title: Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [Hi-C]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Loss of regeneration is a key feature of aging organs, often linked to stem cell exhaustion. Skeletal muscle stem cells (MuSCs) undergo age-related numerical and functional decline, contributing to reduced regenerative potential. Using low-input multi-omics, we systematically profiled the epigenome, transcriptome, and 3D genome of MuSCs from individual mice across 3 age groups (young, old, and geriatric) and both sexes. MuSCs from aged mice, particularly males, exhibited early alterations (evident in old), including enhanced proinflammatory signaling with loss of cell identity. Late alterations (evident in geriatric) included heightened inflammation, widespread enhancer activation, and 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NFκB activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. These progressive molecular shifts may explain the aggravated proliferative deficit observed in MuSCs during aging.

overall_design: Hi-C of sorted MuSCs was performed with a modified low cell number protocol using the Arima-HiC kit (Arima Genomics). ~800,000 MuSCs from 3-4 male mice was used per replicate ((young (n=2), old (n=2), and geriatric (n=4) replicates).

first: Changyou

last: Shi

first: Payel

last: Sen


title: Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [CUT&RUN]

status: Public on Nov 13 2025

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Loss of regeneration is a key feature of aging organs, often linked to stem cell exhaustion. Skeletal muscle stem cells (MuSCs) undergo age-related numerical and functional decline, contributing to reduced regenerative potential. Using low-input multi-omics, we systematically profiled the epigenome, transcriptome, and 3D genome of MuSCs from individual mice across 3 age groups (young, old, and geriatric) and both sexes. At baseline, young male MuSCs showed reduced expression of cell cycle-related mRNAs. In aged mice, particularly males, MuSCs exhibited early alterations (emerging during the transition from young to old age), including enhanced proinflammatory signaling, and loss of cell identity. Late alterations (emerging during the transition from old to geriatric age) included heightened inflammation, widespread enhancer activation, and extensive 3D genome rewiring. Proinflammatory pathways were enriched for interferon signaling and correlated with endogenous retroviral expression and NFκB activity. Late-stage epigenome and 3D genome rewiring reflected downstream degenerative changes in muscle organization, response to cytokines, and loss of myogenic identity. Thus, progressive molecular shifts may explain the aggravated proliferative deficit and functional impairment observed in MuSCs during aging.

overall_design: CUT&RUN was performed to profile enhancer histone modifications H3K4me1 and H3K27ac from sorted MuSCs (young (n=5-6), old (n=7-9), and geriatric (n=4-5)) following guidelines in the CUTANA CUT&RUN Protocol (EpiCypher).


title: Multiomics profiling of molecular and cellular dynamics of spinal cord injury in a rat [miRNA-seq]

city: Vestec

first: Ruslan

last: Klassen

address: Průmyslová 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

type: Non-coding RNA profiling by high throughput sequencing

summary: Spinal cord injury (SCI) is a debilitating condition with no effective treatment. The injury triggers a complex cascade of molecular and cellular events that drive both damage and repair processes. To explore these mechanisms, we performed a comprehensive multiomics analysis in a rat compression model of SCI, focusing on the acute phase. Transcriptomic profiling revealed extensive gene dysregulation, highlighting early inflammation, neuronal death, and synaptic dysfunction, followed by the initiation of reparative processes. Cell type composition analysis showed a rapid infiltration of peripheral immune cells, activation of microglia, and loss of neurons, astrocytes, and oligodendrocytes. miRNA profiling uncovered a highly dysregulated miRNA landscape, with the miR-17~92 cluster emerging as a key regulator of neurogenesis, synaptic activity, and cell survival. Integrative miRNA-mRNA-protein analysis identified potential therapeutic targets, including miR-20a, whose inhibition in vitro supported neurogenesis and reduced apoptosis under oxidative stress. Our findings provide new insights into the molecular mechanisms of SCI and highlight miRNAs as potential targets for therapeutic intervention.

overall_design: Adult male Wistar rats (n=64) were used as an experimental model. The rats were obtained from the facility's breeding center (Physiological Institute of the Academy of Sciences of the Czech Republic, Prague, Czech Republic). Animals undergoing surgery weighed 300 ± 30 g and were 10 weeks old. Animals were maintained on a 12-h light/dark cycle with ad libitum access to food and water. Rats were randomly divided into experimental groups: SCI 3 hpi (n=4), 12 hpi (n=4), 24 hpi (n=4), 3 dpi (n=4), 7 dpi (n=4), time- corresponding shame-operated groups (n=4 for each group) and an intact control group (n=4), also 8 animals were used for behavioral tests and 12 animals were used for immunohistochemical analysis.

middle: A

first: Sarka

last: Chytilova

first: Ivan

last: Arzhanov

first: Daniel

last: Zucha

first: Eva

last: Rohlova

first: Peter

last: Androvic

first: Pavel

last: Abaffy

first: Lucia

last: Urdzikova-Machova

first: Mikael

last: Kubista

first: Nataliya

last: Romanyuk

first: Lukas

last: Valihrach


title: Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [HiChIP]

city: Philadelphia

first: YEQIAO

last: ZHOU

state: PA

address: 3600 Civic Center Blvd 14 114

department: Pathology

institute: University of Pennsylvania

summary: Multiple enhancers, often located across vast genomic distances, regulate key genes in cancer. However, how organization of chromatin topology at individual allele enables cancer type-restricted multi-enhancer gene regulation remains unclear. Using acute protein degradation and time-course population-average chromatin conformation capture in lymphoma, we found that the B-cell lineage-determining transcription factor EBF1 preferentially positions multiple enhancers at loci containing sparsely distributed genes essential for B-cell identity and oncogenesis. Our time-resolved sub-diffraction optical tracing of chromatin architecture of over 100,000 alleles further revealed diverse topological conformations that facilitate multi-enhancer interactions in individual lymphoma cells. Mechanistically, we found that positioning of enhancers at the topological center of the allele is required for their interactions with the target promoter, with EBF1 serving as a barrier to the loop extruding cohesin on the enhancers. These findings, which we demonstrate their generalizability to the T-cell lineage-determining transcription factor TCF1 in T-cell leukemia, suggest that lineage-determining transcription factors establish local radial positioning of enhancers and promoters to enable multi-enhancer regulation of key genes in cancer.

