1
|
Godneeva B, Ninova M, Fejes-Toth K, Aravin A. SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes. eLife 2023; 12:RP89493. [PMID: 37999956 PMCID: PMC10672805 DOI: 10.7554/elife.89493] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 11/25/2023] Open
Abstract
The conserved family of Transcription Intermediary Factors (TIF1) proteins consists of key transcriptional regulators that control transcription of target genes by modulating chromatin state. Unlike mammals that have four TIF1 members, Drosophila only encodes one member of the family, Bonus. Bonus has been implicated in embryonic development and organogenesis and shown to regulate several signaling pathways, however, its targets and mechanism of action remained poorly understood. We found that knockdown of Bonus in early oogenesis results in severe defects in ovarian development and in ectopic expression of genes that are normally repressed in the germline, demonstrating its essential function in the ovary. Recruitment of Bonus to chromatin leads to silencing associated with accumulation of the repressive H3K9me3 mark. We show that Bonus associates with the histone methyltransferase SetDB1 and the chromatin remodeler NuRD and depletion of either component releases Bonus-induced repression. We further established that Bonus is SUMOylated at a single site at its N-terminus that is conserved among insects and this modification is indispensable for Bonus's repressive activity. SUMOylation influences Bonus's subnuclear localization, its association with chromatin and interaction with SetDB1. Finally, we showed that Bonus SUMOylation is mediated by the SUMO E3-ligase Su(var)2-10, revealing that although SUMOylation of TIF1 proteins is conserved between insects and mammals, both the mechanism and specific site of modification is different in the two taxa. Together, our work identified Bonus as a regulator of tissue-specific gene expression and revealed the importance of SUMOylation as a regulator of complex formation in the context of transcriptional repression.
Collapse
Affiliation(s)
- Baira Godneeva
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
- Institute of Gene Biology, Russian Academy of SciencesMoscowRussian Federation
| | - Maria Ninova
- University of California, RiversideRiversideUnited States
| | - Katalin Fejes-Toth
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological EngineeringPasadenaUnited States
| |
Collapse
|
2
|
Lisitskaya L, Petushkov I, Esyunina D, Aravin A, Kulbachinskiy A. Recognition of double-stranded DNA by the Rhodobacter sphaeroides Argonaute protein. Biochem Biophys Res Commun 2020; 533:1484-1489. [PMID: 33333714 DOI: 10.1016/j.bbrc.2020.10.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 10/23/2022]
Abstract
In contrast to eukaryotic Argonaute proteins that act on RNA targets, prokaryotic Argonautes (pAgos) can target DNA, using either small RNA or small DNA guides for its recognition. Since pAgos can recognize only a single strand of DNA and lack a helicase activity, it remains unknown how double-stranded DNA can be bound both in vitro and in vivo. Here, using in vitro reconstitution and footprinting assays we analyze formation of specific complexes with target DNA by a catalytically inactive pAgo, RsAgo from Rhodobacter sphaeroides programmed with small guide RNAs. We showed that RsAgo can recognize a specific site in double-stranded DNA after stepwise reconstitution of the complex from individual oligonucleotides or after prior melting of the DNA target. When bound, RsAgo stabilizes an open DNA bubble corresponding to the length of the guide molecule and protects the target DNA from nuclease cleavage. The results suggest that RsAgo and, possibly, other RNA-guided pAgos cannot directly attack double-stranded DNA and likely require DNA opening by other cellular processes for their action.
Collapse
Affiliation(s)
- Lidia Lisitskaya
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - Ivan Petushkov
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, 123182, Russia
| | - Alexei Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, NRC "Kurchatov Institute", Moscow, 123182, Russia.
