1
|
He L, Sun F, Wu Y, Li Z, Fu Y, Huang Q, Li J, Wang Z, Cai J, Feng C, Deng X, Gu H, He X, Yu J, Sun F. L(1)10Bb serves as a conservative determinant for soma-germline communications via cellular non-autonomous effects within the testicular stem cell niche. Mol Cell Endocrinol 2024; 591:112278. [PMID: 38795826 DOI: 10.1016/j.mce.2024.112278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/21/2024] [Accepted: 05/07/2024] [Indexed: 05/28/2024]
Abstract
The testicular stem cell niche is the central regulator of spermatogenesis in Drosophila melanogaster. However, the underlying regulatory mechanisms are unclear. This study demonstrated the crucial role of lethal (1) 10Bb [l(1)10Bb] in regulating the testicular stem cell niche. Dysfunction of l(1)10Bb in early-stage cyst cells led to male fertility disorders and compromised cyst stem cell maintenance. Moreover, the dysfunction of l(1)10Bb in early-stage cyst cells exerted non-autonomous effects on germline stem cell differentiation, independently of hub signals. Notably, our study highlights the rescue of testicular defects through ectopic expression of L(1)10Bb and the human homologous protein BUD31 homolog (BUD31). In addition, l(1)10Bb dysfunction in early-stage cyst cells downregulated the expression of spliceosome subunits in the Sm and the precursor RNA processing complexes. Collectively, our findings established l(1)10Bb as a pivotal factor in the modulation of Drosophila soma-germline communications within the testicular stem cell niche.
Collapse
Affiliation(s)
- Lei He
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Feiteng Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yunhao Wu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Zhiran Li
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Yangbo Fu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Qiuru Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Jiaxin Li
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Zihan Wang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Jiaying Cai
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Chenrui Feng
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xiaonan Deng
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Han Gu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Xuxin He
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Jun Yu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| |
Collapse
|
2
|
Ray M, Conard AM, Urban J, Mahableshwarkar P, Aguilera J, Huang A, Vaidyanathan S, Larschan E. Sex-specific splicing occurs genome-wide during early Drosophila embryogenesis. eLife 2023; 12:e87865. [PMID: 37466240 PMCID: PMC10400075 DOI: 10.7554/elife.87865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 07/20/2023] Open
Abstract
Sex-specific splicing is an essential process that regulates sex determination and drives sexual dimorphism. Yet, how early in development widespread sex-specific transcript diversity occurs was unknown because it had yet to be studied at the genome-wide level. We use the powerful Drosophila model to show that widespread sex-specific transcript diversity occurs early in development, concurrent with zygotic genome activation. We also present a new pipeline called time2Splice to quantify changes in alternative splicing over time. Furthermore, we determine that one of the consequences of losing an essential maternally deposited pioneer factor called CLAMP (chromatin-linked adapter for MSL proteins) is altered sex-specific splicing of genes involved in diverse biological processes that drive development. Overall, we show that sex-specific differences in transcript diversity exist even at the earliest stages of development..
Collapse
Affiliation(s)
- Mukulika Ray
- MCB department, Brown UniversityProvidenceUnited States
| | | | - Jennifer Urban
- Biology department, Johns Hopkins UniversityBaltimoreUnited States
| | - Pranav Mahableshwarkar
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | | - Annie Huang
- MCB department, Brown UniversityProvidenceUnited States
| | - Smriti Vaidyanathan
- MCB department, Brown UniversityProvidenceUnited States
- CCMB department, Brown UniversityProvidenceUnited States
| | | |
Collapse
|
3
|
Popli P, Chadchan SB, Dias M, Deng X, Gunderson SJ, Jimenez P, Yalamanchili H, Kommagani R. SF3B1-dependent alternative splicing is critical for maintaining endometrial homeostasis and the establishment of pregnancy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541590. [PMID: 37292891 PMCID: PMC10245700 DOI: 10.1101/2023.05.20.541590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The remarkable potential of human endometrium to undergo spontaneous remodeling is shaped by controlled spatiotemporal gene expression patterns. Although hormone-driven transcription shown to govern these patterns, the post-transcriptional processing of these mRNA transcripts, including the mRNA splicing in the endometrium is not studied yet. Here, we report that the splicing factor, SF3B1 is central in driving alternative splicing (AS) events that are vital for physiological responses of the endometrium. We show that loss of SF3B1 splicing activity impairs stromal cell decidualization as well as embryo implantation. Transcriptomic analysis revealed that SF3B1 depletion decidualizing stromal cells led to differential mRNA splicing. Specifically, a significant upregulation in mutually exclusive AS events (MXEs) with SF3B1 loss resulted in the generation of aberrant transcripts. Further, we found that some of these candidate genes phenocopy SF3B1 function in decidualization. Importantly, we identify progesterone as a potential upstream regulator of SF3B1-mediated functions in endometrium possibly via maintaining its persistently high levels, in coordination with deubiquitinating enzymes. Collectively, our data suggest that SF3B1-driven alternative splicing plays a critical role in mediating the endometrial-specific transcriptional paradigms. Thus, the identification of novel mRNA variants associated with successful pregnancy establishment may help to develop new strategies to diagnose or prevent early pregnancy loss.
