nucleolar microdissection (ChIP-Seq)

summary: The three-dimensional architecture of the eukaryotic genome is a critical determinant in the regulation of gene expression programs. Repressive chromatin regions are localized either at the nuclear lamina or the nucleolus. While the role of the nuclear lamina in genome organization has been widely studied, the role of the nucleolus has only recently come under investigation. Here, we present a new method called nucleolus architecture mapping (NAM) for identifying nucleolus-associated genomic domains (NADs) at a single nucleolus resolution. NAM combines laser capture microdissection and DNA sequencing. We applied NAM to embryonic stem cells (ESCs) and neural progenitor cells and observed a distinct pattern of nucleolus-to-nucleolus heterogeneity for NADs. NAM not only identified characteristic features of NADs, such as high levels of H3K9me2, depletion of H3K27me3, low active histone marks, and repressed gene expression but also revealed that the genomic domains seen in cell population studies to contact both nucleoli and nuclear lamina (NAD/LAD regions) can contact the nucleolus in one cell and the NL in another cell, but rarely both nucleolus and NL in the same cell. Additionally, we found that ribosomal protein (RP) genes are frequently associated with the nucleolus, suggesting a potential direct crosstalk between the nucleolus and the regulation of RP genes, and hence ribosome biogenesis. We also performed NAM upon perturbation of the nucleolus structure by inhibiting PolI transcription with Actinomycin D. This showed a loss of mostly NADs from the nucleolus other than the chromosomes containing rRNA genes, demonstrating that nucleolar integrity is required for genomic contacts with the nucleoli. Additionally, NAM applied to hybrid ESCs demonstrates a predominantly monoallelic distribution of NADs in single cells. We identify parental-specific NADs exhibiting a non-uniform distribution across different chromosomes. Our findings underscore NAM as an invaluable tool for investigating nucleolar organization in individual cells and, potentially, genome organization in other large phase-separated organelles in the future.

overall_design: NoLM-seq, ChIP-seq and RNA-seq in E14 ESCs, Actinomycin D treated ESCs, NPCs and F123 hybrid mESCs


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [RNA-seq]

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

institute: Institut Pasteur

summary: Pioneer transcription factors (TF) bind nucleosome-embedded DNA motifs to activate new regulatory elements and promote differentiation. However, the complexity, binding dependencies and temporal effects of their action remain unclear. Here, we dissect how ectopic induction of the pioneer TF GATA6 triggers Primitive Endoderm (PrE) differentiation from pluripotent cells. We show that transient GATA6 binding exploits accessible regions to decommission enhancers and promote pluripotency gene silencing. Simultaneously, GATA6 targets closed chromatin and initiates extensive remodeling culminating in the establishment of fragile nucleosomes flanked by ordered nucleosome arrays and increased accessibility. This is enhanced by rapidly expressed PrE TFs (SOX17) and by pluripotency TFs repurposed for differentiation (OCT4/SOX2). Accordingly, depletion of OCT4 during GATA6 induction decreases Gata6 expression, alters GATA6 and SOX17 binding and impairs differentiation. Therefore, pioneer TFs orchestrate complex regulatory networks involving many if not all available pioneer TFs, including those required to support the original identity of differentiating cells.

overall_design:
differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline
gene expression profiling was carried out at 0,16, 24, 48, 72, 96 and 168 hours of  doxycycline induction as well as in XEN cells.

ES cells carrying the dox-inducible GATA6 transgene were nucleofected with control or oct4 siRNA and plated in doxycycline containing media. RNA sequencing was carried out 48h after nucleofection.

first: Rémi-Xavier

last: Coux


title: Genome structure in single nucleoli by sequencing of laser capture nucleolar microdissection (RNA-Seq)


title: An antagonistic epigenetic mechanism regulating gene expression in pollen revealed through single-nucleus multiomics [snmCT-seq]

first: Colette

last: Picard

overall_design: Goal was to examine DNA methylation dynamics in different pollen nuclei types, and how these change in mbd5/6, mbd7, and mbd5/6/7 mutants. Three experiments were performed (jun2022, sep2022, mar2025). In experiments 1 and 2, 8 x 384-well plates containing 1 FACS-sorted pollen nucleus per well were prepared for each of the two genotypes (Col and mbd5/6) using the snmCT-seq protocol (Luo et al. 2022 Cell Genomics). Note that one plate failed in each of the two sep2022 samples; these are excluded. In experiment 3, 6 x 384 well plates were prepared for each of the four genotypes (Col, mbd7, mbd5/6, mbd5/6/7)investigated in this study. Barcodes for each well of the plate are provided in feature_README.txt.

