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Physiological Reports, 2023 Epidemiological studies have shown that patients who recovered from acute kidney injury (AKI) may subsequently develop chronic kidney disease (CKD). AKI is primarily caused by renal hypoxia, and it causes epigenetic alterations, known as hypoxic memory ...
Tomotaka Yamazaki +4 more
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Opening a Chromatin Gate to Metastasis [PDF]
Cell, 2016 What changes need to occur in a primary tumor to make it metastatic? Denny et al. address this question for small cell lung cancer (SCLC), finding that changes in genomic accessibility mediated by a single transcription factor, NFIB, comprise at least one mechanism influencing metastasis.
John D, Minna, Jane E, Johnson
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Open Chromatin in Plant Genomes [PDF]
Cytogenetic and Genome Research, 2014 Sensitivity to DNase I digestion is an indicator of the accessibility and configuration of chromatin in eukaryotic genomes. Open chromatin exhibits high sensitivity to DNase I cleavage. DNase I hypersensitive sites (DHSs) in eukaryotic genomes can be identified through DNase I treatment followed by sequencing (DNase-seq).
Wenli, Zhang +3 more
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Bibliometric Analysis of ATAC-Seq and Its Use in Cancer Biology via Nucleic Acid Detection
Frontiers in Medicine, 2020 Assay for transposase-accessible chromatin using sequencing (ATAC-seq) is associated with significant progress in biological research and has attracted increasing attention.
Yu Zhao +9 more
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Frontiers in Genetics, 2021 Single-cell open-chromatin profiles have the potential to reveal the pattern of chromatin-interaction in a cell type. However, currently available cis-regulatory network prediction methods using single-cell open-chromatin profiles focus more on local ...
Neetesh Pandey +3 more
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Chromatin higher order structure: Opening up chromatin for transcription [PDF]
Briefings in Functional Genomics and Proteomics, 2004 DNA packaged into chromatin is the physiologically relevant substrate for all DNA-dependent processes inside the nuclei of eukaryotic cells. The highly compacted structures of DNA and histones is inherently repressive for all DNA-dependent processes.
Attila, Németh, Gernot, Längst
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Genome Biology, 2021 Chromatin interactions play important roles in regulating gene expression. However, the availability of genome-wide chromatin interaction data is limited.
Fan Cao +11 more
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Opening the Chromatin by eRNAs [PDF]
Molecular Cell, 2013 Enhancer RNAs (eRNAs) have emerged as an important component of transcriptional activation. In this issue, Mousavi et al. (2013) have uncovered a critical role for eRNAs in regulation of myogenic differentiation program through increasing chromatin accessibility at MyoD and MyoG loci.
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piRNA clusters and open chromatin structure [PDF]
Mobile DNA, 2014 Transposable elements (TEs) are major structural components of eukaryotic genomes; however, mobilization of TEs generally has negative effects on the host genome. To counteract this threat, host cells have evolved genetic and epigenetic mechanisms that keep TEs silenced.
Yamanaka, Soichiro +2 more
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Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome
Protein & Cell, 2016 Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes.
Zhuoya Gu +9 more
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