Tag: H3K27ac

Mechanism by which HDAC3 regulates manganese induced H3K27ac in SH-SY5Y cells and intervention by curcumin

Long-term excessive exposure to manganese can impair neuronal function in the brain, but the underlying pathological mechanism remains unclear. Oxidative stress plays a central role in manganese-induced neurotoxicity. Numerous studies have established a strong link between abnormal histone acetylation levels and the onset of various diseases. Histone deacetylase inhibitors and…

Continue Reading Mechanism by which HDAC3 regulates manganese induced H3K27ac in SH-SY5Y cells and intervention by curcumin

Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…

Continue Reading Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L

Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases | Genome Medicine

Our cohort comprises 34 families in which a presumably autosomal recessive disease defied molecular diagnosis by clinical exome sequencing (short-read sequencing-based) and reanalysis performed on the index individual for each family (Fig. 1). The index patient in each family was subjected to an average of 10 × depth lrWGS except for Family F8602…

Continue Reading Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases | Genome Medicine

RNASEH1-AS1 induced by H3K27ac stabilizes ANXA2 mRNA to promote the progression of colorectal cancer through recruiting BUD13

Colorectal cancer (CRC) is a malignant tumor with high morbidity and mortality. It is well-accepted that dysregulated lncRNAs are closely related to the development of CRC. In this study, the function and mechanism of RNASEH1-AS1 in CRC were investigated. RT-qPCR and western blot detected the expression of targeted genes in…

Continue Reading RNASEH1-AS1 induced by H3K27ac stabilizes ANXA2 mRNA to promote the progression of colorectal cancer through recruiting BUD13

Solved To further examine the transcriptional regulation of

To further examine the transcriptional regulation of the gene–of–interest, you carried out a histone ChIP experiment. Below are results obtained using H3K27Ac antibody in the mutant. What would you expect for the H3K27Ac track for the wild type sample? 0–60 eq 0–20 ‘Ac More reads mapped to the locus, resulting…

Continue Reading Solved To further examine the transcriptional regulation of

Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

Continue Reading Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

A supply of nitrate triggers organ-specific changes of histone modifications at specific gene loci To investigate the organ specificity of dynamic histone modifications in response to N changes, we treated 3-week-old tomato seedlings (Solanum lycopersicum, cultivar M82) with four days of N starvation, followed by N-supply (2.8 mM NO3−; +N) or…

Continue Reading Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato

Profiling of H3K27Ac reveals the influence of asthma on the epigenome of the airway epithelium

Background: Asthma is a chronic airway disease driven by complex genetic-environmental interactions. The role of epigenetic modifications in bronchial epithelial cells (BECs) in asthma is poorly understood. Methods: We piloted genome-wide profiling of the enhancer-associated histone modification H3K27ac in BECs from people with asthma (n=4) and healthy controls (n=3). Results:…

Continue Reading Profiling of H3K27Ac reveals the influence of asthma on the epigenome of the airway epithelium

Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

Continue Reading Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes

Identification of constrained sequence elements across 239 primate genomes

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

Continue Reading Identification of constrained sequence elements across 239 primate genomes

How does H3k27ac change in response to different stimuli?

The provided paper does not mention anything about H3k27ac or its changes in response to different stimuli. The provided paper does not mention anything about H3k27ac or its response to different stimuli. The paper primarily focuses on electrical safety and the effects of electric currents on the human body. Open…

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Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

Continue Reading Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

Continue Reading Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles

Primate-specific ZNF808 is essential for pancreatic development in humans

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

Continue Reading Primate-specific ZNF808 is essential for pancreatic development in humans

The CRTC-1 transcriptional domain is required for COMPASS complex-mediated longevity in C. elegans

CRTC-1-binding proteins To identify CRTC-1 protein interactions, we tagged endogenous CRTC-1 via clustered regularly interspaced short palindromic repeats–associated protein 9 (CRISPR–Cas9) editing to generate a crtc-1::3xFLAG strain and performed immunoprecipitation (IP) followed by liquid chromatography coupled to mass spectrometry (LC–MS). We found 137 potential CRTC-1 interacting proteins (Fig. 1a and…

Continue Reading The CRTC-1 transcriptional domain is required for COMPASS complex-mediated longevity in C. elegans

HDAC3 deacetylates H3K27ac and H3K9ac on the TrkC promoter to exacerbate sevoflurane-induced neurotoxicity

Apai C, Shah R, Tran K, Pandya Shah S (2021) Anesthesia and the developing brain: a review of sevoflurane-induced neurotoxicity in pediatric populations. Clin Ther 43:762–778 Article  CAS  PubMed  Google Scholar  Chai G et al (2022) Sevoflurane inhibits histone acetylation and contributes to cognitive dysfunction by enhancing the expression of…

Continue Reading HDAC3 deacetylates H3K27ac and H3K9ac on the TrkC promoter to exacerbate sevoflurane-induced neurotoxicity

Acetyl-methyllysine is a dual-modification of histone H4

Post-translational modifications (PTMs) of histone proteins, such as methylation and acetylation of lysine residues, are correlated with gene regulation and are proposed to form a ‘histone code’. Lu-Culligan et al. identify the first known dual-modification of lysine residues with both methyl and acetyl groups (Kacme), in Drosophila and human cells….