Collapse
|
4
|
Idrissou M, Maréchal A. The PRP19 Ubiquitin Ligase, Standing at the Cross-Roads of mRNA Processing and Genome Stability. Cancers (Basel) 2022; 14:878. [PMID: 35205626 PMCID: PMC8869861 DOI: 10.3390/cancers14040878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 12/07/2022] Open
Abstract
mRNA processing factors are increasingly being recognized as important regulators of genome stability. By preventing and resolving RNA:DNA hybrids that form co-transcriptionally, these proteins help avoid replication-transcription conflicts and thus contribute to genome stability through their normal function in RNA maturation. Some of these factors also have direct roles in the activation of the DNA damage response and in DNA repair. One of the most intriguing cases is that of PRP19, an evolutionarily conserved essential E3 ubiquitin ligase that promotes mRNA splicing, but also participates directly in ATR activation, double-strand break resection and mitosis. Here, we review historical and recent work on PRP19 and its associated proteins, highlighting their multifarious cellular functions as central regulators of spliceosome activity, R-loop homeostasis, DNA damage signaling and repair and cell division. Finally, we discuss open questions that are bound to shed further light on the functions of PRP19-containing complexes in both normal and cancer cells.
Collapse
Affiliation(s)
- Mouhamed Idrissou
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada;
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N3, Canada
| |
Collapse
|
5
|
Prudêncio P, Savisaar R, Rebelo K, Martinho RG, Carmo-Fonseca M. Transcription and splicing dynamics during early Drosophila development. RNA (NEW YORK, N.Y.) 2022; 28:139-161. [PMID: 34667107 PMCID: PMC8906543 DOI: 10.1261/rna.078933.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/23/2021] [Indexed: 05/03/2023]
Abstract
Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either Saccharomyces cerevisiae or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure cotranscriptional splicing dynamics during the early developmental stages of Drosophila melanogaster embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nt of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes, Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravel novel dynamic features of Pol II transcription and splicing in the developing Drosophila embryo.
Collapse
Affiliation(s)
- Pedro Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Kenny Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Rui Gonçalo Martinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Medical Sciences and Institute for Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| |
Collapse
|
6
|
Vinter DJ, Hoppe C, Minchington TG, Sutcliffe C, Ashe HL. Dynamics of hunchback translation in real-time and at single-mRNA resolution in the Drosophila embryo. Development 2021; 148:dev196121. [PMID: 33722899 PMCID: PMC8077512 DOI: 10.1242/dev.196121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/10/2021] [Indexed: 12/15/2022]
Abstract
The Hunchback (Hb) transcription factor is crucial for anterior-posterior patterning of the Drosophila embryo. The maternal hb mRNA acts as a paradigm for translational regulation due to its repression in the posterior of the embryo. However, little is known about the translatability of zygotically transcribed hb mRNAs. Here, we adapt the SunTag system, developed for imaging translation at single-mRNA resolution in tissue culture cells, to the Drosophila embryo to study the translation dynamics of zygotic hb mRNAs. Using single-molecule imaging in fixed and live embryos, we provide evidence for translational repression of zygotic SunTag-hb mRNAs. Whereas the proportion of SunTag-hb mRNAs translated is initially uniform, translation declines from the anterior over time until it becomes restricted to a posterior band in the expression domain. We discuss how regulated hb mRNA translation may help establish the sharp Hb expression boundary, which is a model for precision and noise during developmental patterning. Overall, our data show how use of the SunTag method on fixed and live embryos is a powerful combination for elucidating spatiotemporal regulation of mRNA translation in Drosophila.
