title: Methylation of SRSF2P95H by SETD2 suppresses myeloid-derived suppressor cell function by inhibiting inflammatory signaling in myelodysplastic syndrome

first: Jiaying

state: Shanghai

address: 320 Yue Yang Road

department: CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health

institute: Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences

summary: Myelodysplastic syndrome (MDS) is a malignant hematologic cancer accompanied with ineffective hematopoietic and myeloid bias. MDS patients with the SRSF2 mutation have a poor prognosis and require specific and effective therapeutic agents. Here, we find that the low expression of SETD2 in the SRSF2P95H background is associated with anomalously increased myeloid derived suppressor cells (MDSCs) differentiation and inflammatory response. Our results reveal that the low expression of SETD2 in the hematopoietic stem and progenitor cells (HSPCs) of MDS patients with SRSF2P95H/+ is associated with patient outcomes. The deletion of Setd2 in Srsf2P95H/+ mice led to lethal MDS in mice, and mechanistic studies showed that Setd2 catalyzing the K17me1 and K65me2 methylation modification of Srsf2P95H/+ protein, to inhibit the aberrant expression of Ceacam1-4 isoforms and inhibit the increased differentiation potential of HSPCs into MDSCs and the formation of Il-1β-related inhibitory tumor microenvironment. Overall, our findings proposed the possibility of targeting the CEACAM1-4- IL-1β signaling axis in the clinical treatment of SRSF2P95H/+ MDS patients

overall_design: Primary HSPCs isolated from mice and analyzed using scRNA-seq. Primary HSPCs isolated from mice and analyzed using RNA-seq.

first: Zi-Juan

last: Li

first: Rou-jia

last: Wang

first: Mu-Ying

last: Zhao

first: Lan


title: Transcriptomic analyses of hMADS cells depleted for hormone-sensitive lipase

status: Public on Oct 25 2025

city: Toulouse Cedex 4

first: Dominique

last: Langin

address: 1 avenue du Professeur Jean Poulhès

country: France

institute: INSERM

summary: Hormone-sensitive lipase HSL is a major metabolic enzyme of adipocyte as the rate limiting enzyme of lipolysis. Recently, a non enzymatic role of HSL as been described in the regulation of the Carbohydrate Responive Element Binding Protein (ChREBP), controlling adipocyte insulin sensitivity. We aimed at further explore new roles of HSL in the control of adipocyte metabolism through gene expression modulation.

overall_design: HSL-depleted (siHSL) and control (siGFP) hMADS white adipocytes at day14 of differenciation were subjected to low glucose/no insulin treatment, then high glucose and insulin to induce de novo lipogenesis. hMADS beige, and white as control, adipocytes were also studied at day 18 of differentiation

first: Emeline

last: Recazens

first: Jeremy

last: Dufau

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: CHAMP1 is an essential regulator for human myoblast fusion and muscle development

status: Public on Oct 24 2025

city: Athens

first: Pengpeng

last: Bi

state: GA

address: 315 Riverbend Rd

country: USA

institute: University of Georgia

type: Expression profiling by high throughput sequencing

summary: Human skeletal muscle is composed of myofibers, each formed by the fusion of thousands of individual myoblasts. This process requires tightly regulated expression of muscle-specific fusogens, which confer both efficiency and muscle specificity to cell-cell fusion. Currently, the genetic regulation of this process remains poorly understood. Here, we identify CHAMP1, a chromosome alignment factor, as a surprising upstream activator of human myoblast fusion. Genetic deletion of CHAMP1 in human myoblasts led to profound fusion defects in vitro and in vivo following transplantation. Leveraging genomics approach and protein interaction assays, we uncovered a noncanonical role for CHAMP1 as a transcriptional cofactor for MyoD, directly activating the expression of the key muscle fusogen Myomaker. CHAMP1 mutations in human patients cause developmental delay, hypotonia, and muscle weakness, hallmarks of fusion myopathy that are also observed with Myomaker mutations. Importantly, CHAMP1 patient-derived cells exhibit severe fusion defects that can be fully rescued by restoring Myomaker expression. Structure and function analysis identified C2H2-type zinc finger motifs on CHAMP1 protein that are both necessary and sufficient for interaction with MyoD, activation of Myomaker transcription and human myoblast fusion. These findings highlight the muscle-autonomous role of CHAMP1 in muscle development and disease, and point to therapeutic avenues for treating muscle development defect caused by CHAMP1 mutations.

overall_design: RNA-Seq profile of CHAMP1 knock-out (KO) or isogenic rescue (RES) human myoblast at different stages, including myoblast in growth medium (GM), differentiate for 2 days (DM2d), differentiate for 6 days (DM6d).

first: Haifeng

last: Zhang

first: Min

last: Zhou

first: Zheng

first: Zhaoning


title: ATAC-seq of memory CD4+ T cells from the HDM-sensitized lungs

city: Chiba-shi

first: Hiroyuki

last: Yagyu

state: Chiba

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

country: Japan

institute: Chiba University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We complehensively investigated the open chromatin regions of ST2hi memory CD4+ T cells from the HDM-sensitized lungs.

overall_design: ST2loCD44hiCD4+ T cells and ST2hiCD44hiCD4+ T cells were freshly isolated from HDM-sensitized mouse lung tissues and subjected to ATAC-seq.

first: Masahiro

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

first: Atsushi

last: Sasaki

first: Chiaki

last: Iwamura

last: Onodera

first: Ami

last: Aoki

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Takuto

last: Hiramoto

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Junya

last: Kurita

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Yu

last: Hara

first: Toyoyuki

last: Hanazawa

first: Takeshi

last: Kaneko

first: Toshinori

last: Nakayama

first: Kiyoshi

last: Hirahara


title: scRNA-seq of CD4+ T cells from mouse allergic airway inflammation model and human patients with eosinophilic chronic rhinosinusitis (ECRS)

first: Hiroyuki

last: Yagyu

summary: A unique subpopulation of memory Th2 cells expressing the interleukin-33 receptor ST2 contributes to the pathogenesis of allergic diseases; however, the immune-metabolic mechanisms that induce ST2hi memory Th2 cells in inflamed tissues remain uncertain. Using single-cell RNA-sequencing (scRNA-seq), we revealed active lipid storage and catabolism during ST2hi memory Th2 cell induction in inflamed murine lungs and nasal polyps from patients with ECRS.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: CD4+ T cells (batch_1) and CD45+ cells (batch_2) were freshly isolated from control and HDM-sensitized mouse lung tissues and subjected to scRNA-seq. For human samples, CD4+ T cells were freshly isolated from nasal polyps and peripheral blood mononuclear cells (PBMCs) of patients with ECRS and subjected to scRNA-seq.

first: Masahiro

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

last: Sasaki


title: Neural stem cell-derived extracellular vesicles inhibit microglial dysfunction in depression through targeting miR-16-5p/Cxcr4 axis

city: shanghai

first: negri

last: li

address: zhennan road 500

country: China

institute: tongji university

summary: Neural stem cell-derived extracellular vesicles (NSC-EVs) have emerged as promising candidates for neurological disease treatment through delivering bioactive cargoes with therapeutic effects, but their roles in major depressive disorder (MDD) remains poorly understood. Here, we collected NSC-EVs and showed these EVs penetrated the blood-brain-barrier and internalized by brain cells via intravenous injection. NSC-EVs alleviated chronic restraint stress (CRS)-induced depression-like behavioral and pathological alterations presumably through inhibiting inflammatory responses and excessive synaptic pruning of microglia. We next identified miR-16-5p as a key component of NSC-EVs responsible for their therapeutic effects by directly targeting Cxcr4 in microglia. We further demonstrated that either microglial Cxcr4 knockout or Cxcr4 inhibitors treatment significantly mitigated depression-like phenotypes of CRS mice. Thus, our findings suggest NSC-EVs as a novel therapeutic strategy and identified Cxcr4 a potential therapeutic target of MDD.

overall_design: RNA-sequencing was performed with fresh hippocampus and mPFC samples from WT mic, chronic restraint stress (CRS) and CRS mice treated with 150μg neural stem cell extracellular vesicles (NSC-Evs) three times a week.

first: Jialin C

last: Zheng

first: Xiaohuan

last: Xia

first: Xiangyu

last: Li

first: Meng

last: Shi

first: Yi

last: Wang

first: Congcong

first: Tiantian

last: Zhao

first: Shengyang

last: Fu

first: Kailing

last: Jia

first: Xinrui

last: Qi

first: Jie

last: Zhu

first: Yanyan

last: Zhang


title: Single nuclei transcriptomics from lumbar spinal cord of EAE mice treated with MIF nuclease inhibitor PAANIB1

city: Baltimore

first: Matthew

middle: D

last: Smith

state: MD

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

summary: Central nervous system inflammation is implicated in neurodegeneration across several disorders, including multiple sclerosis (MS). While marked therapeutic progress has been made through the suppression of immune cell trafficking and function, primary neuroprotection in MS remains elusive. This, in part, is due to an incomplete understanding of the molecular signaling pathways involved in immune-mediated neuronal death. Here, we show that parthanatos, a recently described caspase-independent and DNA damage-induced cell death program, contributes to neuron death in the experimental autoimmune encephalomyelitis (EAE) mouse model of autoimmune neuroinflammation. We revealed that DNA damage increases in neurons during EAE, and that neurons are progressively lost over the disease course. Neurons in affected areas display intercellular hallmarks of the parthanatos cascade. Genetic or pharmacologic blockade of the final step in parthanatos, genomic fragmentation by MIF nuclease, reduces neuron loss and disease severity. Transcriptomic characterization of these neurons reveals parthanatos-dependent differences in response to EAE. Together, this work establishes parthanatos as a key mechanism of neuron cell death during neuroinflammation.

overall_design: 16 wild type C57BL6J mice were treated with either MIF-nuclease inhibitor PAANIB1 (n=8) or vehicle control (n=8) daily starting 2 days prior to immunization with emulsion. Mice were immunized with emulsion containing either MOG35-55 peptide (to induce Experimental Autoimmune Encephalomyelitis, EAE, n = 12) or no peptide (CFA only, n = 4). Mice were then euthanized 16 days post-immunization at which point paralysis had developed and lumbar spinal cords were dissected out, dissociated to single nuclei, then fixed and subjected to single-nucleus transcriptomics with 10X Genomics Flex (probe-based Fixed RNA profiling) technology. Final groups include EAE-PAANIB1 (n=6), EAE-Vehicle (n=6), CFA-PAANIB1 (n=2), and CFA-Vehicle (n=2).

first: Jackson

middle: W

last: Mace

first: Sachin

middle: P

last: Gadani

first: Peter

middle: A

last: Calabresi


title: Identification and validation of KIF20A for predicting prognosis and treatment outcomes in patients with breast cancer

city: Guangzhou

first: Shaohua

last: Qu

state: Guangdong

address: No. 613, Huangpu West Avenue, Tianhe District, Guangzhou, Guangdong, P.R. China

institute: Department of Breast Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China

summary: In the study, we analyzed six pairs of differentially expressed genes between breast cancer tissues and their corresponding adjacent normal tissues, identifying KIF20A as significantly upregulated in breast cancer. Further functional analyses confirmed that KIF20A is a central regulator within the breast cancer regulatory network. It is involved not only in cell proliferation and migration but may also play a role in the invasion and metastasis of breast cancer. The aberrant expression of KIF20A suggests that it could be a potential target for the diagnosis and treatment of breast cancer, providing a critical direction for further research.

