1
|
Bergalet J, Patel D, Legendre F, Lapointe C, Benoit Bouvrette LP, Chin A, Blanchette M, Kwon E, Lécuyer E. Inter-dependent Centrosomal Co-localization of the cen and ik2 cis-Natural Antisense mRNAs in Drosophila. Cell Rep 2021; 30:3339-3352.e6. [PMID: 32160541 DOI: 10.1016/j.celrep.2020.02.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 12/24/2019] [Accepted: 02/10/2020] [Indexed: 11/30/2022] Open
Abstract
Overlapping genes are prevalent in most genomes, but the extent to which this organization influences regulatory events operating at the post-transcriptional level remains unclear. Studying the cen and ik2 genes of Drosophila melanogaster, which are convergently transcribed as cis-natural antisense transcripts (cis-NATs) with overlapping 3' UTRs, we found that their encoded mRNAs strikingly co-localize to centrosomes. These transcripts physically interact in a 3' UTR-dependent manner, and the targeting of ik2 requires its 3' UTR sequence and the presence of cen mRNA, which serves as the main driver of centrosomal co-localization. The cen transcript undergoes localized translation in proximity to centrosomes, and its localization is perturbed by polysome-disrupting drugs. By interrogating global fractionation-sequencing datasets generated from Drosophila and human cellular models, we find that RNAs expressed as cis-NATs tend to co-localize to specific subcellular fractions. This work suggests that post-transcriptional interactions between RNAs with complementary sequences can dictate their localization fate in the cytoplasm.
Collapse
Affiliation(s)
- Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Dhara Patel
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Félix Legendre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Catherine Lapointe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Ashley Chin
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada
| | | | - Eunjeong Kwon
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada; Département de Biochimie et Médecine Moléculaire and Programme de Biologie Moléculaire, Université de Montréal, Montréal, QC, Canada; Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| |
Collapse
|
2
|
Hassine S, Bonnet-Magnaval F, Benoit Bouvrette LP, Doran B, Ghram M, Bouthillette M, Lecuyer E, DesGroseillers L. Staufen1 localizes to the mitotic spindle and controls the localization of RNA populations to the spindle. J Cell Sci 2020; 133:jcs247155. [PMID: 32576666 DOI: 10.1242/jcs.247155] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022] Open
Abstract
Staufen1 (STAU1) is an RNA-binding protein involved in the post-transcriptional regulation of mRNAs. We report that a large fraction of STAU1 localizes to the mitotic spindle in colorectal cancer HCT116 cells and in non-transformed hTERT-RPE1 cells. Spindle-associated STAU1 partly co-localizes with ribosomes and active sites of translation. We mapped the molecular determinant required for STAU1-spindle association within the first 88 N-terminal amino acids, a domain that is not required for RNA binding. Interestingly, transcriptomic analysis of purified mitotic spindles revealed that 1054 mRNAs and the precursor ribosomal RNA (pre-rRNA), as well as the long non-coding RNAs and small nucleolar RNAs involved in ribonucleoprotein assembly and processing, are enriched on spindles compared with cell extracts. STAU1 knockout causes displacement of the pre-rRNA and of 154 mRNAs coding for proteins involved in actin cytoskeleton organization and cell growth, highlighting a role for STAU1 in mRNA trafficking to spindle. These data demonstrate that STAU1 controls the localization of subpopulations of RNAs during mitosis and suggests a novel role of STAU1 in pre-rRNA maintenance during mitosis, ribogenesis and/or nucleoli reassembly.
