101
|
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J. Genetic and mechanistic diversity of piRNA 3'-end formation. Nature 2016; 539:588-592. [PMID: 27851737 PMCID: PMC5164936 DOI: 10.1038/nature20162] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/18/2016] [Indexed: 12/11/2022]
Abstract
Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and therefore have important roles in eukaryotic gene silencing. Of the three small RNA classes, microRNAs and short interfering RNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. PIWI-interacting RNAs (piRNAs)-the 22-30-nt-long guides for PIWI-clade Ago proteins that silence transposons in animal gonads-are generated independently of Dicer from single-stranded precursors. piRNA 5' ends are defined either by Zucchini, the Drosophila homologue of mitoPLD-a mitochondria-anchored endonuclease, or by piRNA-guided target cleavage. Formation of piRNA 3' ends is poorly understood. Here we report that two genetically and mechanistically distinct pathways generate piRNA 3' ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub) or Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3' ends, Aub/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3'-to-5' exoribonuclease Nibbler (Drosophila homologue of Mut-7). The relative activity of these two pathways dictates the extent to which piRNAs are directed to cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Notably, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway in which piRNA 5' and 3' ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data reveal a coherent model for piRNA biogenesis, and should aid the mechanistic dissection of the processes that govern piRNA 3'-end formation.
Collapse
Affiliation(s)
- Rippei Hayashi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Jakob Schnabl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Fabio Mohn
- current address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Stefan L. Ameres
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) Vienna Biocenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| |
Collapse
|
102
|
Fu Q, Pandey RR, Leu NA, Pillai RS, Wang PJ. Mutations in the MOV10L1 ATP Hydrolysis Motif Cause piRNA Biogenesis Failure and Male Sterility in Mice. Biol Reprod 2016; 95:103. [PMID: 27655786 PMCID: PMC5178147 DOI: 10.1095/biolreprod.116.142430] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small noncoding RNAs. piRNAs protect the genome integrity of the germline by silencing active transposable elements and are essential for germ cell development. Most piRNA pathway proteins are evolutionarily conserved. MOV10L1, a testis-specific RNA helicase, binds to piRNA precursors and is a master regulator of piRNA biogenesis in mouse. Here we report that mutation of the MOV10L1 ATP hydrolysis site leads to depletion of piRNAs on Piwi proteins, de-repression of transposable elements, and conglomeration of piRNA pathway proteins into polar granules. The Mov10l1 mutant mice exhibit meiotic arrest and male sterility. Our results show that mutation of the MOV10L1 ATP hydrolysis site perturbs piRNA biogenesis.
Collapse
Affiliation(s)
- Qi Fu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
| | - Radha Raman Pandey
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - N. Adrian Leu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
| | - Ramesh S. Pillai
- Department of Molecular Biology, University of Geneva, Geneva, Switzerland
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania
- Correspondence: P. Jeremy Wang, Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104. E-mail:
| |
Collapse
|
103
|
Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
Collapse
Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
| |
Collapse
|
104
|
Tang W, Tu S, Lee HC, Weng Z, Mello CC. The RNase PARN-1 Trims piRNA 3' Ends to Promote Transcriptome Surveillance in C. elegans. Cell 2016; 164:974-84. [PMID: 26919432 DOI: 10.1016/j.cell.2016.02.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 11/14/2015] [Accepted: 02/03/2016] [Indexed: 02/05/2023]
Abstract
Piwi-interacting RNAs (piRNAs) engage Piwi proteins to suppress transposons and are essential for fertility in diverse organisms. An interesting feature of piRNAs is that, while piRNA lengths are stereotypical within a species, they can differ widely between species. For example, piRNAs are mainly 29 and 30 nucleotides in humans, 24 to 30 nucleotides in D. melanogaster, and uniformly 21 nucleotides in C. elegans. However, how piRNA length is determined and whether length impacts function remains unknown. Here, we show that C. elegans deficient for PARN-1, a conserved RNase, accumulate untrimmed piRNAs with 3' extensions. Surprisingly, these longer piRNAs are stable and associate with the Piwi protein PRG-1 but fail to robustly recruit downstream silencing factors. Our findings identify PARN-1 as a key regulator of piRNA length in C. elegans and suggest that length is regulated to promote efficient transcriptome surveillance.
Collapse
Affiliation(s)
- Wen Tang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heng-Chi Lee
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute.
| |
Collapse
|
105
|
Izumi N, Shoji K, Sakaguchi Y, Honda S, Kirino Y, Suzuki T, Katsuma S, Tomari Y. Identification and Functional Analysis of the Pre-piRNA 3' Trimmer in Silkworms. Cell 2016; 164:962-73. [PMID: 26919431 DOI: 10.1016/j.cell.2016.01.008] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 11/11/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
PIWI-interacting RNAs (piRNAs) play a crucial role in transposon silencing in animal germ cells. In piRNA biogenesis, single-stranded piRNA intermediates are loaded into PIWI-clade proteins and cleaved by Zucchini/MitoPLD, yielding precursor piRNAs (pre-piRNAs). Pre-piRNAs that are longer than the mature piRNA length are then trimmed at their 3' ends. Although recent studies implicated the Tudor domain protein Papi/Tdrkh in pre-piRNA trimming, the identity of Trimmer and its relationship with Papi/Tdrkh remain unknown. Here, we identified PNLDC1, an uncharacterized 3'-5' exonuclease, as Trimmer in silkworms. Trimmer is enriched in the mitochondrial fraction and binds to Papi/Tdrkh. Depletion of Trimmer and Papi/Tdrkh additively inhibits trimming, causing accumulation of ∼35-40-nt pre-piRNAs that are impaired for target cleavage and prone to degradation. Our results highlight the cooperative action of Trimmer and Papi/Tdrkh in piRNA maturation.
