Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells.
Mapping DNase I hypersensitive sites (DHSs) within nuclear chromatin is a traditional and powerful method of identifying genetic regulatory elements. DHSs have been mapped by capturing the ends of long DNase I-cut fragments (>100,000 bp), or 100-1200 bp DNase I-double cleavage fragments (also called double-hit fragments). But next generation sequencing requires a DNA library containing DNA fragments of 100-500 bp. Therefore, we used short DNA fragments released by DNase I digestion to generate DNA libraries for next generation sequencing. The short segments are 100-300 bp and can be directly cloned and used for high-throughput sequencing. We identified 83,897 DHSs in 2,343,479 tags across the human genome. Our results indicate that the DHSs identified by this DHS assay are consistent with those identified by longer fragments in previous studies. We also found: (1) the distribution of DHSs in promoter and other gene regions of similarly expressed genes differs among different chromosomes; (2) silenced genes had a more open chromatin structure than previously thought; (3) DHSs in 3'untranslated regions (3'UTRs) are negatively correlated with level of gene expression.
Department of Biochemistry and Molecular Biology, Cancer Institute, Capital Medical University, Beijing, China.
Ya-Mei
YM
Wang
Ping
P
Zhou
Li-Yong
LY
Wang
Zhen-Hua
ZH
Li
Yao-Nan
YN
Zhang
Yu-Xiang
YX
Zhang
D020413:3' Untranslated Regions; D001665:Binding Sites / Q000235:genetics; D002874:Chromosome Mapping; D018899:CpG Islands; D003850:Deoxyribonuclease I / Q000378:metabolism*; D005786:Gene Expression Regulation; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D058977:Molecular Sequence Annotation; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism
D020413:3' Untranslated Regions; D014157:Transcription Factors; D003850:Deoxyribonuclease I