Nucleosome deposition and DNA methylation at coding region boundaries

Jung K. Choi, Jae Bum Bae, Jaemyun Lyu, Tae Yoon Kim, Young Joon Kim

Research output: Contribution to journalArticlepeer-review

68 Citations (Scopus)


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.

Original languageEnglish
Article numberR89
JournalGenome biology
Issue number9
Publication statusPublished - 2009 Sept 1

Bibliographical note

Funding Information:
This work was supported by the Korea Science and Engineering Foundation (KOSEF) and the Korea Foundation for International Cooperation of Science and Technology (KICOS) through grants provided by the Korean Ministry of Education, Science and Technology (MEST) (M10750030001-08N5003-0011 and K20704000006-08A0500-00610).

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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