Tag: H3K27ac

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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