overall_design: HiChIP was performed in Granta519 cells to assess the EBF1 and SMC1 mediated chromatin folding

first: Robert

middle: B

last: Faryabi

first: Yeqiao

last: Zhou


title: Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [RNA-seq]

first: Supriyo

last: De

type: Expression profiling by high throughput sequencing

overall_design: RNA from sorted MuSCs (young (n=7), old (n=8), and geriatric (n=8)) was converted to Illumina libraries using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s instructions.


title: TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [scRNAseq]

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

summary: Pluripotency is the ability to give rise to all cell types of the body and is first observed in a mass of disorganised cells of the embryo. Upon implantation, pluripotent cells form a columnar epithelium and undergo lumenogenesis. At gastrulation, a portion of the pluripotent epiblast will undergo epithelial to mesenchymal transition (EMT), forming the primitive streak (PS). It still remains unclear what molecular mechanism supports the epithelial identity of the pluripotent epiblast before gastrulation. Here we developed an optimised, chemically defined 3D model of human pluripotent epiblast formation in which conventional pluripotent stem cells (PSCs) self-organise into a columnar epithelium with a lumen in 48 hours. From 72 hours we observed spontaneous symmetry breaking and specification of PS-like cells, as confirmed by single-cell RNA sequencing. We found that Insulin and FGF signalling are both required for the proliferation and survival of the pluripotent epiblast model. Conversely, TGF-beta signalling maintains epithelial identity. Epithelial identity appears uncoupled from the expression of canonical pluripotency markers OCT4, NANOG and PRDM14, but under the control of ZNF398. Once the pluripotent epithelium is established, TGF-beta inhibition is inconsequential, and stimulation with Activin A leads to highly efficient PS induction. We conclude that TGF-beta dynamically orchestrates epithelial identity of human pluripotent cells.

overall_design: scRNA-seq profiling of 3D-hE-gastruloids generated from H9 hESC line, collected at 0, 2 and 6 days of gastrluoid generation. 394 samples.

first: Irene

last: Zorzan

first: Elena

last: Carbognin

first: Valentina

last: Proserpio

first: Davide

last: Benvegnù

first: Susana

last: De Juambelz Urias

first: Caterina

last: Dalrio

first: Giorgia

last: Panebianco

first: Rebecca

last: Scarfò

first: Eleonora

last: Pensabene

first: Mattia

last: Arboit

last: Paolucci

last: Drusin

first: Monika

last: Sledziowska

first: Paola

last: Braghetta

last: Ditadi

first: Gianluca

last: Amadei

first: Salvatore

last: Oliviero

first: Graziano

last: Martello


title: Analysis of chromatin structure of the BCL11A locus in HUDEP-2 cells by Capture-Pore-C (CPC)

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

summary: CRISPR editing of an intronic enhancer within the BCL11A gene reactivates fetal hemoglobin (HbF) in adult erythroid cells, serving as a gene-based therapy for hemoglobinopathies. However, the mechanisms underlying the remarkable efficacy of CRISPR-mediated enhancer ablation remain poorly understood. We describe an evolutionarily conserved, enhancer-dependent chromatin architecture, the enhancer-CTCF rosette, essential for chromatin insulation and the developmental expression of BCL11A in hematopoiesis. CRISPR-mediated disruption of lineage-specific BCL11A enhancers impairs enhancer RNA transcription and NIPBL-cohesin loading, leading to destabilized chromatin configuration, impaired chromatin insulation, and epigenetic silencing of BCL11A. Antisense oligonucleotide-mediated depletion of enhancer RNA silences BCL11A by disrupting chromatin insulation in adult erythroid cells.

overall_design: Capture-Pore-C data were generated from wild-type HUDEP-2 cells, sg1617-edited cells, and enhancer knockout single-cell clones enriched using biotin-labeled probes targeting CTCF binding sites or erythroid enhancers E+55, E+58, and E+62.

first: Kaili

last: Wang

first: Juan


title: Analysis of nascent transcription by PRO-cap in HUDEP-2 cells

summary: CRISPR editing of an intronic enhancer within the BCL11A gene reactivates fetal hemoglobin (HbF) in adult erythroid cells, offering a potential gene-based therapy for hemoglobinopathies. However, the mechanisms underlying the remarkable efficacy of CRISPR-mediated enhancer ablation remain poorly understood. Enhancer RNAs, transcribed from enhancers, play a role in gene regulation. We apply PRO-cap to map the location of active polymerases and transcription start sites.

overall_design: PRO-cap was performed on wild-type HUDEP-2 cells with two biological replicates.