Collapse
Affiliation(s)
- Natsuko Izumi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Keisuke Shoji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Shozo Honda
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.
| |
Collapse
|
106
|
Lee YJ, Starrett GJ, Lee ST, Yang R, Henzler CM, Jameson SC, Hogquist KA. Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst γδ T, Innate Lymphoid, and Th Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:1460-70. [PMID: 27385777 DOI: 10.4049/jimmunol.1600643] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Abstract
Invariant NKT cells differentiate into three predominant effector lineages in the steady state. To understand these lineages, we sorted undifferentiated invariant NK T progenitor cells and each effector population and analyzed their transcriptional profiles by RNAseq. Bioinformatic comparisons were made to effector subsets among other lymphocytes, specifically Th cells, innate lymphoid cells (ILC), and γδ T cells. Myc-associated signature genes were enriched in NKT progenitors, like in other hematopoietic progenitors. Only NKT1 cells, but not NKT2 and NKT17 cells, had transcriptome similarity to NK cells and were also similar to other IFN-γ-producing lineages such as Th1, ILC1, and intraepithelial γδ T cells. NKT2 and NKT17 cells were similar to their analogous subsets of γδ T cells and ILCs, but surprisingly, not to Th2 and Th17 cells. We identified a set of genes common to each effector lineage regardless of Ag receptor specificity, suggesting the use of conserved regulatory cores for effector function.
Collapse
Affiliation(s)
- You Jeong Lee
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455;
| | - Gabriel J Starrett
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455; and
| | - Seungeun Thera Lee
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Rendong Yang
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Christine M Henzler
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, MN 55455
| | - Stephen C Jameson
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota, Minneapolis, MN 55455;
| |
Collapse
|
107
|
Czech B, Hannon GJ. One Loop to Rule Them All: The Ping-Pong Cycle and piRNA-Guided Silencing. Trends Biochem Sci 2016; 41:324-337. [PMID: 26810602 PMCID: PMC4819955 DOI: 10.1016/j.tibs.2015.12.008] [Citation(s) in RCA: 300] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 01/06/2023]
Abstract
The PIWI-interacting RNA (piRNA) pathway is a conserved defense mechanism that protects the genetic information of animal germ cells from the deleterious effects of molecular parasites, such as transposons. Discovered nearly a decade ago, this small RNA silencing system comprises PIWI-clade Argonaute proteins and their associated RNA-binding partners, the piRNAs. In this review, we highlight recent work that has advanced our understanding of how piRNAs preserve genome integrity across generations. We discuss the mechanism of piRNA biogenesis, give an overview of common themes as well as differences in piRNA-mediated silencing between species, and end by highlighting known and emerging functions of piRNAs.
Collapse
Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| |
Collapse
|
108
|
Yang F, Wang PJ. Multiple LINEs of retrotransposon silencing mechanisms in the mammalian germline. Semin Cell Dev Biol 2016; 59:118-125. [PMID: 26957474 DOI: 10.1016/j.semcdb.2016.03.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 02/07/2023]
Abstract
Retrotransposons play an important role in genome evolution but pose acute challenges to host genome integrity, particularly in early stage germ cells where epigenetic control is relaxed to permit genome-wide reprogramming. In most species, the inability to silence retrotransposons in the germline is usually associated with sterility. LINE1 is the most abundant retrotransposon type in the mammalian genome. Mammalian germ cells employ multiple mechanisms to suppress retrotransposon activity, including small non-coding piRNAs, DNA methylation, and repressive histone modifications. Novel factors contributing to the epigenetic silencing of retrotransposons in the germline continue to be identified. Recent studies have provided insight into how epigenetic changes associated with retrotransposon activation impact on fertility.
Collapse
Affiliation(s)
- Fang Yang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, 3800 Spruce Street, Philadelphia, PA 19104, USA.
| |
Collapse
|
109
|
Abstract
For a decade, mystery has surrounded the mechanisms by which piRNA biogenesis yields distinct size classes of small RNAs within individual PIWI proteins. In this issue of Cell, two studies shed light on this process, identifying conserved PARN-family exonucleases that trim piRNAs to their mature size in silkworms and C. elegans.
Collapse
Affiliation(s)
- Benjamin Czech
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Gregory J Hannon
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| |
Collapse
|
110
|
Yatsu R, Miyagawa S, Kohno S, Parrott BB, Yamaguchi K, Ogino Y, Miyakawa H, Lowers RH, Shigenobu S, Guillette LJ, Iguchi T. RNA-seq analysis of the gonadal transcriptome during Alligator mississippiensis temperature-dependent sex determination and differentiation. BMC Genomics 2016; 17:77. [PMID: 26810479 PMCID: PMC4727388 DOI: 10.1186/s12864-016-2396-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/14/2016] [Indexed: 11/26/2022] Open
Abstract
Background The American alligator (Alligator mississippiensis) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the molecular mechanisms governing this process remain a mystery, including the influence of initial environmental temperature on the comprehensive gonadal gene expression patterns occurring during TSD. Results Our characterization of transcriptomes during alligator TSD allowed us to identify novel candidate genes involved in TSD initiation. High-throughput RNA sequencing (RNA-seq) was performed on gonads collected from A. mississippiensis embryos incubated at both a male and a female producing temperature (33.5 °C and 30 °C, respectively) in a time series during sexual development. RNA-seq yielded 375.2 million paired-end reads, which were mapped and assembled, and used to characterize differential gene expression. Changes in the transcriptome occurring as a function of both development and sexual differentiation were extensively profiled. Forty-one differentially expressed genes were detected in response to incubation at male producing temperature, and included genes such as Wnt signaling factor WNT11, histone demethylase KDM6B, and transcription factor C/EBPA. Furthermore, comparative analysis of development- and sex-dependent differential gene expression revealed 230 candidate genes involved in alligator sex determination and differentiation, and early details of the suspected male-fate commitment were profiled. We also discovered sexually dimorphic expression of uncharacterized ncRNAs and other novel elements, such as unique expression patterns of HEMGN and ARX. Twenty-five of the differentially expressed genes identified in our analysis were putative transcriptional regulators, among which were MYBL2, MYCL, and HOXC10, in addition to conventional sex differentiation genes such as SOX9, and FOXL2. Inferred gene regulatory network was constructed, and the gene-gene and temperature-gene interactions were predicted. Conclusions Gonadal global gene expression kinetics during sex determination has been extensively profiled for the first time in a TSD species. These findings provide insights into the genetic framework underlying TSD, and expand our current understanding of the developmental fate pathways during vertebrate sex determination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2396-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ryohei Yatsu
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Shinichi Miyagawa
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Satomi Kohno
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston, SC, 29412, USA.
