Pan‐cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis [PDF]
Cancer Medicine, 2022 Background Open chromatin is associated with gene transcription. Previous studies have shown that the density of mutations in open chromatin regions is lower than that in flanking regions because of the higher accessibility of DNA repair machinery ...
Chie Kikutake, Mikita Suyama
doaj +2 more sources
Molecular Plant-Microbe Interactions, 2022 Nucleosome-free open chromatin often harbors transcription factor (TF)-binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens.
Zhichao Zhang +6 more
doaj +3 more sources
Developing OCHROdb, a comprehensive quality checked database of open chromatin regions from sequencing data [PDF]
Scientific Reports, 2023 International consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available.
Parisa Shooshtari +7 more
doaj +2 more sources
Single cell analysis of transcriptome and open chromatin reveals the dynamics of hair follicle stem cell aging [PDF]
Frontiers in Aging, 2023 Aging is defined as the functional decline of tissues and organisms, leading to many human conditions, such as cancer, neurodegenerative diseases, and hair loss. Although stem cell exhaustion is widely recognized as a hallmark of aging, our understanding
Chi Zhang +7 more
doaj +2 more sources
Butterfly eyespots exhibit unique patterns of open chromatin [version 1; peer review: 2 approved] [PDF]
F1000Research, 2023 Background: How the precise spatial regulation of genes is correlated with spatial variation in chromatin accessibilities is not yet clear. Previous studies that analysed chromatin from homogenates of whole-body parts of insects found little variation in
Suriya Narayanan Murugesan +1 more
doaj +2 more sources
Genome-Wide Open Chromatin Methylome Profiles in Colorectal Cancer
Biomolecules, 2020 The methylome of open chromatins was investigated in colorectal cancer (CRC) to explore cancer-specific methylation and potential biomarkers. Epigenome-wide methylome of open chromatins was studied in colorectal cancer tissues using the Infinium DNA ...
Muhiddin Ishak +9 more
doaj +3 more sources
Open chromatin interaction maps reveal functional regulatory elements and chromatin architecture variations during wheat evolution [PDF]
Genome Biology, 2022 Background Bread wheat (Triticum aestivum) is an allohexaploid that is generated by two subsequent allopolyploidization events. The large genome size (16 Gb) and polyploid complexity impede our understanding of how regulatory elements and their ...
Jingya Yuan +11 more
doaj +2 more sources
Mapping open chromatin by ATAC-seq in bread wheat [PDF]
Frontiers in Plant Science, 2022 Gene transcription is largely regulated by cis-regulatory elements. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an emerging technology that can accurately map cis-regulatory elements in animals and plants.
Xin Wang +4 more
doaj +2 more sources
PATTY corrects open-chromatin bias for improved bulk and single-cell CUT&Tag profiling [PDF]
Nature CommunicationsAccurate epigenomic profiling is essential for understanding chromatin and gene regulation. Cleavage Under Targets & Tagmentation (CUT&Tag) enables efficient epigenomic profiling for low-input and single-cell samples and is increasingly adopted in ...
Shengen Shawn Hu +7 more
doaj +2 more sources
OCRClassifier: integrating statistical control chart into machine learning framework for better detecting open chromatin regions [PDF]
Frontiers in GeneticsOpen chromatin regions (OCRs) play a crucial role in transcriptional regulation and gene expression. In recent years, there has been a growing interest in using plasma cell-free DNA (cfDNA) sequencing data to detect OCRs. By analyzing the characteristics
Xin Lai +6 more
doaj +2 more sources