title: TGF-beta dynamically controls epithelial identity in a 3D model of human epiblast [scRNAseq_HES3-MIXL1-GFP_hESC]

first: Andrea

last: Lauria

overall_design: scRNA-seq profiling of 3D-hE-gastruloids generated from MIXL1-GFP HES3 reporter hESC line, collected at 0, 2 and 5 days of gastrluoid generation. 654 samples.

first: Irene

last: Zorzan

first: Elena

last: Carbognin

last: Proserpio

last: Benvegnù


title: Analysis of CTCF-mediated chromatin interactions at the BCL11A locus in HUDEP-2 cells by Micro-Capture-C (MCC)

summary: Three-dimensional chromatin structures, including promoter-enhancer interactions and CTCF looping, are essential for gene regulation. In this study, we apply Micro-Capture-C (MCC) to analyze chromatin structures at the BCL11A locus.

overall_design: Micro-Capture-C was performed at the BCL11A locus using probes targeting seven CTCF binding sites (CBS) as baits, with experiments conducted in two biological replicates.

first: YoonJung

last: Kim


title: Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [RNA-seq]

first: YEQIAO

last: ZHOU

overall_design: RNA was performed to assess gene expression in Granta519 with or without EBF1

first: Robert

last: Faryabi

first: Yeqiao

last: Zhou


title: Identification of the bacterial actors of the anaerobic plant biomass delignification

city: MARSEILLE

first: Nicolas

last: VITA

address: 31 ch Joseph Aiguier

country: France

institute: CNRS

summary: The anaerobic plant biomass delignification was questioned till recently despite being a key process for plant cell wall degradation in anaerobic biotopes where plant debris accumulate, the carbon mineralization being the limiting step of the Carbon cycle. Besides no actors were identified till now and no data were available on this processus performed by anaerobic cellulolytic bacteria or even on its existence  Using RNAseq, we here report the idenfication of secreted (including cellulosomal) enzymes, especially SGNH hydrolase family members known to be esterases but never described to act on lignin.  We also propose based on our genetic, biochemical and bioinformatic approaches, a new role for the SGNHs in the remodeling of lignin to favor the access to polysaccharides by plant polysaccharides degrading proteins, function that could be useful for the design of biotechnological applications.

overall_design: RNA-seq profiling of R. cellulolyticum grown on more or less lignified substrates at the mid and end of the exponential growth phases

last: Vita

first: Séverine

last: Gagnot

first: Felipe

last: Meija

first: Marion

last: Holmière


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

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 Thermoplasma acidophilum strain 122-1B2 grown at either pH1, pH2, or pH3, 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 - Sente

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


title: Enhancer rewiring orchestrates inflammation and loss of cell identity during muscle stem cell aging [ATAC-seq]

first: Supriyo

last: De

overall_design: Sorted MuSCs (young (n=8), old (n=8), and geriatric (n=7)) were pelleted by centrifugation, lysed, and transposed. The transposed DNA fragments were PCR-amplified, purified, and sequenced on the Illumina platform.

first: Changyou

last: Shi

first: Payel

last: Sen


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


title: Allelic topological centering by transcription factors drives oncogenic multi-enhancer transcriptional regulation [ATAC-seq]

first: YEQIAO

last: ZHOU

overall_design: ATAC-seq was performed to assess chromatin accessibility in Granta519 Cas9 cells with or without EBF1

first: Robert

last: Faryabi

first: Yeqiao

last: Zhou


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: Analysis of nascent transcription by PRO-seq in HUDEP-2 cells following CRISPR editing of BCL11A enhancer

first: Jian

last: Xu

summary: CRISPR editing of an intronic enhancer within the BCL11A gene reactivates fetal hemoglobin (HbF) in adult erythroid cells, serving as a gene-based therapy for hemoglobinopathies. However, the mechanisms underlying the remarkable efficacy of CRISPR-mediated enhancer ablation remain poorly understood. Ehancer RNAs transcribes from enhancer play a role in gene regulation. Here, we apply PRO-seq in wild-type and sg1617-edited HUDEP-2 cells to determine the effects of sg1617 editing on enhancer RNA transcription.

overall_design: PRO-seq was performed in wild-type HUDEP-2 cells and sg1617-edited single-cell clones with 1 bp insertion, 13 bp deletion, or 15 bp deletion.

first: Kaili

last: Wang


title: Analysis of chromatin occupancy in erythroid cells by CUT&Tag following CRISPR editing of BCL11A enhancer

summary: The mechanisms underlying the remarkable efficacy of CRISPR-mediated enhancer ablation remain poorly understood. Here, we employ CUT&Tag to investigate histone modifications following BCL11A enhancer editing or CTCF disruption.

overall_design: CUT&Tag analysis of H3K27ac was performed in wild-type HUDEP-2 cells, enhancer knockout cells, sg1617-edited cells, and double CBS knockout single-cell clones, each with two independent biological replicates. CUT&Tag analysis of NIPBL was perfromed in wild-type HUDEP-2 cells, sg1617-edited cells, and ASO treated cells. Additionally, CUT&Tag of H3K27ac was conducted in control AAVS-edited and sg1617-edited CD34+ HSPCs following erythroid differentiation.


