SynthesisNucleic acids research2011
Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.
Synthesis in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed, 54 citations in OpenAlex.
- Regulation of chromatin accessibility and gene expression in the developing hippocampal primordium by LIM-HD transcription factor LHX2.PLoS genetics · 2023Article
- Chromatin Dynamics in Digestive System Cancer: Commander and Regulator.Frontiers in oncology · 2022Review
- Epitome: predicting epigenetic events in novel cell types with multi-cell deep ensemble learning.Nucleic acids research · 2021Article
- A Newly Assigned Role of CTCF in Cellular Response to Broken DNAs.Biomolecules · 2021Review
- Chromatin accessibility profiling methods.Nature reviews. Methods primers · 2021Article
- Construction of the gene regulatory network identifies MYC as a transcriptional regulator of SWI/SNF complex.Scientific reports · 2020Article
- Transcriptional Regulation ofGenes · 2019Review
- Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.PLoS computational biology · 2019Article
- Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana.Molecular biology and evolution · 2018Article
- GLANET: genomic loci annotation and enrichment tool.Bioinformatics (Oxford, England) · 2017Article
- Denoising genome-wide histone ChIP-seq with convolutional neural networks.Bioinformatics (Oxford, England) · 2017Article
- NicE-seq: high resolution open chromatin profiling.Genome biology · 2017Article
- Insights into inner ear-specific gene regulation: Epigenetics and non-coding RNAs in inner ear development and regeneration.Seminars in cell & developmental biology · 2017Review
- Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation.Nucleic acids research · 2017Article
- RGmatch: matching genomic regions to proximal genes in omics data integration.BMC bioinformatics · 2016Article
- Prenatal exposures and DNA methylation in newborns: a pilot study in Durban, South Africa.Environmental science. Processes & impacts · 2016Article
- The genome-wide DNA sequence specificity of the anti-tumour drug bleomycin in human cells.Molecular biology reports · 2016Article
- Massively parallel cis-regulatory analysis in the mammalian central nervous system.Genome research · 2016Article
- Non-targeted transcription factors motifs are a systemic component of ChIP-seq datasets.Genome biology · 2014Article
- Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To understand the molecular mechanisms that underlie global transcriptional regulation, it is essential to first identify all the transcriptional regulatory elements in the human genome. The advent of next-generation sequencing has provided a powerful platform for genome-wide analysis of different species and specific cell types; when combined with traditional techniques to identify regions of open chromatin [DNaseI hypersensitivity (DHS)] or specific binding locations of transcription factors [chromatin immunoprecipitation (ChIP)], and expression data from microarrays, we become uniquely poised to uncover the mysteries of the genome and its regulation. To this end, we have performed global meta-analysis of the relationship among data from DNaseI-seq, ChIP-seq and expression arrays, and found that specific correlations exist among regulatory elements and gene expression across different cell types. These correlations revealed four distinct modes of chromatin domain structure reflecting different functions: repressive, active, primed and bivalent. Furthermore, CCCTC-binding factor (CTCF) binding sites were identified based on these integrative data. Our findings uncovered a complex regulatory process involving by DNaseI HS sites and histone modifications, and suggest that these dynamic elements may be responsible for maintaining chromatin structure and integrity of the human genome. Our integrative approach provides an example by which data from diverse technology platforms may be integrated to provide more meaningful insights into global transcriptional regulation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.