A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.

Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study t...

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Main Authors: Ivan Liachko, Anand Bhaskar, Chanmi Lee, Shau Chee Claire Chung, Bik-Kwoon Tye, Uri Keich
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2010-05-01
Series:PLoS Genetics
Online Access:http://europepmc.org/articles/PMC2869322?pdf=render
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spelling doaj-910ede6ff9a340368023a5016bf001882020-11-24T21:47:52ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042010-05-0165e100094610.1371/journal.pgen.1000946A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.Ivan LiachkoAnand BhaskarChanmi LeeShau Chee Claire ChungBik-Kwoon TyeUri KeichEukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.http://europepmc.org/articles/PMC2869322?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Ivan Liachko
Anand Bhaskar
Chanmi Lee
Shau Chee Claire Chung
Bik-Kwoon Tye
Uri Keich
spellingShingle Ivan Liachko
Anand Bhaskar
Chanmi Lee
Shau Chee Claire Chung
Bik-Kwoon Tye
Uri Keich
A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
PLoS Genetics
author_facet Ivan Liachko
Anand Bhaskar
Chanmi Lee
Shau Chee Claire Chung
Bik-Kwoon Tye
Uri Keich
author_sort Ivan Liachko
title A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
title_short A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
title_full A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
title_fullStr A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
title_full_unstemmed A comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
title_sort comprehensive genome-wide map of autonomously replicating sequences in a naive genome.
publisher Public Library of Science (PLoS)
series PLoS Genetics
issn 1553-7390
1553-7404
publishDate 2010-05-01
description Eukaryotic chromosomes initiate DNA synthesis from multiple replication origins. The machinery that initiates DNA synthesis is highly conserved, but the sites where the replication initiation proteins bind have diverged significantly. Functional comparative genomics is an obvious approach to study the evolution of replication origins. However, to date, the Saccharomyces cerevisiae replication origin map is the only genome map available. Using an iterative approach that combines computational prediction and functional validation, we have generated a high-resolution genome-wide map of DNA replication origins in Kluyveromyces lactis. Unlike other yeasts or metazoans, K. lactis autonomously replicating sequences (KlARSs) contain a 50 bp consensus motif suggestive of a dimeric structure. This motif is necessary and largely sufficient for initiation and was used to dependably identify 145 of the up to 156 non-repetitive intergenic ARSs projected for the K. lactis genome. Though similar in genome sizes, K. lactis has half as many ARSs as its distant relative S. cerevisiae. Comparative genomic analysis shows that ARSs in K. lactis and S. cerevisiae preferentially localize to non-syntenic intergenic regions, linking ARSs with loci of accelerated evolutionary change.
url http://europepmc.org/articles/PMC2869322?pdf=render
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