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: Analysis of chromatin accessbility in erythroid cells following CRISPR editing or ASO perturbation of BCL11A enhancer

overall_design: ATAC-seq analysis was performed on wild-type and sg1617-edited HUDEP-2 cells, as well as control AAVS-edited CD34+ HSPCs and Cas9-sg1617 RNP-edited CD34+ HSPCs following erythroid differentiation. Additionally, ATAC-seq was conducted on HUDEP-2 cells treated with either control ASO or E+58 eRNA ASO.


title: Analysis of chromatin occupancy in erythroid cells by CUT&RUN following CRISPR editing of BCL11A enhancer

summary: The mechanisms underlying the remarkable efficacy of CRISPR-mediated BCL11A enhancer ablation remain poorly understood. Here, we employ CUT&RUN to investigate active and repressive histone modifications, as well as cohesin and CTCF binding, to uncover epigenetic changes under various editing conditions.

overall_design: The CUT&RUN assay was performed following enhancer knockout or sg1617 editing to assess chromatin alterations. The inactive chromatin mark H3K27me3, as well as the occupancy of cohesin, and CTCF, were examined in wild-type cells, single-cell clones with different INDELs, and bulk-edited CD34+ HSPCs.


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

first: Jianfei

last: Qi

state: MD

address: 655W baltimore street

department: Biochemistry and Molecular Biology

institute: University of Maryland

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: 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: 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: 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: 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.


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

city: Taipei

first: Lavakau

last: Thalimaraw

address: 128 Sec. 2, Academia Rd, Nankang

country: Taiwan

institute: Institute of Plants and Microbial biology, Academia Sinica

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: 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.

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: Analysis of nascent transcription by EU-seq in HUDEP-2 cells following CTCF degredation

summary: CTCF plays a crucial role in looping and insulation, yet its role in BCL11A regulation remains unclear. Here, we utilize EU-seq to measure nascent transcription in HUDEP-2 cells with CTCF-AID.

overall_design: EU-seq of CTCF-AID HUDEP-2 cells with 5-ph-IAA treatment for 0h, 2h, 4h and 7h.


title: Senataxin Promotes RNA Polymerase II Elongation [RChIPseq]

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 R-loop accumulation by RChIPseq  under DMSO vs dTAGV1 treatment (4h)

first: Jesper

middle: Q

last: Svejstrup


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

first: Miguel

last: Garcia-Campos

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

first: Schraga

last: Schwartz

first: Joe

last: Georgeson

first: Ronit

last: Nir

first: Vinithra

last: Iyer

first: Anatoly

last: Kustanovich


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

overall_design:
DAP-seq of Marchantia polymorpha HSFA1 in Tak-1 genomic DNA at Day14 of germmalings.
We investigated the binding sites and locations of MpHSFA1 in regulating chromatin dynamics and gene expression under heat stress (HS) using DNA Affinity Purification Sequencing (DAP-seq). The HSFA1_DAP sample consists of in vitro translated MpHSFA1 proteins incubated with Tak-1 genomic DNA. The sequencing results represent the MpHSFA1-bound DNA fragments. For peak calling, we used the Golden Gate expression vector pICH47732 (which was used to express the MpHSFA1 CDS) as a negative control to remove non-specific binding sites. The Empty_DAP sample represents this control.


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

platform_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.


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

first: Anne

last: Fiebig

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.

first: Yi-Tzu

last: Kuo

first: Andreas

last: Houben


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

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

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


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

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


title: Senataxin Promotes RNA Polymerase II Elongation [PROseq]

first: Zhong

last: Han

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


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

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


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: 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: 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

middle: W

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

middle: R

last: Schöler

first: Christian

last: Thomas

first: Ulrich

last: Schüller

first: Jan

middle: M

last: Bruder

first: Kornelius

last: Kerl


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


title: Senataxin Promotes RNA Polymerase II Elongation [DRBrelease_TTseq]

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


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

sample_organism:
Homo sapiens
Mus musculus

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

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

last: Sandmann-Varghese


title: GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling

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

first: Jacquelyne

last: Sun

first: Kim Hei-Man

last: CHOW


title: Molecular and epistatic interactions between pioneer transcription factors shape nucleosome dynamics and cell differentiation [ChIP-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
ChIPseq against GATA6, SOX17, OCT4, SOX2 and ESRRB were carried out at various differentiation time points

ES cells carrying a dox-inducible GATA6 transgene were nucleofected with control or oct4 siRNA and plated in doxycycline containing media. ChIPseq against SOX17 and GATA6 was carried out 48h after nucleofection.

first: Remi-Xavier

last: Coux


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)

first: Carolin

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.

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

last: Bedhzov

first: Sarah

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

first: Jacquelyne

last: Sun

first: Kim Hei-Man

last: CHOW


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

city: Los Angeles

first: Colette

middle: L

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 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: 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

middle: J

last: Behrendt

first: Su May Lei

last: Soe

first: Chongyuan

last: Luo

first: Steven

middle: E

last: Jacobsen


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

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

last: Varghese

first: Hans

last: Schöler

first: Christian

last: Thomas

first: Ulrich

last: Schüller

first: Jan

last: Bruder


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

first: Raffaella

last: Santoro

first: Kaivalya

last: Walavalkar


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

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


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

city: Nanjing

first: Bowen

last: Wang

address: 12 Xue-fu Road, Pukou District

country: China

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

first: Pablo

last: Navarro

overall_design: differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline, MNase-seq was carried out at various differentiation time points

first: Rémi-Xavier

last: Coux


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

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.


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

first: Fanghao

last: Guo

first: Qing

first: Qianhui

last: Hu

first: Di

last: Sun

first: Yongjian

last: Ma

first: Yanquan

last: Li

first: Mengxi

first: Haixia

last: Ding

first: Ying

first: Baicai

last: Yang

first: Songmao

first: Ningxia

first: Wen


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

city: Houston

first: Jian

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

middle: G

last: Bovee

first: Hendrik

last: Marks

first: Véronique


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

first: Colette

last: Picard

type: Methylation profiling by high throughput sequencing

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

first: SuMay

last: Soe

first: Chongyuan

first: Steven


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

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.


