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dc.contributor.authorYu, Shoukai
dc.contributor.authorSilva, Bernardo Lemos
dc.date.accessioned2016-11-07T17:14:29Z
dc.date.issued2016
dc.identifierQuick submit: 2016-10-27T06:57:16-0400
dc.identifier.citationYu, Shoukai, and Bernardo Lemos. 2016. “A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome.” Genome Biology and Evolution (October 25): evw257. doi:10.1093/gbe/evw257.en_US
dc.identifier.issn1759-6653en_US
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:29360404
dc.description.abstractRibosomal rRNAs account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, while the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. We conclude that portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.en_US
dc.language.isoen_USen_US
dc.publisherOxford University Press (OUP)en_US
dc.relation.isversionofdoi:10.1093/gbe/evw257en_US
dash.licenseLAA
dc.titleA portrait of ribosomal DNA contacts with Hi-C reveals 5S and 45S rDNA anchoring points in the folded human genomeen_US
dc.typeJournal Articleen_US
dc.date.updated2016-10-27T10:57:36Z
dc.description.versionVersion of Recorden_US
dc.relation.journalGenome Biology and Evolutionen_US
dash.depositing.authorSilva, Bernardo Lemos
dc.date.available2016
dc.date.available2016-11-07T17:14:29Z
dc.identifier.doi10.1093/gbe/evw257*
dash.authorsorderedfalse
dash.contributor.affiliatedYu, Shoukai
dash.contributor.affiliatedLemos, Bernardo


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