last: Ichino

first: Su May Lei

last: Soe


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [Esrra_shRNA]

first: Jacquelyne

last: Sun

summary: Sex-biased differences in Alzheimer’s disease (AD) are well documented, but the mechanisms underlying increased vulnerability in postmenopausal women remain unclear. This study aimed to model the effects of perimenopausal hormonal fluctuations on AD pathophysiology. Using a VCD-induced accelerated ovarian failure model in young female C57BL/6J and 3xTg mice, we simulated a perimenopausal state with hormonal changes characterized by elevated oestradiol levels and reduced progesterone levels. Supporting human brain transcriptomic and metabolomic data from the ROSMAP study revealed that impaired oestrogen-related receptor alpha (ERRα) function was a key driver of female sex-biased vulnerability. In female mice, progesterone-guided oestrogen receptor signalling maintained ERRα activity by regulating neuronal cholesterol homeostasis and the TCA cycle. Hormonal imbalances disrupted this mechanism, triggering an aspartate-driven “minicycle,” which increased glutamate release, neuronal excitability, ATP depletion, and energy crisis susceptibility. This study demonstrates how perimenopausal hormonal imbalances exacerbate AD risk via ERRα dysfunction, linking neuronal cholesterol and energy homeostasis to disease vulnerability.

overall_design: To investigate the effect of peripheral loss in estradiol to progesterone balance, whole cerebral cortex tissues harvested from animals treated with or without 4-vinylcyclohexene diepoxide (VCD) were harvested for bulk transcriptomics analysis

first: Kim

middle: H

last: CHOW


title: Spatial transcriptomic characteristics of the aging human ovary

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

summary: Ovarian aging is a complex process that compromises fertility and elevates the risk of reproductive disorders. To elucidate its spatiotemporal dynamics, we integrated single-nucleus RNA sequencing and spatial transcriptomics to construct a comprehensive aging atlas of 12 human ovarian tissues spanning ages 12-54. Our analysis revealed aging-associated transcriptomic shifts, including impaired mitochondrial oxidative phosphorylation and reproductive structure development in aged human ovaries. We identified a novel endothelial cell (EDC) subtype, CLDN5⁺ blood EDCs, which exhibited unique functional specialization as (semi-professional) antigen-presenting cells. In contrast to other cell types that lost cell identity during aging, CLDN5⁺ blood EDCs displayed transcriptomic sensitivity to aging, characterized by enhanced antigen-presenting capabilities, and heightened inflammatory activity. Spatial mapping further uncovered immunoglobulin-expressing cell (IGHG1+/IGKC+) accumulation in the ovarian periphery, correlating with advancing age. Critically, aging disrupted global cellular connectivity while amplifying the DLK1:NOTCH3 axis between theca cells and CLDN5⁺ blood EDCs, which may contribute to the dysregulation of ovarian functions. The progressively upregulation of DLK1 indicates it as a robust biomarker of ovarian aging. This study significantly enhances our comprehension of the underlying mechanisms of human ovarian aging and concurrently pinpoints potential therapeutic avenues for addressing related disorders.

overall_design:
To understand the regional specification of somatic and germ cells in the aging human ovary, 57,970 single cells from three human ovary samples of ages 12, 32, 34, and 42 were profiled using 10× Genomics snRNA-seq technique. To decode the spatial aging event of the human ovary at single-cell resolution, spatial transcriptomic analysis of ages 12, 32, 34, and 42 human ovary samples was performed using scStereo-seq technique.

***************************************************************
The raw snRNA-seq and scStereo-seq data reported in this study have been deposited in Genome Sequence Archive (GSA) for Human under the accession number HRA010703.
***************************************************************

first: Meiling

last: Zhang

first: Fanghao

last: Guo

first: Qing

first: Qianhui

last: Hu

first: Di

first: Yongjian

last: Ma

first: Yanquan

first: Mengxi

first: Haixia

last: Ding

first: Ying

first: Baicai

last: Yang

first: Songmao

first: Ningxia

first: Wen


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [microarray 3]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary: Gene expression profiling of WT and Opa1-deficient Treg cells.

overall_design: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreOpa1fl/fl mixed BM chimera mice (n = 4 biological replicates per group).

