Nucleosome deposition and DNA methylation at coding region boundaries.
BACKGROUND
Nucleosome deposition downstream of transcription initiation and DNA methylation in the gene body suggest that control of transcription elongation is a key aspect of epigenetic regulation.


RESULTS
Here we report a genome-wide observation of distinct peaks of nucleosomes and methylation at both ends of a protein coding unit. Elongating polymerases tend to pause near both coding ends immediately upstream of the epigenetic peaks, causing a significant reduction in elongation efficiency. Conserved features in underlying protein coding sequences seem to dictate their evolutionary conservation across multiple species. The nucleosomal and methylation marks are commonly associated with high sequence-encoded DNA-bending propensity but differentially with CpG density. As the gene grows longer, the epigenetic codes seem to be shifted from variable inner sequences toward boundary regions, rendering the peaks more prominent in higher organisms.


CONCLUSIONS
Recent studies suggest that epigenetic inhibition of transcription elongation facilitates the inclusion of constitutive exons during RNA splicing. The epigenetic marks we identified here seem to secure the first and last coding exons from exon skipping as they are indispensable for accurate translation.
Choi
Jung Kyoon
JK
Department of Biochemistry, College of Life Science and Technology, Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul, Korea.
Bae
Jae-Bum
JB
Lyu
Jaemyun
J
Kim
Tae-Yoon
TY
Kim
Young-Joon
YJ
D000818:Animals; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D019143:Evolution, Molecular; D023281:Genomics / Q000379:methods; D006801:Humans; D009707:Nucleosomes / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics
D009707:Nucleosomes