Continue Reading Acetyl-methyllysine is a dual-modification of histone H4

DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…

Continue Reading DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice

DIAMOND mice develop HCC in the context of obesity and insulin resistance To investigate in depth the genome-wide transcriptional and epigenetic changes that occur during development of MAFLD and obesity-related hepatocellular carcinoma (HCC), we performed RNA-sequencing (RNA-seq) and Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) of liver tumours (HCC) and liver control tissue (FL)…

Continue Reading Diet-induced rewiring of the Wnt gene regulatory network connects aberrant splicing to fatty liver and liver cancer in DIAMOND mice

Index of /compbio1/eGTEx-H3K27ac/Processed_files/haQTL/gAREandhaQTL_hg38

Name Last modified Size Description Parent Directory   –   Brain.emp.pvals.hg38.tsv.gz 2022-12-25 15:40 9.8M   Brain_allPairs/ 2022-12-28 00:07 –   Heart.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 6.8M   Heart_allPairs/ 2022-12-28 00:09 –   Lung.RSC0.8OrMatched.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 5.1M   Lung_allPairs/ 2022-12-28 00:10 –   Muscle.emp.pvals.hg38.tsv.gz 2022-12-25 15:41 7.4M   Muscle_allPairs/ 2022-12-28 00:09 –  …

Continue Reading Index of /compbio1/eGTEx-H3K27ac/Processed_files/haQTL/gAREandhaQTL_hg38

TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

Continue Reading TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells

Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

     Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull    mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…

Continue Reading Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455

Mechanism of HDAC3 Regulation of Manganese-Induced SH-SY5Y Cytotoxicity H3K27ac and Intervention by Curcumin by Ying Liu, Hua Zhao, Yue Yang, Yan Liu, Chun-Yan Ao, Jia-Min Zeng, Jia-Qi Ban, Jun Li :: SSRN

49 Pages Posted: 18 Oct 2023 See all articles by Ying Liu Guizhou Medical University (Guiyang Medical University) Guizhou Medical University (Guiyang Medical University) Guiyang Hospital of Stomatology Guizhou Medical University (Guiyang Medical University) Guizhou Medical University (Guiyang Medical University) Guizhou…

Continue Reading Mechanism of HDAC3 Regulation of Manganese-Induced SH-SY5Y Cytotoxicity H3K27ac and Intervention by Curcumin by Ying Liu, Hua Zhao, Yue Yang, Yan Liu, Chun-Yan Ao, Jia-Min Zeng, Jia-Qi Ban, Jun Li :: SSRN

Delineating the dynamic transcriptional and epigenetic landscape regulating hematopoiesis

Credit: iScience (2023). DOI: 10.1016/j.isci.2023.107893 A research team led by Professor Megumu K. Saito (Department of Clinical Application) examined the dynamic transcriptional and epigenetic landscape during definitive hematopoiesis and revealed the non-redundant roles of ZEB2 and MEIS1 vital to producing hematopoietic stem cells from the hemogenic endothelium. The study is…

Continue Reading Delineating the dynamic transcriptional and epigenetic landscape regulating hematopoiesis

LOC127815786 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124216027-124216526 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

Continue Reading LOC127815786 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:124216027-124216526 [Homo sapiens (human)] – Gene

The histone acetyl transferases CBP and p300 regulate stress response pathways in synovial fibroblasts at transcriptional and functional levels

Hypoxia, the formation of reactive oxygen species (ROS), and subsequent oxidative stress in synovial tissues are key events in the pathogenesis of RA1. We provide here evidence that CBP and p300 are pivotal regulators of the adaptive response of SF that integrate the cell`s transcriptional and functional regulation of stress…

Continue Reading The histone acetyl transferases CBP and p300 regulate stress response pathways in synovial fibroblasts at transcriptional and functional levels

Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…

Continue Reading Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

Novel method of isolating nuclei of human oligodendrocyte precursor cells reveals substantial developmental changes in gene expression and H3K27ac histone modification

doi: 10.1002/glia.24462. Online ahead of print. Affiliations Expand Affiliations 1 Research & Development, James J. Peters VA Medical Center, Bronx, New York, USA. 2 Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA. 3 Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander Universität…

Continue Reading Novel method of isolating nuclei of human oligodendrocyte precursor cells reveals substantial developmental changes in gene expression and H3K27ac histone modification