overall_design: To investigate gene expression changes associated with breast cancer, we conducted transcriptome sequencing on six pairs of breast cancer tissues and their corresponding normal tissues. By comparing the gene expression profiles of cancerous and normal tissues, we identified a series of differentially expressed genes that may play a role in tumor initiation and progression. This study helps to elucidate the molecular mechanisms of breast cancer and provides new insights into potential therapeutic targets.

first: Mei

last: Yang


title: Large scale cell-based transcriptome data treated with Jakyakgamcho-tang in PC12 cell

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

summary: Whole transcriptomic analysis in PC12 cells was conducted, comparing cells treated with a vehicle control to those treated with three different concentrations of JGT-E and JGT-W. All experiments were performed in triplicate.

overall_design: we constructed the pharmacological transcriptome data obtained through combinatorial conditions, such as extraction orders (individual herbs extracted or the herb-mixed JGT extracted), combination ratios (two herbs into 2:1, 1:1, and 1:2), two extracting methods (hot water or 70% ethanol).

first: Seongwon

last: Cha

first: Jin-Mu

last: Yi


title: Large scale cell-based transcriptome data treated with Jakyakgamcho-tang

summary: Whole transcriptomic analysis in C2C12 cells was conducted, comparing cells treated with a vehicle control to those treated with three different concentrations of JGT-E and JGT-W. All experiments were performed in triplicate.

overall_design: we constructed the pharmacological transcriptome data obtained through combinatorial conditions, such as extraction orders (individual herbs extracted or the herb-mixed JGT extracted), combination ratios (two herbs into 2:1, 1:1, and 1:2), two extracting methods (hot water or 70% ethanol), and three cell lines (muscle-related C2C12, neuropathic pain-related PC12, and drug metabolism-related HepG2).


title: Active aldehydes accelerate CD8+ T cell exhaustion through metabolic alteration in tumor microenvironment

city: Kyoto

first: Kenji

last: Chamoto

address: Yoshida Konoe-cho, Sakyo-ku

department: Department of Immunology and Genomic Medicine

institute: Graduate School of Medicine, Kyoto University

summary: We employed a 10x Genomics single-cell RNA sequencing (scRNA-seq) approach to investigate the characteristics of distinct mitochondrial states within PD1+ CD8+ T cells in tumors. This study demonstrates that mitochondrial status correlates with the depth of exhaustion in PD1+ CD8+ T cells and further characterizes distinct functional stages of exhaustion within the tumor microenvironment (TME).

overall_design:
We conducted single-cell RNA sequencing (scRNA-seq) on the isolated PD1- CD8+ T cells and D1, D2, and D3 populations from PD1+ CD8+ T cells in the MC38 tumor on day14.
Since cellranger multi was executed, the main output files can be found consolidated in GSM9214854 (CD8+ T cells in MC38 tumor, GEX).
The ADT data includes information on cell hashing (hashtags), surface protein markers, and corresponding isotype controls.

first: Yasuharu

last: Haku

first: Koji

last: Kitaoka

first: Koki

last: Ichimaru

first: Tomoko

last: Hirano

first: Jun

first: Kazuhiro

last: Sonomura

first: Asuka

last: Maruo

first: Shuhei

last: Hirose

first: Yu

first: Katsuhiro

last: Ito

first: Tomohiro

last: Kozuki

first: Keiko

last: Yurimoto

first: Mai

last: Kiyono

first: Hidetaka

last: Kosako

first: Toshi

last: Menju

first: Hiroshi

last: Date

first: Takashi

last: Kobayashi

first: Koichi

last: Omori

first: Tomonori

last: Yaguchi

first: Tasuku

last: Honjo


title: eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

institute: Nagoya University

summary: Although eukaryotic initiation factor 2D (eIF2D) is implicated in translation initiation, re-initiation, and ribosome recycling, its precise role remains unclear. Here, we show that eIF2D promotes 40S ribosome recycling during intrinsic ribosome destabilization (IRD), a process in which ribosomes stochastically destabilize while translating proteins with consecutive acidic amino acids at their NH2-terminus. Unrecycled 40S ribosomes accumulate in eIF2D-deficient cells, leading to 80S ribosome stalling. Selective translation complex profiling (TCP-seq) reveals that eIF2D preferentially associates with IRD-prone regions. The winged-helix (WH) domain, unique to eIF2D but absent in MCTS1–DENR, enhances its binding to 40S subunits, but likely clashes with ABCE1 during stop codon-associated recycling. Loss of eIF2D reduces the expression of IRD-inducing proteins, including splicing factors. Together, these findings define a previously unappreciated role for eIF2D in 40S recycling and clarify its mechanistic divergence from the MCTS1–DENR complex.

overall_design: Translatome and transcriptome analysis of eIF2D-deficient HEK293T cells

first: Akinobu

last: Matsumoto


title: Mpox virus OPG175 negatively regulates viral replication via controlling Wnt signaling

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

summary: Mpox virus (MPXV) infection has different case fatality rates and symptoms depending on its clade. However, there has not been sufficient molecular biological analysis of the differences between clades. Here, we investigated whether we can distinguish between clades by focusing on the expression of MPXV genes. The replication efficiency of MPXV clade IIb, responsible for the 2022 Mpox outbreak, was lower than that of clades Ia and IIa. We found that OPG175 was highly expressed in MPXV clade IIb-infected cells. Suppression of OPG175 expression significantly upregulated the infectious titer of MPXV, while OPG175 overexpression significantly decreased the infectious titer of MPXV. We found OPG175 overexpression to enhance the expression of Wnt signaling-related genes and activation of Wnt signaling to decrease the replication efficiency of MPXV. Therefore, high OPG175 expression in MPXV clade IIb-infected cells likely inhibits MPXV replication via activation of Wnt signaling.

overall_design: HEK293 cells were transfected with plasmids-expressing OPG175 or human superoxide dismutase (SOD) 1, and then total RNA was collected and RNA-seq was performed.


title: Overlooked contributions of ionic strength to cell envelope dynamics modulating outer membrane vesiculation and metal mineralization

city: East Lansing

first: Morgen

last: Clark

state: Michigan

address: 567 Wilson Rd

department: Microbiology, Genetics, & Immunology

institute: Michigan State University

summary: Electrically active Geobacter bacteria assemble conductive pili and release redox-active outer membrane vesicles to drive metal transformations critical to environmental and energy systems. Mechanistic understanding of these processes largely derives from studies of Geobacter sulfurreducens cultivated in mineral media that mimic natural geochemical conditions. Here, we show that modest drops (90 to 80 mM) in sodium ionic strength of common media did not impact cell permeability, but stimulated vesiculation, growth, and covalent anchoring of the outer membrane to the cell wall via a long Lpp peptide to accommodate cell wall expansions and periplasmic enlargement. However, cations that neutralize peptidoglycan carboxylates and contract the cell wall rescued these phenotypes and promoted the assembly of conductive pili over vesiculation for the extracellular mineralization of uranium. These findings reveal cation-driven cell wall dynamics modulating cell envelope structure and functions ultimately determining the fate of metals and the effectiveness of bioremediation and bioenergy solutions.

overall_design: RNA-seq profiles of mid-exponential phase Geobacter sulfurreducens strain PCA cultures grown in NB or DB medium with 15 mM acetate and 40 mM fumarate

middle: M

first: Kazem

last: Kashefi

first: Gemma

last: Reguera


title: Establishing competence for trophectoderm specification in mouse embryos before the first lineage bifurcation

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

summary: How embryonic blastomeres transition from totipotency to differentiation remains a fundamental question in developmental biology. Here, we uncover the transcription factor CEBPa as an orchestrator of this process. CEBPa expression is first activated by NR5A2 at the 2-cell to 4-cell transition and in a second wave peaks in the trophectoderm of blastocysts. Loss of CEBPa disrupts timely blastocyst formation and impairs trophectoderm development, while its forced expression in embryonic stem cells drives differentiation into trophectoderm-like cells. Mechanistically, CEBPa sequentially activates key trophectoderm enhancers in a dose-dependent manner. At the 4-cell stage, some of these trophectoderm enhancers are already active while others are primed or still closed, placing blastomeres in a state of alert. These findings establish CEBPa as a molecular switch that equips 4-cell blastomeres with the competence for trophectoderm differentiation, defining the earliest steps in cell fate bifurcation and shedding new light on the mechanisms driving embryonic lineage specification.

overall_design: Temporal study of gene expression and chromatin accessibility changes after CEBPa induction in mouse embryonic stem cells, via single cell methodologies.

first: Xiao

last: Wei

first: Irepan

last: Salvador-Martinez

first: Maciej

last: Meglicki

first: Marcos

last: Plana-Carmona

first: Antonios

last: Klonizakis

first: Barbara

last: Pernaute

first: Manuel

last: Irimia

first: Gregoire

last: Stik

first: Mina

last: Popovic

first: Guillem

last: Torcal Garcia

first: Holger

last: Heyn

first: Magdalena

last: Zernicka-Goetz


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [CUT&RUN]

city: Boston

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

institute: Boston Children's Hospital

summary: Embryonic patterning relies on the ability of cells to record and process spatial cues they receive from the environment. In vertebrates, this process is orchestrated by the activation of signal transduction patterns by secreted ligands, which provide cells with positional information. How embryonic progenitors encode these spatial values within their regulatory states has remained a central question in developmental biology. Here, we report that spatial gradients of chromatin activation impart cells with positional values during axial specification. By utilizing spatially-resolved genomic analysis, we identified a set of positional cis-regulatory elements (pCREs) that can predict the location of cells in the developing avian embryo. pCREs are located in the loci of spatially-restricted genes and display graded activation patterns along the embryonic axes. pCRE gradients are established in the early gastrula, and their patterns of accessibility are controlled by the signaling systems involved in axial specification. Our results support the existence of a Cartesian system of chromatin activation that ensures the spatial coordination of cell differentiation in vertebrate embryos.

overall_design: Spatially-resolved transcriptomic and epigenomic analysis of early gastrula embryos

first: Ana

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [RNA-seq]


title: RNA-seq analysis for rRNA-depleted RNA in Caenorhabditis elegans.

city: Kobe

first: Hiroki

last: Shibuya

state: Hyogo

address: 2-2-3 Minatojima-minamimachi

department: BDR

institute: RIKEN institute

type: Non-coding RNA profiling by high throughput sequencing

summary: To investigate the expression of coding and non-coding RNAs, we performed RNA-seq analysis on total RNA from wild-type C. elegans after rRNA depletion.