first: Hao

last: Shi

first: Jordy

last: Saravia


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [microarray 2]

summary: Gene expression profiling of WT, Cd4CreFlcnfl/fl, Cd4CreTfebfl/fl, Cd4CreFlcnfl/flTfebfl/fl, or Cd4CreFlcnfl/flTfebfl/flTfe3–/– iTreg cells.

overall_design: iTreg cells were generated in vitro by culturing naïve CD4+ T cells for 3 d in the presence of anti-CD3 (5 mg mL-1; plate-bound), anti-CD28 (2 mg mL-1), rIL-2 (100 U mL-1), and rTGF-b (5 ng mL-1) (n = 2 biological replicates per group).


title: Perimenopausal State Oestradiol to Progesterone Imbalance Drives Alzheimer’s Risk via ERRα Dysregulation and Energy Dyshomeostasis [VCD_Treatment]

city: Sha Tin

first: Jacquelyne

address: Room 612A, Mong Man Wai Building,

institute: The Chinese University of Hong Kong

first: Kim Hei-Man


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [microarray 1]

summary: Gene expression profiling of Treg cell states from DT-treated DTR chimera mice.

overall_design: DTR chimera mice were treated with DT and, 7 d later, CD4+Foxp3-YFP+ Treg cells were sorted into four states based upon expression of PD-1 and CXCR3 (n = 4 biological replicates per group).


title: Effect of FGF9 on human renal tubular epithelial cells in high glucose culture

first: wen

middle: qing

last: chen

address: Huangpu Avenue, Tianhe District, Guangzhou City

institute: Jinan University

summary: Diabetic nephropathy is characterised by the accumulation of extracellular matrix in the glomerular tunica and tubular interstitium, which ultimately leads to excessive renal scarring and decreased excretory function. The main pathological changes of renal fibrosis are: glomerulosclerosis, tubulointerstitial fibrosis, infiltration of inflammatory mediators and activation of α-SMA-positive myofibroblasts. Among them, tubulointerstitial fibrosis is an important link in the development of end-stage renal disease (ESRD).Previous experiments verified that FGF9 expression was decreased in kidneys of STZ-induced diabetic mice and HK2 cells cultured with high glucose, while overexpression of FGF9 inhibited HK2 cell migration under high glucose. To investigate the role of FGF9 in tubulointerstitial fibrosis in diabetic nephropathy, we performed high-throughput sequencing of different subgroups of HK2 cells.

overall_design: HK2 cells were divided into four groups: normal glucose group (NG), high glucose group (HG), high glucose + FGF9 overexpression group, and normal glucose + siRNA-FGF9 group.

first: Wenqing

last: Chen

first: Chengyang


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [scRNA-seq3]

summary: Gene expression profiling of Treg cells from DT-treated WT DTR chimera and Foxp3CreOpa1fl/fl DTR chimera mice.

overall_design: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre (called WT) or Foxp3CreOpa1fl/fl (called Opa1 KO) mice) were treated with DT, and, 7 days later, CD4+Foxp3-YFP+ Treg cells sorted for input to scRNA-seq.


title: Mitochondria-lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [ATAC-seq2]

summary: Chromatin profiling in WT and Opa1-deficient Treg cells.

overall_design: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera (n = 4) and Foxp3CreOpa1fl/fl mixed BM chimera (n = 3) mice.


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [scRNA-seq1]

summary: Gene expression profiling in Treg cells and non-Treg immune cells under steady-state and inflammation conditions.

overall_design: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre mice) were treated with DT (called inflammation) or PBS (called steady-state), and, 7 days later, CD4+Foxp3-YFP+ Treg cells and CD45+ (non-Treg) cells were sorted and then mixed 1:1 for input to scRNA-seq and scTCR-seq.


title: Mitochondria-lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [bulk RNA-seq]

summary: Gene expression profiling of WT and Flcn-deficient Treg cells.

overall_design: CD45.2+CD45.1-CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreFlcnfl/fl mixed BM chimera mice (n = 5 biological replicates per group)


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [scRNA-seq2]

summary: Gene expression profiling of Treg cells from DT-treated WT DTR chimera and Foxp3CreFlcnfl/fl DTR chimera mice.

overall_design: DTR chimera mice (generated at a 9:1 ratio with BM from Foxp3DTR and Foxp3Cre (called WT) or Foxp3CreFlcnfl/fl (called Flcn KO) mice) were treated with DT, and, 7 days later, CD4+Foxp3-YFP+ Treg cells sorted for input to scRNA-seq.