A Novel Therapeutic Target Identified for Pancreatic Ductal Adenocarcinoma

Researchers have identified a novel therapeutic target for pancreatic ductal adenocarcinoma (PDAC), a lethal type of pancreatic cancer. Pancreatic cancer is responsible for over 90% of all cases. Previous studies have not been able to identify the master regulator of cell cycle entry and proliferative metabolism in PDAC. The researchers…

Continue Reading A Novel Therapeutic Target Identified for Pancreatic Ductal Adenocarcinoma

Role of Super-Enhancers in Triggering Pancreatic Cancer Tumor Growth Explored in Study

NEW YORK — Researchers have identified how gene regulatory regions called super-enhancers can fuel the growth of pancreatic ductal adenocarcinoma (PDAC), which accounts for over 90 percent of all pancreatic cancer cases. In a study published in Nature Communications on Wednesday, a team led by researchers from the Salk Institute…

Continue Reading Role of Super-Enhancers in Triggering Pancreatic Cancer Tumor Growth Explored in Study

Pig H3K4me3, H3K27ac and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

Tao Jiang, Zhimin Zhou, Ziqi Ling, Qing Zhang, Zhongzi Wu, Jiawen Yang, Siyu Yang, Bin Yang, Lusheng Huang. Pig H3K4me3, H3K27ac and gene expression profiles reveal reproductive tissue-specific activity of transposable elements. Zoological Research. doi: 10.24272/j.issn.2095-8137.2023.060 Citation: Tao Jiang, Zhimin Zhou, Ziqi Ling, Qing Zhang,…

Continue Reading Pig H3K4me3, H3K27ac and gene expression profiles reveal reproductive tissue-specific activity of transposable elements

The H3K27ac track in the human genome browser

The H3K27ac track in the human genome browser (genome.ucsc.edu) shows experimentally measured levels of histone acetylation. Specifically, this data measures acetylation on one lysine (K27) on one histone subunit (H3) at all locations across the genome. This histone modification is typically found in promoter and enhancer regions of genes: high…

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Abstract PR008: The SLC1A1/EAAT3 dicarboxylic amino acid transporter: An actionable, HIF-independent, hub that links epigenetic dysregulation to nucleotide metabolism in kidney cancer | Cancer Research

Significance: The clear cell renal cell carcinomas (ccRCCs), which harbor the hallmark inactivation of the von Hippel Lindau tumor suppressor protein (pVHL), represent the majority of adult kidney cancers. Although, early stage/localized ccRCC is effectively managed by surgery and surveillance, therapeutic options for advanced stage disease are limited, highlighting the…

Continue Reading Abstract PR008: The SLC1A1/EAAT3 dicarboxylic amino acid transporter: An actionable, HIF-independent, hub that links epigenetic dysregulation to nucleotide metabolism in kidney cancer | Cancer Research

Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Cell culture Mammary epithelial, non-transformed MCF10A cells (ATCC CRL-10317) were grown in DMEM:F-12 (Dulbecco’s Modified Eagle Medium:Nutrient Mixture F-12) (1:1) medium (Gibco, 11330057) supplemented with 5% Horse Serum (HS), 2 mM l-glutamine and 1% penicillin/streptomycin (Sigma-Aldrich, G6784), 10 µg/ml insulin (Sigma-Aldrich, I9278) and 0.5 µg/ml hydrocortisone (Sigma-Aldrich, H0888). Human Epidermal Growth Factor (hEGF,…

Continue Reading Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model

Differential exon usage of developmental genes is associated with deregulated epigenetic marks

H3K36me3 mark is most relevant to AS events The first task was to prepare a suitable data set where differentially used exons (DEUs) can be clearly associated with individual genes. Hence, out of 19,240 clusters of protein coding genes generated for the DEXSeq analysis (see “Materials and methods” section), we…

Continue Reading Differential exon usage of developmental genes is associated with deregulated epigenetic marks

Rewiring cancer drivers to activate apoptosis

Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985). Article  ADS  CAS  PubMed  Google Scholar  Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Sanchez-Vega,…

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Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

Continue Reading Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Chip-Seq replicates from different experiments

Chip-Seq replicates from different experiments 1 Hi, I have two replicate Chip-seq samples of H3K27Ac in the same condition. However, they are from two experiments carried out at different times and on different mice. I would like to compare/merge them in order to create heatmaps etc. The correlation is high…

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Biomolecules | Free Full-Text | Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure

1. Introduction The digestive tract greatly influences the maintenance of energy requirements in cattle due to its crucial role in digesting and absorbing nutrients. The rumen is an essential organ in the digestive tract for feed efficiency, with relatively high metabolic activities. The digestion of solid-feeding materials generates short-chain fatty…

Continue Reading Biomolecules | Free Full-Text | Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure

Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice | BMC Medicine

The strategy and logic of choosing VRK2 SNPs for genetic analyses We retrieved the summary statistics of VRK2 SNPs in 23andMe, UK Biobank, and PGC2 samples [2, 3], and 256 SNPs region were available in all three GWAS datasets (a total of 246,363 cases and 561,190 controls). An overview about…

Continue Reading Reduced Vrk2 expression is associated with higher risk of depression in humans and mediates depressive-like behaviors in mice | BMC Medicine

Identify binding motifs within large super enhancer region

Identify binding motifs within large super enhancer region 1 Hello, From my H3K27ac ChIP seq data, I have identified 500 super enhancer regions using Homer’s findPeaks -style super. From the super enhancer regions, I found 4 enriched binding motifs within the 500 super enhancer regions using Homer’s findMotifsGenome.pl. First, I…

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LOC127890413 H3K27ac hESC enhancers GRCh37_chr19:10362245-10362818 and GRCh37_chr19:10362819-10363392 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

Continue Reading LOC127890413 H3K27ac hESC enhancers GRCh37_chr19:10362245-10362818 and GRCh37_chr19:10362819-10363392 [Homo sapiens (human)] – Gene

NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization

NUP98 and RAE1 are enriched in progenitors and constitute a distinct complex Between the progenitor-state versus the differentiation state keratinocytes, we identified that 4 out of 5 nuclear-basket NUPs are significantly downregulated in differentiation (Fig. 1a), leveraging the RNA-seq data that we recently generated20. To determine how the enrichment of these…

Continue Reading NUP98 and RAE1 sustain progenitor function through HDAC-dependent chromatin targeting to escape from nucleolar localization

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Timecourse of Hox gene activation in stembryos In gastrulating mouse embryos, Wnt signaling contributes to the formation of the primitive streak from epiblast cells. Likewise, in stembryos cultured as described in ref. 34, a pulse of the Wnt agonist Chiron 48 h after aggregation of mES cells, that is, between 48 h…

Continue Reading Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Solved The data displayed above show both evolutionary and

Transcribed image text: [Questions 14-16] To test the function of the H3K27ac region found 8 kb upstream of a gene that is commonly deleted in tumor samples (information from the genome browser diagrammed below), experiments were performed targeting Cas9-sgRNA upstream and downstream of the region to introduce two double-stranded breaks that…

Continue Reading Solved The data displayed above show both evolutionary and

Index of /compbio1/eGTEx-H3K27ac/code/Fig.3/QTL.mapping

Name Last modified Size Description Parent Directory   –   a.2.callTisshaQTL.paral.R 2021-05-30 06:55 2.8K   a.2.callTisshaQTL_V1.2.2.2_filtPeaks_gINT.Peer_rmAgeBatch.RSC0.8.R 2022-05-16 09:56 9.8K   a.2.callTisshaQTL_V1.2.2_filtPeaks_gINT.Peer_rmAgeBatch.R 2021-11-18 15:07 9.2K   a.3.visHaQTLNumVSCovNum.R 2022-05-11 16:37 1.9K   a.4.callTisshaQTL_fixedCov_V1.2.2_filtPk_gINT.Peer_rmAgeBatch.R 2022-11-17 14:54 11K   a.4.callTisshaQTL_fixedCov_V1.2.2_filtPk_gINT.Peer_rmAgeBatch.para.R 2022-05-16 09:57 2.5K   a.4_2.haQTL2bed.R 2021-03-06 00:13 2.7K   a.5.multipleTestOnQTL_forPeer.R 2022-12-15 23:38 9.9K  …

Continue Reading Index of /compbio1/eGTEx-H3K27ac/code/Fig.3/QTL.mapping

Heritable transcriptional defects from aberrations of nuclear architecture

Cell culture and cell line construction Cells were cultured at 37 °C in 5% CO2 atmosphere with 100% humidity. Telomerase-immortalized RPE-1 retinal pigment epithelium cells (CRL-4000, American Type Culture Collection), U2OS osteosarcoma cells (HTB-96, American Type Culture Collection) and derivative cell lines were grown in DMEM/F12 (1:1) medium without phenol red…

Continue Reading Heritable transcriptional defects from aberrations of nuclear architecture

Finding Enhancers using Genomation library

Finding Enhancers using Genomation library 1 I am able to find CpG islands and shores, but now i want to find enhancers. please help me find a way to get information about enhancers using genomation library. Genomation • 18 views • link updated 7 minutes ago by ATpoint 72k •…

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LOC127888533 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

Continue Reading LOC127888533 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80054421-80055336 [Homo sapiens (human)] – Gene

A New AI Research From Google Declares The Completion of The First Human Pangenome Reference

Researchers have spent decades piecing together a human genome map, a comprehensive copy of each individual’s genetic instructions. In 2000, researchers completed the first draft, but it needed key components. After completing the reference genome in 2022, they still had a ways to go. Genomics has spent the past three…

Continue Reading A New AI Research From Google Declares The Completion of The First Human Pangenome Reference

