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      Principles of chromosomal organization: lessons from yeast

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          Abstract

          The spatial organization of genes and chromosomes plays an important role in the regulation of several DNA processes. However, the principles and forces underlying this nonrandom organization are mostly unknown. Despite its small dimension, and thanks to new imaging and biochemical techniques, studies of the budding yeast nucleus have led to significant insights into chromosome arrangement and dynamics. The dynamic organization of the yeast genome during interphase argues for both the physical properties of the chromatin fiber and specific molecular interactions as drivers of nuclear order.

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          Population genomics of domestic and wild yeasts

          Gianni Liti, David Carter, Alan M. Moses … (2009)
          Since the completion of the genome sequence of Saccharomyces cerevisiae in 19961,2, there has been an exponential increase in complete genome sequences accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions3,4, population structure5-8, and sexual versus asexual reproduction9,10. Less well understood at the whole genome level are the evolutionary processes acting within populations and species leading to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to four-fold or more coverage of the genome sequences of over seventy isolates of the baker's yeast, S. cerevisiae, and its closest relative, S. paradoxus. We examine variation in gene content, SNPs, indels, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. Interestingly, S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variation.
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            High-density mapping of single-molecule trajectories with photoactivated localization microscopy.

            Suliana Manley, Jennifer Gillette, George Patterson … (2008)
            We combined photoactivated localization microscopy (PALM) with live-cell single-particle tracking to create a new method termed sptPALM. We created spatially resolved maps of single-molecule motions by imaging the membrane proteins Gag and VSVG, and obtained several orders of magnitude more trajectories per cell than traditional single-particle tracking enables. By probing distinct subsets of molecules, sptPALM can provide insight into the origins of spatial and temporal heterogeneities in membranes.
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              Life with 6000 genes.

              A Goffeau, B G Barrell, H Bussey … (1996)
              The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration. The sequence of 12,068 kilobases defines 5885 potential protein-encoding genes, approximately 140 genes specifying ribosomal RNA, 40 genes for small nuclear RNA molecules, and 275 transfer RNA genes. In addition, the complete sequence provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history. The genome shows a considerable amount of apparent genetic redundancy, and one of the major problems to be tackled during the next stage of the yeast genome project is to elucidate the biological functions of all of these genes.
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Cell Biol
                Journal ID (iso-abbrev): J. Cell Biol
                Journal ID (hwp): jcb
                Title: The Journal of Cell Biology
                Publisher: The Rockefeller University Press
                ISSN (Print): 0021-9525
                ISSN (Electronic): 1540-8140
                Publication date (Print): 7 March 2011
                Volume: 192
                Issue: 5
                Pages: 723-733
                Affiliations
                [1 ]Groupe Imagerie et Modélisation, Département Biologie Cellulaire et Infection , [2 ]Unité de Génétique Moléculaire des Levures, Département Génomes et Génétique ; and [3 ]Laboratoire Régulation Spatiale des Fonctions Génomiques, Département Génomes et Génétique, Institut Pasteur, F-75015 Paris, France
                [4 ]URA 2582 and [5 ]URA 2171, Centre National de la Recherche Scientifique, F-75015 Paris, France
                Author notes
                Correspondence to Emmanuelle Fabre: emmanuelle.fabre@ 123456pasteur.fr
                Article
                Publisher ID: 201010058
                DOI: 10.1083/jcb.201010058
                PMC ID: 3051815
                PubMed ID: 21383075
                SO-VID: b153d09a-953d-4bb8-8ad8-fb033678cba8
                Copyright © © 2011 Zimmer and Fabre
                License:

                This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

                History
                Date received : 11 October 2010
                Date accepted : 15 February 2011
                Categories
                Subject: Reviews
                Subject: Review

                ScienceOpen disciplines: Cell biology
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                ScienceOpen disciplines: Cell biology

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