Dynamic regulation of nucleosome positioning in the human genome.

By Dustin E. Schones, Kairong Cui, Suresh Cuddapah, Tae-Young Roh, A. Barski, Zhibin Wang, Gang Wei, Keji Zhao. Cell, 2008

1,438 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/761d1165b0ee18c577f86929ccc29f9b6de6d796

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In Molecular Biology

1. Keji Zhao
2. Kairong Cui
3. A. Bird
4. Jason Ernst
5. Manolis Kellis
6. Dustin E. Schones
7. A. Deaton
8. Manel Esteller

Citations in the corpus

• ChIP-Seq: advantages and challenges of a maturing technology (2009, background): “, MNase treatment is generally preferred because it removes linker DNA more efficiently than sonication and therefore allows more precise mapping of each nucleosom”
• Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. (2011, background): “…every step of transcriptional regulation, i.e., analyses of nucleosome structures in regions surrounding TSSs (nucleosome-seq) (Albert et al. 2007; Schones et al. 2008; Jiang and Pugh 2009), the binding status of transcription factors, RNA polymerase II (pol II) and histone modifications…”
• Discovery and characterization of chromatin states for systematic annotation of the human genome (2010, background): “4-fold signal enrichment for the elongating form of PolII surveyed in an independent stud”
• Chromatin organization marks exon-intron structure (2009, methodology): “We next obtained a data set of nucleosome positioning within the human genome derived through Solexa high-throughput sequencing of DNA fragments attached to nucleosomes in activated T cells, following micrococcal nuclease (MNase) digestio”
• CpG islands and the regulation of transcription. (2011, positive): “Also, global nuclear run-on analysis examining the products of transcriptionally engaged RNAPII molecules detected bidirectional transcription of short nonproductive RNAs as well as full-length transcripts at many CGI promoters (Core et al. 2008; Seila et al. 2008).”
• H3.3/H2A.Z double variant-containing nucleosomes mark ‘nucleosome-free regions’ of active promoters and other regulatory regions in the human genome (2009, background): “Z NCPs) are unusually unstable under the conditions normally used in nucleosome preparations for such studies; it therefore seemed possible that preferential loss could account for earlier report”
• Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. (2009, methodology): “Genome-wide Maps of H3K4me3 and H3K27me3 Modifications in CD4 Effector and Regulatory T Cell Lineages To reveal epigenetic features acquired during CD4 T cell differentiation, we generated global maps of H3K4me3 and H3K27me3 modifications via the ChIP-seq approach (Barski et al., 2007; Schones et al”
• Histone modification levels are predictive for gene expression (2010, methodology): “Furthermore, we examined microarray data measuring the transcript abundance of each of these genes in CD4þ T-cells (18), where the logarithm of the intensity served as expression value.”