LOC127271744 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226270255-226271122 [Homo sapiens (human)] – Gene

NEW Try the new Transcript table RefSeqs maintained independently of Annotated Genomes These reference sequences exist independently of genome builds. Explain These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by…

Continue Reading LOC127271744 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226270255-226271122 [Homo sapiens (human)] – Gene

Large-scale long terminal repeat insertions found to produce a significant set of novel transcripts in cotton

Comparisons of the gene numbers obtained from diploid cotton G. arboreum transcriptomes at different sequencing depths. Credit: Science China Press TEs (transposable elements), especially LTRs, are known to play an important role in determining the basic genome structure and influencing the expression of functional genes. Insertion of TE or LTR…

Continue Reading Large-scale long terminal repeat insertions found to produce a significant set of novel transcripts in cotton

Histone modifications regulate pioneer transcription factor cooperativity

Protein expression, mutagenesis and purification Xenopus laevis histones for nucleosome assembly were overexpressed in the Escherichia coli BL21(DE3) pLysS strain and purified from inclusion body as previously described48. The cells were grown in LB medium at 37 °C and induced with 1 mM IPTG when OD600 reached 0.6. After 3 h of expression,…

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Mechanism of histone deacetylase HDAC2 in FOXO3-mediated trophoblast pyroptosis in preeclampsia

Histone deacetylase 2 (HDAC2) has been demonstrated to regulate trophoblast behaviors. However, its role in trophoblast pyroptosis remains unknown. This study sought to analyze the molecular mechanism of HDAC2 in trophoblast pyroptosis in PE. Expression levels of HDAC2, forkhead box O3 (FOXO3), and protein kinase R-like endoplasmic reticulum kinase (PERK)…

Continue Reading Mechanism of histone deacetylase HDAC2 in FOXO3-mediated trophoblast pyroptosis in preeclampsia

Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0

In this section, we derive a simplified expression for the proportionality constant \(\alpha\) that enables quantitative ChIP-seq and we introduce some consequences for track building. This new expression is more intuitive to understand, easier to evaluate, and more accurate to sequencing outcomes than the previous expression. While values derived from…

Continue Reading Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0

Solved rs610037/MAP3K11 rs61895677/MAP3K11 | Chegg.com

Transcribed image text:  rs610037/MAP3K11  rs61895677/MAP3K11  rs12801731/MAP3K11  rs44205/OVOL1-AS1  201465898/OVOL1-AS1  s34016202/OVOL1-AS1  s76152641/OVOL1-AS1  202039555/OVOL1-AS1  s59927298/OVOL1-AS1 ​ Layered H3 K4M3 H3K27Ac Mark (Often Found Near Active Regulatory Elements) on 7 cell lines from ENCODE Layered H3K27Ac 0.0457.96​ H3K4Me1 Mark (Otten Found Near Regulatory Elements) on 7 cell lines from ENCODE Layered H3 K4Me1 .04 Placental Mammal Basewise Conservation by PhyloP Mammal Cons (1) −4…

Continue Reading Solved rs610037/MAP3K11 rs61895677/MAP3K11 | Chegg.com

1. The GWAS data shown below are from the recent

Transcribed image text: 1. The GWAS data shown below are from the recent paper published in Nature Genetics Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus doi.org/10.1038/s41588-021-00955-3 (citation) The authors focus on the SNP rs17713054. DNAse I sensitivity is suggestive of euchromatin DNA, and H3K27Ac…

Continue Reading 1. The GWAS data shown below are from the recent

H2BNTac Represents a Novel Marker of Active Enhancers

Science has moved on since William Shakespeare put quill to parchment around 1600 to write the Tragedy of Hamlet, Prince of Denmark, but his legacy has survived to influence a new manuscript that describes the quest to discover histone modifications that better distinguish active enhancers. “H2B, or not H2B, that…

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The Allis code | Nature Genetics

David Allis (1951–2023) was a leading figure in the field of chromatin biology. He inspired many generations of scientists both through his work and his own personal example as a mentor and colleague. His influential ‘histone code’ theory remains an important guiding principle to study and understand gene regulation. In…

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A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs

Genome-scale CRISPR screen to identify regulators that maintain mESC pluripotency To establish a function-based PGRN, we first performed a CRISPR-Cas9 mediated genome-wide screen to detect genes essential for self-renewal. mESCs were cultured under Leukaemia inhibitory factors (LIF)/serum condition (L/S), which was commonly used in similar tasks and confer a naïve…

Continue Reading A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs

Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

Multiple H2BNTac sites occupy the same genomic regions H2BNTac sites are similarly regulated by CBP/p30018 (Supplementary Fig. 1a), yet the reported genome occupancy patterns of H2BNTac sites are dissimilar from each other22,23 (Supplementary Note 1). To resolve this conundrum, we systematically compared H3K27ac and H2BNTac genomic occupancy and regulation by…

