title: Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain.
abstract: Nucleosome positioning maps of several organisms have shown that Transcription Start Sites (TSSs) are marked by nucleosome depleted regions flanked by strongly positioned nucleosomes. Using genome-wide nucleosome maps and histone variant occupancy in the mouse liver, we show that the majority of genes were associated with a single prominent H2A.Z containing nucleosome in their promoter region. We classified genes into clusters depending on the proximity of H2A.Z to the TSS. The genes with no detectable H2A.Z showed lowest expression level, whereas H2A.Z was positioned closer to the TSS of genes with higher expression levels. We confirmed this relation between the proximity of H2A.Z and expression level in the brain. The proximity of histone variant H2A.Z, but not H3.3 to the TSS, over seven consecutive nucleosomes, was correlated with expression. Further, a nucleosome was positioned over the TSS of silenced genes while it was displaced to expose the TSS in highly expressed genes. Our results suggest that gene expression levels in vivo are determined by accessibility of the TSS and proximity of H2A.Z.
authors: Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi 110 007, India.
authors: Rhishikesh
authors: R
authors: Bargaje
authors: Mohammad Parwez
authors: MP
authors: Alam
authors: Ashok
authors: A
authors: Patowary
authors: Maharnob
authors: M
authors: Sarkar
authors: Tamer
authors: T
authors: Ali
authors: Shivani
authors: S
authors: Gupta
authors: Manali
authors: M
authors: Garg
authors: Meghna
authors: M
authors: Singh
authors: Ramya
authors: R
authors: Purkanti
authors: Vinod
authors: V
authors: Scaria
authors: Sridhar
authors: S
authors: Sivasubbu
authors: Vani
authors: V
authors: Brahmachari
authors: Beena
authors: B
authors: Pillai
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D005260:Female; D005786:Gene Expression Regulation; D020868:Gene Silencing; D006657:Histones / Q000032:analysis*; D008099:Liver / Q000378:metabolism*; D051379:Mice; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism*; D024363:Transcription Initiation Site
chemical_list: D006657:Histones; D009707:Nucleosomes