| | - Benjamin B Parrott
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston, SC, 29412, USA.
| | - Katsushi Yamaguchi
- National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
| | - Yukiko Ogino
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| | - Hitoshi Miyakawa
- Center for Bioscience Research and Education, Utsunomiya University, 350 Mine-machi, Utsunomiya, Tochigi, 321-8505, Japan.
| | - Russell H Lowers
- Innovative Health Applications, Kennedy Space Center, Merritt Island, FL, 32899, USA.
| | - Shuji Shigenobu
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,National Institute for Basic Biology, National Institutes of Natural Sciences, 38 Nishigonaka, Myodaiji, Okazaki, Aichi, 444-8585, Japan.
| | - Louis J Guillette
- Department of Obstetrics and Gynecology, Medical University of South Carolina, and Marine Biomedicine and Environmental Science Center, Hollings Marine Laboratory, Charleston, SC, 29412, USA.
| | - Taisen Iguchi
- Department of Basic Biology, Faculty of Life Science, SOKENDAI (Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan. .,Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| |
Collapse
|
111
|
Kobayashi H, Tomari Y. RISC assembly: Coordination between small RNAs and Argonaute proteins. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:71-81. [DOI: 10.1016/j.bbagrm.2015.08.007] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 08/11/2015] [Accepted: 08/20/2015] [Indexed: 12/18/2022]
|
112
|
piRNA biogenesis in the germline: From transcription of piRNA genomic sources to piRNA maturation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:82-92. [DOI: 10.1016/j.bbagrm.2015.09.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/25/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
|
113
|
Zhang J, Wang Q, Wang M, Jiang M, Wang Y, Sun Y, Wang J, Xie T, Tang C, Tang N, Song H, Cui D, Chao R, Ding S, Ni B, Chen X, Wang Y. GASZ and mitofusin-mediated mitochondrial functions are crucial for spermatogenesis. EMBO Rep 2015; 17:220-34. [PMID: 26711429 DOI: 10.15252/embr.201540846] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/19/2015] [Indexed: 12/13/2022] Open
Abstract
Nuage is an electron-dense cytoplasmic structure in germ cells that contains ribonucleoproteins and participates in piRNA biosynthesis. Despite the observation that clustered mitochondria are associated with a specific type of nuage called intermitochondrial cement (pi-body), the importance of mitochondrial functions in nuage formation and spermatogenesis is yet to be determined. We show that a germ cell-specific protein GASZ contains a functional mitochondrial targeting signal and is largely localized at mitochondria both endogenously in germ cells and in somatic cells when ectopically expressed. In addition, GASZ interacts with itself at the outer membrane of mitochondria and promotes mitofusion in a mitofusin/MFN-dependent manner. In mice, deletion of the mitochondrial targeting signal reveals that mitochondrial localization of GASZ is essential for nuage formation, mitochondrial clustering, transposon repression, and spermatogenesis. MFN1 deficiency also leads to defects in mitochondrial activity and male infertility. Our data thus reveal a requirement for GASZ and MFN-mediated mitofusion during spermatogenesis.
Collapse
Affiliation(s)
- Jingjing Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Qian Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Mingsong Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Manxi Jiang
- Department of Laboratory Animal Science, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Yongsheng Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yun Sun
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Junpeng Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Taorong Xie
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao Tang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Nannan Tang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huili Song
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Cui
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China
| | - Ruihua Chao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuzhe Ding
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention, Ministry of Education, East China Normal University, Shanghai, China
| | - Bing Ni
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xuejin Chen
- Department of Laboratory Animal Science, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Yuan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| |
Collapse
|
114
|
Abstract
Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the "germ-line multipotency program" and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.