| |
Collapse
|
3
|
Bamezai S, Mulaw M, Vegi N, Zhou F, Rohde C, Döhner K, Döhner H, Feuring-Buske M, Höll J, Kloetgen A, Borkhardt A, Aravin A, Plass C, Müller-Tidow C, Rawat V, Buske C. Aberrantly expressed stem cell associated protein PIWIL4 acts as a piRNA binding, epigenetically active and growth regulatory factor in human acute myeloid leukemia. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
4
|
Ciabrelli F, Comoglio F, Fellous S, Bonev B, Ninova M, Szabo Q, Xuéreb A, Klopp C, Aravin A, Paro R, Bantignies F, Cavalli G. Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila. Nat Genet 2017; 49:876-886. [PMID: 28436983 PMCID: PMC5484582 DOI: 10.1038/ng.3848] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [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: 08/09/2016] [Accepted: 03/27/2017] [Indexed: 12/15/2022]
Abstract
Transgenerational Epigenetic Inheritance (TEI) studies the transmission of alternative functional states through multiple generations in the presence of the same genomic DNA sequence. Very little is known on the principles and the molecular mechanisms governing this type of inheritance. Here, by transiently enhancing 3D chromatin interactions, we established stable and isogenic Drosophila epilines that carry alternative epialleles, defined by differential levels of the Polycomb-dependent H3K27me3 mark. Once established, epialleles can be dominantly transmitted to naïve flies and induce paramutation. Importantly, epilines can be reset to a naïve state by disrupting chromatin interactions. Finally, we show that environmental changes can modulate the expressivity of the epialleles and we extend our paradigm to naturally occurring phenotypes. Our work sheds light on how nuclear organization and Polycomb group proteins contribute to epigenetically inheritable phenotypic variability.
Collapse
Affiliation(s)
- Filippo Ciabrelli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Boyan Bonev
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Maria Ninova
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Quentin Szabo
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | | | - Christophe Klopp
- Unité de Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet Tolosan, France
| | - Alexei Aravin
- Division of Biology, California Institute of Technology, Pasadena, California, USA
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Frédéric Bantignies
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, Montpellier, France
| |
Collapse
|
5
|
Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K. The histone chaperone CAF-1 safeguards somatic cell identity. Nature 2016; 528:218-24. [PMID: 26659182 PMCID: PMC4866648 DOI: 10.1038/nature15749] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [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: 02/23/2015] [Accepted: 09/28/2015] [Indexed: 12/25/2022]
Abstract
Cellular differentiation involves profound remodeling of chromatic landscapes, yet the mechanisms by which somatic cell identity is subsequently maintained remain incompletely understood. To further elucidate regulatory pathways that safeguard the somatic state, we performed two comprehensive RNAi screens targeting chromatin factors during transcription factor-mediated reprogramming of mouse fibroblasts to induced pluripotent stem cells (iPSCs). Remarkably, subunits of the chromatin assembly factor-1 (CAF-1) complex emerged as the most prominent hits from both screens, followed by modulators of lysine sumoylation and heterochromatin maintenance. Optimal modulation of both CAF-1 and transcription factor levels increased reprogramming efficiency by several orders of magnitude and facilitated iPSC formation in as little as 4 days. Mechanistically, CAF-1 suppression led to a more accessible chromatin structure at enhancer elements early during reprogramming. These changes were accompanied by a decrease in somatic heterochromatin domains, increased binding of Sox2 to pluripotency-specific targets and activation of associated genes. Notably, suppression of CAF-1 also enhanced the direct conversion of B cells into macrophages and fibroblasts into neurons. Together, our findings reveal the histone chaperone CAF-1 as a novel regulator of somatic cell identity during transcription factor-induced cell fate transitions and provide a potential strategy to modulate cellular plasticity in a regenerative setting.
Collapse
Affiliation(s)
- Sihem Cheloufi
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Barbara Hopfgartner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Youngsook L Jung
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Jernej Murn
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Maria Ninova
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Maria Hubmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Aimee I Badeaux
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Cheen Euong Ang
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Danielle Tenen
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Daniel J Wesche
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nadezhda Abazova
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Max Hogue
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Nilgun Tasdemir
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Justin Brumbaugh
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Philipp Rathert
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Julian Jude
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Francesco Ferrari
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Andres Blanco
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Michaela Fellner
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Daniel Wenzel
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Marietta Zinner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Simon E Vidal
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Matthias Stadtfeld
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Howard Y Chang
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Scott W Lowe
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA.,Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - John Rinn
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology and Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Alexei Aravin
- California Institute of Technology, Division of Biology and Biological Engineering, Pasadena, California 91125, USA
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), A-1030 Vienna, Austria
| | - Konrad Hochedlinger
- Department of Molecular Biology, Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| |
Collapse
|
6
|
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ. Preparation of small RNA libraries for high-throughput sequencing. Cold Spring Harb Protoc 2012; 2012:1067-77. [PMID: 23028068 DOI: 10.1101/pdb.prot071431] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This protocol details the process of small RNA cloning for sequencing on the Illumina/Solexa sequencing platform, but it can be easily modified for use on other next-generation platforms (e.g., SOLiD, 454). This procedure is designed to clone canonical small RNA molecules with 5'-monophosphate and 3'-hydroxyl termini. Modifications, such as the presence of a 2'-O-methyl group, can reduce efficiency, although not sufficiently to negate the utility of the approach. Other termini modifications, such as a 5' triphosphate or a 3' phosphate, can be altered by enzymatic treatment before cloning.