Continue Reading Acetylation of histone H2B marks active enhancers and predicts CBP/p300 target genes

Catching active enhancers via H2B N-terminal acetylation

Specific chromatin features, especially histone H3 lysine 27 acetylation, are widely used to identify active enhancers, yet current methods are imprecise. New work suggests that histone H2B N terminus multisite lysine acetylation (H2BNTac) is a notable signature of active enhancers and could substantially improve enhancer prediction. In this issue of…

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NAD+ is critical for maintaining acetyl-CoA and H3K27ac in embryonic stem cells by Sirt1-dependent deacetylation of AceCS1

NAD+ is critical for maintaining acetyl-CoA and H3K27ac in embryonic stem cells by Sirt1-dependent deacetylation of AceCS1 Yi Wu1,2, Yang Liu1,2,3, Zhihong Hao1,2,3, Xingguo Liu1,2,4() 1. CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University,…

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SARS-CoV-2 rewires host chromatin | Nature Reviews Microbiology

The conformation of the mammalian 3D genome is highly regulated and has a key role in various biological processes, such as transcription, DNA replication or repair, cell division or cell differentiation. By high-throughput chromosome conformation capture (Hi-C) and analysis, chromatin architecture is structured into A compartments (transcriptionally active euchromatin) and B compartments…

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COVID-19 activates endogenous retroviruses within our genome

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is otherwise known as the coronavirus disease 2019 (COVID-19), continues to pose significant…

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Spatial multiomics map of trophoblast development in early pregnancy

Human samples Placental and decidual samples used for the in vivo and in vitro profiling were obtained from elective terminations from: The MRC and Wellcome-funded Human Developmental Biology Resource (HDBR, www.hdbr.org), with appropriate maternal written consent and approval from the Fulham Research Ethics Committee (REC reference 18/LO/0822) and Newcastle and…

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The loss of epigenetic information: not only consequences but a cause of mammalian aging

In a recent study published in Cell, Yang et al. revealed that changes in epigenetic landscapes caused by faithful DNA repair are key drivers accelerating aging of mammalian organs or tissues.1 Impressively, changes in H3K27ac landscape during aging process influence cell identity maintenance, and this aging process can be reversed…

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DiffBind with ChIPseq from histone analysis: EdgeR or Deseq2?

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I…

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Hematopoietic/erythroid enhancers activate nearby target genes by extending histone H3K27ac and transcribing intergenic RNA

doi: 10.1096/fj.202201891R. Affiliations Expand Affiliations 1 Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, South Korea. 2 Department of Biomedical Laboratory Science, College of Healthcare Medical Science and Engineering, Inje University, Gimhae, South Korea. Item in Clipboard Yea Woon Kim et al. FASEB J. 2023 Apr. Show…

Continue Reading Hematopoietic/erythroid enhancers activate nearby target genes by extending histone H3K27ac and transcribing intergenic RNA

Study Finds Cannabinoids “May Have Utility in Cancer Immunotherapy Regimens”

According to a new Frontiers in Immunology study, specific cannabinoids “may have utility in cancer immunotherapy regimens by overcoming immune escape and augmenting cancer immune surveillance in metastatic disease.” Titled Specific cannabinoids revive adaptive immunity by reversing immune evasion mechanisms in metastatic tumours, the study was conducted by researchers at…

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New technology maps where and how cells read their genome

Design and evaluation of spatial epigenome–transcriptome cosequencing with E13 mouse embryo. a, Schematic workflow. b, Comparison of number of unique fragments and fraction of reads in peaks (FRiP) in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. c, Gene and UMI count distribution in spatial ATAC–RNA-seq and spatial CUT&Tag–RNA-seq. Number of pixels in…

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Epigenetic and epitranscriptomic regulation of axon regeneration

Goldberg JL, Klassen MP, Hua Y, Barres BA. Amacrine-signaled loss of intrinsic axon growth ability by retinal ganglion cells. Science. 2002;296:1860–4. Article  CAS  PubMed  Google Scholar  Blackmore M, Letourneau PC. Changes within maturing neurons limit axonal regeneration in the developing spinal cord. J Neurobiol. 2006;66:348–60. Article  CAS  PubMed  Google Scholar …

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A gene silencing screen uncovers diverse tools for targeted gene repression in Arabidopsis

A gain-of-function screen for regulators of gene silencing We utilized the native Arabidopsis gene FWA as a reporter to screen for regulators of gene silencing. FWA encodes a transcription factor that causes a late flowering phenotype when overexpressed, resulting in a greater number of leaves produced before flowering. In Col-0…

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Assessing the risk of excess folic acid intake

Both high FA and low FA intake increases de novo mutation rate and disrupt genome DNA methylation in the offspring. a Violin Plot of DNSNV/DNM (de novo mutation) counts among the three different FA dietary groups (sample size for each group was as follows; combined panel: 0.3 ppm group n = 26;…