overall_design: We used two biological duplicates. RNA-seq libraries were prepared by Novogene and sequenced using Illumina Novaseq 6000 (PE150)

first: Michiaki

last: Hamada

first: Masahiro

last: Onoguchi


title: PRC1-mediated H2A.Zub promotes gene expression by preventing H3.1K27me1 incorporation in Arabidopsis

city: Coventry

first: Javier

last: Antunez Sanchez

address: Gibbet Hill Campus

department: Life Sciences

country: United Kingdom

institute: University of Warwick

summary: The PcG complexes guarantee the correct temporal and spatial expression of genes. As such, they are crucial in orchestrating plant developmental phase transitions. While PRC2-mediated H3K27me3 is primarily associated with gene repression, PRC1 has a more versatile role that is not fully understood. Moreover, although PRC1 can monoubiquitinate canonical H2A or its variant H2A.Z, the circumstances under which this occurs remain unknown. Here, we show that in Arabidopsis H2A.Z is the variant that undergoes monoubiquitination during the transition from seed-to-seedling. H2A.Zub incorporation recruits PRC2 to repress seed-specific genes; nevertheless, it also activates gene expression by preventing the incorporation of H3K27me1. Interestingly, the removal of two methyl groups from H3K27me3-marked genes is a prerequisite for H2A.Zub incorporation, placing REF6 activity at the onset of gene reprogramming. Our data also indicate that H2A.Zub plays a role in promoting histone exchange to maintain gene expression patterns. These findings extend our understanding of PRC1-mediated gene regulation.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modification H3K27me3 on Arabidopsis seeds 48 hours after imbibition (48 HAI) as well as ChIP-seq for histon variant H2A.Z and histone modifications H3K27me3 and H3K27me1 in Arabidopsis seedlings 10 days after germination (10 DAG).

first: Fernando

last: Baile

last: Antunez-Sanchez

first: Jose

last: Gutierrez-Marcos

first: Myriam

last: Calonje


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes [scRNA-seq]

city: Taipei city

first: Gilbert

middle: Aaron

last: Lee

address: 250 Wu-Hsing Street,

country: Taiwan

institute: Taipei Medical University

summary: Meningeal lymphatic system governs immune cell trafficking in the brain via brain-to-cervical lymph node (CLN) pathway. However, the role of meningeal lymphatics in brain–CLN axis after stroke remains unclear. Here, we showed that meningeal lymphatic ablation (MLA) reduced brain infarct and neuronal loss levels and inhibited inflammatory pathways in the hippocampus after MCAO–reperfusion. Single-cell transcriptome analysis demonstrated that MLA reduced monocyte/macrophage and polymorphonuclear cell counts and T and natural killer cell effector function. MLA reprogrammed the transcriptome profile related to chemotaxis and leukocyte migration in CLN LECs and downregulated expression of the CCN1 in floor LECs. Mechanistically, MLA inhibited inflammatory macrophage infiltration by repressing CCN1 and CD147 (thromboinflammatory marker) expression in blood vessels, thus inhibiting detrimental inflammatory responses. Blockade of VEGF-C-mediated signaling in meningeal lymphatic system improved memory function after ischemic stroke. Collectively, MLA reprograms the LEC transcriptome and inhibits CCN1-mediated proinflammatory responses during poststroke brain–CLN signaling.

overall_design: We used scRNA-seq analysis to investigate the effects of saline and meingeal lymphatic ablation treatment on brain infiltrating lymphocytes after stroke


title: Screening for H/ACA snoRNAs in Caenorhabditis elegans by GFP-FLAG-DKC-1 eCLIP.

summary: To identify H/ACA snoRNAs, we generated a C. elegans strain overexpressing GFP-FLAG-DKC-1 and biochemically screened for GFP-FLAG-DKC-1-binding RNAs by enhanced crosslinking and immunoprecipitation (eCLIP) assay.

overall_design: eCLIP studies were performed by Eclipse Bioinnovations Inc (San Diego, www.eclipsebio.com) according to the published single-end CLIP protocol.

first: Takefumi

last: Kondo

first: Osamu

last: Nishimura

first: Mitsutaka

last: Kadota


title: ATAC-seq and CUT&Tag of memory CD4+ T cells from patients with eosinophilic chronic rhinosinusitis (ECRS)

first: Hiroyuki

last: Yagyu

summary: We complehensively investigated the open chromatin regions and enhancer landscape of CD45RO+ memory CD4+ T cells from PBMCs and nasal polyps of ECRS patients.

overall_design: CD45RO+CD4+ T cells were freshly isolated from PBMCs and nasal polyps and subjected to ATAC-seq and CUT&Tag for H3K27Ac.

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

first: Atsushi

last: Sasaki

first: Chiaki

last: Iwamura

last: Onodera

first: Ami

last: Aoki

first: Takahisa

last: Hishiya

first: Kaori

last: Tsuji

first: Takuto

last: Hiramoto

first: Rie

last: Shinmi

first: Yuri

last: Sonobe

first: Junya

last: Kurita

first: Tomohisa

last: Iinuma

first: Syuji

last: Yonekura

first: Yu

last: Hara

first: Toyoyuki

last: Hanazawa

first: Takeshi

last: Kaneko

first: Toshinori

last: Nakayama

first: Kiyoshi

last: Hirahara


title: DDX5 alleviates osteoarthritic temporomandibular joint by maintaining homeostasis of cartilage metabolism

city: 南京

first: liang qingqing

middle: liang qingqing

last: liang qingqing

address: 栖霞区仙林大道163号南京大学仙林校区

institute: 南京市口腔医院

summary: Temporomandibular joint osteoarthritis (TMJOA) is a prevalent musculoskeletal disease without effective therapeutic measure. DDX5 regulated the progression of cancer，immune disease, as well as skin inflammation by activating a series of signal transduction pathways. However, the role of DDX5 in TMJOA has not been reported yet. The distribution of DDX5 in human cartilage was performed by HE, Safranin O and Masson staining. Moreover, the expression of DDX5 was unveiled by immunofluorescent analyses. The role of DDX5 in TMJOA was verified by UAC-induced TMJOA mice and Aggrecan-CreERT; DDX5flox/flox mice. The downstream protein expression profile of DDX5 were examined by RNA-Seq analysis. The DDX5 expression remarkably decreased in the condylar cartilage of patients with TMJOA. DDX5 decreased with cartilage degradation in UAC-Induced TMJOA mice. Cartilage specific DDX5 knockout induced cartilage degeneration. Mechanistically, the inhibition expression of DDX5 accelerates cartilage degeneration by activating NF-κB Signaling. Additionally, DDX5 overexpression alleviated the progression of TMJOA under excessive mechanical stress.

first: Qingqing

last: Liang

first: Ji

last: Jun


title: ChIP-seq for PPARg, RXRa, and H3K27Ac in inflammation-associated unsaturated fatty acid-supplemented Th2 cells

first: Hiroyuki

last: Yagyu

summary: A unique subpopulation of memory Th2 cells expressing the interleukin-33 receptor ST2 contributes to the pathogenesis of allergic diseases; however, the immune-metabolic mechanisms that induce ST2hi memory Th2 cells in inflamed tissues remain uncertain. We revealed that linoleic and oleic acids increased in the inflamed lungs induced ST2 expression through activating PPARg. Furthermore, this activation of PPARg was dependent on ATGL activity.

overall_design: Each fatty acid complexed to BSA was added to the cell culture medium at a final concentration of 20 µM during the differentiation of Th2 cells from splenic naïve CD4+ T cells. Cells were treated with DMSO or ATGL inhibitor atglistatin (15 µM in DMSO; Sigma-Aldrich) were added to the cell culture medium from day 4. ChIP-seq were conducted on day 5.

first: Masahiro

last: Kiuchi

first: Eisuke

last: Itakura

first: Kota

last: Kokubo

first: Atsushi

last: Sasaki

first: Chiaki

last: Iwamura

last: Onodera

first: Ami

last: Aoki


title: Quercetin promotes the proliferation and maturation of NK cells by binding to MYH9 and improves cognitive functions in aged mice

city: Shanghai

first: Hailiang

last: Liu

address: NO 1239, siping road

institute: Tongji university

summary: We implemented transcriptomic analyses of hippocampus of 10M mice; These mice with the treatment of quercetin for 24 days.


title: Time-restricted feeding reduces kidney damage and preserves renal function upon injury in mice.

city: La Jolla

first: Terry

last: Lin

state: CA

address: 10010 N Torrey Pines Rd, RBIO-P

department: RBIO

institute: Salk Institute

summary: Investigating the mechanisms of time-restricted feeding that can prevent weight gain, fibrosis, and inflammation in folic-acid induced nephropathy.

overall_design: Kidneys of vehicle or FAN-treated mice fed a high-fat diet ad libitum or time-restricted were sequenced 15 days after treatment.

first: Carlos

last: Rey-Serra

first: Amandine

last: Chaix

first: Santiago

last: Lamas

first: Satchidananda

last: Panda


title: Acidosis-mediated inhibition of cancer cell dissemination is restored by hypoxia via regulation of NHE1-dependent signaling

city: Washington

first: Jiaxiang

last: Tao

state: DC

address: 3970 Reservoir Road NW

department: Oncology

institute: Georgetown University

summary: Tumors develop an acidic pH due to shifts in metabolism towards glycolysis and lactic acid production, a phenomenon known as the Warburg effect. Multiple studies have shown that acidosis promotes an aggressive tumor phenotype, characterized by higher migratory, invasive, and metastatic potentials1-3. We instead demonstrate that cancer cell exposure to acidic extracellular pH (pHe=6.4) suppresses proliferation, cell dissociation from tumor spheroids, and migration. Acidosis acutely inhibits motility by downregulating the activity of sodium-hydrogen exchanger isoform-1 (NHE1), which in turn suppresses phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt). Inhibition of PI3K/Akt then blocks Yes-associated protein (YAP) translocation to the nucleus, thereby reducing NHE1 expression. Although cells rapidly adjust their intracellular pH in response to pHe changes, prolonged cell exposure to acidosis downregulates NHE1 expression, which is restored in a delayed fashion upon switching to physiological pHe. This lag phase may explain the reduced extravasation of tumor cells preconditioned at acidic pHe prior to their injection in chick embryos and mice. The reduced migratory potential due to acidosis is rescued by hypoxia. Cumulatively, acidosis alone suppresses aggressive tumor phenotypes but has minimal effect in the presence of hypoxia.

overall_design: Cells (500,000) were plated into T75 flasks and allowed to reach 70-80% confluence using cell culture medium with pHe=7.4. At that point, cells were washed with 2.5 mL of cell culture media with pH of 7.4, 6.7 or 6.4, and then incubated with media of prescribed pH for 24 h.

first: Se

middle: J

last: Lee

first: Chen-Ming

last: Fan

first: Konstantinos

last: Konstantopoulos


title: Histone modification and accessibility dynamics during human cardiomyocyte differention

