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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Citations
CLM-access: A Specialized Foundation Model for High-dimensional Single-cell ATAC-seq analysis
Ziqiang Liu,Bowen Li,Zhenyu Xu,Yantao Li,Junwei Zhang,Chulin Sha,Xiaolin Li +6 more
- 12 Aug 2025
TL;DR: Researchers introduce CLM-access, a specialized foundation model for high-dimensional single-cell ATAC-seq analysis, incorporating innovations in data processing, patching, and masking to outperform existing methods in downstream tasks, including batch effect correction and cell type annotation.
Dynamic chromatin accessibility modeled by Markov process of randomly-moving molecules in the 3D genome
TL;DR: A Markov process model to derive a chromosomal equilibrium distribution of randomly-moving molecules as a functional consequence of spatially organized genome 3D structures is proposed and concludes that SSD is a novel and better measure of dynamic chromatin activity and accessibility.
Epigenetic Landscape during Coronavirus Infection.
Alexandra Schäfer,Ralph S. Baric +1 more
TL;DR: By combining measures of epigenome reorganization with RNA and proteomic datasets, this article articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host’s innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection.
An increased expression of PI-PLCβ1 is associated with myeloid differentiation and a longer response to azacitidine in myelodysplastic syndromes.
Lucio Cocco,Carlo Finelli,Sara Mongiorgi,Cristina Clissa,Domenico Russo,Costanza Bosi,Marilisa Quaranta,Michele Malagola,Sarah Parisi,Marta Stanzani,Giulia Ramazzotti,Giulia Adalgisa Mariani,Anna Maria Billi,Lucia Manzoli,Matilde Y. Follo +14 more
TL;DR: Results show that PI‐PLCβ1 quantification in MDS predicts the response to azacitidine and is associated with an increased myeloid differentiation.
Defining transcription factor nucleosome binding with Pioneer-seq
Maria Tsompana,Patrick Wilson,Vijaya Murugaiyan,Christopher Raymond Handelmann,Michael J. Buck +4 more
TL;DR: Pioneer-Seq as mentioned in this paper uses a library of nucleosomes containing thousands of DNA sequences with TF binding sites in all possible nucleosome orientations and the protein-nucleosome complex is isolated and quantified.
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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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