Collapse
|
115
|
Yang Z, Chen KM, Pandey RR, Homolka D, Reuter M, Janeiro BKR, Sachidanandam R, Fauvarque MO, McCarthy AA, Pillai RS. PIWI Slicing and EXD1 Drive Biogenesis of Nuclear piRNAs from Cytosolic Targets of the Mouse piRNA Pathway. Mol Cell 2015; 61:138-52. [PMID: 26669262 PMCID: PMC4712191 DOI: 10.1016/j.molcel.2015.11.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/12/2015] [Accepted: 10/28/2015] [Indexed: 11/19/2022]
Abstract
PIWI-interacting RNAs (piRNAs) guide PIWI proteins to suppress transposons in the cytoplasm and nucleus of animal germ cells, but how silencing in the two compartments is coordinated is not known. Here we demonstrate that endonucleolytic slicing of a transcript by the cytosolic mouse PIWI protein MILI acts as a trigger to initiate its further 5'→3' processing into non-overlapping fragments. These fragments accumulate as new piRNAs within both cytosolic MILI and the nuclear MIWI2. We also identify Exonuclease domain-containing 1 (EXD1) as a partner of the MIWI2 piRNA biogenesis factor TDRD12. EXD1 homodimers are inactive as a nuclease but function as an RNA adaptor within a PET (PIWI-EXD1-Tdrd12) complex. Loss of Exd1 reduces sequences generated by MILI slicing, impacts biogenesis of MIWI2 piRNAs, and de-represses LINE1 retrotransposons. Thus, piRNA biogenesis triggered by PIWI slicing, and promoted by EXD1, ensures that the same guides instruct PIWI proteins in the nucleus and cytoplasm.
Collapse
Affiliation(s)
- Zhaolin Yang
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Kuan-Ming Chen
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Radha Raman Pandey
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - David Homolka
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Michael Reuter
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Bruno Kotska Rodino Janeiro
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Ravi Sachidanandam
- Department of Oncological Sciences, Icahn School of Medicine at Sinai, One Gustave L. Levy Place, NY 10029, USA
| | | | - Andrew A McCarthy
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France; Unit for Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, 38042 France.
| |
Collapse
|
116
|
Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
Collapse
Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| |
Collapse
|
117
|
Kim M, Ki BS, Hong K, Park SP, Ko JJ, Choi Y. Tudor Domain Containing Protein TDRD12 Expresses at the Acrosome of Spermatids in Mouse Testis. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:944-51. [PMID: 26954166 PMCID: PMC4932588 DOI: 10.5713/ajas.15.0436] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/31/2015] [Accepted: 09/26/2015] [Indexed: 12/24/2022]
Abstract
Tdrd12 is one of tudor domain containing (Tdrd) family members. However, the expression pattern of Tdrd12 has not been well studied. To compare the expression levels of Tdrd12 in various tissues, real time-polymerase chain reaction was performed using total RNAs from liver, small intestine, heart, brain, kidney, lung, spleen, stomach, uterus, ovary, and testis. Tdrd12 mRNA was highly expressed in testis. Antibody against mouse TDRD12 were generated using amino acid residues SQRPNEKPLRLTEKKDC of TDRD12 to investigate TDRD12 localization in testis. Immunostaining assay shows that TDRD12 is mainly localized at the spermatid in the seminiferous tubules of adult testes. During postnatal development, TDRD12 is differentially expressed. TDRD12 was detected in early spermatocytes at 2 weeks and TDRD12 was localized at acrosome of the round spermatids. TDRD12 expression was not co-localized with TDRD1 which is an important component of piRNA pathway in germ cells. Our results indicate that TDRD12 may play an important role in spermatids and function as a regulator of spermatogenesis in dependent of TDRD1.
Collapse
Affiliation(s)
- Min Kim
- Department of Biomedical Science, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Byeong Seong Ki
- Department of Biomedical Science, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Kwonho Hong
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 330-714, Korea
| | - Se-Pill Park
- Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju 690-756, Korea
| | - Jung-Jae Ko
- Department of Biomedical Science, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Youngsok Choi
- Department of Biomedical Science, CHA University, 335 Pangyo-ro, Seongnam-si, Gyeonggi-do 13488, Korea
| |
Collapse
|
118
|
Han BW, Wang W, Li C, Weng Z, Zamore PD. Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 2015; 348:817-21. [PMID: 25977554 PMCID: PMC4545291 DOI: 10.1126/science.aaa1264] [Citation(s) in RCA: 260] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PIWI-interacting RNAs (piRNAs) protect the animal germ line by silencing transposons. Primary piRNAs, generated from transcripts of genomic transposon "junkyards" (piRNA clusters), are amplified by the "ping-pong" pathway, yielding secondary piRNAs. We report that secondary piRNAs, bound to the PIWI protein Ago3, can initiate primary piRNA production from cleaved transposon RNAs. The first ~26 nucleotides (nt) of each cleaved RNA becomes a secondary piRNA, but the subsequent ~26 nt become the first in a series of phased primary piRNAs that bind Piwi, allowing piRNAs to spread beyond the site of RNA cleavage. The ping-pong pathway increases only the abundance of piRNAs, whereas production of phased primary piRNAs from cleaved transposon RNAs adds sequence diversity to the piRNA pool, allowing adaptation to changes in transposon sequence.
Collapse
Affiliation(s)
- Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Wei Wang
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Chengjian Li
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Zhiping Weng
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
| |
Collapse
|
119
|
Mohn F, Handler D, Brennecke J. Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science 2015; 348:812-817. [PMID: 25977553 PMCID: PMC4988486 DOI: 10.1126/science.aaa1039] [Citation(s) in RCA: 243] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In animal gonads, PIWI-clade Argonaute proteins repress transposons sequence-specifically via bound Piwi-interacting RNAs (piRNAs). These are processed from single-stranded precursor RNAs by largely unknown mechanisms. Here we show that primary piRNA biogenesis is a 3'-directed and phased process that, in the Drosophila germ line, is initiated by secondary piRNA-guided transcript cleavage. Phasing results from consecutive endonucleolytic cleavages catalyzed by Zucchini, implying coupled formation of 3' and 5' ends of flanking piRNAs. Unexpectedly, Zucchini also participates in 3' end formation of secondary piRNAs. Its function can, however, be bypassed by downstream piRNA-guided precursor cleavages coupled to exonucleolytic trimming. Our data uncover an evolutionarily conserved piRNA biogenesis mechanism in which Zucchini plays a central role in defining piRNA 5' and 3' ends.