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type-specific gene regulatory networks in eukaryotic cells.  How pluripotent stem cells (PSC) alter their chromatin architecture to direct cell fate specification remains to be elucidated.  Here, using a human PSC cardiomyocyte differentiation model, we analyze the dynamic reorganization of chromatin structure and gene regulatory networks during key transitional stages of cardiomyocyte development.  We show that many human PSC-specific topologically associating domains (TADs) are driven by active transcription of the primate-specific retroviruses HERVH.  These HERVH are silenced at the earliest stages of differentiation , accompanied by loss of TAD borders and subsequent merging of cognate TADs during differentiation, which leads to repression of gene expression within these domains .  In line with these findings, deletion of select HERVHs results in elimination of corresponding TAD boundaries in human PSCs. We further discovered developmental stage-specific chromatin loop interactions that predict target genes of cardiac-related trait/disease non-coding genetic variants.  Overall, our results not only highlight a novel role for endogenous retroviruses in shaping species-specific PSC chromatin architecture during evolution but also provide a genomic blueprint for understanding the impact of non-coding variants in congenital and adult heart disease/traits.

overall_design: hESCs are differentiated into cardiomyocyte. We used a transgenic H9 hESC line expressing a H2B-GFP fusion protein under control of the ventricular cardiomyocyte specific MYL2 promoter. We collected samples at six critical time points during differentiation: human embryonic stem cells (hESC) (Day 0), hESC mesodermal cells (Day 2), hESC-cardiac mesodermal cells (Day 5), hESC-cardiac progenitor cell (Day 7), hESC-primitive cardiomyocytes (Day 15) and hESC-ventricular cardiomyocytes (Day 80). We performed HiC, ATAC-seq, RNA-seq, and ChIP-seq for H3K27ac, H3K27me3, H3K4me1, H3K4me3, H3K9me3 and CTCF for every time point, each with two biological replicates.

first: Neil

last: Chi

first: Yanxiao

last: Zhang


title: Studies of eRF1 in mammalian cells

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

summary: We performed ribosome profiles in the eRF1 depleted cells under the wild-type backgound and GCN2 knockout background in mouse embryonic stem cells

overall_design: After RNase1 digestion of cell lysate, 80S ribosomes were isolated by sucrose density gradient. Then the ribosome protected fragments were isolated, followed by library constructions for high throughput sequencing.

first: Katharine

last: Maschhoff


title: Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

status: Public on Oct 23 2025

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

institute: ENS Lyon

summary: Although significant progress has been made in our understanding of DNA replication and spatial chromosome organization in eukaryotes, how they both interplay remains elusive. In particular, from the local structure of two diverging sister-forks to the higher-level organization of the replication machinery into nuclear domains, the mechanistic details of chromatin duplication in the 3D nuclear space remain debated. In this study, we use a computational model of the Saccharomyces cerevisiae genome to explore how replication influences chromatin folding. By integrating both a realistic description of the genome 3D architecture and 1D replication timing, simulations reveal that the colocalization of sister-forks produces a characteristic “fountain” pattern around early origins of replication. We confirm the presence of similar features in vivo in early S-phase with new Hi-C data in various conditions, showing that it is replication-dependent and cohesin-independent. At a larger scale, we show that the 3D genome leads to forks being highly enriched at one pole of the nucleus in early S-phase, before later redistributing more homogeneously, and may favor the higher-order clustering of forks into Replication Foci, as observed in earlier microscopy experiments. Additionally, replication causes temporary chromatin slowdown and reduced mobility due to fork passage and sister chromatid intertwining. Overall, our model offers new insights into the spatial and dynamic organization of chromatin during replication in eukaryotes.

overall_design: Hi-C experiments were performed on S. cerevisiae cultures released from an alpha-factor arrest for 20 minutes.

first: Vinciane

last: Piveteau

first: Aurèle


title: Type I and Type II fibre-type-specific and whole muscle DNA methylation profiles across both males and females before and after 12 weeks High Intensity Interval Training

city: Clayton

first: Nir

last: Eynon

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

type: Methylation profiling by genome tiling array

summary: Skeletal muscle is an important organ for health and movement, largely driven by specific muscle fibres. However, the assessment of fibre-type-specific DNA methylation in human skeletal muscle has been limited. We generated methylome profiles of Type I muscle fibres (T1), Type II muscle fibres (T2) and whole skeletal muscle (WM) from males and females before and after 12 weeks high intensity interval training. We compared the TI and TII pooled fibre samples (per individual) and whole muscle samples at the baseline timepoint and generated TI, TII and WM profiles of human skeletal muscle from both males and females.

overall_design:
We generated the following DNAm profiles: 12 TI samples from 7 males and 5 females before HIIT; 11 TI samples from 7 males and 4 females after 12 weeks HIIT; 12 TII samples from 7 males and 5 females before HIIT; 11 TII samples from 7 males and 4 females after 12 weeks HIIT; 1 pooled TIIX sample from all individuals before HIIT; 1 pooled TIIX sample from all individuals after HIIT; 1 global TI sample pooled from all individuals before HIIT; and 1 global TII sample pooled from all individuals before HIIT; 15 whole muscle samples from before HIIT, 14 whole muscle samples after 4 weeks HIIT; and 14 whole muscle samples after 12 weeks HIIT. To total 96 samples we replicated a baseline whole muscle sample three times and another sample two times.
TIIX: These samples were collected as MYH7 and MYH2 negative but ponceau positive potential Type IIx human muscle fibres. Type IIx fibres were pooled from all available samples and are therefore mixed individuals and sexes.

first: Andrew

middle: S

last: Palmer


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [Multiome]

first: Marcos

last: Simoes-Costa

first: Ana

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


title: Genome-wide profiling reveals a dual role for histone H2A monoubiquitylation at Polycomb-repressed and enhancer chromatin [RNA-seq]

city: Toronto

first: Daniel

last: Fusca

state: ON

address: 25 Willcocks Street

department: Department of Ecology and Evolutionary Biology

country: Canada

institute: University of Toronto

summary: Histone modifications are an integral component of eukaryotic genome regulation. Polycomb Repressive Complex 1 (PRC1) is responsible for depositing histone H2A lysine 119 mono-ubiquitylation (H2AK119ub) and can work cooperatively with PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) to maintain gene repression. However, H3K27me3-independent functions and roles in gene activation have also been described for PRC1. Thus, the extent to which Polycomb complexes and their corresponding histone modifications function together or independently is unclear. Using C. elegans as a model, we investigated the relationship between H2AK119ub and H3K27me3. Here we show that the majority of H2AK119ub and H3K27me3 enrichment across the genome in embryos is distinct, and that the bulk levels of these modifications are regulated independently. We identify many genes related to nervous system development and functionality that have H2AK119ub-enriched promoters and are misregulated in H2AK119ub-deficient mutants, including a subset of genes that are normally H3K27me3-repressed. Surprisingly, we also find an enrichment of H2AK119ub at enhancers, including enhancers proximal to genes which are both up-regulated and down-regulated following the loss of this histone modification. Together, our results indicate a dual role for H2AK119ub in the regulation of both H3K27me3-repressed and enhancer chromatin states.

overall_design: RNA-seq in wild-type worms, mig-32 mutants, spat-3 mutants, and mig-32;spat-3 double mutants

first: Kailynn

last: MacGillivray

first: Luomeng

last: Tan

first: Reta

last: Aram

first: Arneet

middle: L

last: Saltzman


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes [RNA-seq]

first: Gilbert

last: Lee

overall_design: We used RNA-seq analysis to investigate the effects of saline and meingeal lymphatic ablation treatment on hippocampus


title: Radiofrequency radiation impairs the human cortical organoid development

city: New Haven

first: In-Hyun

last: Park

state: CT

address: 10 AMISTAD ST # 201B

department: Genetics

institute: Yale University

summary: Neurodevelopmental disorders pose a severe health burden in our society, with remarkably increasing prevalence in children. Though radiofrequency radiation (RF) exposure to the prenatal brain is one of the environmental risks strongly associated with neurobehavioral disorders, its direct impact on human brain development remains largely unknown. Here we use human brain organoids representing the cortex, namely cortical organoids (hCOs) from human embryonic stem cells (hESC), to examine the effects of RF from mobile phones on corticogenesis. We found that RF exposure to brain organoids leads to structural impairment and the defective mitotic behaviors of radial glia progenitors, which carry out critical roles in neocortical expansion. We further uncovered that RF-treated organoids acquire the dysregulation in the transcriptional program, including the aberrant expression of autism risk genes and the morphologically and functionally abnormal neurons. Moreover, the RF shield made complete protection of the detrimental impact of RF on corticogenesis. Finally, we identified small molecule inhibitors for BET proteins that ameliorated RF-induced damages in cortical organoids. Our findings demonstrate how RF exposure impairs brain development and suggest new strategies to prevent RF-mediated brain damage.

overall_design: Human cortical organoids were treated by mobile phone-emitted radiation and analyzed by scRNA-seq

first: Bilal

last: Cakir

first: Yoshiaki

last: Tanaka


title: Multimodal Single-Cell Integration Across Time, Individuals, and Batches

city: Somerville

first: Mauricio

last: Cortes

state: MA

address: 101 South Street

institute: Cellarity

summary: In the past decade, the advent of single-cell genomics has enabled the measurement of DNA, RNA, and proteins in single cells. These technologies allow the study of biology at an unprecedented scale and resolution. Among the outcomes have been detailed maps of early human embryonic development, the discovery of new disease-associated cell types, and cell-targeted therapeutic interventions. Moreover, with recent advances in experimental techniques it is now possible to measure multiple genomic modalities in the same cell.  While multimodal single-cell data is increasingly available, data analysis methods are still scarce. Due to the small volume of a single cell, measurements are sparse and noisy. Differences in molecular sampling depths between cells (sequencing depth) and technical effects from handling cells in batches (batch effects) can often overwhelm biological differences. When analyzing multimodal data, one must account for different feature spaces, as well as shared and unique variation between modalities and between batches. Furthermore, current pipelines for single-cell data analysis treat cells as static snapshots, even when there is an underlying dynamical biological process. Accounting for temporal dynamics alongside state changes over time is an open challenge in single-cell data science.  Generally, genetic information flows from DNA to RNA to proteins. DNA must be accessible (ATAC data) to produce RNA (GEX data), and RNA in turn is used as a template to produce protein (ADT data). These processes are regulated by feedback: for example, a protein may bind DNA to prevent the production of more RNA. This genetic regulation is the foundation for dynamic cellular processes that allow organisms to develop and adapt to changing environments. In single-cell data science, dynamic processes have been modeled by so-called pseudotime algorithms that capture the progression of the biological process. Yet, generalizing these algorithms to account for both pseudotime and real time is still an open problem.

overall_design: The dataset for this competition comprises single-cell multiomics data collected from mobilized peripheral CD34+ hematopoietic stem and progenitor cells (HSPCs) isolated from four healthy human donors. More information about the cells can be found on the vendor website.  Measurements were taken at five time points over a ten-day period. During this time, cells were cultured with StemSpan SFEM media supplemented with CC100 and thrombopoietin (TPO) and incubated at 37ºC. Media was changed every 2-3 days. No additional media supplements were added to the cell culture conditions.  From each culture plate at each sampling time point, cells were collected for measurement with two single-cell assays. The first is the 10x Chromium Single Cell Multiome ATAC + Gene Expression technology (Multiome) and the second is the 10x Genomics Single Cell Gene Expression with Feature Barcoding technology technology using the TotalSeq™-B Human Universal Cocktail, V1.0 (CITEseq).