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Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson’s disease

Case selection In this prospective case‒control study, we enrolled PD patients and healthy controls at Asan Medical Center (AMC), Seoul, South Korea, between 2018 and 2020. PD diagnosis was based on the UK PD Society Brain Bank criteria15. Batch 1 (n = 210) and 2 (n = 100) PD cohorts were recruited from January…

Continue Reading Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson’s disease

Segmentation

Segmentation Segmentation algorithms partition the genome into regions with distinct epigenomic profiles. These are genomic regions of similar signal pattern over a selected number of assays. To segment the genome for each cell type we currently use either ChromHMM (Ernst et al., 2011) or Segway (Hoffman et al., 2011). These…

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NIH Team Links Single-Nucleotide Mutations to Higher Brain Functioning in Humans

Many small mutations may be responsible for driving the features of the human brain that enable advanced cognition, according to a study appearing this week in Science Advances. The neocortex is a mammalian brain innovation that handles higher functioning, and its size and complexity in humans underlies our unique brain…

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FLI1 and FRA1 transcription factors drive the transcriptional regulatory networks characterizing muscle invasive bladder cancer

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021). Article  PubMed  Google Scholar  Sanli, O. et al. Bladder cancer. Nat. Rev. Dis. Prim. 3, 17022 (2017). Article  PubMed  Google Scholar  International…

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Transcription factor binding sites are frequently under accelerated evolution in primates

Pooling-based phylogenetic inference of accelerated evolution In the current study, we introduce a novel software application, GroupAcc, which includes two pooling-based phylogenetic approaches with improved statistical power to infer weakly accelerated evolution. The key idea of GroupAcc is to group TFBSs by the bound transcription factor and then examine whether…

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Reference epigenome reveals transcription and chromatin state reprogramming during wheat embryogenesis

Stage-specific transcriptional divergence regulation model in wheat embryogenesis. Credit: IGDB Embryogenesis is one of the most fundamental and remarkable processes in both animals and plants. It’s amazing that after fertilization, a single maternal egg cell can develop into an organism with a multilayered body plan only in just a few…

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FitHiChIP producing very few peaks for H3K27ac and H3K4me3

FitHiChIP producing very few peaks for H3K27ac and H3K4me3 0 I am running fitHiChIP on publicly available datasets found at hichip.readthedocs.io/en/latest/data_sets.html I have gotten CTCF to work well and produce arcs but when running fitHiChIP for H3K4me3 and H3K27ac I have used the following settings and have found almost no…

Continue Reading FitHiChIP producing very few peaks for H3K27ac and H3K4me3

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)? 0 Hi, I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings. Is there any good tools to annotate these broad peaks to coding genes? I know GREAT(great.stanford.edu/public/html/)…

Continue Reading Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Human fetal cerebellar cell atlas informs medulloblastoma origin and oncogenesis

Wang, J., Garancher, A., Ramaswamy, V. & Wechsler-Reya, R. J. Medulloblastoma: from molecular subgroups to molecular targeted therapies. Annu. Rev. Neurosci. 41, 207–232 (2018). Article  CAS  PubMed  Google Scholar  Cavalli, F. M. G. et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell 31, 737–754.e736 (2017). Article  CAS  PubMed  PubMed Central …

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Human hg38 chr7:73,678,750-73,740,129 UCSC Genome Browser v435

Use drop-down controls below and press refresh to alter tracks displayed.Tracks with lots of items will automatically be displayed in more compact modes.    Custom Tracks H3K27ac Meta NeuN SCZhidedensesquishpackfull H3K27ac NeuN SCZ del_CRDhidedensesquishpackfull H3K27ac NeuN SCZ del_CRD_del_peakshidedensesquishpackfull H3K27ac Tissuehidedensesquishpackfull H3K27ac Tissue BDhidedensesquishpackfull H3K27ac Tissue BD del_CRDhidedensesquishpackfull H3K27ac Tissue BD…

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The SMC5/6 complex leads to a loss of H3K27ac on KSHV chromatin.

(a-c) Ectopic expression of SMC6 decreases the levels of H3K27ac on KSHV genome. (a) H3K27ac on viral RTA was measured with ChIP-qPCR assay. ChIP was performed among latently infected control cells and SMC6-overexpressing cells by using antibodies against total H3 or H3K27ac. The recruitment of H3 and H3K27ac on KSHV…

Continue Reading The SMC5/6 complex leads to a loss of H3K27ac on KSHV chromatin.

