PT - JOURNAL ARTICLE AU - Jie Xiong AU - Shan Gao AU - Wen Dui AU - Wentao Yang AU - Xiao Chen AU - Sean D. Taverna AU - Ronald E. Pearlman AU - Wendy Ashlock AU - Wei Miao AU - Yifan Liu TI - Distinct nucleosome distribution patterns in two structurally and functionally differentiated nuclei of a unicellular eukaryote AID - 10.1101/018754 DP - 2015 Jan 01 TA - bioRxiv PG - 018754 4099 - http://biorxiv.org/content/early/2015/04/30/018754.short 4100 - http://biorxiv.org/content/early/2015/04/30/018754.full AB - 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 (TSS) likely connected with promoter proximal pausing of RNA polymerase II, as well as in exonic regions flanking both the 5’ and 3’ splice sites. In contrast, nucleosomes in MIC are more delocalized. Nucleosome occupancy in MAC and MIC are nonetheless highly correlated with each other and with predictions based upon DNA sequence features. Arrays of well-positioned nucleosomes are often correlated with GC content oscillations, suggesting significant contributions from cis-determinants. We propose that cis- and trans-determinants may coordinately accommodate some well-positioned nucleosomes with important functions, driven by a process in which positioned nucleosomes shape the mutational landscape of associated DNA sequences, while the DNA sequences in turn reinforce nucleosome positioning.