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

first: Jacquelyne

last: Sun

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: 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

last: Walter

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

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

last: Varghese

first: Hans

last: Schöler

first: Christian

last: Thomas

first: Ulrich

last: Schüller

first: Jan

last: Bruder

first: Kornelius

last: Kerl


title: Transcription factor ZNF263 primes human embryonic stem cells for pluripotency dissolution and early differentiation [CUT&Tag]

city: shanghai

first: Liu

last: Xin

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology, CAS

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: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology. Cleavage Under Targets & Tagmentation (CUT&Tag) of H1 KO hESCs (1-10) for ZIC2 transcription factor was performed to explore the ZIC2 chromatin binding changes upon ZNF263 loss.

first: Zhen

last: Shao


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

overall_design: To investigate the role of ZNF263 in the regulation of hESC pluripotency dissolution, we treated H1 KO (1-10) and WT hESCs with MEK inhibitor, and then performed gene expression profiling using RNA-seq.


title: Immune-Epithelial Interactions and Tissue Remodeling in the Inflammatory Respiratory Nasal Tract [NanoString GeoMx spatial transcriptomics]

first: Guanrui

last: Liao

state: Massachusetts

address: 3 Blackfan Circle

institute: BIDMC

summary: Chronic rhinosinusitis (CRS) is a common inflammatory disease of the nasal cavity and sinuses that affects millions of individuals worldwide. The complex pathophysiology of CRS remains poorly understood, with emerging evidence implicating diverse immune and epithelial cell types in the disease process. We employed NanoString GeoMx spatial transcriptomics in both intact tissues to investigate the cellular and molecular heterogeneity of CRS with and without nasal polyps.

overall_design:
Samples from patients with CRS with and without nasal polyps and healthy controls were collected and analyzed using NanoString GeoMx spatial transcriptomics.

*** FASTQ raw data files are unavailable (cannot be located). ***

first: Jayakar

middle: V

last: Nayak


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

overall_design: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology. Chromatin immunoprecipitation DNA sequencing (ChIP-seq) of H1 KO hESCs (1-10) for histone modifications (H3K4me3, H3K27ac and H3K27me3) were performed to elucidate the chromatin state changes upon ZNF263 loss. Genomic occupancy profiling of ZNF263 was conducted in wildtype H1 hESCs with an endogeneous antibody or in H1 KO hESCs that expressed a FLAG-tagged version of ZNF263 with a FLAG antibody.


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

first: Pablo

last: Navarro

overall_design:
differentiation of ES cells carrying a dox-inducible GATA6 transgene was induced using doxycycline
ATACseq was carried out at various differentiation time points

first: Rémi-Xavier

last: Coux


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

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

first: Jacquelyne

last: Sun

first: Kim

middle: H

last: CHOW


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.

first: Lucia

last: Ichino

first: Tyler

last: Buckley

first: Brandon

last: Boone

first: Jaewon

last: Yun

first: Kevin

last: Abuhanna

first: Yi

last: Zhang

first: Noah

last: Behrendt

first: Su May Lei

last: Soe

first: Chongyuan

last: Luo

first: Steven

last: Jacobsen


title: Single-Cell Analysis of Heterogeneity in Reverted Human iPSC-Derived Hepatic Stellate Cells

status: Public on Nov 12 2025

city: Cleveland

first: Xianfang

last: Wu

state: Ohio

address: 9500 Euclid Avenue/NE20, Office NE2-308, Office NE2-308

department: Infection Biology

institute: Cleveland Clinic

summary: We employed a single-cell RNA sequencing (scRNA-seq) approach using the 10x Genomics platform to investigate the heterogeneity of reverted hepatic stellate cells (HSCs) derived from human induced pluripotent stem cells (hiPSCs). HSCs are key mediators of liver fibrosis; although their activation is well known to drive fibrogenesis, their fate following removal of the fibrogenic insult remains poorly understood. To address this, we utilized a hiPSC-derived liver culture system comprising hepatocytes, HSCs, and macrophages. HSCs were activated by hepatitis C virus (HCV) infection and subsequently treated with antivirals to achieve viral clearance. Reverted HSCs were then characterized through gene expression profiling, vitamin A quantification, functional assays, and scRNA-seq. Our data reveal that activated HSCs exhibit plasticity and can revert to a quiescent-like state upon removal of the activating stimulus, although they retain heightened sensitivity to re-stimulation. These findings enhance our understanding of HSC dynamics and highlight potential therapeutic strategies targeting HSC reversion to treat liver fibrosis.

overall_design: HSCs were activated through hepatitis C virus (HCV) infection and subsequently treated with antiviral agents to achieve viral clearance. To enable single-cell RNA sequencing (scRNA-seq), reverted HSCs were isolated by depleting co-cultured hepatocytes.