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchE

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

summary: This study aimed to identify transcript expression induced by digestion-related herbal medicines (DHM) and modes of action (MOA) of DHM in SW1783 cell line. For the production of THM-induced transcripts, digestion herbal medicines water extract (THW) and digestion herbal medicines ethanol extract (THE) were used.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THW (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), THE (500 ug/mL, 100 ug/mL, and 20 ug/mL, respectively), positive control (wortmannin, LY294002, and thioridazine 10uM, respectively), and vehicle control (2% DMSO). However, in extracts with IC20 of less than 500ug/mL, the concentration at IC20 and the concentration diluted to 1/5 and 1/25 of the IC20 concentration were used, respectively.


title: Mitochondria–lysosome crosstalk dictates the progressive differentiation of Treg cells to limit inflammation-associated immunopathology [ATAC-seq1]

summary: Chromatin profiling in WT and Flcn-deficient Treg cells.

overall_design: CD45.2+CD45.1–CD4+Foxp3-YFP+ Treg cells were sorted from WT mixed BM chimera and Foxp3CreFlcnfl/fl mixed BM chimera mice (n = 4 biological replicates per group).


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [RNA-seq_ME_EC]

city: shanghai

first: shao

last: zhen

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: Conventional human embryonic stem cells (hESCs) are capable of self-renewal and simultaneously poised for differentiation, and thus have been considered to resemble a primed pluripotent state. But the underlying regulatory mechanisms remain largely underexplored. Especially, little was known about the pivotal transcription factors (TFs) driving hESCs through the naïve-to-primed transition to prepare for differentiation. Here, we conduct a large-scale in-silico screening and identify ZNF263 as a new key TF in primed hESCs, as evidenced by its extensive binding capacity at the active and poised genes. Genetic and functional assays reveal that ZNF263 directly initiates the incipient expression of early differentiation genes and concurrently dampens the core pluripotency circuitry in hESCs, greatly tilting the balance from pluripotency maintenance to lineage priming. Importantly, ZNF263 deficiency in hESCs further led to clear defects in pluripotency dissolution and lineage commitment, suggesting it’s indispensably required for the whole process. Together, our results demonstrate a pivotal role of ZNF263 in coordinating the establishment of primed pluripotency state in hESCs and facilitating the differentiation into primary germ layer lineages, which opens a new gate for understanding the central regulatory network governing human early development.

overall_design: To investigate the role of ZNF263 in the process of lineage differentiation, we conducted in vitro directed differentiation into mesoderm and ectoderm with H1 KO (1-10) and WT hESCs, and then performed gene expression profiling using RNA-seq.

first: Zhen

last: Shao


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchC


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchB


title: The exit of naïve pluripotency contains a metabolism-induced checkpoint for telomere homeostasis [scRNA-seq]

first: Veronique

last: Azuara

summary: During peri-implantation development, the pluripotent tissue of the early embryo undergoes profound cellular and biochemical reprogramming. These transformations are essential for subsequent development, yet how they are coordinated with the preservation of genome integrity remains poorly understood. Here, we uncover a telomere length checkpoint that is elicited by metabolic remodeling as mouse embryonic stem cells (ESCs) transition from the naïve to formative pluripotent state. We show that the exit of naïve pluripotency is marked by accelerated mitochondrial respiration and de novo lipogenesis, fueling lipid droplet accumulation required for tissue remodeling. Unexpectedly, these acute metabolic shifts trigger transient telomere shortening and activate ZSCAN4, a pluripotency-associated regulator of telomeres, followed by telomere re-elongation as cells adopt a more glycolytic metabolic profile. Our findings reveal a feedback mechanism in which metabolism-induced telomere stress engages ZSCAN4 as a protective response, thereby linking metabolic state to telomere homeostasis during early developmental progression.

overall_design: Three clonal mESC cultures with distinct LD profiles (L, H1 and H2) and their parental wild type E14 cell line were subjected to droplet-based scRNAseq on a 10X Genomics platform. All ESCs were cultured in routine FBS/LIF medium.

first: Roshni

last: de Souza

first: Nick

last: Bovee

first: Hendrik

last: Marks

first: Véronique


title: Digital transformation of herbal medicine: Conversion to biological entity data using digestive herbal medicine-induced transcriptome sequencing_second_SW1783_batchA