Collapse
|
7
|
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007; 129:1401-14. [PMID: 17604727 PMCID: PMC2681231 DOI: 10.1016/j.cell.2007.04.040] [Citation(s) in RCA: 2892] [Impact Index Per Article: 170.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2006] [Revised: 03/03/2007] [Accepted: 04/16/2007] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.
Collapse
Affiliation(s)
- Pablo Landgraf
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Mirabela Rusu
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Robert Sheridan
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Alain Sewer
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics
| | - Nicola Iovino
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Alexei Aravin
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Sébastien Pfeffer
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Amanda Rice
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Alice O. Kamphorst
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Markus Landthaler
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Carolina Lin
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
| | - Nicholas D. Socci
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | | | - Valerio Fulci
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma “La Sapienza”, 00185 Roma, Italy
| | - Sabina Chiaretti
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma “La Sapienza”, 00185 Roma, Italy
| | - Robin Foà
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma “La Sapienza”, 00185 Roma, Italy
| | - Julia Schliwka
- Div. Molecular Genetics B060, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Uta Fuchs
- Oncology and Hematology Department, Dr. v. Hauner Children’s Hospital, University of Munich, 80337 Munich, Germany
| | - Astrid Novosel
- Oncology and Hematology Department, Dr. v. Hauner Children’s Hospital, University of Munich, 80337 Munich, Germany
| | - Roman-Ulrich Müller
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
- Renal Division, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Bernhard Schermer
- Renal Division, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Ute Bissels
- Miltenyi Biotec GmbH, 50829 Cologne, Germany
| | - Jason Inman
- TIGR (The Institute for Genomic Research), Rockville, MD 20850, USA
| | - Quang Phan
- J. Craig Venter Institute, Functional Genomics, Rockville, MD 20850, USA
| | - Minchen Chien
- Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
| | - David B. Weir
- Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
| | - Ruchi Choksi
- Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
| | - Gabriella De Vita
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Universita’ di Napoli FedericoII, 80131 Napoli, Italy
| | - Daniela Frezzetti
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Universita’ di Napoli FedericoII, 80131 Napoli, Italy
| | - Hans-Ingo Trompeter
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Medical Center, 40225 Düsseldorf, Germany
| | | | - Grace Teng
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10021, USA
| | - Gunther Hartmann
- Division of Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
| | - Miklos Palkovits
- Laboratory of Neuromorphology, Hungarian Academy of Sciences-Semmelweis University, Budapest, Hungary
| | - Roberto Di Lauro
- Dipartimento di Biologia e Patologia Cellulare e Molecolare, Universita’ di Napoli FedericoII, 80131 Napoli, Italy
- IRGS, Biogem s.c.ar.l., 83031, Ariano Irpino (AV), Italy
| | - Peter Wernet
- Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Medical Center, 40225 Düsseldorf, Germany
| | - Giuseppe Macino
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma “La Sapienza”, 00185 Roma, Italy
| | - Charles E. Rogler
- Ullman Bldg Room 509, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - James W. Nagle
- DNA Sequencing Facility, NINDS, NIH, Bethesda, MD 20892, USA
| | - Jingyue Ju
- Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - F. Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10021, USA
| | - Thomas Benzing
- Renal Division, University Hospital Freiburg, 79106 Freiburg, Germany
| | - Peter Lichter
- Div. Molecular Genetics B060, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, the Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10021, USA
| | | | | | - Arndt Borkhardt
- Oncology and Hematology Department, Dr. v. Hauner Children’s Hospital, University of Munich, 80337 Munich, Germany
| | - James J. Russo
- Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Mihaela Zavolan
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics
