Evidence for nucleosome depletion at active regulatory regions genome-wide

By Cheol-Koo Lee, Yoichiro Shibata, Bhargavi Rao, Brian D. Strahl, J. Lieb. Nature Genetics, 2004

809 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/ca4c2928367dfc2d7a10cd76fc092fc1fc934c3e

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Citations in the corpus

Chromatin remodelling: the industrial revolution of DNA around histones (2006, background): “Many promoters are slightly histone deficient, and become more deficient following activation, which raises the possibility that the ejection of histones helps to regulate transcription by enabling promoter acces”
Whole-Genome Analysis of Histone H3 Lysine 27 Trimethylation in Arabidopsis (2007, result): “similar to that observed in animals and fungi [31,37–41], Figure 4.”
A dual role of linker histone H1.4 Lys 34 acetylation in transcriptional activation. (2012, background): “S4D,E), consistent with nucleosome depletion from active regulatory regions (Lee et al. 2004; Heintzman et al. 2007).”
Genome-wide map of nucleosome acetylation and methylation in yeast. (2005, neutral): “genome-wide studies (Bernstein et al., 2004; Boeger et al., 2003; Lee et al., 2004; Reinke and Horz, 2003).”
Histone variant H2A.Z marks the 5' ends of both active and inactive genes in euchromatin. (2005, background): “Studies of global nucleosome density have also shown that the abundance of motifs containing dT:dA tracts correlate with nucleosome depletion from promoters (Bernstein et al., 2004; Lee et al., 2004).”
G+C content dominates intrinsic nucleosome occupancy (2009, background): “Active regulatory sequences are often depleted of nucleosomes[ 5-7 ], presumably due to steric hindrance constraints between nucleosomes and binding of most other DNA-binding proteins.”
A high-resolution atlas of nucleosome occupancy in yeast (2007, background): “Large-scale studies of nucleosome positions have shown that promoters are often depleted of nucleosome”
FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. (2007, methodology): “…by FAIRE has a very strong negative correlation with nucleosome occupancy (Hogan et al. 2006), as measured by comparison with nucleosome ChIP– chip experiments (Bernstein et al. 2004; Lee et al. 2004) and high-resolution mapping of nucleosomes with micrococcal nuclease digestion (Yuan et al. 2005).”
Dynamic regulation of nucleosome positioning in the human genome. (2008, methodology): “For example, a similar nucleosome depletion in the promoter region has been observed using both the MNase digestion strategy and sonication followed by H3-ChIP (Bernstein et al., 2004; Lee et al., 2004; Yuan et al., 2005).”
Genome-wide dynamics of Htz1, a histone H2A variant that poises repressed/basal promoters for activation through histone loss. (2005, neutral): “However, whereas mRPGs show typical levels of H2A (mMPR 50%), H2A is virtually absent at cRPG promoters (mMPR 10%; Figure S3), in keeping with the observations of others that cRPG promoters are deficient in histone H3 (Bernstein et al., 2004; Lee et al., 2004 ).”
Nucleosome positioning and gene regulation: advances through genomics (2009, background): “Nevertheless, for the first time, these pioneering studies showed a general depletion of nucleosomes in the intergenic regions where promoters are foun”
Nutritional Control of Growth and Development in Yeast (2012, background): “…factors Rap1 or Abf1, which generate a nucleosome-free domain and recruit the forkheadlike transcription factor, Fhl1, which in turn recruits the transcriptional activator Ifh1 to drive gene expression (Morse 2000; Boeger et al. 2003; Lee et al. 2004; Wade et al. 2004; Zhao et al. 2006).”
High-resolution profiling of histone methylations in the human genome. (2007, background): “The general picture emerging from these studies is that promoter regions of active genes have reduced nucleosome occupancy and elevated histone acetylation (Bernstein et al., 2002, 2004; Lee et al., 2004; Liu et al., 2005; Pokholok et al., 2005; Sekinger et al., 2005; Yuan et al., 2005).”