first: Allegra

last: Lord

first: Samuel

last: Miller

first: Sunil

last: Kuppasani

first: Aakash

last: Kabbin

first: Benjamin

last: DeMeo

first: Jonathan

last: Bloom

first: Peter

last: Holderrieth

first: Hiyab

last: Stefanos

first: Qing

last: Liu

first: Kaylie

last: Scheneider

first: Cameron

last: Reilly

first: Aquib

last: Hasnain

first: Ethan

last: French

first: Karen

last: Gaffney

first: Aishwarya

last: Chandler

first: Mrunali

last: Manjrekar

first: Sophie

last: Guo

first: Yash

last: Raj

first: Sakina

last: Saif

first: Laura

last: Issaco

first: Scott

last: Steelman

last: Burkhardt

first: Malte

last: Lücken

first: Christopher

last: Lance


title: Neutrophils after mouse subarachnoid hemorrhage

city: Houston

first: John

middle: P.

last: Hagan

state: Texas

address: 6431 Fannin St.

department: Neurosurgery

institute: UTHealth

summary: Subarachnoid hemorrhage causes an increase in inflammation and may effect neutrophils. Here, we test if there are differences in expression from neutrophils after subarachnoid hemorrhage in mice on days 1 and 3 (compared with a sham control).

overall_design: Comparison of neutrophil gene expression profile after SAH in mice, each sample is a unique mouse

first: Devin

last: McBride


title: RNA-seq of superficial-zone articular cartilage in a DMM-induced osteoarthritis mouse model

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

institute: Osaka University

summary: C57BL/6J male mice underwent destabilization of the medial meniscus (DMM) or sham surgery. Superficial-zone cartilage from the medial femoral condyle was microdissected 8 weeks postoperatively. Total RNA was purified and poly(A)+ libraries were sequenced on Illumina HiSeq 2500 (single-end).

overall_design: Four samples: WT_DMM_SFZ_M04, WT_Sham_SFZ_M04, KO_DMM_SFZ_M05, KO_Sham_SFZ_M05; one library per sample.

first: Shiori

last: Yamamoto

first: Riko

last: Nishimura


title: Candidate genes underlying hypomelanistic morphs in squamate reptiles

city: Geneva

first: Athanasia

last: Tzika

address: Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Reptiles exhibit a broad variety of adaptive colours and colours patterns but little is known of the mechanisms responsible for these traits. We focus here on the Hypomelanistic traits of 1 corn snake color morph and 3 leopard gecko color morphs. We use mapping-by-sequencing and and differential expression analysis to identify the causative mutation and identify the genes involved in the phenotypes of these color morphs.

overall_design: Paired-end RNA-Seq of dorsal skin from E40 corn snake embryos WT and Homozygous Hypomelanistic

first: Pierre

last: Beaudier

first: Asier

last: Ullate-Agote

middle: C


title: Hepatocyte-specific epidermal growth factor receptor (EGFR) deletion attenuates acetaminophen-induced liver injury in mice

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

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

overall_design: Refer to individual Series


title: Spatial gradients of chromatin accessibility endow embryonic cells with positional information [Epi ATAC-seq]

city: Boston

first: Marcos

last: Simoes-Costa

address: 300 Longwood Ave

institute: Boston Children's Hospital

summary: Embryonic patterning relies on the ability of cells to record and process spatial cues they receive from the environment. In vertebrates, this process is orchestrated by the activation of signal transduction patterns by secreted ligands, which provide cells with positional information. How embryonic progenitors encode these spatial values within their regulatory states has remained a central question in developmental biology. Here, we report that spatial gradients of chromatin activation impart cells with positional values during axial specification. By utilizing spatially-resolved genomic analysis, we identified a set of positional cis-regulatory elements (pCREs) that can predict the location of cells in the developing avian embryo. pCREs are located in the loci of spatially-restricted genes and display graded activation patterns along the embryonic axes. pCRE gradients are established in the early gastrula, and their patterns of accessibility are controlled by the signaling systems involved in axial specification. Our results support the existence of a Cartesian system of chromatin activation that ensures the spatial coordination of cell differentiation in vertebrate embryos.

overall_design: Spatially-resolved transcriptomic and epigenomic analysis of early gastrula embryos

first: Ana

last: Azambuja

first: Megan

last: Rothstein

first: Tatiane

last: Kanno


title: Perturbational single-cell RNA-seq time course of CD34+ HSPC megakaryocyte differentiation with CMO multiplexing (Days 0–7, 1 uM compounds)

first: Mauricio

last: Cortes

summary: We profiled transcriptomic responses of a panel of small molecules during in vitro megakaryocyte (Mk) differentiation of CD34+ hematopoietic progenitors from a single donor. Cells were cultured in SFEM with TPO and CC100; an untreated Day 0 sample (unhashed) was collected, and additional samples on Days 1, 2, 5, and 7 were multiplexed with Cell Multiplexing Oligos (CMOs) and pooled 12 samples per library (~100k cells per well contributed), with duplicates for each compound distributed across libraries and plate-level positive/negative controls. Libraries were prepared with 10x Genomics Single Cell 3’ v3.1 and sequenced on Illumina NovaSeq 6000. FASTQs were generated with bcl2fastq and processed with Cell Ranger (STAR/GRCh38). Hashed data were QC-filtered, demultiplexed by Gaussian mixture modeling of CLR-normalized CMO counts, and further filtered to singlets; counts were then normalized to 10,000 per cell and log-transformed. For consistent annotation, the dataset was mapped to a hematopoiesis reference using harmony-corrected PCs and SymphonyPy KNN label transfer, with robustness assessed by distance/similarity metrics and marker expression. This submission provides Day 0 raw counts, Days 1–7 raw counts (pre-demultiplexing), demultiplexed singlet counts with well/treatment assignments, and normalized counts with transferred cell-type labels.

overall_design: Dual-mobilized peripheral blood CD34+ HSPCs were thawed and cultured; on Day 0 cells were plated for Mk differentiation (60,000 cells per well, round-bottom plates). Compounds were applied at a final concentration of 1 uM (DMSO controls included); treatments occurred on Days 0, 2, and 5. Sampling for scRNA-seq occurred at Day 0 (unhashed) and at Days 1, 2, 5, and 7 (hashed). For hashed time points, 12 CMO-tagged samples were pooled per library; each compound was sequenced in biological duplicate with duplicates distributed across libraries, and each library contained positive and negative controls alongside hit and non-hit compounds. Sequencing used 10x Genomics Single Cell 3’ v3.1 and Illumina NovaSeq 6000. Processing included bcl2fastq, Cell Ranger on GRCh38 (STAR), pre-demultiplexing QC (counts 5,000–80,000; mitochondrial fraction <20%), demultiplexing by Gaussian mixtures on CLR-normalized CMO counts (singlets retained), post-demultiplexing QC (<2,500 or >60,000 counts and <1,600 or >9,000 genes removed), per-cell normalization to 10,000 counts with log transform, and reference mapping plus label transfer with harmony and SymphonyPy.

first: Inna

last: Lipchina

first: Daniel

first: Charlotte

last: Nesbitt

first: Samuel

last: Miller

first: Benjamin

last: DeMeo

first: Thomas

last: Pfefer

first: Doris

last: Fu


title: Bulk mRNAseq in control and Plp-CreER_Ddx20 cKO mouse spinal cords

city: Niigata City

first: Norihisa

last: Bizen

address: 757 Ichibancho, Asahimachi-dori, Chuo Ward

department: Graduate School of Medical and Dental Sciences

institute: Niigata University

summary: We sequenced mRNA extracted from the spinal cords of mice at 4 and 4.5 weeks after tamoxifen administration and compared the gene expression levels between the control group and the Ddx20 conditional knockout (Plp-CreER; Ddx20 cKO) group.

overall_design: At 4 and 4.5 weeks after tamoxifen administration, mRNA was extracted from the spinal cords of three control mice and three Ddx20 cKO mice. The extracted mRNA was sequenced using the Illumina NovaSeq 6000 platform to generate mRNA expression profiles.

first: Masataka

last: Ise

first: Hirohide

last: Takebayashi


title: Meningeal lymphatic ablation reduces ischemic stroke-induced inflammation via reprograming transcriptome profiling in cervical lymph nodes

city: Taipei city

first: Gilbert

last: Lee

institute: Taipei Medical University


title: The brain neurovascular epigenome and its association with dementia

city: London

first: Alexander

last: Nott

address: 86 Wood Lane

institute: Imperial College London

summary: Cerebral small vessel disease (SVD) is frequently comorbid with Alzheimer’s disease (AD) and vascular brain endothelial cells (BECs) are enriched for the expression of genes associated with AD genetic risk. However, the gene regulatory landscapes of neurovascular cells and their intersection with genetic risk for disease remains unexplored. Here we have generated gene regulomes for human BECs, mural cells and other brain cell types to show that AD heritability is primarily immune-related and that it shows modest enrichment in BECs. By contrast, genetic risk for SVD is enriched across cells of the neurovascular unit, including astrocytes. Enhancer-to-gene interactomes implicate amyloid processes in both AD and SVD, though the risk genes are mostly distinct for the two disorders. Motifs for putative partners of lineage transcription factors in microglia and BECs were enriched for AD and SVD variants at genes linked to disease pathways. Gene prioritization and enrichment analyses further identified potential repurposable drugs for AD. Our findings highlight novel regulatory mechanisms and therapeutic targets within the neurovascular system.

overall_design:
H3K27ac CUT&Tag on ERG+, NeuN+, NOTCH3+, PU.1+, OLIG2+ and RFX4+ sorted cortical nuclei from aged postmortem tissue.
H3K4me3 CUT&Tag on ERG+, NeuN+, NOTCH3+, PU.1+, OLIG2+ and RFX4+ sorted cortical nuclei from aged postmortem tissue.

first: Kevin

last: Ziegler

first: Aydan

last: Askarova

first: Charbel

last: Gergian

first: Reuben

last: Yaa

first: Janna

last: van Dalen

first: Janis

last: Transfeld

first: Filippo

last: Zoppi

first: Jia

last: Du

last: Clode

first: Fatemeh

last: Rahbar

first: Rebecca

middle: E

last: Graham

first: Muralidharan

last: Sargurupremraj

first: Stéphanie

last: Debette

first: David

last: Gonda

first: Michael

last: Levy

first: Siddharthan

last: Chandran

first: Sven

last: Falk

first: Marisa

last: Karow

first: Paul

last: Matthews

first: Nicole

middle: G

last: Coufal

first: Alexi


title: Uncovering changes in 3D-chromatin structure and dynamic gene expression during spermatogenesis [Hi-C]

city: Yinchuan

first: Jin

last: Haoyan

state: NingXia

address: No. 489, West Helanshan Road

department: colllege of animal science and technology

institute: NingXia University

summary: We conducted a high-throughput analysis of the chromatin structural organisation and gene expression by using porcine spermatogonia (SPG), spermatocytes (SPY) and round spermatids (RS). We found that during spermatogenesis, SPY showed a weaker pattern of chromosomal interactions, attenuated compartmentalisation and a reduction in the number of TADs, which was restored during the subsequent  period of round spermatids. This suggests a reprogramming of chromatin higher-order structures during porcine spermatogonia differentiation. Our results reveal that chromatin structure changes during porcine spermatogenesis, along with changes in gene expression.