Collapse
Affiliation(s)
- Fabio Mohn
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
| |
Collapse
|
120
|
Vourekas A, Zheng K, Fu Q, Maragkakis M, Alexiou P, Ma J, Pillai RS, Mourelatos Z, Wang PJ. The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing. Genes Dev 2015; 29:617-29. [PMID: 25762440 PMCID: PMC4378194 DOI: 10.1101/gad.254631.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Piwi-piRNA ribonucleoproteins (piRNPs) enforce retrotransposon silencing, a function critical for preserving genome integrity of germ cells. Vourekas et al. found that MOV10L1 exhibits 5? to 3? directional RNA unwinding activity in vitro and that a point mutation that abolishes this activity causes a failure in primary piRNA biogenesis in vivo. MOV10L1 selectively binds piRNA precursor transcripts and is essential for the generation of intermediate piRNA processing fragments that are subsequently loaded to Piwi proteins. Piwi–piRNA (Piwi-interacting RNA) ribonucleoproteins (piRNPs) enforce retrotransposon silencing, a function critical for preserving the genome integrity of germ cells. The molecular functions of most of the factors that have been genetically implicated in primary piRNA biogenesis are still elusive. Here we show that MOV10L1 exhibits 5′-to-3′ directional RNA-unwinding activity in vitro and that a point mutation that abolishes this activity causes a failure in primary piRNA biogenesis in vivo. We demonstrate that MOV10L1 selectively binds piRNA precursor transcripts and is essential for the generation of intermediate piRNA processing fragments that are subsequently loaded to Piwi proteins. Multiple analyses suggest an intimate coupling of piRNA precursor processing with elements of local secondary structures such as G quadruplexes. Our results support a model in which MOV10L1 RNA helicase activity promotes unwinding and funneling of the single-stranded piRNA precursor transcripts to the endonuclease that catalyzes the first cleavage step of piRNA processing.
Collapse
Affiliation(s)
- Anastassios Vourekas
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ke Zheng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China;
| | - Qi Fu
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jing Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 210029, China
| | - Ramesh S Pillai
- European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| | - P Jeremy Wang
- Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
| |
Collapse
|
121
|
Abstract
Piwi proteins and Piwi-interacting RNAs (piRNAs) are essential for gametogenesis, embryogenesis, and stem cell maintenance in animals. Piwi proteins act on transposon RNAs by cleaving the RNAs and by interacting with factors involved in RNA regulation. Additionally, piRNAs generated from transposons and psuedogenes can be used by Piwi proteins to regulate mRNAs at the posttranscriptional level. Here we discuss piRNA biogenesis, recent findings on posttranscriptional regulation of mRNAs by the piRNA pathway, and the potential importance of this posttranscriptional regulation for a variety of biological processes such as gametogenesis, developmental transitions, and sex determination.
Collapse
Affiliation(s)
- Toshiaki Watanabe
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06519, USA.
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06519, USA.
| |
Collapse
|
122
|
MORC1 represses transposable elements in the mouse male germline. Nat Commun 2014; 5:5795. [PMID: 25503965 PMCID: PMC4268658 DOI: 10.1038/ncomms6795] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 12/30/2022] Open
Abstract
The Microrchidia (Morc) family of GHKL ATPases are present in a wide variety of prokaryotic and eukaryotic organisms but are of largely unknown function. Genetic screens in Arabidopsis thaliana have identified Morc genes as important repressors of transposons and other DNA-methylated and silent genes. MORC1-deficient mice were previously found to display male-specific germ cell loss and infertility. Here we show that MORC1 is responsible for transposon repression in the male germline in a pattern that is similar to that observed for germ cells deficient for the DNA methyltransferase homologue DNMT3L. Morc1 mutants show highly localized defects in the establishment of DNA methylation at specific classes of transposons, and this is associated with failed transposon silencing at these sites. Our results identify MORC1 as an important new regulator of the epigenetic landscape of male germ cells during the period of global de novo methylation. The Microrchidia (Morc) family of GHKL ATPases are important repressors of transposons and other DNA-methylated and silent genes in A. thaliana. Here, the authors show that MORC1 is responsible for repression and methylation of specific classes of transposons in the mouse male germline.
Collapse
|
123
|
Abstract
Distinguishing self from non-self plays a crucial role in safeguarding the germlines of metazoa from mobile DNA elements. Since their discovery less than a decade ago, Piwi-interacting RNAs (piRNAs) have been shown to repress transposable elements in the germline and, hence, have been at the forefront of research aimed at understanding the mechanisms that maintain germline integrity. More recently, roles for piRNAs in gene regulation have emerged. In this Review, we highlight recent advances made in understanding piRNA function, highlighting the divergent nature of piRNA biogenesis in different organisms, and discussing the mechanisms of piRNA action during transcriptional regulation and in transgenerational epigenetic inheritance.
