From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data

Cui, Ya; Li, Jason Sheng; Li, Wei

doi:10.1016/j.gpb.2021.06.002

Cited by 4 publications

(3 citation statements)

References 24 publications

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“…The fragment distribution plots show clear peaks corresponding to nucleosome-free regions (NFR) with sizes below 100 bp, as well as peaks for mono-(~200 bp), di-(~400 bp), and tri-(~600 bp) nucleosomes, similar in both the select young and old samples (Figure S1A). As expected, a high proportion of the ATAC-seq libraries contain short reads (~100bp) from nucleosome-free regions (Figure S1A), indicating high quality of the libraries since the Tn5 transposase prefers more accessible chromatin regions 22,31,[40][41][42] . The presence of mono-nucleosome fragments (Figure S1A)…”

Section: Resultssupporting

confidence: 72%

Changes in microglia chromatin accessibility in aged female mice

Ansere,

Tooley,

Srividya

et al. 2024

Preprint

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Aged female microglia display a more inflammatory and disease-associated phenotype compared to age-matched males. Epigenetic mechanisms, such as chromatin accessibility, are key drivers of microglial plasticity and phenotypes necessary for development, priming, and immune activation. Therefore, alterations in chromatin accessibility patterns can potentially regulate the neuroimmune responses and phenotypes observed in female microglia with aging, but to date have not been assessed. In this study, hippocampal microglia chromatin accessibility in young (4-5 months) and old (23-24 months) female mice was interrogated by Assay for Transposable Accessible Chromatin using Sequencing (ATAC-Seq). Cx3cr1-cre/ERT2+: NuTRAP mice were used to tag microglia and enable INTACT (isolation of nuclei tagged in specific cell types) collection of microglia-specific nuclei. With aging, loci specific gains and losses in chromatin accessibility were observed. Notably, changes in chromatin accessibility were skewed, with aged female microglia having more regions gaining accessibility than loosing accessibility. These changes were under-represented in the proximal promoter region (≤1kb) of genes but were enriched in intergenic regions. Regions that gained accessibility were more concentrated around genes responsible for myeloid cell differentiation and the regulation of immune and inflammatory responses. In contrast, regions that became less accessible were closest to genes involved in neuronal and synaptic function. In addition, X Chromosome accessibility changes were less common compared to autosomal changes, which argues against increased X Chromosome escape from inactivation with aging in female microglia. Overall, our data demonstrate age-related chromatin accessibility changes in female microglia, which may be regulated within enhancers and distal regulatory elements, and that these changes have potential downstream implications for the inflammatory phenotype of microglia in aging female mice.

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Section: Resultssupporting

confidence: 72%

Changes in microglia chromatin accessibility in aged female mice

Ansere,

Tooley,

Srividya

et al. 2024

Preprint

View full text Add to dashboard Cite

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“…ATAC-seq detects the regions bound by TFs or occupied by nucleosomes. It is faster and more sensitive than DNase-seq and MNase-seq [13] , [14] . FAIRE-seq overcomes the enzymatic cleavage preference that may be present in the aforementioned methods and directly detects DNA sequences occupied by nucleosomes [12] .…”

Section: Introductionmentioning

confidence: 99%

PlantCADB: A Comprehensive Plant Chromatin Accessibility Database

Ding

Sun

Luo

et al. 2022

Genomics, Proteomics &Amp; Bioinformatics

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Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular basis underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated for humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB) from 649 samples of 37 species. These samples are abiotic stress-related (such as heat, cold, drought, and salt; 159 samples), development-related (232 samples), and/or tissue-specific (376 samples). Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factor footprint, motif, and single-nucleotide polymorphisms (SNPs). Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility resource, which can aid in better understanding genetic regulatory networks underlying development, important traits, stress adaptations, and evolution. PlantCADB is freely available at https://bioinfor.nefu.edu.cn/PlantCADB/.

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“…ATAC-seq detects the regions bound by transcription factors or occupied by nucleosomes. It is faster and more sensitive than DNase-seq and MNase-seq [13, 14]. FAIRE-seq overcomes the enzymatic cleavage preference that may present in the above methods and directly detects DNA sequences occupied by nucleosomes [12].…”

Section: Introductionmentioning

confidence: 99%

PlantCADB: A comprehensive plant chromatin accessibility database

Ding

Sun

Long

et al. 2022

Preprint

View full text Add to dashboard Cite

Chromatin accessibility landscapes are essential for detecting regulatory elements, illustrating the corresponding regulatory networks, and, ultimately, understanding the molecular bases underlying key biological processes. With the advancement of sequencing technologies, a large volume of chromatin accessibility data has been accumulated and integrated in humans and other mammals. These data have greatly advanced the study of disease pathogenesis, cancer survival prognosis, and tissue development. To advance the understanding of molecular mechanisms regulating plant key traits and biological processes, we developed a comprehensive plant chromatin accessibility database (PlantCADB, https://bioinfor.nefu.edu.cn/PlantCADB/) from 649 samples of 37 species. Among these samples, 159 are abiotic stress-related (including heat, cold, drought, salt, etc.), 232 are development-related and 376 are tissue-specific. Overall, 18,339,426 accessible chromatin regions (ACRs) were compiled. These ACRs were annotated with genomic information, associated genes, transcription factors footprint, motif, and SNPs. Additionally, PlantCADB provides various tools to visualize ACRs and corresponding annotations. It thus forms an integrated, annotated, and analyzed plant-related chromatin accessibility information which can aid to better understand genetic regulatory networks underlying development, important traits, stress adaptions, and evolution.

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From Reads to Insights: Integrative Pipelines for Biological Interpretation of ATAC-Seq Data

Cited by 4 publications

References 24 publications

Changes in microglia chromatin accessibility in aged female mice

Changes in microglia chromatin accessibility in aged female mice

PlantCADB: A Comprehensive Plant Chromatin Accessibility Database

PlantCADB: A comprehensive plant chromatin accessibility database

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