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      Nuclear pore proteins and the control of genome functions

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          Abstract

          Nuclear pore complexes (NPCs) are composed of several copies of proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules, and NPC components influence genome functions in a transport-independent manner. Here, Ibarra and Hetzer discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.

          Abstract

          Nuclear pore complexes (NPCs) are composed of several copies of ∼30 different proteins called nucleoporins (Nups). NPCs penetrate the nuclear envelope (NE) and regulate the nucleocytoplasmic trafficking of macromolecules. Beyond this vital role, NPC components influence genome functions in a transport-independent manner. Nups play an evolutionarily conserved role in gene expression regulation that, in metazoans, extends into the nuclear interior. Additionally, in proliferative cells, Nups play a crucial role in genome integrity maintenance and mitotic progression. Here we discuss genome-related functions of Nups and their impact on essential DNA metabolism processes such as transcription, chromosome duplication, and segregation.

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          The spindle-assembly checkpoint in space and time.

          Andrea Musacchio, Edward Salmon (2007)
          In eukaryotes, the spindle-assembly checkpoint (SAC) is a ubiquitous safety device that ensures the fidelity of chromosome segregation in mitosis. The SAC prevents chromosome mis-segregation and aneuploidy, and its dysfunction is implicated in tumorigenesis. Recent molecular analyses have begun to shed light on the complex interaction of the checkpoint proteins with kinetochores--structures that mediate the binding of spindle microtubules to chromosomes in mitosis. These studies are finally starting to reveal the mechanisms of checkpoint activation and silencing during mitotic progression.
          Article 0 comments Cited 688 times – based on 0 reviews     Review now
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            ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage.

            S Matsuoka, B. Ballif, A Smogorzewska … (2007)
            Cellular responses to DNA damage are mediated by a number of protein kinases, including ATM (ataxia telangiectasia mutated) and ATR (ATM and Rad3-related). The outlines of the signal transduction portion of this pathway are known, but little is known about the physiological scope of the DNA damage response (DDR). We performed a large-scale proteomic analysis of proteins phosphorylated in response to DNA damage on consensus sites recognized by ATM and ATR and identified more than 900 regulated phosphorylation sites encompassing over 700 proteins. Functional analysis of a subset of this data set indicated that this list is highly enriched for proteins involved in the DDR. This set of proteins is highly interconnected, and we identified a large number of protein modules and networks not previously linked to the DDR. This database paints a much broader landscape for the DDR than was previously appreciated and opens new avenues of investigation into the responses to DNA damage in mammals.
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              A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability.

              Renee D Paulsen, Deena V. Soni, Roy Wollman … (2009)
              Signaling pathways that respond to DNA damage are essential for the maintenance of genome stability and are linked to many diseases, including cancer. Here, a genome-wide siRNA screen was employed to identify additional genes involved in genome stabilization by monitoring phosphorylation of the histone variant H2AX, an early mark of DNA damage. We identified hundreds of genes whose downregulation led to elevated levels of H2AX phosphorylation (gammaH2AX) and revealed links to cellular complexes and to genes with unclassified functions. We demonstrate a widespread role for mRNA-processing factors in preventing DNA damage, which in some cases is caused by aberrant RNA-DNA structures. Furthermore, we connect increased gammaH2AX levels to the neurological disorder Charcot-Marie-Tooth (CMT) syndrome, and we find a role for several CMT proteins in the DNA-damage response. These data indicate that preservation of genome stability is mediated by a larger network of biological processes than previously appreciated.
              Article 0 comments Cited 223 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genes Dev
                Journal ID (iso-abbrev): Genes Dev
                Journal ID (hwp): genesdev
                Journal ID (pmc): genesdev
                Journal ID (publisher-id): GAD
                Title: Genes & Development
                Publisher: Cold Spring Harbor Laboratory Press
                ISSN (Print): 0890-9369
                ISSN (Electronic): 1549-5477
                Publication date (Print): 15 February 2015
                Volume: 29
                Issue: 4
                Pages: 337-349
                Affiliations
                Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
                Author notes
                Corresponding author: hetzer@ 123456salk.edu
                Article
                Medline ID: 8711660
                DOI: 10.1101/gad.256495.114
                PMC ID: 4335290
                PubMed ID: 25691464
                SO-VID: d1204f28-9150-449e-bf40-3312436ccd13
                Copyright © © 2015 Ibarra and Hetzer; Published by Cold Spring Harbor Laboratory Press
                License:

                This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genesdev.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

                History
                Page count
                Pages: 13
                Funding
                Funded by: National Institutes of Health
                Award ID: R01GM098749
                Funded by: American Cancer Society
                Award ID: P30CA014195
                Categories
                Subject: 2
                Subject: 17
                Subject: Review

                Keywords: nuclear genome,nuclear envelope,nuclear pore complex,nucleoporin,transcription control,mitosis,dna damage
                Data availability:
                Keywords: nuclear genome, nuclear envelope, nuclear pore complex, nucleoporin, transcription control, mitosis, dna damage

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