first: Xinjia

last: Wang

first: Eun Hee

last: Ha

first: Yifei

last: Zheng


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [RNA-Seq]

city: Seoul

first: Mi-Kyung

last: Oh

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences

country: South Korea

institute: Seoul National University

summary: Current treatments for inflammatory bowel disease (IBD) primarily rely on systemic immunosuppression, which often exhibits limited efficacy and off-target toxicity. Here we present a bioengineered extracellular vesicle (EV) platform designed for inflammatory bowel-targeted delivery of dual-action therapeutics, enabling precise modulation of T cell responses to enhance IBD treatment efficacy. EVs derived from Wharton’s jelly mesenchymal stem cells ( WJ-MSCs) were engineered to display membrane-bound PD-L1 and encapsulate miRNA 27a-3p (miR-27a-3p). The platform leverages WJ-MSCs’ intrinsic immunomodulatory properties and CXCR4-mediated recruitment to inflamed tissues. PD-L1 not only promotes immunosuppression of effector T cells, but also may enhance EV retention within inflamed sites. Meanwhile, miR-27a-3p shifts the Th17/Treg balance from a pro-inflammatory Th17 phenotype toward an anti-inflammatory Treg phenotype by targeting prohibitin 1. Bulk RNA sequencing of human CD4⁺ T cells treated with the EVs revealed downregulated of Th1/Th17-associated transcripts. In a humanized mouse model of colitis, EV treatment significantly reduced disease severity, diminished intestinal T cell infiltration, and restored mucosal integrity. Single-cell RNA sequencing demonstrated expansion of Treg cells and contraction of effector memory subsets, indicating durable immune modulation. This engineered EV platform represents a novel therapeutic paradigm that combines inflamed tissue targeting and dual immunomodulatory mechanisms to restore immune tolerance in IBD, addressing key limitations of conventional immunosuppressive approaches.

overall_design: RNA sequencing was performed on CD4⁺ T cells from spleens of IBD humanized mouse models (human graft), CD4⁺ T cells from human PBMCs, WJ-MSCs, and WJ-MSC–derived exosomes. The study includes single-cell RNA-seq, bulk mRNA-seq, and small RNA-seq to assess transcriptomic and miRNA profiles in the context of IBD and engineered exosome therapy.

first: Hyun Sung

last: Park

first: Kyung-Rok

last: Yu


title: Nascent RNA profiling reveals genome-wide productive reiterative initiation regulating gene transcription in bacteria

city: Tianjin

first: Zhe

last: Sun

address: 32 West 7th Ave

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Productive reiterative initiation at promoters is an alternative transcription mechanism characterized by RNA slippage relative to the template DNA and RNA polymerase, resulting in the incorporation of extra nucleotides into transcripts. A comprehensive understanding of the mechanisms underlying productive reiterative initiation, and its functional implications has been hindered due to the complexity of heterogeneous slippage transcripts. Here, we develop and employ 5’ Terminal Native Elongating Transcript Sequencing (5’TNET-seq) to identify and quantify productive reiterative initiation events in Escherichia coli. Using this method, we reveal that more than half of promoters exhibit productive reiterative initiation. The conserved promoter –10 region, an appropriate spacer between the –10 region and the TSS, and the transcription initiation region associated with weak RNA-DNA hybrid stability, particularly “AAA” and “TTT” trinucleotide tracts, contribute to high productive reiterative initiation. In addition, up to four consecutive nucleotides can be added in a single cycle of productive reiterative initiation. A smaller transcription bubble is observed during productive reiterative initiation, which may stabilize the transcription initiation complex to stimulate gene transcription. Our results suggest that productive reiterative initiation emerges as an inherent transcription process regulating biological processes independent of protein regulators.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: To identify the genome-wide productive reiterative initiation,5prime terminal native elongating transcript sequencing (5primeTNET-seq) was designed and developed. 5primeTNET-seq was performed using the E. coli strain β'-WT with His-tag fusion to RpoC (β’) collected at log phase and stationary phase. Nascent RNA in the native elongating ternary complexes pulled down were extracted and size fractioned. The short nascent RNA was purified, treated with or without 5’-monophosphate-dependent terminator exonuclease, and applied to construct library for high-throughput sequencing. RNA-seq was performed using the same strains and conditions to monitor the changes of gene transcription.

first: Sun

last: Zhe

first: Mikhail

last: Kashlev


title: CDK4/6 Inhibition reprograms the Breast Cancer immunopeptidome via Rb-Dependent chromatin and transcriptomic remodeling

city: Montréal

first: Robin

last: Minati

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

summary: The Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) are standard-of-care therapies for metastatic hormone receptor-positive (HR+) breast cancer, yet their immunomodulatory effects remain underexplored. Here, we demonstrate that CDK4/6 inhibition with Abemaciclib reprograms the tumor antigen landscape by increasing MHC-I presentation and reshaping the immunopeptidome in HR+ and triple-negative breast cancer (TNBC) cells. Through multiomics integration, we reveal that this remodeling is driven by retinoblastoma protein (Rb)-dependent transcriptional and chromatin reprogramming, reflected by increased H3K27ac deposition and enhanced chromatin accessibility revealed by ATAC-seq. CDK4/6 inhibition dephosphorylates Rb, enhancing its interaction with BET family proteins and inducing chromatin remodeling that upregulates antigen-source transcripts. We identify immunogenic Abemaciclib-induced MHC-I peptides, including antigens derived from non-coding genomic regions, which can enhance tumor immunogenicity. These findings reveal a previously unrecognized role of CDK4/6is in shaping tumor antigenicity and suggest that combining CDK4/6is with immunotherapy could broaden antigenic targets in breast cancer.