Collapse
Affiliation(s)
- Eva-Maria Weick
- Wellcome Trust Cancer Research UK Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, Department of Biochemistry and Department of Genetics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| |
Collapse
|
124
|
Ichiyanagi T, Ichiyanagi K, Ogawa A, Kuramochi-Miyagawa S, Nakano T, Chuma S, Sasaki H, Udono H. HSP90α plays an important role in piRNA biogenesis and retrotransposon repression in mouse. Nucleic Acids Res 2014; 42:11903-11. [PMID: 25262350 PMCID: PMC4231750 DOI: 10.1093/nar/gku881] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male germ cells. The knockout mutation of Hsp90α resulted in a large reduction in the expression of primary and secondary piRNAs and mislocalization of MIWI2, a PIWI homolog. Whereas the mutation in Fkbp6 encoding a co-chaperone reduced piRNAs of 28–32 nucleotides in length, the Hsp90α mutation reduced piRNAs of 24–32 nucleotides, suggesting the presence of both FKBP6-dependent and -independent actions of HSP90α. Although DNA methylation and mRNA levels of L1 retrotransposon were largely unchanged in the Hsp90α mutant testes, the L1-encoded protein was increased, suggesting the presence of post-transcriptional regulation. This study revealed the specialized function of the HSP90α isofom in the piRNA biogenesis and repression of retrotransposons during the development of male germ cells in mammals.
Collapse
Affiliation(s)
- Tomoko Ichiyanagi
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Ayako Ogawa
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Toru Nakano
- Department of Pathology, Medical School and Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
| | - Shinichiro Chuma
- Department of Development and Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Kita-ku, Okayama 700-8558, Japan
| |
Collapse
|
125
|
Deutsch DR, Fröhlich T, Otte KA, Beck A, Habermann FA, Wolf E, Arnold GJ. Stage-Specific Proteome Signatures in Early Bovine Embryo Development. J Proteome Res 2014; 13:4363-76. [DOI: 10.1021/pr500550t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Daniela R. Deutsch
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Kathrin A. Otte
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Andrea Beck
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Felix A. Habermann
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Eckhard Wolf
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| | - Georg J. Arnold
- Laboratory for Functional Genome Analysis LAFUGA, Gene Center, ‡Molecular Animal Breeding
and Biotechnology, Department of Veterinary Sciences and Gene Center, and §Institute of Anatomy,
Histology and Embryology, Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich 81377, Germany
| |
Collapse
|
126
|
Gayatri S, Bedford MT. Readers of histone methylarginine marks. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1839:702-10. [PMID: 24583552 PMCID: PMC4099268 DOI: 10.1016/j.bbagrm.2014.02.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/31/2014] [Accepted: 02/14/2014] [Indexed: 11/15/2022]
Abstract
Arginine methylation is a common posttranslational modification (PTM) that alters roughly 0.5% of all arginine residues in the cells. There are three types of arginine methylation: monomethylarginine (MMA), asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). These three PTMs are enriched on RNA-binding proteins and on histones, and also impact signal transduction cascades. To date, over thirty arginine methylation sites have been cataloged on the different core histones. These modifications alter protein structure, impact interactions with DNA, and also generate docking sites for effector molecules. The primary "readers" of methylarginine marks are Tudor domain-containing proteins. The complete family of thirty-six Tudor domain-containing proteins has yet to be fully characterized, but at least ten bind methyllysine motifs and eight bind methylarginine motifs. In this review, we will highlight the biological roles of the Tudor domains that interact with arginine methylated motifs, and also address other types of interactions that are regulated by these particular PTMs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
Collapse
Affiliation(s)
- Sitaram Gayatri
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mark T Bedford
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.
| |
Collapse
|
127
|
Castañeda J, Genzor P, van der Heijden GW, Sarkeshik A, Yates JR, Ingolia NT, Bortvin A. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. EMBO J 2014; 33:1999-2019. [PMID: 25063675 DOI: 10.15252/embj.201386855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Pachytene piRNAs are a class of Piwi-interacting small RNAs abundant in spermatids of the adult mouse testis. They are processed from piRNA primary transcripts by a poorly understood mechanism and, unlike fetal transposon-derived piRNAs, lack complementary targets in the spermatid transcriptome. We report that immunopurified complexes of a conserved piRNA pathway protein Maelstrom (MAEL) are enriched in MIWI (Piwi partner of pachytene piRNAs), Tudor-domain proteins and processing intermediates of pachytene piRNA primary transcripts. We provide evidence of functional significance of these complexes in Mael129 knockout mice that exhibit spermiogenic arrest with acrosome and flagellum malformation. Mael129-null mutant testes possess low levels of piRNAs derived from MAEL-associated piRNA precursors and exhibit reduced translation of numerous spermiogenic mRNAs including those encoding acrosome and flagellum proteins. These translation defects in haploid round spermatids are likely indirect, as neither MAEL nor piRNA precursors associate with polyribosomes, and they may arise from an imbalance between pachytene piRNAs and MIWI.
Collapse
Affiliation(s)
- Julio Castañeda
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Pavol Genzor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | | | - Ali Sarkeshik
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nicholas T Ingolia
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Alex Bortvin
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| |
Collapse
|
128
|
Gou LT, Dai P, Liu MF. Small noncoding RNAs and male infertility. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:733-45. [PMID: 25044449 DOI: 10.1002/wrna.1252] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 11/07/2022]
Abstract
Small noncoding RNAs (ncRNAs) are a novel class of gene regulators that modulate gene expression at transcriptional, post-transcriptional, and epigenetic levels, and they play crucial roles in almost all cellular processes in eukaryotes. Recent studies have indicated that several types of small noncoding RNAs, including microRNAs (miRNAs), endo-small interference RNAs (endo-siRNAs), and Piwi-interacting RNAs (piRNAs), are expressed in the male germline and are required for spermatogenesis in animals. In this review, we summarize the recent knowledge of these small noncoding RNAs in male germ cells and their biological functions and mechanisms of action in animal spermatogenesis.
