Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

By Nathaniel D. Heintzman, R. Stuart, Gary Chung Hon, Yutao Fu, Christina W. Ching, R. Hawkins, Leah Barrera, Sara Van Calcar, Chunxu Qu, K. Ching and 5 more. Nature Genetics, 2007

3,418 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d45f613ed448ff7d5c094bd1181ab6ef230cf871

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Citations in the corpus

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers (2010, background): “Conversely, enhancers display high levels of H3K4me1, usually distributed over several kilobases, associated with low or no H3K4me3 (H3K4me1/H3K4me3 domains) [52,53].”
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. (2010, methodology): “…the identification of a specific enhancer-associated chromatin signature consisting in a broad (several kilobases-long) domain of histone H3K4 monomethylation (H3K4me1) combined with low amounts of H3K4me3 (a modification associated with the TSSs of active or poised genes) (Heintzman et al., 2007).”
Distinct Epigenomic Landscapes of Pluripotent and Lineage-committed Human Cells (2010, methodology): “Cell Stem Cell, Volume 6 Supplemental Information”
Dynamic regulation of nucleosome positioning in the human genome. (2008, positive): “During the past few years, large amounts of data pertaining to genome-wide profiles of histone modifications have been generated for a number of human cell types (Barski et al., 2007; Bernstein et al., 2005, 2006; Boyer et al., 2006; Guenther et al., 2007; Heintzman et al., 2007; Kim et al., 2005; L”
Opposing regulation of the Il17 locus through direct, reciprocal actions of STAT3 and STAT5 (2011, background): “Genome-wide studies have identified binding of the histone acetyltransferase p300 as a marker of gene-enhancer element”
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. (2007, background): “The distribution of H3K27me3 regions is rather unique: 6162 out of 10,554 (58%) modified loci are solely found on chromosome X as a result of X chromosome inactivation (XCI) ( Heard, 2004 ), and the karyotype of hES3 cells used in this study is 46; X, X. XCI has also been observed in female H9 human”
Genomic Views of Distant-Acting Enhancers (2009, background): “In contrast to promoters, which are marked by trimethylation of histone H3 at lysine residue 4 (H3K4me3), active enhancers are marked by monomethylation at this position (H3K4me1”
DEEP: a general computational framework for predicting enhancers (2014, background): “The second category is based on more sophisticated algorithms (15) that associate enhancers and promoters with certain types of histone modification marks and transcription regulators.”
Determinants of enhancer and promoter activities of regulatory elements (2019, background): “Heintzman (2007) and Robertson (2008) identify a signature of high H3K4me1 and low H3K4me3 at candidate enhancers that could be used to discern enhancers from promoters and predict their locations genome- wide.”
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. (2011, result): “been discussed in previous reports (Heintzman et al. 2007; Kim et al. 2008); however, this is the first study to provide direct evidence”
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007, background): “The strong association between TSSs and both histone modifications and DHSs prompted us to investigate whether the location and activity of TSSs could be predicted solely on the basis of chromatin structure information.”