- *Contact: Mihaela Zavolan, , phone: +41 61 267-1577; Thomas Tuschl, , phone: +1 212 327-7651
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
- *Contact: Mihaela Zavolan, , phone: +41 61 267-1577; Thomas Tuschl, , phone: +1 212 327-7651
| |
Collapse
|
8
|
Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, Chien M, Russo JJ, Ju J, Sheridan R, Sander C, Zavolan M, Tuschl T. A novel class of small RNAs bind to MILI protein in mouse testes. Nature 2006; 442:203-7. [PMID: 16751777 DOI: 10.1038/nature04916] [Citation(s) in RCA: 1056] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2006] [Accepted: 05/17/2006] [Indexed: 11/09/2022]
Abstract
Small RNAs bound to Argonaute proteins recognize partially or fully complementary nucleic acid targets in diverse gene-silencing processes. A subgroup of the Argonaute proteins--known as the 'Piwi family'--is required for germ- and stem-cell development in invertebrates, and two Piwi members--MILI and MIWI--are essential for spermatogenesis in mouse. Here we describe a new class of small RNAs that bind to MILI in mouse male germ cells, where they accumulate at the onset of meiosis. The sequences of the over 1,000 identified unique molecules share a strong preference for a 5' uridine, but otherwise cannot be readily classified into sequence families. Genomic mapping of these small RNAs reveals a limited number of clusters, suggesting that these RNAs are processed from long primary transcripts. The small RNAs are 26-31 nucleotides (nt) in length--clearly distinct from the 21-23 nt of microRNAs (miRNAs) or short interfering RNAs (siRNAs)--and we refer to them as 'Piwi-interacting RNAs' or piRNAs. Orthologous human chromosomal regions also give rise to small RNAs with the characteristics of piRNAs, but the cloned sequences are distinct. The identification of this new class of small RNAs provides an important starting point to determine the molecular function of Piwi proteins in mammalian spermatogenesis.
Collapse
Affiliation(s)
- Alexei Aravin
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Sewer A, Paul N, Landgraf P, Aravin A, Pfeffer S, Brownstein MJ, Tuschl T, van Nimwegen E, Zavolan M. Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics 2005; 6:267. [PMID: 16274478 PMCID: PMC1315341 DOI: 10.1186/1471-2105-6-267] [Citation(s) in RCA: 198] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 11/07/2005] [Indexed: 11/20/2022] Open
Abstract
Background MicroRNAs (miRNAs) are endogenous 21 to 23-nucleotide RNA molecules that regulate protein-coding gene expression in plants and animals via the RNA interference pathway. Hundreds of them have been identified in the last five years and very recent works indicate that their total number is still larger. Therefore miRNAs gene discovery remains an important aspect of understanding this new and still widely unknown regulation mechanism. Bioinformatics approaches have proved to be very useful toward this goal by guiding the experimental investigations. Results In this work we describe our computational method for miRNA prediction and the results of its application to the discovery of novel mammalian miRNAs. We focus on genomic regions around already known miRNAs, in order to exploit the property that miRNAs are occasionally found in clusters. Starting with the known human, mouse and rat miRNAs we analyze 20 kb of flanking genomic regions for the presence of putative precursor miRNAs (pre-miRNAs). Each genome is analyzed separately, allowing us to study the species-specific identity and genome organization of miRNA loci. We only use cross-species comparisons to make conservative estimates of the number of novel miRNAs. Our ab initio method predicts between fifty and hundred novel pre-miRNAs for each of the considered species. Around 30% of these already have experimental support in a large set of cloned mammalian small RNAs. The validation rate among predicted cases that are conserved in at least one other species is higher, about 60%, and many of them have not been detected by prediction methods that used cross-species comparisons. A large fraction of the experimentally confirmed predictions correspond to an imprinted locus residing on chromosome 14 in human, 12 in mouse and 6 in rat. Our computational tool can be accessed on the world-wide-web. Conclusion Our results show that the assumption that many miRNAs occur in clusters is fruitful for the discovery of novel miRNAs. Additionally we show that although the overall miRNA content in the observed clusters is very similar across the three considered species, the internal organization of the clusters changes in evolution.