overall_design: Abemaciclib (Cat#A115153) was procured from Toronto Research Chemicals Inc. The powder was dissolved in DMSO to prepare a 5 mM stock solution, filtered through a 0.22 µm filter for sterility, aliquoted, and stored at -20°C for no more than 6 months. For Abemaciclib treatment, the 5 mM stock was diluted in complete culture media to the indicated final concentrations. Cells were treated with the indicated final concentration of Abemaciclib or DMSO for 96 h before collection. Total RNA was isolated using TRIzol reagent (Thermo Scientific, cat#15596018) followed by RNeasy purification (Qiagen, Cat. #74104). RNA was quantified using Qubit (Thermo Scientific), and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific). Sequencing was performed on the Illumina Novaseq 2000.

first: Maxime

last: Cahuzac

first: Julie

last: Perrault

first: Véronique

last: Lullier

first: Anca

last: Apavaloaei

first: Eric

last: Bonneil

first: Mathieu

last: Courcelles

first: Joel

last: Lanoix

first: Eralda

last: Kina

first: Claude

last: Perreault

first: Pierre

last: Thibault


title: NSUN7 is an RNA:m5C catalytically inactive protein that regulates sperm flagellum assembly [scRNA-seq]

first: Jing

last: Li

address: Haike Road 230

department: School of Life Science and Technology

institute: ShanghaiTech University

summary: Defects in Nsun7, a member of the main RNA:m5C modifying enzymes, known as the NOL1/NOP2/Sun domain (NSUN) family, cause male infertility. The NSUN family includes NSUN1-7, all possessing conserved motifs IV and VI essential for RNA:m5C formation. However, due to the controversy regarding the catalytic activity and RNA substrates of NSUN7, the pathogenic mechanism underlyingof NSUN7-related male infertility remains unclear. Here, we showed that NSUN7 is predominantly enriched in adult mouse testes, particularly in elongated spermatids. Through m5C mass spectrometry detection and bisulfite sequencing, we found that knockout of Nsun7 has no impact on testicular RNA:m5C modification. Mechanistically, NSUN7 loses its ability to bind S-adenosylmethionine (SAM) due to sequence variations in motif IV compared towith the conserved residues observed in NSUN1-6. Notably, the key SAM-binding Asp in motif IV is replaced by Leu in NSUN7, thereby abolishing SAM binding. Nsun7 deficiency impairs sperm progressive motility, accompanied by defects in axonemes and mispositioning of longitudinal columns. Single-cell RNA sequencing showed that knockout of Nsun7 results in a significantly decrease in the levels of a cohort of mRNAs related to cilium organization in elongated spermatids. Collectively, our study demonstrateds that NSUN7 is the only RNA:m5C catalytically inactive member in the NSUN family, and that it regulates sperm flagellum assembly by modulating the expression of cilium organization-associated genes.

overall_design: single cell RNA sequencing of  WT and Nsun7 KO adult mouse testes

first: Wen-Yu

last: Zhu

first: Zhen

last: Wang


title: Simultaneous Targeting of KRAS and CDK4 Synergistically Induces Durable Growth Arrest in Pancreatic Cancer Cells [51T-2D_RNA_Seq]

city: Göttingen

first: Maj-Britt

last: Paulsohn

address: Justus-von-Liebig-Weg 11

department: Department of Molecular Oncology

institute: University Medical Center Göttingen

summary: We report that the KRAS-G12C inhibitor Sotorasib synergizes with the CDK4/6 inhibitor Palbociclib to eliminate pancreatic ductal adenocarcinoma (PDAC) cells (51T-2D cells) harboring KRAS-G12C mutations. This synergy was especially pronounced following drug washout, indicating a durable cellular response. Mechanistically, the combinations induced sustained cell cycle arrest.

overall_design: RNA-Sequencing of 51T-2D cells treated for 48 h with DMSO, Palbociclib (5 µM), Sotorasib (2.5 µM) or the combination (day3), or 48 h treatment + 4 days of recovery in normal cultivation medium (Day7).

first: Matthias

last: Dobbelstein


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

first: Liu

last: Xin

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.

last: Shao


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [scRNA-Seq]

first: Mi-Kyung

last: Oh

first: Hyun Sung

last: Park

first: Kyung-Rok

last: Yu


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

overall_design: We established H1 KO hESCs in which ZNF263 has been deleted using cas9 technology, then cell population heterogeneity of WT and KO hESCs was analyzed using scRNA-seq.


title: NSUN7 is an RNA:m5C catalytically inactive protein that regulates sperm flagellum assembly

overall_design: ultrafast bisufite-seq profiling of m5C modification levels in mRNA, large RNA, and small RNA from  WT and Nsun7 KO adult mouse testes


title: Bioengineered Extracellular Vesicles Co-delivering PD-L1 and miR-27a-3p Synergistically Reprogram T cells To Treat Inflammatory Bowel Disease [miRNA-Seq]


title: Supplementation with short-chain fatty acids and a prebiotic improves clinical outcome in Parkinson’s disease: A randomized double-blind prospective study

city: Ramat Gan

first: Nissan

last: Yissachar

address: Bar-Ilan University

institute: Bar-Ilan University

summary: Background: Parkinson’s disease is associated with a dysbiotic, proinflammatory gut microbiome, disruptions to intestinal barrier functions, and immunological imbalance. Microbiota-produced short-chain fatty acids, such as propionic and butyric acid promote gut barrier integrity and immune regulation, but their impact on Parkinson’s disease pathology remains mostly unknown .Methods: In a randomized double-blind prospective study, 72 people with Parkinson’s disease received propionic and butyric acid and/or the prebiotic fiber 2′-fucosyllactose supplementation over 6 months in combination with existing Parkinson’s disease-specific therapy. Patients underwent complete neurological assessment and provided blood and stool samples before as well as 3 and 6 months after supplementation. Results: We observed improvement in motor and nonmotor symptoms, in addition to modulation of peripheral immunity and improved mitochondrial respiration in immunocytes. Postintervention microbiota remodeled inflammatory and barrier-related gene sets in gut organ cultures and improved in vitro barrier functions. Treatment response was associated with microbiome composition, distinct patterns of colonic transcription and permeability ex vivo. Multiobjective analysis revealed immune parameters associated with an optimal response to supplementation. Conclusion: Short-chain fatty acids ameliorate clinical symptoms in Parkinson’s disease patients and modulate intestinal and peripheral immunity.

