The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

Abstract The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To...

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Autores principales:	Jung-Hyun Kim, Vladimir N. Noskov, Aleksey Y. Ogurtsov, Ramaiah Nagaraja, Nikolai Petrov, Mikhail Liskovykh, Brian P. Walenz, Hee-Sheung Lee, Natalay Kouprina, Adam M. Phillippy, Svetlana A. Shabalina, David Schlessinger, Vladimir Larionov
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3fe958d0148f47c1a2f569bdf90256d7
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spelling	oai:doaj.org-article:3fe958d0148f47c1a2f569bdf90256d72021-12-02T14:06:56ZThe genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning10.1038/s41598-021-82565-x2045-2322https://doaj.org/article/3fe958d0148f47c1a2f569bdf90256d72021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82565-xhttps://doaj.org/toc/2045-2322Abstract The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.Jung-Hyun KimVladimir N. NoskovAleksey Y. OgurtsovRamaiah NagarajaNikolai PetrovMikhail LiskovykhBrian P. WalenzHee-Sheung LeeNatalay KouprinaAdam M. PhillippySvetlana A. ShabalinaDavid SchlessingerVladimir LarionovNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jung-Hyun Kim Vladimir N. Noskov Aleksey Y. Ogurtsov Ramaiah Nagaraja Nikolai Petrov Mikhail Liskovykh Brian P. Walenz Hee-Sheung Lee Natalay Kouprina Adam M. Phillippy Svetlana A. Shabalina David Schlessinger Vladimir Larionov The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
description	Abstract The rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.
format	article
author	Jung-Hyun Kim Vladimir N. Noskov Aleksey Y. Ogurtsov Ramaiah Nagaraja Nikolai Petrov Mikhail Liskovykh Brian P. Walenz Hee-Sheung Lee Natalay Kouprina Adam M. Phillippy Svetlana A. Shabalina David Schlessinger Vladimir Larionov
author_facet	Jung-Hyun Kim Vladimir N. Noskov Aleksey Y. Ogurtsov Ramaiah Nagaraja Nikolai Petrov Mikhail Liskovykh Brian P. Walenz Hee-Sheung Lee Natalay Kouprina Adam M. Phillippy Svetlana A. Shabalina David Schlessinger Vladimir Larionov
author_sort	Jung-Hyun Kim
title	The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
title_short	The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
title_full	The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
title_fullStr	The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
title_full_unstemmed	The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning
title_sort	genomic structure of a human chromosome 22 nucleolar organizer region determined by tar cloning
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3fe958d0148f47c1a2f569bdf90256d7
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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

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