overall_design: Sequencing of collected porcine spermatogonia, spermatocytes and round spermatids to study chromatin interactions during spermatogenesis

first: Haoyan

last: Jin

first: Lingkai

last: Zhang


title: Uncovering changes in 3D-chromatin structure and dynamic gene expression during spermatogenesis [RNA-seq]

overall_design: Sequencing of collected porcine spermatogonia, spermatocytes, and round spermatids to study changes in chromatin structure and gene expression during spermatogenesis


title: Epigenetic Profiling Reveals Key Super-Enhancer Networks Driving Oncogenesis in HPV-Positive HNSCC

city: Baltimore

first: Fernando

last: Zamuner

address: 1550 Orleans Street

department: Department of Otolaryngology - Head and Neck Surgery

institute: Johns Hopkins University, School of Medicine

summary: The objective was to investigate the impact of JQ1, a bromodomain inhibitor, on two cell lines of HPV+ HNSCC by comparing it to a control group that did not receive any treatment (DMSO).

overall_design: For every experiment conducted on the UM-SCC-47 or UPCI-SCC-090 cell line treated with JQ1 or DMSO, we sequenced three repeats, and each of these was performed twice (2 different lanes).

middle: T

first: Daria

last: Gaykalova


title: Cutibacterium acnes induces skin region-specific innate immune memory alterations in human keratinocytes

city: Szeged

first: Fanni

last: Balogh

address: Temesvári krt. 62

country: Hungary

institute: Biological Research Centre

summary: External insults can cause immune activation in immune cells, resulting in persistent molecular changes that can lead to innate immune memory (IIM) changes in these cells. This study investigated the potential for cellular reprogramming in response to Cutibacterium acnes in keratinocytes. We exposed normal human epidermal keratinocytes obtained by mammoplasty (NHEK-B) or abdominoplasty (NHEK-A) to C. acnes, followed by stimulation with Pam3CSK4 to assess immune activation and cellular responses. In NHEK-B cells, C. acnes and Pam3CSK4 treatment induced trained immunity-type responses, with higher expression of selected immune target genes, and a diminished response compared with that in nontrained but Pam3CSK4-induced NHEK-A cells. Total transcriptome analysis delineated regional differences, with the activation of immune-related pathways in NHEK-B cells and increased skin development in NHEK-A cells. We detected differences in metabolic regulation, and utilizing pharmacological inhibitors, we demonstrated the necessity of the optimal regulation of histone acetylation and DNA methylation for the aforementioned changes. This study demonstrated that C. acnes triggers IIM-like processes in keratinocytes, characterized by signaling, epigenetic, and metabolic reprogramming that influences cellular responses to subsequent stimuli. The observation that analogous insults might elicit skin region specific responses offers novel insights into the etiology and mechanisms underlying common inflammatory skin diseases.

overall_design: RNA-seq profiling of mammary or abdomen-derived NHEKs after C. acnes training (day 2) and Pam3CSK4 induction (day 8) at day 8.

first: Anett

last: Magyari

first: Lilla

last: Erdei

first: Beáta Szilvia

last: Bolla

first: Balázs

last: Koncz

first: Laura

last: Bagi

first: Máté

last: Manczinger

first: Blanka

last: Toldi

first: Bálint

last: Baráth

first: Katalin

last: Burián

first: Rolland

last: Gyulai

first: Lajos

last: Kemény

first: Kornélia

last: Szabó


title: Fagopyrum acutatum extract attenuates influenza A virus-stimulated inflammation and lung injury via NF-kB signaling pathway in vitro and in vivo

city: Guangzhou

first: liu

last: lifu

address: Panyu xinzao NO.1 Road

institute: Guangzhou Medical University

summary: This research aimed to determine the effects of Fagopyrum acutatum extract (FAE) on IAV-induced inflammation and its underlying mechanisms.

overall_design: A549 cells were infected with H1N1 virus and subjected to FDE intervention or not. After a period of culture, total RNA was extracted for sequencing.


title: Repair of DNA double-strand breaks leaves heritable impairment to genome function

city: Copenhagen N

first: Nils

last: Krietenstein

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: Upon DNA breakage, a genomic locus undergoes alterations in 3-D chromatin architecture to facilitate signaling and repair. While cells possess mechanisms to repair damaged DNA, it is unknown whether the surrounding chromatin is restored to its naïve state. We show that a single DNA double-strand break (DSB) within a topologically-associated domain (TAD) harboring conformation-sensitive genes causes lasting chromatin alterations, which persist after completion of DNA repair and feature structural changes, chromatin compaction and loss of local RNA species. Unexpectedly, these newly-acquired features of post-repair chromatin are transmitted to daughter cells and manifest as heritable impairments of gene expression. These findings uncover a hitherto concealed dimension of DNA breakage, which we term post-repair chromatin fatigue, and which confers heritable impairment of gene function beyond DNA repair.

overall_design: Region Capture Micro-C of the c-MYC locus of untreated HeLa cells and Hela cells after Cas9 cleavages. c-MYC ORF and CTCF sites were analyzed over a time course of 72 hours, whereas upstream-TAD#1, upstream-TAD#2, downstream-TAD#1 and downstream-TAD#2 cut sites were analyzed 48 hours after DNA cleavage.

first: Susanne

last: Bantele

first: Irene

last: Mordini

first: Alva

last: Biran

first: Nicolas

last: Alcaraz

first: Gijs

last: Zonderland

first: Alice

last: Wenger

first: Anja

last: Groth

first: Jiri

last: Lukas


first: Athanasia

last: Tzika

overall_design: Paired-end RNA-Seq of dorsal skin from E40 leopard geckos embryos WT and Homozygous Hypomelanistic 1, 2 and 3

first: Pierre

last: Beaudier

first: Asier

last: Ullate-Agote


title: Differentially expressed genes in Bone-Marrow Derived Macrophages (M0) from DKO (Cdk8 flox/flox Vav-iCre Cdk19null) or VavCre control

first: Chen

last: Chu

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary: In this experiment, we use RNA-seq to examine the differentially expressed genes in macrophages derived from bone marrows of mice with whole body Cdk19 deletion and bone-marrow Cdk8 deletion.

overall_design: Bone marrow derived macrophages were collected on day 7 of differentiation.

first: Aleksandra

last: Kolodziejczyk

first: Piotr

last: Sicinski


title: Characterization of the CCR4-NOT complex subunits CNOT1 and CNOT4 using rapid auxin-induced degradation in cultured cells

city: State College

first: Shardul

last: Kulkarni

address: 463 North Frear Laboratory

institute: Penn State University

summary: CCR4-NOT regulates multiple steps in gene regulation, including transcription, mRNA decay, protein ubiquitylation and translation. Originally discovered in yeast, this complex is highly conserved across eukaryotes, although its composition and functions differ between mammals and yeast.  For example, unlike yeast Not4, human CNOT4 (E3 Ubiquitin Ligase) does not form a stable complex with CCR4-NOT, and its functions are less clear compared to its yeast counterpart.  To investigate the roles of CNOT1 (the central scaffold subunit) and CNOT4, we developed a rapid auxin-induced degron cell culture system that allows for the acute depletion of these proteins. We studied the effects of their absence on complex integrity, cell growth, and mRNA expression and turnover. Our transcriptome-wide analysis revealed that depleting CNOT1 altered the expression of thousands of transcripts, with the majority showing increased abundance and a general decrease in mRNA decay. Although CNOT4 does not associate with the complex through standard biochemical methods, BioID proximity labelling confirmed its association with the complex in cells.  However, depleting CNOT4 did not affect the integrity of CCR4-NOT. In contrast to the effects observed with CNOT1 depletion, reducing CNOT4 levels led to only modest changes in RNA steady-state levels and unexpectedly accelerated global mRNA decay.  Finally, we show that the changes in mRNA stability in CCR4-NOT depleted cells correlated with the codon optimality of the transcripts. Our data suggest that CNOT4 exerts opposite effects on mRNA metabolism compared to CNOT1, and that CNOT4 may have functions distinct from those of complex subunits that promote mRNA degradation.

overall_design:
To study the roles of human CCR4-NOT complex, we generated auxin inducible degron tagged cells at the genomic locus of CNOT1 and CNOT4 genes.
Cells were treated with auxin to deplete CNOT1 or CNOT4, and total RNA was extracted from the cells to analyze gene expression changes.
We performed RNA-seq to investigate the effects of CNOT1 or CNOT4 depletion on steadystate RNA levels and RNA halflives
Differential expression analysis was carried out on RNA-seq data obtained from multiple timepoints/treatments.

first: Aswathy

last: Sebastian

first: Joseph

last: Reese


title: Structural mechanism of the Retron-Eco7 anti-phage defense system

city: Shinjuku-ku

first: Aa

middle: Haeruman

last: Azam

state: Tokyo

address: Toyama 1-23-1

department: Research Center for Therapeutic Drugs and Vaccines Development

institute: The National Institute of Infectious Diseases

summary: Retrons are prokaryotic genetic elements involved in anti-phage defense and consist of a non-coding RNA, a reverse transcriptase (RT), and various effector proteins. Retron-Eco7 (previously known as Retron-Ec78) from Escherichia coli encodes two effector proteins (a PtuA ATPase and a PtuB nuclease) and degrades host tRNATyr upon phage infection, thereby protecting host cells against invading phages. However, its defense mechanism remains elusive. Here, we report the cryo-electron microscopy structures of the Retron-Eco7 complex, comprising the RT, multicopy single-stranded DNA (msDNA), PtuA, and PtuB. The Retron-Eco7 structure reveals that the RT–msDNA complex associates with two PtuA–PtuB complexes, potentially inhibiting their nuclease activity and suppressing bacterial growth arrest prior to phage infection. Furthermore, we found that a phage-encoded D15 nuclease acts as a trigger for the Retron-Eco7 system, cleaving the msDNA bound to the complex and facilitating the dissociation of PtuA–PtuB from RT–msDNA. Our data indicate that msDNA cleavage by D15 is the initial step required for the specific cleavage of host tRNATyr by the PtuA–PtuB nuclease, which leads to abortive infection. Overall, this study provides mechanistic insights into the Retron-Eco7 system and highlights the diversity of prokaryotic anti-phage defense mechanisms.

