TY - JOUR
T1 - A novel mechanism of epigenetic regulation
T2 - Nucleosome-space occupancy
AU - Cui, Peng
AU - Zhang, Lingfang
AU - Lin, Qiang
AU - Ding, Feng
AU - Xin, Chengqi
AU - Fang, Xiangdong
AU - Hu, Songnian
AU - Yu, Jun
N1 - Funding Information:
The study is supported by grants from the National Basic Research Program (973 Program; 2006CB910401 , 2006CB910403 , and 2006CB910404 ), the Ministry of Science and Technology of the People’s Republic of China .
PY - 2010/1/1
Y1 - 2010/1/1
N2 - Nucleosome positioning around the gene space (or transcriptional unit) plays a crucial role for gene regulation but we do not know if the spatial organization-nucleosome-space occupancy or nucleosome density in a defined sequence unit length-contributes to the regulation complexity of mammalian gene expression. Using our own rmRNA-Seq (ribosomal RNA-minus RNA sequencing) and publically available ChIP-Seq (H3) data from mouse stem cells, we discovered a non-random distribution of nucleosomes along chromosomes, and further genome-wide studies on histone modifications, DNA methylation, transcriptional activity, gene density, and base compositional dynamics, demonstrated that nucleosome-space occupancy of genomic regions-clustered genes and their intergenic spaces-show distinctive features, where a high occupancy coincides with active transcription, intensive histone modifications, poor DNA methylation, and higher GC contents as compared to the nucleosome-poor regions. We therefore proposed that nucleosome-space occupancy as a novel mechanism of epigenetic gene regulation, creating a vital environment for transcriptional activation.
AB - Nucleosome positioning around the gene space (or transcriptional unit) plays a crucial role for gene regulation but we do not know if the spatial organization-nucleosome-space occupancy or nucleosome density in a defined sequence unit length-contributes to the regulation complexity of mammalian gene expression. Using our own rmRNA-Seq (ribosomal RNA-minus RNA sequencing) and publically available ChIP-Seq (H3) data from mouse stem cells, we discovered a non-random distribution of nucleosomes along chromosomes, and further genome-wide studies on histone modifications, DNA methylation, transcriptional activity, gene density, and base compositional dynamics, demonstrated that nucleosome-space occupancy of genomic regions-clustered genes and their intergenic spaces-show distinctive features, where a high occupancy coincides with active transcription, intensive histone modifications, poor DNA methylation, and higher GC contents as compared to the nucleosome-poor regions. We therefore proposed that nucleosome-space occupancy as a novel mechanism of epigenetic gene regulation, creating a vital environment for transcriptional activation.
KW - Epigenetic regulation
KW - Histone modification
KW - Nucleosome
UR - http://www.scopus.com/inward/record.url?scp=72949095318&partnerID=8YFLogxK
U2 - 10.1016/j.bbrc.2009.11.157
DO - 10.1016/j.bbrc.2009.11.157
M3 - Article
C2 - 19948147
AN - SCOPUS:72949095318
SN - 0006-291X
VL - 391
SP - 884
EP - 889
JO - Biochemical and biophysical research communications
JF - Biochemical and biophysical research communications
IS - 1
ER -