Collapse
Affiliation(s)
| | | | | | | | - Hilary L. Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| |
Collapse
|
7
|
Bayega A, Oikonomopoulos S, Gregoriou ME, Tsoumani KT, Giakountis A, Wang YC, Mathiopoulos KD, Ragoussis J. Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest. Sci Rep 2021; 11:7878. [PMID: 33846393 PMCID: PMC8042104 DOI: 10.1038/s41598-021-86753-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
The olive fruit fly, Bactrocera oleae, is the most important pest for the olive fruit but lacks adequate transcriptomic characterization that could aid in molecular control approaches. We apply nanopore long-read RNA-seq with internal RNA standards allowing absolute transcript quantification to analyze transcription dynamics during early embryo development for the first time in this organism. Sequencing on the MinION platform generated over 31 million reads. Over 50% of the expressed genes had at least one read covering its entire length validating our full-length approach. We generated a de novo transcriptome assembly and identified 1768 new genes and a total of 79,810 isoforms; a fourfold increase in transcriptome diversity compared to the current NCBI predicted transcriptome. Absolute transcript quantification per embryo allowed an insight into the dramatic re-organization of maternal transcripts. We further identified Zelda as a possible regulator of early zygotic genome activation in B. oleae and provide further insights into the maternal-to-zygotic transition. These data show the utility of long-read RNA in improving characterization of non-model organisms that lack a fully annotated genome, provide potential targets for sterile insect technic approaches, and provide the first insight into the transcriptome landscape of the developing olive fruit fly embryo.
Collapse
Affiliation(s)
- Anthony Bayega
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Maria-Eleni Gregoriou
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Konstantina T Tsoumani
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Antonis Giakountis
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Yu Chang Wang
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Kostas D Mathiopoulos
- Laboratory of Molecular Biology and Genomics, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada.
- Department of Bioengineering, McGill University, Montréal, Québec, Canada.
| |
Collapse
|
8
|
Rathore OS, Silva RD, Ascensão-Ferreira M, Matos R, Carvalho C, Marques B, Tiago MN, Prudêncio P, Andrade RP, Roignant JY, Barbosa-Morais NL, Martinho RG. NineTeen Complex-subunit Salsa is required for efficient splicing of a subset of introns and dorsal-ventral patterning. RNA (NEW YORK, N.Y.) 2020; 26:1935-1956. [PMID: 32963109 PMCID: PMC7668242 DOI: 10.1261/rna.077446.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The NineTeen Complex (NTC), also known as pre-mRNA-processing factor 19 (Prp19) complex, regulates distinct spliceosome conformational changes necessary for splicing. During Drosophila midblastula transition, splicing is particularly sensitive to mutations in NTC-subunit Fandango, which suggests differential requirements of NTC during development. We show that NTC-subunit Salsa, the Drosophila ortholog of human RNA helicase Aquarius, is rate-limiting for splicing of a subset of small first introns during oogenesis, including the first intron of gurken Germline depletion of Salsa and splice site mutations within gurken first intron impair both adult female fertility and oocyte dorsal-ventral patterning, due to an abnormal expression of Gurken. Supporting causality, the fertility and dorsal-ventral patterning defects observed after Salsa depletion could be suppressed by the expression of a gurken construct without its first intron. Altogether, our results suggest that one of the key rate-limiting functions of Salsa during oogenesis is to ensure the correct expression and efficient splicing of the first intron of gurken mRNA. Retention of gurken first intron compromises the function of this gene most likely because it undermines the correct structure and function of the transcript 5'UTR.