sample_organism: Escherichia coli str. K-12 substr. DH10B

overall_design: Overnight cultures of E. coli (DH10B) cells containing either the plasmid pBAD-PtuA–PtuB or the full set of retron-Eco7 (pLG008) were grown in 10 mL of LB medium until reaching an OD₆₀₀ of 0.3. The bacteria carrying pBAD-PtuA–PtuB were induced with 0.2% arabinose to promote PtuAB expression, whereas those containing pLG008 were infected with phage SP15 and cultured at 37°C with shaking at 200 rpm for either 1 hour or 20 minutes, respectively. Following incubation, the cultures were centrifuged at 6,000 × g for 5 minutes, and the pellets were washed twice with PBS buffer. Total RNA was extracted using a miRNA isolation kit (Qiagen) following the manufacturer’s instructions. Additionally, E. coli (DH10B) cells containing the Retron-Eco7 plasmid or an empty vector were infected with SP15 (MOI = 10) for 20 minutes, with uninfected cells serving as negative controls. The cells were then centrifuged at 10,000 × g for 10 minutes and washed twice with SM buffer. Total RNA was extracted using the miRNA isolation kit (Qiagen). The extracted RNAs were then submitted for tRNA-fragment sequencing.

first: Ishikawa

last: Junichiro

first: Yoneyama

last: Kanta

first: Azam

last: Aa Haeruman

first: Nagao

last: Asuteka

first: Mitsuda

last: Yoshihisa

first: Nakazaki

last: Ren

first: Kotaro

last: Chihara

first: Hiraizumi

last: Masahiro

first: Yamashita

last: Keitaro

first: Suzuki

last: Tsutomu

first: Kiga

last: Kotaro

first: Nishimasu

last: Hiroshi


title: Distinct maternofetal immune signatures delineate preterm birth onset following urinary tract infection

first: Samantha

last: Ottinger

state: TX

address: 1 Baylor Plaza

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

summary: Preterm birth is the leading cause of infant mortality resulting in over one million neonatal deaths annually. Maternal urinary tract infection (UTI) during pregnancy increases risk for preterm birth; however, biological processes mediating UTI-associated preterm birth are not well-described. We established a murine maternal UTI model in which challenge with uropathogenic E. coli resulted in preterm birth in about half of dams. Dams experiencing preterm birth displayed excessive bladder inflammation and altered uteroplacental T cell polarization compared to non-laboring infected dams, with no differences in bacterial burdens. Additional factors associated with preterm birth included higher proportions of male fetuses and lower maternal serum IL-10. Furthermore, exogenous maternal IL-10 treatment absolved UTI-associated preterm birth but contributed to fetal growth restriction in this model.

overall_design: 129/sv dams and nonpregnant controls were transurethrally infected with 5e7 UTI89 on E13.5. Four hours later, dams were euthanized and bladder, placenta, and uterus were resected. Total RNA was extracted using Rneasy Plus mini kits (Qiagen 74134). mRNA was purified from total RNA using poly-T beads, then cDNA was synthesized and sequenced on an Illumina NovaSeq 6000 sequencer. Differential gene expression was determined using DESeq2.

first: Kathryn

last: Patras


title: Differentially expressed genes in bone marrows from C57/BL6 wild-type, Cdk19null, Cdk8flox/flox VaviCe or DKO (Cdk8 flox/flox Vav-iCre Cdk19null) or iVavCre control

first: Chen

last: Chu

summary: In this experiment, we use RNA-seq to examine the differentially expressed genes in bone marrows from DKO (Cdk8 flox/flox Vav-iCre Cdk19null) or iVavCre control mice

overall_design: Tibiae and femurs of 8-wks old mice were flushed with cold PBS, spun and flash frozen in LN

first: Aleksandra

last: Kolodziejczyk

first: Piotr

last: Sicinski


title: Single-Cell Transcriptomic Analysis of Periodontal Granulation Tissue from Surgical Patients

city: Solna

first: Wentao

last: Zhu

address: 17177 Solna

country: Sweden

institute: Karolinska Institutet

summary: This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.

overall_design: This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Illumina Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.


title: Monitoring rapid degradation of NANOG reveals UTP15 maintains pluripotency by regulating nascent transcripts

city: Guanzhou

first: dongmei

last: he

address: Yunpu Street

institute: University of Chinese Academy of Sciences

summary: Master transcription factors (MTFs) are key regulators in cell fate determination. However, an approach to profile MTF’s direct transcriptional targets together with their associated RNA-binding proteins (RBPs), is still lacking. Here, we applied 5-ethynyluridine RNA metabolic labelling and click chemistry to map the dynamics of the transcriptional targets and the RBPs interacting with the newly transcribed RNAs upon acute NANOG degradation in mouse embryonic stem cells (mESCs). We identified UTP15, a classic rRNA-biogenesis regulator, acts as a key activator of pluripotency-associated gene transcription independently of rRNA biogenesis. Importantly, NANOG-regulated transcription enhances UTP15 binding to transcription start sites (TSSs), associated with increased Pol II binding and more active transcription. Moreover, UTP15 promotes the assembly of Pol II biomolecular condensates, thereby potentially driving pluripotency gene transcription. Collectively, our study uncovers a NANOG-nascent transcript-UTP15 regulatory axis to activate pluripotency gene transcription, providing a distinct approach for studying MTF’s function during cell fate determination.

overall_design: To investigate the cooperative function NANOG/UTP15 in the regulation of pluripotency, we established NANOG-AID and UTP15-AID cell lines in which each target protein was allowed to be acute degradation.We then performed gene transcription profiling analysis using data obtained from nascent RNA-seq at different time points after target protein degradation.Comparative gene transcription profiling analysis of nascent RNA-seq data from NANOG-AID/UTP15-AID cells at different time points after target protein degradation

first: Mingqiang

last: Deng

first: Dongmei

last: He

first: Xiwei

last: Wang

first: Xichen

last: Bao


title: Targeting CD11b+ regulatory B cells via RAS/RAF/PI3K pathway inhibition augments response to immune checkpoint blockade or CD40 agonism in metastatic melanoma

city: Nashville

first: Chi

last: Yan

state: Tennessee

address: 432A Preston Res Building, 2220 Pierce Ave

institute: Vanderbilt University

summary: Abstract Development of effective second-line treatment options for immune checkpoint blockade (ICB) resistant patients with BRAFWTNRASWT or BRAFWTNRASmut melanoma is crucial. While systemic delivery of agonist CD40 (aCD40) plus anti-PD1 (αPD1) showed activity in patients with ICB-resistant melanoma, the objective response rate was modest (15%), in part due to induction of B regulatory cells (Bregs) which suppress CD8+ effector T cells. We previously reported that RAS/RAF/PI3K-inhibition elevated CD40 expression in melanoma cells and sensitized tumors to ICB. Here, we show that treatment of ICB-resistant BRAFWTNRASWT and BRAFWTNRASmut melanoma tumors with the combination of rigosertib (RGS), a RAS/PI3K/AKT-pathway inhibitor, and/or trametinib (T), a MEK1/2 inhibitor, plus aCD40 overcomes ICB resistance. Overexpression of CD40 in melanoma cells effectively reverses ICB-resistance and induces tumor regression upon aCD40+αPD1 treatment. Mechanistically, RGS+T suppressed aCD40-associated CD11b+PD-L1+ B regulatory cells (B11regs), which promoted CD8+ T-cell killing in melanoma. scRNA-Seq analyses confirmed CD40-associated B11regs across cancer types in patients.  Statement of Significance Addition of aCD40 treatment to PD1 fails to overcome ICB resistance due to aCD40-induction of B11regs and low expression of CD40 in melanoma cells. Our data demonstrate that addition of RAS/RAF/PI3K inhibitors to aCD40 resolves these issues and provides alternative therapeutic options for ICB-resistant BRAFWTNRASWT or BRAFWTNRASmut metastatic melanoma.

overall_design: CD40 overexpression (CD40-OE) and CD40-ctrl clones of 1014 NRAS-mut melanoma cells were generated and injected in C57BL/6 mice. Treatment with 200μg/mouse αPD1 (every 3 days, intraperitoneal), 30μg/mouse aCD40 (every 3 days, intraperitoneal), or 300mg/kg rigosertib (RGS, 5 days a week, oral gavage), starts at day 8 post tumor cell inoculation. Tumor samples were harvested 22 days post-treatment and proceeded with bulk RNA-Seq and TCR-Seq (n=3 per treatment group).

first: Yan

last: Chi

first: Richmond

last: Ann


title: Testosterone exposure during fetal masculinization programming window determines the kidney size in adult mice

city: Turku

first: Petra

last: Sipilä

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: To study the role of fetal testosterone exposure in the development of male mouse kidney, we compared fetal kidneys from WT and testosterone deficient Hsd17b3 KO mice at E16.5, after 2 day testosterone propionate or vehicle treatment.

overall_design: RNA-seq was performed from E16.5 kidneys from testosterone and vehicle treated WT and KO male mice.

first: Arttu

last: Junnila

first: Mats

last: Perk

first: Asta

last: Laiho


title: H3K36 Methylation - a Guardian of Epigenome Integrity [BiSulfite-seq]

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

institute: McGill University

type: Methylation profiling by high throughput sequencing

summary: H3K36 methylation is emerging as a key epigenetic modification with strong involvement in genetic disease and cancer. The mechanisms through which H3K36me impacts the epigenome and asserts its functional consequences are far from understood. Here, we use mouse mesenchymal stem cell lines with successive knockouts of the H3K36 methyltransferases: NSD1, NSD2, SETD2, NSD3, and ASH1L, which result in progressive depletion of H3K36me and its complete absence in the quintuple KO cells, to finely dissect the role of H3K36me2 in shaping the epigenome and transcriptome. We show that H3K36me2, which targets active enhancers, is important for maintaining enhancer activity, and its depletion results in downregulation of enhancer-dependent genes. We demonstrate the roles of H3K36me2/3 in preventing the invasion of gene bodies by the silencing H3K27me modifications. Finally, we observe a previously undescribed relationship between H3K36me and H3K9me3: Following the depletion of H3K36me2, H3K9me3 is redistributed away from large heterochromatic domains and towards euchromatin. This results in a drastic decompartmentalization of the genome, weakening the boundaries between active and inactive compartments, and a catastrophic loss of long-range inter-compartment interactions. By studying cells totally devoid of H3K36 methyltransferase activity, we uncover a broad range of crucial functions of H3K36me in maintaining epigenome integrity.

overall_design: Whole genome bisulfite sequencing in C3H10T1/2 mouse mesechymal stem cells to assess methylation levels following successive knockouts of H3K36 methyltransferases NSD1, NSD2, SETD2, NSD3 and ASH1L.