Collapse
Affiliation(s)
- Sami Hassine
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Florence Bonnet-Magnaval
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Louis Philip Benoit Bouvrette
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Bellastrid Doran
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Mathieu Bouthillette
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| | - Eric Lecuyer
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Luc DesGroseillers
- Département de biochimie et médecine moléculaire, Faculté de médecine, Université de Montréal, 2900 Édouard Montpetit, Montréal, QC H3T 1J4, Canada
| |
Collapse
|
3
|
Van Nostrand EL, Freese P, Pratt GA, Wang X, Wei X, Xiao R, Blue SM, Chen JY, Cody NAL, Dominguez D, Olson S, Sundararaman B, Zhan L, Bazile C, Bouvrette LPB, Bergalet J, Duff MO, Garcia KE, Gelboin-Burkhart C, Hochman M, Lambert NJ, Li H, McGurk MP, Nguyen TB, Palden T, Rabano I, Sathe S, Stanton R, Su A, Wang R, Yee BA, Zhou B, Louie AL, Aigner S, Fu XD, Lécuyer E, Burge CB, Graveley BR, Yeo GW. A large-scale binding and functional map of human RNA-binding proteins. Nature 2020; 583:711-719. [PMID: 32728246 PMCID: PMC7410833 DOI: 10.1038/s41586-020-2077-3] [Citation(s) in RCA: 508] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 07/10/2019] [Indexed: 11/09/2022]
Abstract
Many proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.
Collapse
Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter Freese
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Xiaofeng Wang
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Xintao Wei
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Rui Xiao
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Medical Research Institute, Wuhan University, Wuhan, China
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Neal A L Cody
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Daniel Dominguez
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Balaji Sundararaman
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lijun Zhan
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Cassandra Bazile
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Julie Bergalet
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada
| | - Michael O Duff
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Keri E Garcia
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Myles Hochman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicole J Lambert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hairi Li
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Michael P McGurk
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thai B Nguyen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tsultrim Palden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ines Rabano
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Rebecca Stanton
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amanda Su
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Bing Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ashley L Louie
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Quebec, Canada.
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada.
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
| | - Christopher B Burge
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Brenton R Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, UConn Health, Farmington, CT, USA.
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
4
|
Benoit Bouvrette LP, Bovaird S, Blanchette M, Lécuyer E. oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. Nucleic Acids Res 2020; 48:D166-D173. [PMID: 31724725 PMCID: PMC7145663 DOI: 10.1093/nar/gkz986] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/11/2019] [Accepted: 10/28/2019] [Indexed: 01/26/2023] Open
Abstract
Protein-RNA interactions are essential for controlling most aspects of RNA metabolism, including synthesis, processing, trafficking, stability and degradation. In vitro selection methods, such as RNAcompete and RNA Bind-n-Seq, have defined the consensus target motifs of hundreds of RNA-binding proteins (RBPs). However, readily available information about the distribution features of these motifs across full transcriptomes was hitherto lacking. Here, we introduce oRNAment (o RNA motifs enrichment in transcriptomes), a database that catalogues the putative motif instances of 223 RBPs, encompassing 453 motifs, in a transcriptome-wide fashion. The database covers 525 718 complete coding and non-coding RNA species across the transcriptomes of human and four prominent model organisms: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster and Mus musculus. The unique features of oRNAment include: (i) hosting of the most comprehensive mapping of RBP motif instances to date, with 421 133 612 putative binding sites described across five species; (ii) options for the user to filter the data according to a specific threshold; (iii) a user-friendly interface and efficient back-end allowing the rapid querying of the data through multiple angles (i.e. transcript, RBP, or sequence attributes) and (iv) generation of several interactive data visualization charts describing the results of user queries. oRNAment is freely available at http://rnabiology.ircm.qc.ca/oRNAment/.
Collapse
Affiliation(s)
- Louis Philip Benoit Bouvrette
- Institut de Recherches Cliniques de Montréal (IRCM) Montréal, Québec, Canada.,Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec, Canada
| | - Samantha Bovaird
- Institut de Recherches Cliniques de Montréal (IRCM) Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | | | - Eric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM) Montréal, Québec, Canada.,Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| |
Collapse
|
5
|
Kong J, Han H, Bergalet J, Bouvrette LPB, Hernández G, Moon NS, Vali H, Lécuyer É, Lasko P. A ribosomal protein S5 isoform is essential for oogenesis and interacts with distinct RNAs in Drosophila melanogaster. Sci Rep 2019; 9:13779. [PMID: 31551467 PMCID: PMC6760144 DOI: 10.1038/s41598-019-50357-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 07/01/2019] [Indexed: 11/09/2022] Open
Abstract
In Drosophila melanogaster there are two genes encoding ribosomal protein S5, RpS5a and RpS5b. Here, we demonstrate that RpS5b is required for oogenesis. Females lacking RpS5b produce ovaries with numerous developmental defects that undergo widespread apoptosis in mid-oogenesis. Females lacking germline RpS5a are fully fertile, but germline expression of interfering RNA targeting germline RpS5a in an RpS5b mutant background worsened the RpS5b phenotype and blocked oogenesis before egg chambers form. A broad spectrum of mRNAs co-purified in immunoprecipitations with RpS5a, while RpS5b-associated mRNAs were specifically enriched for GO terms related to mitochondrial electron transport and cellular metabolic processes. Consistent with this, RpS5b mitochondrial fractions are depleted for proteins linked to oxidative phosphorylation and mitochondrial respiration, and RpS5b mitochondria tended to form large clusters and had more heterogeneous morphology than those from controls. We conclude that RpS5b-containing ribosomes preferentially associate with particular mRNAs and serve an essential function in oogenesis.