overall_design: CaCo-2 cells were cultured to full confluency with penicillin/streptomycin for 4 days. Fecal samples were resuspended in cell culture media without antibiotics to a concentration of 15 mg/ml. Suspensions were passed through a sterile cell strainer and then added to CaCo-2 cells. Following incubation for 30 min, cells were washed 3 times with PBS to remove nonadherent bacteria. DNA was extracted using the PureLink™ Microbiome DNA Purification Kit (Invitrogen).

first: Tobias

last: Hegelmaier

first: Alexander

last: Duscha

first: Christiane

last: Desel

first: Sabrina

last: Fuchs

first: Michal

last: Shapira

first: Sivan

last: Amidror

first: Qihao

last: Shan

first: Gabriele

middle: I

last: Stangl

first: Frank

last: Hirche

first: Stefan

last: Kempa

first: András

last: Maifeld

first: Lisa-Marie

last: Würtele

first: Jana

last: Peplinski

first: Diana

last: Jauk

first: Gitali

last: Naim

first: Nuphar

last: Shidlovsky

first: Adva

last: Cohen

first: Yifat

last: Bennet

first: Lisa

last: Paschold

first: Claudia

last: Dumitru

first: Ute

last: Obermüller-Jevic

first: Svein-Olaf

last: Hustvedt

first: Nina

last: Timmesfeld

first: Ralf

last: Gold

first: Antonia

last: Zapf

first: Mascha

last: Binder

first: Ibrahim

last: Sandalcioglu

first: Sanaz

last: Mostaghim

first: Horst

last: Przuntek

first: Eran

last: Segal

first: Aiden

last: Haghikia


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

first: Liu

last: Xin

overall_design: To investigate the role of ZNF263 in the regulation of hESC pluripotency, we established H1 and H9 KO hESCs in which ZNF263 has been deleted using cas9 technology. We then performed gene expression profiling using RNA-seq data of two cell lines. Comparative analysis was conducted between wildtype hESCs and its KO derivatives (1-5, 1-10, 9-1, 9-D).

first: Zhen

last: Shao


first: Robin

last: Minati

summary: The Cyclin-dependent kinase 4/6 inhibitors (CDK4/6is) are standard-of-care therapies for metastatic hormone receptor-positive (HR+) breast cancer, yet their immunomodulatory effects remain underexplored. Here, we demonstrate that CDK4/6 inhibition with Abemaciclib reprograms the tumor antigen landscape by increasing MHC-I presentation and reshaping the immunopeptidome in HR+ and triple-negative breast cancer (TNBC) cells. Through multiomics integration, we reveal that this remodeling is driven by retinoblastoma protein (Rb)-dependent transcriptional and chromatin reprogramming, reflected by increased H3K27ac deposition and enhanced chromatin accessibility revealed by ATAC-seq. CDK4/6 inhibition dephosphorylates Rb, enhancing its interaction with BET family proteins and inducing chromatin remodeling that upregulates antigen-source transcripts. We identify novel Abemaciclib-induced MHC-I peptides, including antigens derived from non-coding genomic regions, which can enhance tumor immunogenicity. These findings reveal a previously unrecognized role of CDK4/6is in shaping tumor antigenicity and suggest that combining CDK4/6is with immunotherapy could broaden antigenic targets in breast cancer.

overall_design: Abemaciclib (Cat#A115153) was procured from Toronto Research Chemicals Inc. The powder was dissolved in DMSO to prepare a 5 mM stock solution, filtered through a 0.22 µm filter for sterility, aliquoted, and stored at -20°C for no more than 6 months. For Abemaciclib treatment, the 5 mM stock was diluted in complete culture media to the indicated final concentrations. Cells were treated with the indicated final concentration of Abemaciclib or DMSO for 96 h before collection. Total RNA was isolated using TRIzol reagent (Thermo Scientific, cat#15596018) followed by RNeasy purification (Qiagen, Cat. #74104). RNA was quantified using Qubit (Thermo Scientific), and quality was assessed with the 2100 Bioanalyzer (Agilent Technologies). Transcriptome libraries were generated using the KAPA RNA HyperPrep (Roche) using a poly-A selection (Thermo Scientific). Sequencing was performed on the Illumina NextSeq500 or Novaseq. For each triplicate, one sample was sequenced at 160-280M paired-end reads per sample (80-140M clusters) for database generation and the others at 50-70M paired-end reads per sample (35-25M clusters) for RNAseq analysis.

first: Maxime

last: Cahuzac

first: Julie

last: Perrault

first: Veronique

last: Lullier

first: Anca

last: Apavaloaei

first: Eric

last: Bonneil

first: Mathieu

last: Courcelles

first: Joel

last: Lanoix

first: Eralda

last: Kina

first: Claude

last: Perreault

first: Pierre

last: Thibault