Charting histone modifications and the functional organization of mammalian genomes

By Vicky W. Zhou, Amir Goren, Bradley E. Bernstein. Nature reviews genetics, 2011

1,182 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/a7f160d3a53773e8ca9afd960b5ea8fa983c57f2

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In Molecular Biology

Citations in the corpus

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage (2012, neutral): “Modifications included H3K27me3 and H3K4me3 (associated with inactive and active promoters respectively) and H3K4me1 and H3K27ac (associated with promoters and enhancers) (Barski et al., 2007; Cui et al., 2009; Ernst et al., 2011; Mikkelsen et al., 2007; Zhou et al., 2011).”
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. (2012, methodology): “Our transcript assemblies are also consistent with chromatin marks known to be associated with promoters (Zhou et al. 2011) (see also below).”
Satellite Cells and Skeletal Muscle Regeneration (2015, neutral): “Alternatively, other modifications are associated to gene repression, including trimethylation of histone H3 lysine 27 (H3K27me3) and methylation of lysine 9 of histone H3 (H3K9me) (Table 2) (335).”
Integrative epigenomic mapping defines four main chromatin states in Arabidopsis (2011, background): “…al, 2007), indicate a low combinatorial complexity of chromatin marks in Arabidopsis, as recently reported for metazoans (Wang et al, 2008; Hon et al, 2009; Ernst and Kellis, 2010; Gerstein et al, 2010; Roy et al, 2010; Kharchenko et al, 2011; Liu et al, 2011; Riddle et al, 2011; Zhou et al, 2011).”
Interpreting thelanguage of histone and DNA modifications (2014, background): “In addition to combinatorial PTMs that function together both synergistically and antagonistically, there is now an appreciation for PTM asymmetry within individual nucleosomes [35], novel types of PTMs with unique functions [36], nucleosomes bearing histone variants [7], and nuclear compartmentaliz”
A double take on bivalent promoters. (2013, background): “…in ES cells have revealed the presence of distinct histone marks at certain genomic domains, such as H3K4me1 and acetylation of H3K27 (H3K27ac) within active enhancers as well as H3K4me3 and H3K27me3 within active and repressed promoters, respectively (Zhou et al. 2011; Calo and Wysocka 2013).”
Revealing the vectors of cellular identity with single-cell genomics (2016, methodology): “These methods hold promise for elucidating the epigenetic controls of cellular identity 193,194 .”
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, background): “CpG islands, H3K4me2, and H3K27me3 were commonly selected features for the three-class models, in agreement with existing knowledge that CpG islands mark promoter regions, and inactive regions are enriched for H3K27me3 [36, 2].”
THE HISTONE DEACETYLASE SIRT6 IS A NOVEL TUMOR SUPPRESSOR THAT CONTROLS CANCER METABOLISM (2012, positive): “As expected, MYC binding exhibited a sharp peak on the promoters, colocalizing with the signal of H3K4me3 (a mark of activated as well as poised promoters) (Schneider et al., 2004; Zhou et al., 2011) (Figure 4D).”
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants (2013, background): “Regulatory elements such as promoters, enhancers, insulators, transcribed, and repressed regions are marked by distinct patterns of histone modifications (1), including histone H3 lysine 27 acetylation (H3K27ac), H3K27 trimethylation (H3K27me3), H3K36me3, H3K4 monomethylation (H3K4me1), H3K4me3, and”
Methylation multiplicity and its clinical values in cancer (2021, positive): “Lysine methylation could either activate or repress gene expression, depending on the location and degree of methylation (Refs 38, 41 – 44 , 46 ).”
An Integrated Encyclopedia of DNA Elements in the Human Genome (2012, background): “Table 2 describes the different histone modifications, their peak characteristics, and a summary of their known roles (reviewed in refs 36–39 ).”
Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters (2015, background): “H3K27me3 Enriched in closed or poised enhancers [21] and poised promoters [27].”