Collapse
Affiliation(s)
- Jian Kong
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hong Han
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Julie Bergalet
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Louis Philip Benoit Bouvrette
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.,Département de Biochimie, Université de Montréal, Montréal, QC, H3C 3J7, Canada
| | - Greco Hernández
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.,Unit of Biomedical Research on Cancer, National Institute of Cancer, Tlalpan, 14080, Mexico City, Mexico
| | - Nam-Sung Moon
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, Faculty of Dentistry, McGill University, Montréal, QC, Canada
| | - Éric Lécuyer
- Montreal Clinical Research Institute (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Paul Lasko
- Department of Biology, McGill University, 3649 Promenade Sir William Osler, Montréal, QC, H3G 0B1, Canada.
| |
Collapse
|
6
|
Benoit Bouvrette LP, Cody NAL, Bergalet J, Lefebvre FA, Diot C, Wang X, Blanchette M, Lécuyer E. CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells. RNA 2018; 24:98-113. [PMID: 29079635 PMCID: PMC5733575 DOI: 10.1261/rna.063172.117] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/13/2017] [Indexed: 05/26/2023]
Abstract
Cells are highly asymmetrical, a feature that relies on the sorting of molecular constituents, including proteins, lipids, and nucleic acids, to distinct subcellular locales. The localization of RNA molecules is an important layer of gene regulation required to modulate localized cellular activities, although its global prevalence remains unclear. We combine biochemical cell fractionation with RNA-sequencing (CeFra-seq) analysis to assess the prevalence and conservation of RNA asymmetric distribution on a transcriptome-wide scale in Drosophila and human cells. This approach reveals that the majority (∼80%) of cellular RNA species are asymmetrically distributed, whether considering coding or noncoding transcript populations, in patterns that are broadly conserved evolutionarily. Notably, a large number of Drosophila and human long noncoding RNAs and circular RNAs display enriched levels within specific cytoplasmic compartments, suggesting that these RNAs fulfill extra-nuclear functions. Moreover, fraction-specific mRNA populations exhibit distinctive sequence characteristics. Comparative analysis of mRNA fractionation profiles with that of their encoded proteins reveals a general lack of correlation in subcellular distribution, marked by strong cases of asymmetry. However, coincident distribution profiles are observed for mRNA/protein pairs related to a variety of functional protein modules, suggesting complex regulatory inputs of RNA localization to cellular organization.
Collapse
Affiliation(s)
- Louis Philip Benoit Bouvrette
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
- Département de Biochimie, Université de Montréal, Montréal H3C 3J7, Canada
| | - Neal A L Cody
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
| | - Julie Bergalet
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
| | - Fabio Alexis Lefebvre
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
- Département de Biochimie, Université de Montréal, Montréal H3C 3J7, Canada
| | - Cédric Diot
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
- Département de Biochimie, Université de Montréal, Montréal H3C 3J7, Canada
| | - Xiaofeng Wang
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
| | - Mathieu Blanchette
- McGill School of Computer Science, McGill University, Montréal H3A 0E9, Canada
| | - Eric Lécuyer
- Institut de Recherches Clinique de Montréal (IRCM), Montréal H2W 1R7, Canada
- Département de Biochimie, Université de Montréal, Montréal H3C 3J7, Canada
- Division of Experimental Medicine, McGill University, Montréal H4A 3J1, Canada
| |
Collapse
|