Dissecting relative contributions of cis-and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin

Jie Xiong, Shan Gao, Wen Dui, Wentao Yang, Xiao Chen, Sean D. Taverna, Ronald E. Pearlman, Wendy Ashlock, Wei Miao, Yifan Liu

Research output: Contribution to journalArticlepeer-review

Abstract

The ciliate protozoan Tetrahymena thermophila contains two types of structurally and functionally differentiated nuclei: The transcriptionally active somatic macronucleus (MAC) and the transcriptionally silent germ-line micronucleus (MIC). Here, we demonstrate that MAC features well-positioned nucleosomes downstream of transcription start sites and flanking splice sites. Transcription-Associated trans-determinants promote nucleosome positioning in MAC. By contrast, nucleosomes in MIC are dramatically delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other, as well as with in vitro reconstitution and predictions based upon DNA sequence features, revealing unexpectedly strong contributions from cisdeterminants. In particular, well-positioned nucleosomes are often matched with GC content oscillations. As many nucleosomes are coordinately accommodated by both cis-and trans-determinants, we propose that their distribution is shaped by the impact of these nucleosomes on the mutational and transcriptional landscape, and driven by evolutionary selection.

Original languageEnglish (US)
Pages (from-to)10091-10105
Number of pages15
JournalNucleic acids research
Volume44
Issue number21
DOIs
StatePublished - Dec 2016

ASJC Scopus subject areas

  • Genetics

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