first: Reinnier

last: Padilla

first: Gerald

last: Shipman

first: Cynthia

last: Horth

first: Eric

last: Bareke


title: H3K36 Methylation - a Guardian of Epigenome Integrity [RNA-seq]

summary: H3K36 methylation is a key epigenetic mark with critical roles in development and disease, yet its genome-wide functions remain incompletely understood. Here, we systematically dissect the role of H3K36 methylation using a series of CRISPR-engineered mouse mesenchymal stem cell lines with progressive knockouts of the five H3K36 methyltransferases: NSD1, NSD2, NSD3, SETD2 and ASH1L—culminating in quintuple knockout (QuiKO) cells entirely lacking H3K36me2/3. We demonstrate that H3K36me2 enriched at active cis-regulatory elements predominantly influences enhancer activity and supports the expression of enhancer-dependent genes. Within gene bodies, loss of H3K36me2/3 permits invasion by the repressive H3K27me2/3 modifications, thereby disrupting transcriptional fidelity. Unexpectedly, we uncover a previously undescribed relationship between H3K36me and H3K9me3: upon H3K36me2 depletion, SUV39H1-mediated H3K9me3 redistributes from large constitutive heterochromatic domains into euchromatin, leading to widespread epigenome restructuring and transcriptional changes. This redistribution is accompanied by a collapse of 3D genome organization, including weakened compartment boundaries and a profound loss of long-range interactions. Finally, we validate key findings in two human HNSCC cell lines overexpressing the H3K36M oncohistone, highlighting the conserved role of H3K36 methylation in maintaining epigenome integrity across species and cell types, and providing further mechanistic insights into the downstream consequences of this oncogenic mutation. Together, these data reveal that H3K36me is essential not only for local gene regulation but also for safeguarding the higher-order structure and functional balance of the genome.

overall_design: RNA-sequencing in C3H10T1/2 mouse mesechymal stem cells to perform gene expression analysis following knockouts of lysine 36 methyltransferases (NSD1,NSD2,SETD2,NSD3 and ASH1L) and in HNSCC (head and neck squamous cell carcinoma) cell lines following overexpression of H3.3K36M.

first: Michel

last: Gravel


title: H3K36 Methylation - a Guardian of Epigenome Integrity

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

overall_design: Refer to individual Series


title: Complex-specific inhibitor for interrogating ATAC histone acetyltransferase complex

city: Hong Kong

first: Sha

last: Liu

address: Pokfulam Road, Hong Kong

department: Department of Chemistry

institute: The University of Hong Kong

summary: Histone acetyltransferases (HATs) modify chromatin to regulate gene expression. Instead of acting alone, HATs function in complexes with other proteins, leading to variations in substrate specificity, genomic localization, and cellular function. To understand the complex-dependent roles of HATs, we present a chemical approach to specifically dissociate ATAC (Ada-two-A-containing) HAT complex from chromatin without perturbing other complexes. Rather than targeting the shared HAT enzyme, we developed chemical probes for an ATAC-specific subunit, YEATS2. The most effective probe, LS-170, specifically reduced the chromatin occupancy of the ATAC complex, decreased the ATAC-dependent histone acetylation level, and downregulated the expression of ATAC-governed genes, leading to significantly suppressed tumor growth in a lung cancer mouse model. This study not only sheds light on the regulatory roles of the ATAC HAT complex in gene transcription, but also provides evidence that the chemical inhibition of the ATAC complex can be a promising therapeutic strategy.

overall_design: H1299 cells were treated with LS-170 or DMSO. RNA-seq was performed with 4 replicates DMSO and 3 replicates LS-170. ChIP-seq were performed in duplicates with matched input control for each condition and antibody.

first: Xiang David

last: Li


title: Involvement of Naïve CD4+ T cells in the Pathogenesis of Osimertinib-induced Pneumonitis

city: Fukuoka

first: Kazuya

last: Tsubouchi

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Respiratory Medicine

institute: Kyushu University

summary: Background: Osimertinib, a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI), has exhibited significant efficacy in the treatment of EGFR-mutated non-small cell lung cancer. Drug-induced interstitial lung disease is a potentially fatal complication of osimertinib therapy. Although there is often an elevated number of lymphocytes in the bronchoalveolar lavage fluid (BALF) in patients with drug-induced pneumonitis, the precise involvement of lymphocytes in osimertinib-induced pneumonitis remains unclear. Therefore, we investigated the pathogenesis of osimertinib-induced pneumonitis using BALF obtained from patients with osimertinib-induced pneumonitis and a mouse model of osimertinib-induced pneumonitis. Methods: Mass cytometry was used to analyze BALF cells obtained from patients with osimertinib-induced pneumonitis. A mouse model of osimertinib-induced pneumonitis was established by the administration of naphthalene and osimertinib. Histopathological evaluation, body weight measurements, BALF analysis, and RNA sequencing were performed to investigate immune cell involvement and the mechanisms underlying osimertinib-induced pneumonitis. Results: Analysis of BALF cells obtained from patients with osimertinib-induced pneumonitis revealed the expansion of CCR7+ CD45RA+ naïve T cells. In the mouse model, osimertinib administration following naphthalene-induced club cell injury exacerbated lung inflammation, leading to increased inflammatory cell infiltration and body weight loss. BALF analysis revealed elevated proportions of T cells, including CD4+ and double-negative T cells, in mice administered osimertinib after naphthalene treatment. Bulk RNA sequencing identified upregulation of chemokine-related biological processes, with increased the expression of C-C motif chemokine ligand 21 (Ccl21) and C-C motif chemokine ligand 8 (Ccl8) in lung tissue, and immunostaining confirmed elevated expression of Ccl21 and Ccl8 in the distal bronchiolar epithelium. Conclusion: This study provides insights into the immune mechanisms underlying osimertinib-induced pneumonitis, which are crucial for overcoming this fatal complication in EGFR-positive non-small cell lung cancer.

overall_design: Lung mRNA profiles of untreated mice, osimertinib-treated mice after naphthalene treatment and naphthalene-treated mice.

first: Hiroyuki

last: Ando

first: Toyoshi

last: Yanagihara

first: Kentaro

last: Hata

first: Daisuke

last: Eto

first: Kunihiro

last: Suzuki

first: Naoki

last: Hamada

first: Isamu

last: Okamoto


title: H3K36 Methylation - a Guardian of Epigenome Integrity [ChIP-Seq]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for histone modifications H3K27ac, H3K4me3, H3K27me1/2/3 and H3K9me3 in C3H10T1/2 mouse mesenchymal stem cells. ChIP-Seq for SUV39H1-FLAG and HP1 was also performed in C3H10T1/2 mouse mesechymal stem cells. In human head and neck squamous cell carcinoma (HNSCC) cell lines, ChIP-Seq was performed for H3K9me3, H3K27ac and H3K27me3.


title: H3K36 Methylation - a Guardian of Epigenome Integrity [ATAC-seq]

overall_design: ATAC sequencing in C3H10T1/2 mouse mesechymal stem cells with successive knockouts of the lysine 36 methyltransferases NSD1, NSD2, SETD2, NSD3 and ASH1L, as well as in HNSCC (head and neck squamous cell carcinoma) cell lines overexpressing H3.3K36M.


title: Gestational Feed Restriction Induces Differential Expression of Novel Long Non-Coding RNAs in Offspring Skeletal Muscle

status: Public on Oct 22 2025

city: Viçosa

first: Maria Malane

last: Muniz

state: MG

address: Av Peter Henry Rolfs S

department: Animal Science

country: Brazil

institute: University Federal of Vicosa

summary: Fetal programming via maternal nutrition during gestation plays a key role in shaping skeletal muscle development, directly affecting meat quality and production efficiency. This study examines how maternal feed restriction at different gestational stages alters the expression of novel long non-coding RNAs (lncRNAs) in the skeletal muscle of goat offspring. LncRNAs are emerging as important regulators of biological processes, including myogenesis, yet their role in fetal programming remains largely unexplored. Using RNA sequencing (RNA-Seq), we analyzed lncRNA expression in the Longissimus thoracis muscle of kids born to goats exposed to two feeding regimens: early gestation restriction (50% of maintenance from day 8–84 of gestation, then 100% until parturition; RM, n=6) and late gestation restriction (100% from day 8–84, then 50% until parturition; MR, n=8). RNA-Seq data underwent quality control, alignment, transcript assembly, and differential expression analysis using Cufflinks and FEELnc pipelines. Three differentially expressed (DE; FDR ≤ 0.05) lncRNAs were identified and classified based on genomic context and potential regulatory function. The upregulated lncRNA_10996.1 in the RM group was linked to ENSCHIG00000020055 and ENSCHIG00000024132. Downregulated lncRNA_1180.1 and lncRNA_7992.1 were associated with ZNF546, PSMC4, SNORA65, ZNF79, LRSAM1, and ENSCHIG00000023017. These results suggest that maternal nutrition-induced shifts in lncRNA expression may influence muscle development through regulatory interactions with protein-coding genes. Our findings identify candidate lncRNAs as potential biomarkers and contribute novel insights into the molecular mechanisms underlying fetal programming in livestock.

overall_design: RNA-Seq profilling of Longissimus thoracis muscle  from newborn male goat kids.60 nulliparous Saanen dairy goats underwent estrous synchronization using prostaglandin administered at a 7-day interval, followed by artificial insemination with semen from a single male.The day of the insemination was considered the day 0 of the pregnancy and the beginning of the experiment. All the animals were kept under the same diet and management conditions for an adaptation period of 7 days. After that, the animals were randomly assigned to one of two feeding regimens: Restriction-Maintenance (RM) group (n = 6): fed 50% of maintenance requirements from days 8–84 of gestation, followed by 100% from day 85 to parturition. Maintenance-Restriction (MR) group (n = 8): fed 100% of maintenance requirements from days 8–84, followed by 50% from day 85 to parturition. Both groups received the same diet composition; only the timing of the restriction varied according to gestational stage.

first: Maria

first: Thais

last: Costa

first: Nicola

last: Serão

first: Mateus

last: Gionbelli

first: Marcio

last: Duarte


title: Guanine- and cytosine-rich genes are actively transcribed at the nuclear Lmnb1 compartment

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Chromatin organization in the mammalian cell nucleus plays a vital role in the regulation of gene expression. The lamina-associated domain at the inner nuclear membrane has been proposed to harbor heterochromatin, while the nuclear interior has been shown to contain most of the euchromatin. Here, we show that a sub-set of actively transcribing genes, marked by RNA Pol II pSer2, are associated with Lmnb1 at the inner nuclear envelop in mESCs and the number of genes proportionally increases upon in vitro differentiation of mESC to olfactory precursor cells. These nuclear periphery-associated actively transcribing genes primarily represent housekeeping genes, and their gene bodies are significantly enriched with guanine and cytosine compared to genes actively transcribed at the nuclear interior. We found the promoters of these gene’s to also be significantly enriched with guanine and to be predominantly regulated by zinc finger protein transcription factors. We provide evidence supporting the emerging notion that the Lmnb1 region is not solely transcriptionally silent.

overall_design: Lmnb1-associated actively transcribing gene in male mESCs and mESC derived OPCs immunoprecipitation by sequential ChIP assay (Lmnb1 and RNA Pol II pSer2) and DNA-sequencing.

middle: I

first: David

last: Spector


title: Identification of DNA methylation biomarkers for evaluating cardiovascular disease risk from epigenome profiles altered by low-dose ionizing radiation

city: Cheonan

first: Jihye

last: Park

address: Cheonan Campus 119 Dan-daero

institute: Dankook university

overall_design: Bisulphite converted DNA from the 10 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip.

first: Hae

last: Lee

first: Yukyeong

last: Han

first: Keunsoo

last: Kang

first: Joo

last: Yi