title: Genomic characterization of the mouse ribosomal DNA locus.
abstract: The transcription of rRNA is critical to all living cells and is tightly controlled at the level of chromatin structure. Although the widespread adoption of genomic technologies including chromatin immunoprecipitation with massively parallel short-read sequencing (ChIP-seq) has allowed for the interrogation of chromatin structure on a genome-wide scale, until recently rDNA has not been analyzed by this technique. We extended genomic analysis of rDNA to mouse (Mus musculus), in which rDNA is similar in structure but highly divergent in sequence compared with human rDNA. Comparison of rDNA histone marks between mouse embryonic stem cells (mESCs) and more differentiated mouse cell types revealed differences between pluripotent and differentiated states. We also observed substantial divergence in rDNA histone modification patterns between mESCs and human embryonic stem cells (hESCs). Surprisingly, we found that the pluripotency factor OCT4 was bound to rDNA in similar patterns in mESCs and hESCs. Extending this analysis, we found that an additional 17 pluripotency-associated factors were bound to rDNA in mESCs, suggesting novel modes of rDNA regulation in pluripotent cells. Taken together, our results provide a detailed view of rDNA chromatin structure in an important model system and enable high-resolution comparison of rDNA regulation between mouse and human.
authors.affiliation: Department of Genetics and Genome Sciences, Case Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106.
authors.forename: Gabriel E
authors.initials: GE
authors.lastname: Zentner
authors.forename: Stephanie A
authors.initials: SA
authors.lastname: Balow
authors.forename: Peter C
authors.initials: PC
authors.lastname: Scacheri
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002843:Chromatin / Q000737:chemistry / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism; D056426:Genetic Loci; D016678:Genome; D006657:Histones / Q000378:metabolism; D006801:Humans; D051379:Mice; D050814:Octamer Transcription Factor-3 / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D011485:Protein Binding; D012335:RNA, Ribosomal / Q000235:genetics*; D013045:Species Specificity
chemical_list: D002843:Chromatin; D006657:Histones; D050814:Octamer Transcription Factor-3; C494173:POU5F1 protein, human; C494174:Pou5f1 protein, mouse; D012335:RNA, Ribosomal
keywords: ChIP-seq; Oct4; polycomb; rDNA; rRNA