title: Integrative genomic analysis of human ribosomal DNA.
abstract: The transcription of ribosomal RNA (rRNA) is critical to life. Despite its importance, ribosomal DNA (rDNA) is not included in current genome assemblies and, consequently, genomic analyses to date have excluded rDNA. Here, we show that short sequence reads can be aligned to a genome assembly containing a single rDNA repeat. Integrated analysis of ChIP-seq, DNase-seq, MNase-seq and RNA-seq data reveals several novel findings. First, the coding region of active rDNA is contained within nucleosome-depleted open chromatin that is highly transcriptionally active. Second, histone modifications are located not only at the rDNA promoter but also at novel sites within the intergenic spacer. Third, the distributions of active modifications are more similar within and between different cell types than repressive modifications. Fourth, UBF, a positive regulator of rRNA transcription, binds to sites throughout the genome. Lastly, the insulator binding protein CTCF associates with the spacer promoter of rDNA, suggesting that transcriptional insulation plays a role in regulating the transcription of rRNA. Taken together, these analyses confirm and expand the results of previous ChIP studies of rDNA and provide novel avenues for exploration of chromatin-mediated regulation of rDNA.
authors.affiliation: Department of Genetics, Case Western Reserve University, Cleveland, OH 44106, USA.
authors.forename: Gabriel E
authors.initials: GE
authors.lastname: Zentner
authors.forename: Alina
authors.initials: A
authors.lastname: Saiakhova
authors.forename: Pavel
authors.initials: P
authors.lastname: Manaenkov
authors.forename: Mark D
authors.initials: MD
authors.lastname: Adams
authors.forename: Peter C
authors.initials: PC
authors.lastname: Scacheri
mesh_terms: D000076246:CCCTC-Binding Factor; D002843:Chromatin / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004275:DNA, Ribosomal / Q000737:chemistry* / Q000378:metabolism; D015894:Genome, Human; D023281:Genomics; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D006801:Humans; D020014:K562 Cells; D009707:Nucleosomes / Q000378:metabolism; D035463:Pol1 Transcription Initiation Complex Proteins / Q000378:metabolism; D011401:Promoter Regions, Genetic; D012318:RNA Polymerase I / Q000378:metabolism; D012335:RNA, Ribosomal / Q000096:biosynthesis*; D012097:Repressor Proteins / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D002843:Chromatin; D004275:DNA, Ribosomal; D006657:Histones; D009707:Nucleosomes; D035463:Pol1 Transcription Initiation Complex Proteins; D012335:RNA, Ribosomal; D012097:Repressor Proteins; C063844:transcription factor UBF; D012318:RNA Polymerase I