Collapse
Affiliation(s)
- Om Singh Rathore
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Rui D Silva
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Mariana Ascensão-Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ricardo Matos
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Bruno Marques
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Margarida N Tiago
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
| | - Pedro Prudêncio
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Raquel P Andrade
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
- Department of Medicine and Biomedical Sciences and Algarve Biomedical Center, Universidade do Algarve, 8005-139 Faro, Portugal
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Nuno L Barbosa-Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Rui Gonçalo Martinho
- Center for Biomedical Research (CBMR), Universidade do Algarve, Faro, 8005-139 Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Department of Medical Sciences and Institute for Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| |
Collapse
|
9
|
Bajpai A, Quazi TA, Tang HW, Manzar N, Singh V, Thakur A, Ateeq B, Perrimon N, Sinha P. A Drosophila model of oral peptide therapeutics for adult intestinal stem cell tumors. Dis Model Mech 2020; 13:dmm044420. [PMID: 32540914 PMCID: PMC7390633 DOI: 10.1242/dmm.044420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
Peptide therapeutics, unlike small-molecule drugs, display crucial advantages of target specificity and the ability to block large interacting interfaces, such as those of transcription factors. The transcription co-factor of the Hippo pathway, YAP/Yorkie (Yki), has been implicated in many cancers, and is dependent on its interaction with the DNA-binding TEAD/Sd proteins via a large Ω-loop. In addition, the mammalian vestigial-like (VGLL) proteins, specifically their TONDU domain, competitively inhibit YAP-TEAD interaction, resulting in arrest of tumor growth. Here, we show that overexpression of the TONDU peptide or its oral uptake leads to suppression of Yki-driven intestinal stem cell tumors in the adult Drosophila midgut. In addition, comparative proteomic analyses of peptide-treated and untreated tumors, together with chromatin immunoprecipitation analysis, reveal that integrin pathway members are part of the Yki-oncogenic network. Collectively, our findings establish Drosophila as a reliable in vivo platform to screen for cancer oral therapeutic peptides and reveal a tumor suppressive role for integrins in Yki-driven tumors.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Anjali Bajpai
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Taushif Ahmad Quazi
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Hong-Wen Tang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nishat Manzar
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Virender Singh
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ashwani Thakur
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Bushra Ateeq
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Pradip Sinha
- Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| |
Collapse
|
10
|
Moonlighting in Mitosis: Analysis of the Mitotic Functions of Transcription and Splicing Factors. Cells 2020; 9:cells9061554. [PMID: 32604778 PMCID: PMC7348712 DOI: 10.3390/cells9061554] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Moonlighting proteins can perform one or more additional functions besides their primary role. It has been posited that a protein can acquire a moonlighting function through a gradual evolutionary process, which is favored when the primary and secondary functions are exerted in different cellular compartments. Transcription factors (TFs) and splicing factors (SFs) control processes that occur in interphase nuclei and are strongly reduced during cell division, and are therefore in a favorable situation to evolve moonlighting mitotic functions. However, recently published moonlighting protein databases, which comprise almost 400 proteins, do not include TFs and SFs with secondary mitotic functions. We searched the literature and found several TFs and SFs with bona fide moonlighting mitotic functions, namely they localize to specific mitotic structure(s), interact with proteins enriched in the same structure(s), and are required for proper morphology and functioning of the structure(s). In addition, we describe TFs and SFs that localize to mitotic structures but cannot be classified as moonlighting proteins due to insufficient data on their biochemical interactions and mitotic roles. Nevertheless, we hypothesize that most TFs and SFs with specific mitotic localizations have either minor or redundant moonlighting functions, or are evolving towards the acquisition of these functions.
Collapse
|
11
|
Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade in Caenorhabditis Endoderm Specification. G3-GENES GENOMES GENETICS 2020; 10:333-356. [PMID: 31740453 PMCID: PMC6945043 DOI: 10.1534/g3.119.400724] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene regulatory networks and their evolution are important in the study of animal development. In the nematode, Caenorhabditis elegans, the endoderm (gut) is generated from a single embryonic precursor, E. Gut is specified by the maternal factor SKN-1, which activates the MED → END-1,3 → ELT-2,7 cascade of GATA transcription factors. In this work, genome sequences from over two dozen species within the Caenorhabditis genus are used to identify MED and END-1,3 orthologs. Predictions are validated by comparison of gene structure, protein conservation, and putative cis-regulatory sites. All three factors occur together, but only within the Elegans supergroup, suggesting they originated at its base. The MED factors are the most diverse and exhibit an unexpectedly extensive gene amplification. In contrast, the highly conserved END-1 orthologs are unique in nearly all species and share extended regions of conservation. The END-1,3 proteins share a region upstream of their zinc finger and an unusual amino-terminal poly-serine domain exhibiting high codon bias. Compared with END-1, the END-3 proteins are otherwise less conserved as a group and are typically found as paralogous duplicates. Hence, all three factors are under different evolutionary constraints. Promoter comparisons identify motifs that suggest the SKN-1, MED, and END factors function in a similar gut specification network across the Elegans supergroup that has been conserved for tens of millions of years. A model is proposed to account for the rapid origin of this essential kernel in the gut specification network, by the upstream intercalation of duplicate genes into a simpler ancestral network.
