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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain
PLoS Genetics, Volume 8, No. 9, Article e1002954, Year 2012
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Description
Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs), HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low Tm downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA. © 2012 Riddle et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s001.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s002.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s003.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s004.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s005.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s006.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s007.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s008.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s009.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s010.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s011.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s012.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s013.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s014.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s015.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s016.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s017.xls
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s018.xlsx
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s019.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s020.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s021.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s022.docx
https://efashare.b-cdn.net/share/pmc/articles/PMC3447959/bin/pgen.1002954.s023.docx
Authors & Co-Authors
Riddle, Nicole C.
United States, St. Louis
Washington University in St. Louis
Jung, Youngsook Lucy
United States, Boston
Harvard Medical School
Gu, Tingting
United States, St. Louis
Washington University in St. Louis
Alekseyenko, Artyom A.
United States, Boston
Brigham and Women's Hospital
Asker, Dalal
United States, New Brunswick
Rutgers University–new Brunswick
Egypt, Alexandria
Faculty of Agriculture
Gui, Hongxing
United States, New Brunswick
Rutgers University–new Brunswick
Kharchenko, Peter V.
United States, Boston
Harvard Medical School
Minoda, Aki
United States, Berkeley
University of California, Berkeley
United States, Berkeley
Lawrence Berkeley National Laboratory
Plachetka, Annette
United States, Boston
Brigham and Women's Hospital
Schwartz, Yuri B.
United States, New Brunswick
Rutgers University–new Brunswick
Sweden, Umea
Umeå Universitet
Tolstorukov, Michael Y.
United States, Boston
Harvard Medical School
Kuroda, Mitzi I.
United States, Boston
Brigham and Women's Hospital
Pirrotta, Vincenzo
United States, New Brunswick
Rutgers University–new Brunswick
Karpen, Gary H.
United States, Berkeley
University of California, Berkeley
United States, Berkeley
Lawrence Berkeley National Laboratory
Park, Peter J.
United States, Boston
Harvard Medical School
Elgin, Sarah C.R.
United States, St. Louis
Washington University in St. Louis
Statistics
Citations: 52
Authors: 16
Affiliations: 8
Identifiers
Doi:
10.1371/journal.pgen.1002954
e-ISSN:
15537404
Research Areas
Cancer
Genetics And Genomics
Study Design
Cohort Study