Collapse
Affiliation(s)
- Alain Sewer
- Biozentrum, Universität Basel, Basel, Switzerland
| | | | - Pablo Landgraf
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, USA
| | - Alexei Aravin
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, USA
| | - Sébastien Pfeffer
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, USA
- IBMP-CNRS, Strasbourg, France
| | | | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, Rockefeller University, New York, USA
| | | | | |
Collapse
|
10
|
Abstract
Double-stranded RNA (dsRNA) is a potent trigger of sequence-specific gene silencing mechanisms known as RNA silencing or RNA interference. The recognition of the target sequences is mediated by ribonucleoprotein complexes that contain 21- to 28-nucleotide (nt) guide RNAs derived from processing of the trigger dsRNA. Here, we review the experimental and bioinformatic approaches that were used to identify and characterize these small RNAs isolated from cells and tissues. The identification and characterization of small RNAs and their expression patterns is important for elucidating gene regulatory networks.
Collapse
Affiliation(s)
- Alexei Aravin
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021, USA.
| | | |
Collapse
|
11
|
Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005; 33:2697-706. [PMID: 15891114 PMCID: PMC1110742 DOI: 10.1093/nar/gki567] [Citation(s) in RCA: 592] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
MicroRNAs (miRNAs) are ∼22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of known miRNAs in human. We show that human miRNA gene clustering is significantly higher than expected at random. A total of 37% of the known human miRNA genes analyzed in this study appear in clusters of two or more with pairwise chromosomal distances of at most 3000 nt. Comparison of the miRNA sequences with their homologs in four other organisms reveals a typical conservation pattern, persistent throughout the clusters. Furthermore, we show enrichment in the typical conservation patterns and other miRNA-like properties in the vicinity of known miRNA genes, compared with random genomic regions. This may imply that additional, yet unknown, miRNAs reside in these regions, consistent with the current recognition that there are overlooked miRNAs. Indeed, by comparing our predictions with cloning results and with identified miRNA genes in other mammals, we corroborate the predictions of 18 additional human miRNA genes in the vicinity of the previously known ones. Our study raises the proportion of clustered human miRNAs that are <3000 nt apart to 42%. This suggests that the clustering of miRNA genes is higher than currently acknowledged, alluding to its evolutionary and functional implications.
Collapse
Affiliation(s)
| | - Pablo Landgraf
- Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, Box 186, New York, NY 10021, USA
| | | | | | - Sébastien Pfeffer
- Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, Box 186, New York, NY 10021, USA
| | - Alexei Aravin
- Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, Box 186, New York, NY 10021, USA
| | - Michael J. Brownstein
- Laboratory of Genetics NIMH/NHGRI, National Institutes of HealthBuilding 36, Room 3D06 Bethesda, MD 20892, USA
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University1230 York Avenue, Box 186, New York, NY 10021, USA
| | - Hanah Margalit
- To whom correspondence should be addressed. Tel: +972 2 6758614; Fax: +972 2 6757308;
| |
Collapse
|
12
|
Abstract
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted target sites on the 3' untranslated regions of human gene transcripts for all currently known 218 mammalian miRNAs to facilitate focused experiments. We report about 2,000 human genes with miRNA target sites conserved in mammals and about 250 human genes conserved as targets between mammals and fish. The prediction algorithm optimizes sequence complementarity using position-specific rules and relies on strict requirements of interspecies conservation. Experimental support for the validity of the method comes from known targets and from strong enrichment of predicted targets in mRNAs associated with the fragile X mental retardation protein in mammals. This is consistent with the hypothesis that miRNAs act as sequence-specific adaptors in the interaction of ribonuclear particles with translationally regulated messages. Overrepresented groups of targets include mRNAs coding for transcription factors, components of the miRNA machinery, and other proteins involved in translational regulation, as well as components of the ubiquitin machinery, representing novel feedback loops in gene regulation. Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at http://www.microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes.
Collapse
Affiliation(s)
- Bino John
- 1Computational Biology Center, Memorial Sloan-Kettering Cancer CenterNew York, New YorkUnited States of America
| | - Anton J Enright
- 1Computational Biology Center, Memorial Sloan-Kettering Cancer CenterNew York, New YorkUnited States of America
- 2Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Alexei Aravin
- 3Laboratory of RNA Molecular Biology, The Rockefeller UniversityNew York, New YorkUnited States of America
| | - Thomas Tuschl
- 3Laboratory of RNA Molecular Biology, The Rockefeller UniversityNew York, New YorkUnited States of America
| | - Chris Sander
- 1Computational Biology Center, Memorial Sloan-Kettering Cancer CenterNew York, New YorkUnited States of America
| | - Debora S Marks
- 4Department of Systems Biology, Harvard Medical SchoolBoston, MassachusettsUnited States of America
| |
Collapse
|