ArticleBMC bioinformatics2011
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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
27 citing papers in PubMed, 40 citations in OpenAlex.
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- Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research.Nature communications · 2021Article
- Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance.Journal of biosciences · 2021Review
- Binding of anGenetics · 2019Article
- Expression of Micro-RNA-492 (MiR-492) in Human Cervical Cancer Cell Lines is Upregulated by Transfection with Wild-Type P53, Irradiation, and 5-Fluorouracil Treatment In Vitro.Medical science monitor : international medical journal of experimental and clinical research · 2018Article
- HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures.BMC bioinformatics · 2018Article
- Molecular mechanism(s) involved in differential expression of vitamin C transporters along the intestinal tract.American journal of physiology. Gastrointestinal and liver physiology · 2017Article
- Striatal H3K27 Acetylation Linked to Glutamatergic Gene Dysregulation in Human Heroin Abusers Holds Promise as Therapeutic Target.Biological psychiatry · 2017Article
- The upstreams and downstreams of H3K79 methylation by DOT1L.Chromosoma · 2016Review
- Mesodermal iPSC-derived progenitor cells functionally regenerate cardiac and skeletal muscle.The Journal of clinical investigation · 2015Article
- Genome-wide analysis of DNA methylation and gene expression patterns in purified, uncultured human liver cells and activated hepatic stellate cells.Oncotarget · 2015Article
- Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation.Molecular and cellular biology · 2015Article
- A liver-enriched long non-coding RNA, lncLSTR, regulates systemic lipid metabolism in mice.Cell metabolism · 2015Article
- Epigenetic modulation of intestinal cholesterol transporter Niemann-Pick C1-like 1 (NPC1L1) gene expression by DNA methylation.The Journal of biological chemistry · 2014Article
- Modelling epigenetic regulation of gene expression in 12 human cell types reveals combinatorial patterns of cell-type-specific genes.IET systems biology · 2014Article
- Regression hidden Markov modeling reveals heterogeneous gene expression regulation: a case study in mouse embryonic stem cells.BMC genomics · 2014Article
- ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.BMC genomics · 2014Article
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Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundGene expression is regulated at both the DNA sequence level and through modification of chromatin. However, the effect of chromatin on tissue/cell-type specific gene regulation (TCSR) is largely unknown. In this paper, we present a method to elucidate the relationship between histone modification/variation (HMV) and TCSR.
resultsA classifier for differentiating CD4+ T cell-specific genes from housekeeping genes using HMV data was built. We found HMV in both promoter and gene body regions to be predictive of genes which are targets of TCSR. For example, the histone modification types H3K4me3 and H3K27ac were identified as the most predictive for CpG-related promoters, whereas H3K4me3 and H3K79me3 were the most predictive for nonCpG-related promoters. However, genes targeted by TCSR can be predicted using other type of HMVs as well. Such redundancy implies that multiple type of underlying regulatory elements, such as enhancers or intragenic alternative promoters, which can regulate gene expression in a tissue/cell-type specific fashion, may be marked by the HMVs. Finally, we show that the predictive power of HMV for TCSR is not limited to protein-coding genes in CD4+ T cells, as we successfully predicted TCSR targeted genes in muscle cells, as well as microRNA genes with expression specific to CD4+ T cells, by the same classifier which was trained on HMV data of protein-coding genes in CD4+ T cells.
conclusionWe have begun to understand the HMV patterns that guide gene expression in both tissue/cell-type specific and ubiquitous manner.
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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.