Tag: H3K27ac

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…

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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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Tools for Normalizing and Comparing ChIP-seq Samples

data(H3K27Ac, package = “MAnorm2”) attr(H3K27Ac, “metaInfo”) ## Make a comparison between GM12891 and GM12892 cell lines and create an MA ## plot on the comparison results. # Perform MA normalization and construct bioConds to represent the two cell # lines. norm <- normalize(H3K27Ac, 5:6, 10:11) norm <- normalize(norm, 7:8, 12:13)…

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Intersecting Encode peaks to search for tissue specific peaks?

Intersecting Encode peaks to search for tissue specific peaks? 0 As per the title, I have a list of H3K27ac peaks from my lab, and I would like to find out which of those are specific to my organ of interest. What I’ve decided to do was to download a…

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