Cargando…

A Three-Dimensional Model of the Yeast Genome

Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes1-3. Interphase chromosomes are not positioned randomly within the nucleus but instead adopt preferred conformations4-7....

Descripción completa

Detalles Bibliográficos
Autores principales: Duan, Zhijun, Andronescu, Mirela, Schutz, Kevin, Mcllwain, Sean, Kim, Yoo Jung, Lee, Choli, Shendure, Jay, Fields, Stanley, Blau, C. Anthony, Noble, William S.
Formato: Texto
Lenguaje:English
Publicado: 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874121/
https://www.ncbi.nlm.nih.gov/pubmed/20436457
http://dx.doi.org/10.1038/nature08973
_version_ 1782181439159140352
author Duan, Zhijun
Andronescu, Mirela
Schutz, Kevin
Mcllwain, Sean
Kim, Yoo Jung
Lee, Choli
Shendure, Jay
Fields, Stanley
Blau, C. Anthony
Noble, William S.
author_facet Duan, Zhijun
Andronescu, Mirela
Schutz, Kevin
Mcllwain, Sean
Kim, Yoo Jung
Lee, Choli
Shendure, Jay
Fields, Stanley
Blau, C. Anthony
Noble, William S.
author_sort Duan, Zhijun
collection PubMed
description Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes1-3. Interphase chromosomes are not positioned randomly within the nucleus but instead adopt preferred conformations4-7. Disparate DNA elements co-localize into functionally defined aggregates or “factories” for transcription8 and DNA replication9. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope10-12. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among tRNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome.
format Text
id pubmed-2874121
institution National Center for Biotechnology Information
language English
publishDate 2010
record_format MEDLINE/PubMed
spelling pubmed-28741212010-11-20 A Three-Dimensional Model of the Yeast Genome Duan, Zhijun Andronescu, Mirela Schutz, Kevin Mcllwain, Sean Kim, Yoo Jung Lee, Choli Shendure, Jay Fields, Stanley Blau, C. Anthony Noble, William S. Nature Article Layered on top of information conveyed by DNA sequence and chromatin are higher order structures that encompass portions of chromosomes, entire chromosomes, and even whole genomes1-3. Interphase chromosomes are not positioned randomly within the nucleus but instead adopt preferred conformations4-7. Disparate DNA elements co-localize into functionally defined aggregates or “factories” for transcription8 and DNA replication9. In budding yeast, Drosophila and many other eukaryotes, chromosomes adopt a Rabl configuration, with arms extending from centromeres adjacent to the spindle pole body to telomeres that abut the nuclear envelope10-12. Nonetheless, the topologies and spatial relationships of chromosomes remain poorly understood. Here we developed a method to globally capture intra- and inter-chromosomal interactions, and applied it to generate a map at kilobase resolution of the haploid genome of Saccharomyces cerevisiae. The map recapitulates known features of genome organization, thereby validating the method, and identifies new features. Extensive regional and higher order folding of individual chromosomes is observed. Chromosome XII exhibits a striking conformation that implicates the nucleolus as a formidable barrier to interaction between DNA sequences at either end. Inter-chromosomal contacts are anchored by centromeres and include interactions among tRNA genes, among origins of early DNA replication and among sites where chromosomal breakpoints occur. Finally, we constructed a three-dimensional model of the yeast genome. Our findings provide a glimpse of the interface between the form and function of a eukaryotic genome. 2010-05-02 2010-05-20 /pmc/articles/PMC2874121/ /pubmed/20436457 http://dx.doi.org/10.1038/nature08973 Text en Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Duan, Zhijun
Andronescu, Mirela
Schutz, Kevin
Mcllwain, Sean
Kim, Yoo Jung
Lee, Choli
Shendure, Jay
Fields, Stanley
Blau, C. Anthony
Noble, William S.
A Three-Dimensional Model of the Yeast Genome
title A Three-Dimensional Model of the Yeast Genome
title_full A Three-Dimensional Model of the Yeast Genome
title_fullStr A Three-Dimensional Model of the Yeast Genome
title_full_unstemmed A Three-Dimensional Model of the Yeast Genome
title_short A Three-Dimensional Model of the Yeast Genome
title_sort three-dimensional model of the yeast genome
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874121/
https://www.ncbi.nlm.nih.gov/pubmed/20436457
http://dx.doi.org/10.1038/nature08973
work_keys_str_mv AT duanzhijun athreedimensionalmodeloftheyeastgenome
AT andronescumirela athreedimensionalmodeloftheyeastgenome
AT schutzkevin athreedimensionalmodeloftheyeastgenome
AT mcllwainsean athreedimensionalmodeloftheyeastgenome
AT kimyoojung athreedimensionalmodeloftheyeastgenome
AT leecholi athreedimensionalmodeloftheyeastgenome
AT shendurejay athreedimensionalmodeloftheyeastgenome
AT fieldsstanley athreedimensionalmodeloftheyeastgenome
AT blaucanthony athreedimensionalmodeloftheyeastgenome
AT noblewilliams athreedimensionalmodeloftheyeastgenome
AT duanzhijun threedimensionalmodeloftheyeastgenome
AT andronescumirela threedimensionalmodeloftheyeastgenome
AT schutzkevin threedimensionalmodeloftheyeastgenome
AT mcllwainsean threedimensionalmodeloftheyeastgenome
AT kimyoojung threedimensionalmodeloftheyeastgenome
AT leecholi threedimensionalmodeloftheyeastgenome
AT shendurejay threedimensionalmodeloftheyeastgenome
AT fieldsstanley threedimensionalmodeloftheyeastgenome
AT blaucanthony threedimensionalmodeloftheyeastgenome
AT noblewilliams threedimensionalmodeloftheyeastgenome