Collapse
Affiliation(s)
- Lan-Tao Gou
- Center for RNA Research, State Key Laboratory of Molecular Biology-University of Chinese Academy of Sciences, Shanghai, China; Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | | | | |
Collapse
|
129
|
Ku HY, Lin H. PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. Natl Sci Rev 2014; 1:205-218. [PMID: 25512877 DOI: 10.1093/nsr/nwu014] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a complex class of small non-coding RNAs that are mostly 24-32 nucleotides in length and composed of at least hundreds of thousands of species that specifically interact with the PIWI protein subfamily of the ARGONAUTE family. Recent studies revealed that PIWI proteins interact with a number of proteins, especially the TUDOR-domain-containing proteins, to regulate piRNA biogenesis and regulatory function. Current research also provides evidence that PIWI proteins and piRNAs are not only crucial for transposon silencing in the germline, but also mediate novel mechanisms of epigenetic programming, DNA rearrangements, mRNA turnover, and translational control both in the germline and in the soma. These new discoveries begin to reveal an exciting new dimension of gene regulation in the cell.
Collapse
Affiliation(s)
- Hsueh-Yen Ku
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Haifan Lin
- Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06511, USA
| |
Collapse
|
130
|
Connecting the dots of RNA-directed DNA methylation in Arabidopsis thaliana. Chromosome Res 2014; 22:225-40. [PMID: 24846724 DOI: 10.1007/s10577-014-9425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Noncoding RNAs are the rising stars of genome regulation and are crucial to an organism's metabolism, development, and defense. One of their most notable functions is its ability to direct epigenetic modifications through small RNA molecules to specific genomic regions, ensuring transcriptional regulation, proper genome organization, and maintenance of genome integrity. Here, we review the current knowledge of the spatial organization of the Arabidopsis thaliana RNA-directed DNA methylation pathway within the cell nucleus, which, while known to be essential for the proper establishment of epigenetic modifications, remains poorly understood. We will also discuss possible future cytological approaches that have the potential of unveiling functional insights into how small RNA-directed epigenetics is regulated through the spatiotemporal regulation of its major components within the cell.
Collapse
|
131
|
Izumi N, Tomari Y. Diversity of the piRNA pathway for nonself silencing: worm-specific piRNA biogenesis factors. Genes Dev 2014; 28:665-71. [PMID: 24696451 PMCID: PMC4015490 DOI: 10.1101/gad.241323.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The PIWI-interacting RNA (piRNA) pathway protects animal germline cells from transposable elements and other genomic invaders. Although the genome defense function of piRNAs has been well established, the mechanisms of their biogenesis remain poorly understood. In this issue of Genes & Development, three groups identify novel factors required for piRNA biogenesis in Caenorhabditis elegans. These works greatly expand our understanding of the piRNA pathway in worms, highlighting both its shared and its unique properties.
Collapse
Affiliation(s)
- Natsuko Izumi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | | |
Collapse
|
132
|
Hirose T, Mishima Y, Tomari Y. Elements and machinery of non-coding RNAs: toward their taxonomy. EMBO Rep 2014; 15:489-507. [PMID: 24731943 PMCID: PMC4210095 DOI: 10.1002/embr.201338390] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 12/26/2022] Open
Abstract
Although recent transcriptome analyses have uncovered numerous non-coding RNAs (ncRNAs), their functions remain largely unknown. ncRNAs assemble with proteins and operate as ribonucleoprotein (RNP) machineries, formation of which is thought to be determined by specific fundamental elements embedded in the primary RNA transcripts. Knowledge about the relationships between RNA elements, RNP machinery, and molecular and physiological functions is critical for understanding the diverse roles of ncRNAs and may eventually allow their systematic classification or "taxonomy." In this review, we catalog and discuss representative small and long non-coding RNA classes, focusing on their currently known (and unknown) RNA elements and RNP machineries.
Collapse
Affiliation(s)
- Tetsuro Hirose
- Institute for Genetic Medicine, Hokkaido UniversitySapporo, Hokkaido, Japan
| | - Yuichiro Mishima
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| | - Yukihide Tomari
- Institute of Molecular and Cellular Biosciences, The University of TokyoBunkyo-ku, Tokyo, Japan
- Department of Medical Genome Sciences, The University of TokyoBunkyo-ku, Tokyo, Japan
| |
Collapse
|
133
|
Zhou J, Leu NA, Eckardt S, McLaughlin KJ, Wang PJ. STK31/TDRD8, a germ cell-specific factor, is dispensable for reproduction in mice. PLoS One 2014; 9:e89471. [PMID: 24586802 PMCID: PMC3929691 DOI: 10.1371/journal.pone.0089471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 01/20/2014] [Indexed: 02/07/2023] Open
Abstract
Tudor domain containing (Tdrd) proteins that are expressed in germ cells are divided into two groups. One group, consisting of TDRD1, TDRKH, TDRD9 and TDRD12, function in piRNA biogenesis and retrotransposon silencing, while the other group including RNF17/TDRD4 and TDRD5-7 are required for spermiogenesis. These Tdrd proteins play distinct roles during male germ cell development. Here, we report the characterization of STK31/TDRD8 in mice. STK31 contains a tudor domain and a serine/threonine kinase domain. We find that STK31 is a cytoplasmic protein in germ cells. STK31 is expressed in embryonic gonocytes of both sexes and postnatal spermatocytes and round spermatids in males. Disruption of the tudor domain and kinase domain of STK31 respectively does not affect fertility in mice. Our data suggest that the function of STK31 may be redundant with other Tdrd proteins in germ cell development.