Simultaneous Mapping of Enhancers and Enhancer RearrangementsEnhancer Rearrangements with Paired-End H3K27ac ChIP-seq

We describe a protocol for H3K27ac ChIP paired-end sequencing and computational analysis of rearrangements. Our approach can be used to simultaneously map enhancers and their activity and to identify structural variations at enhancers. Since changes in enhancer activity and new enhancer translocations both play a major role in tumor initiation,…

Continue Reading Simultaneous Mapping of Enhancers and Enhancer RearrangementsEnhancer Rearrangements with Paired-End H3K27ac ChIP-seq

New study investigates the epigenetic drift of time passing

A new research paper was published in Aging (Aging-US) on the cover of Volume 14, Issue 12, entitled, “Time makes histone H3 modifications drift in mouse liver.” Aging is known to involve epigenetic histone modifications, which are associated with transcriptional changes, occurring throughout the entire lifespan of an individual. “So…

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Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Subjects Normal breast and tumor samples were obtained with the written informed consent from donors and appropriate approval from local ethical committees, with the detailed information described in the respective original publications: normal tissue9, METABRIC14, TCGA35. Differential allelic expression analysis DNA and total RNA from 64 samples of normal breast…

Continue Reading Allelic expression imbalance of PIK3CA mutations is frequent in breast cancer and prognostically significant

Full Text Journal Articles by Author And Robin Andersson (Page 1)

PDF.MPro – Full Text Journal Articles by Author And Robin Andersson (Page 1) Home / Search / Author And Robin Andersson (Page 1) Advertisement Find full text journal articles The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription Kirill Jefimov, Nicolas Alcaraz, Susan Kloet, Signe Värv, Siri Aastedatter…

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Understanding the relationship between large-scale chromatin structure and gene expression

Abstract Eukaryotic genomes are packaged into a complex DNA, RNA, and protein rich chromatin fibre, creating an interdependent functional relationship between the structure of the chromatin and the activity of the genetic features stored within. The composition of active genomic regions is weighted towards transcription factors, co-activating proteins, and active …

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Transcriptional and H3K27ac related genome profiles in oral squamous cell carcinoma cells treated with metformin

. 2022 Mar 21;13(6):1859-1870. doi: 10.7150/jca.63234. eCollection 2022. Affiliations Expand Affiliations 1 State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, China. 2 Department of Oral and Maxillofacial Surgery, Binzhou…

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TET2 regulates immune tolerance in chronically activated mast cells

This article was originally published here JCI Insight. 2022 Apr 8;7(7):e154191. doi: 10.1172/jci.insight.154191. ABSTRACT Mutation of the TET2 DNA-hydroxymethylase has been associated with a number of immune pathologies. The disparity in phenotype and clinical presentation among these pathologies leads to questions regarding the role of TET2 mutation in promoting disease…

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Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar Macrophages Following LPS or PolyIC Exposure

Date created: | Last Updated: : DOI | ARK Creating DOI. Please wait… Create DOI Category: Data Description: Supplementary data for publication: Juber Herrera-Uribe, Haibo Liu, Kristen A. Byrne, Zahra F. Bond, Crystal L. Loving and Christopher K. Tuggle. (2020). Changes in H3K27ac at Gene Regulatory Regions in Porcine Alveolar…

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice

O304 treatment prevents islet gene expression signature changes induced by HFD We have previously demonstrated that the AMPK activator O304 improves blood glucose homeostasis in both human T2D subjects as well as in high-fat diet induced obese and diabetic mouse models. In the present study, we have now analysed the…

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Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | BMC Genomics

1. Yin H, Price F, Rudnicki MA. Satellite cells and the muscle stem cell niche. Physiol Rev. 2013;93(1):23–67. CAS  PubMed  PubMed Central  Google Scholar  2. Hoppeler H, Fluck M. Plasticity of skeletal muscle mitochondria: structure and function. Med Sci Sport Exer. 2003;35(1):95–104. CAS  Google Scholar  3. Astruc T: Carcass Composition,…

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P-value cut-off to identify SNPs at ChIP-seq peaks? [BedTools]

P-value cut-off to identify SNPs at ChIP-seq peaks? [BedTools] 0 Hi all, I have a bed file of SNPs and also H3K27ac ChIP-seq .broadpeak file from Roadmap epigenome… I want to find the SNPs in my list that intersects a H3K27ac peak using BedTools intersect However, should I filter the…

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Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??!

Intersecting Roadmap’s Histone ChIP-seq data using BedTools?!?!??! 0 Hi all, I want to prioritise my list of 112 SNPs by looking at those that lie within open chromatin regions and/or active promoter/enhancer histone marks In order to do that I have downloaded several Histone modification ChIP-seq data from Roadmap epigenomics…

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Is there any software that can use ATAC-seq to identify super enhancer

Is there any software that can use ATAC-seq to identify super enhancer 1 Hello Everyone! Has anyone tried to identify super-enhancers by using ATAC-seq? I am wondering whether some one can recommend some software 🙂 Thanks a lot in advance for your comments and ideas! Best wishes Guandong Shang ATAC-seq…

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