Chromatin accessibility: a window into the genome
Maria Tsompana,Michael J. Buck +1 more
TL;DR: The limitations and advantages of current genome-wide chromatin accessibility assays are discussed with especial attention on experimental precautions and sequence data analysis and the perspective on future improvements necessary for moving the field of chromatin profiling forward is concluded.
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Abstract: Transcriptional activation throughout the eukaryotic lineage has been tightly linked with disruption of nucleosome organization at promoters, enhancers, silencers, insulators and locus control regions due to transcription factor binding. Regulatory DNA thus coincides with open or accessible genomic sites of remodeled chromatin. Current chromatin accessibility assays are used to separate the genome by enzymatic or chemical means and isolate either the accessible or protected locations. The isolated DNA is then quantified using a next-generation sequencing platform. Wide application of these assays has recently focused on the identification of the instrumental epigenetic changes responsible for differential gene expression, cell proliferation, functional diversification and disease development. Here we discuss the limitations and advantages of current genome-wide chromatin accessibility assays with especial attention on experimental precautions and sequence data analysis. We conclude with our perspective on future improvements necessary for moving the field of chromatin profiling forward.
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Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq.
TL;DR: This study performs ATAC-seq on Bombus terrestris samples derived from four developmental stages to provide clues for all possible regulatory elements in the bumblebee genome and identify 36,390 chromatin accessible regions in total.
Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton.
Corrine E Grover,Daniel L Vera,Pei-Yau Lung,S.B. Girimurugan,Emma R. Miller,Justin L. Conover,Shujun Ou,De Zhu,Dongming Li,Joseph P Gallagher,Joshua A. Udall,Xin Sui,Jinfeng Zhang,Hank W. Bass,Jonathan F. Wendel +14 more
TL;DR: Evolutionary dynamics of chromatin structure and duplicate gene expression in diploid and allopolyploid cotton reveal coordinated regulation through chromatin accessibility.
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Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset
TL;DR: Translator is presented, an efficient transfer learning approach to capture generalizable chromatin interactions from high-quality (HQ) reference scATAC-seq data to obtain robust cell representations in low-to-moderate quality target scATac-seqData, and could learn more biologically meaningful cell representations than other methods.
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A chromatin accessibility landscape during early adipogenesis of human adipose-derived stem cells
TL;DR: The ATAC-seq method was applied to depict a high-quality genome‐wide time-resolved accessible chromatin atlas during adipogenesis of human adipose-derived stem cells (hASCs) and indicated that the chromatin accessibility drastic dynamically reformed during the adipogenic of hASCs and 8 h may be the critical transition node of adipogenesis chromatin states from commitment phase to determination phase.
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Epigenetic Effects of Resveratrol on Oncogenic Signaling in Breast Cancer
Lucinda Kurzava Kendall,Yuexi Ma,Tony Yang,Katarzyna Lubecka,Barbara Stefanska +4 more
TL;DR: Resveratrol epigenetically targets oncogenes in breast cancer by modulating DNA methylation and inhibiting signal transduction pathways.
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•Journal Article
An integrated encyclopedia of DNA elements in the human genome.
TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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