Collapse
Affiliation(s)
- Jian Zhou
- Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - N. Adrian Leu
- Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Sigrid Eckardt
- Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - K. John McLaughlin
- Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States of America
| | - P. Jeremy Wang
- Department of Animal Biology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
134
|
Fu Q, Wang PJ. Mammalian piRNAs: Biogenesis, function, and mysteries. SPERMATOGENESIS 2014; 4:e27889. [PMID: 25077039 DOI: 10.4161/spmg.27889] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/23/2013] [Accepted: 01/16/2014] [Indexed: 12/20/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a distinct class of small non-coding RNAs specifically expressed in the germline of many species. They are most notably required for transposon silencing. Loss of piRNAs results in defects in germ cell development, and thus, infertility. Most studies of piRNAs have been done in Drosophila, but much progress has also been made on piRNAs in the germline of mammals and other species in the past few years. This review provides a summary of our current knowledge of the biogenesis and functions of piRNAs during mouse spermatogenesis and discusses challenges in the mammalian piRNA field.
Collapse
Affiliation(s)
- Qi Fu
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
| | - P Jeremy Wang
- Department of Animal Biology; University of Pennsylvania School of Veterinary Medicine; Philadelphia, PA USA
| |
Collapse
|
135
|
Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
|
136
|
Clark JP, Lau NC. Piwi Proteins and piRNAs step onto the systems biology stage. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:159-97. [PMID: 25201106 PMCID: PMC4248790 DOI: 10.1007/978-1-4939-1221-6_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Animal germ cells are totipotent because they maintain a highly unique and specialized epigenetic state for its genome. To accomplish this, germ cells express a rich repertoire of specialized RNA-binding protein complexes such as the Piwi proteins and Piwi-interacting RNAs (piRNAs): a germ-cell branch of the RNA interference (RNAi) phenomenon which includes microRNA and endogenous small interfering RNA pathways. Piwi proteins and piRNAs are deeply conserved in animal evolution and play essential roles in fertility and regeneration. Molecular mechanisms for how these ribonucleoproteins act upon the transcriptome and genome are only now coming to light with the application of systems-wide approaches in both invertebrates and vertebrates. Systems biology studies on invertebrates have revealed that transcriptional and heritable silencing is a main mechanism driven by Piwi proteins and piRNA complexes. In vertebrates, Piwi-targeting mechanisms and piRNA biogenesis have progressed, while the discovery that the nuclease activity of Piwi protein is essential for vertebrate germ cell development but not completely required in invertebrates highlights the many complexities of this pathway in different animals. This review recounts how recent systems-wide approaches have rapidly accelerated our appreciation for the broad reach of the Piwi pathway on germline genome regulation and what questions facing the field await to be unraveled.
Collapse
Affiliation(s)
- Josef P. Clark
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| | - Nelson C. Lau
- Department of Biology and Rosenstiel Biomedical Research Center, Brandeis University, 415 South Street, Waltham, MA 02454, USA
| |
Collapse
|
137
|
Honda S, Kirino Y, Maragkakis M, Alexiou P, Ohtaki A, Murali R, Mourelatos Z, Kirino Y. Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA (NEW YORK, N.Y.) 2013; 19:1405-18. [PMID: 23970546 PMCID: PMC3854531 DOI: 10.1261/rna.040428.113] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/08/2013] [Indexed: 05/18/2023]
Abstract
PIWI proteins and their associated PIWI-interacting RNAs (piRNAs) protect genome integrity by silencing transposons in animal germlines. The molecular mechanisms and components responsible for piRNA biogenesis remain elusive. PIWI proteins contain conserved symmetrical dimethylarginines (sDMAs) that are specifically targeted by TUDOR domain-containing proteins. Here we report that the sDMAs of PIWI proteins play crucial roles in PIWI localization and piRNA biogenesis in Bombyx mori-derived BmN4 cells, which harbor fully functional piRNA biogenesis machinery. Moreover, RNAi screenings for Bombyx genes encoding TUDOR domain-containing proteins identified BmPAPI, a Bombyx homolog of Drosophila PAPI, as a factor modulating the length of mature piRNAs. BmPAPI specifically recognized sDMAs and interacted with PIWI proteins at the surface of the mitochondrial outer membrane. BmPAPI depletion resulted in 3'-terminal extensions of mature piRNAs without affecting the piRNA quantity. These results reveal the BmPAPI-involved piRNA precursor processing mechanism on mitochondrial outer membrane scaffolds.
Collapse
Affiliation(s)
- Shozo Honda
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Yoriko Kirino
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Akashi Ohtaki
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yohei Kirino
- Department of Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
- Corresponding authorE-mail
| |
Collapse
|
138
|
Tudor domain containing 12 (TDRD12) is essential for secondary PIWI interacting RNA biogenesis in mice. Proc Natl Acad Sci U S A 2013; 110:16492-7. [PMID: 24067652 DOI: 10.1073/pnas.1316316110] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are gonad-specific small RNAs that provide defense against transposable genetic elements called transposons. Our knowledge of piRNA biogenesis is sketchy, partly due to an incomplete inventory of the factors involved. Here, we identify Tudor domain-containing 12 (TDRD12; also known as ECAT8) as a unique piRNA biogenesis factor in mice. TDRD12 is detected in complexes containing Piwi protein MILI (PIWIL2), its associated primary piRNAs, and TDRD1, all of which are already implicated in secondary piRNA biogenesis. Male mice carrying either a nonsense point mutation (reproductive mutant 23 or repro23 mice) or a targeted deletion in the Tdrd12 locus are infertile and derepress retrotransposons. We find that TDRD12 is dispensable for primary piRNA biogenesis but essential for production of secondary piRNAs that enter Piwi protein MIWI2 (PIWIL4). Cell-culture studies with the insect ortholog of TDRD12 suggest a role for the multidomain protein in mediating complex formation with other participants during secondary piRNA biogenesis.
Collapse
|