Genomic maps and comparative analysis of histone modifications in human and mouse.

By Bradley E. Bernstein, Michael Kamal, Kerstin Lindblad-Toh, S. Bekiranov, D. Bailey, Dana J. Huebert, S. McMahon, Elinor K. Karlsson, E. Kulbokas, Thomas R. Gingeras and 2 more. Cell, 2005

1,605 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/22d5a2d2e52aaf61a9795c90315c8b4a8d84a0ad

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

1. Richard A. Young
2. Yi Zhang
3. D. Reinberg
4. Howard Y. Chang
5. A. Bird
6. C. D. Allis
7. Keji Zhao
8. Eric S. Lander

Citations in the corpus

• FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. (2008, positive): “Considering that H3K4me2 is typically associated with gene transcription (Bernstein et al., 2005), these results highlight the critical interplay between the pioneer factor FoxA1 and H3K4me2 at enhancers for efficient gene regulation.”
• Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease. (2008, background): “While H3K4me3 is highly enriched around transcriptional start sites, H3K4me2 seems to be present throughout the coding region of transcribed genes (Noma et al. 2001; Santos-Rosa et al. 2002; Liang et al. 2004; R. Schneider et al. 2004; Bernstein et al. 2005).”
• Modeling gene expression using chromatin features in various cellular contexts (2012, neutral): “Z) were generated by the Broad/ MGH ENCODE group using ChIP-Seq [42], and are available from the Gene Expression Omnibus (GEO; accession number GSE29611).”
• Genome-wide map of nucleosome acetylation and methylation in yeast. (2005, neutral): “…relative levels of intergenic and genic DNA are recovered using various extraction strategies (Nagy et al., 2003), but control data of this type have not yet been used to normalize the results of histone ChIP studies (Bernstein et al., 2004, 2005; Kurdistani et al., 2004; Lee et al., 2004 ).”
• A double take on bivalent promoters. (2013, result): “As observed in previous studies (Bernstein et al. 2005; Kim et al. 2005), the vast majority of transcriptional start sites (TSSs) were found as being marked by H3K4me3.”
• Genomic Views of Distant-Acting Enhancers (2009, background): “; and histone methylation present at orthologous loci in humans and mice did not correlate with overall increased levels of sequence conservatio”
• Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. (2007, methodology): “This corresponds well with recently published ChIP-chip results for these factors (Bernstein et al., 2005; Heintzman et al., 2007).”
• A bivalent chromatin structure marks key developmental genes in embryonic stem cells. (2006, methodology): “ChIP and control DNA samples were amplified by in vitro transcription, converted into double-stranded cDNA with random primers, fragmented with DNase I, and end-labeled with biotin as described (Kapranov et al., 2002; Liu et al., 2003; Cawley et al., 2004; Bernstein et al., 2005).”
• Androgen Receptor Regulates a Distinct Transcription Program in Androgen-Independent Prostate Cancer (2009, background): “We have recently defined a role for the active enhancer histone marks H3 lysine 4 monoand di-methyl (H3K4me1 and H3K4me2) (Bernstein et al., 2005; Heintzman et al., 2007) in specifying sites of FoxA1 recruitment in various cell types (Lupien et al.”
• Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation (2009, background): “Studies using ESCs suggest that bivalent modifications maintain the activation or silencing potential of critical differentiation genes (Azuara et al., 2006; Bernstein et al., 2006).”