Collapse
|
12
|
Kulichová K, Kumar V, Steinbachová L, Klodová B, Timofejeva L, Juříček M, Honys D, Hafidh S. PRP8A and PRP8B spliceosome subunits act co-ordinately to control pollen tube attraction in Arabidopsis. Development 2020; 147:dev.186742. [DOI: 10.1242/dev.186742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023]
Abstract
Precise guided pollen tube growth by the female gametophyte is a pre-requisite for successful sexual reproduction in flowering plants. Cysteine-rich proteins (CRPs) secreted from the embryo sac are known pollen tube attractants perceived by pollen tube receptor-like kinases (RLK's). How pre-mRNA splicing facilitates this cell-to-cell communication is not understood. Here, we report novel function of Pre-mRNA PROCESSING factor 8 paralogs, PRP8A and PRP8B, as regulators of pollen tube attraction. Double mutant prp8a prp8b ovules cannot attract pollen tubes, and prp8a prp8b pollen tubes fail in sensing ovules attraction signals. Only 3% of ovule-expressed genes were misregulated in prp8a prp8b. Combination of RNA-seq and MYB98/LURE1.2-YFP reporter revealed the expression of MYB98, LUREs and 49 other CRPs were downregulated suggesting loss of synergid cell fate. Differential Exon usage (DEU) and Intron-retention (IR) analysis revealed autoregulation of PPR8A/PRP8B splicing. In vivo, PRP8A coimmunoprecipitates with splicing enhancer AtSF3A1, suggesting involvement of PRP8A in 3′-splice site selection. Our data hint that PRP8A/PRP8B module exhibit spliceosome-autoregulation to facilitate pollen tube attraction via transcriptional regulation of MYB98, CRPs and LURE pollen tube attractants.
Collapse
Affiliation(s)
- Katarína Kulichová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Vinod Kumar
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Božena Klodová
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Ljudmilla Timofejeva
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - Miloslav Juříček
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
- Department of Plant Experimental Biology, Faculty of Science, Charles University, Viničná 5, 128 44, Prague 2, Czech Republic
| | - Said Hafidh
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Rozvojová 263, 165 02 Prague 6, Czech Republic
| |
Collapse
|
13
|
Abstract
Nucleotide excision repair (NER) is a highly conserved mechanism to remove helix-distorting DNA lesions. A major substrate for NER is DNA damage caused by environmental genotoxins, most notably ultraviolet radiation. Xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy are three human disorders caused by inherited defects in NER. The symptoms and severity of these diseases vary dramatically, ranging from profound developmental delay to cancer predisposition and accelerated ageing. All three syndromes include developmental abnormalities, indicating an important role for optimal transcription and for NER in protecting against spontaneous DNA damage during embryonic development. Here, we review the current knowledge on genes that function in NER that also affect embryonic development, in particular the development of a fully functional nervous system.
Collapse
Affiliation(s)
- Sofia J Araújo
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain.,Institute of Biomedicine, University of Barcelona (IBUB), Barcelona, Spain
| | - Isao Kuraoka
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| |
Collapse
|
14
|
Minocha R, Popova V, Kopytova D, Misiak D, Hüttelmaier S, Georgieva S, Sträßer K. Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. Nucleic Acids Res 2019; 46:9749-9763. [PMID: 30053068 PMCID: PMC6182176 DOI: 10.1093/nar/gky640] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 07/20/2018] [Indexed: 01/31/2023] Open
Abstract
The different steps of gene expression are intimately linked to coordinate and regulate this complex process. During transcription, numerous RNA-binding proteins are already loaded onto the nascent mRNA and package the mRNA into a messenger ribonucleoprotein particle (mRNP). These RNA-binding proteins are often also involved in other steps of gene expression than mRNA packaging. For example, TREX functions in transcription, mRNP packaging and nuclear mRNA export. Previously, we showed that the Prp19 splicing complex (Prp19C) is needed for efficient transcription as well as TREX occupancy at transcribed genes. Here, we show that the splicing factor Mud2 interacts with Prp19C and is needed for Prp19C occupancy at transcribed genes in Saccharomyces cerevisiae. Interestingly, Mud2 is not only recruited to intron-containing but also to intronless genes indicating a role in transcription. Indeed, we show for the first time that Mud2 functions in transcription. Furthermore, these functions of Mud2 are likely evolutionarily conserved as Mud2 is also recruited to an intronless gene and interacts with Prp19C in Drosophila melanogaster. Taken together, we classify Mud2 as a novel transcription factor that is necessary for the recruitment of mRNA-binding proteins to the transcription machinery. Thus, Mud2 is a multifunctional protein important for transcription, splicing and most likely also mRNP packaging.
Collapse
Affiliation(s)
- Rashmi Minocha
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
| | - Varvara Popova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Daria Kopytova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Danny Misiak
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle Wittenberg, Halle 06120, Germany
| | - Sofia Georgieva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Katja Sträßer
- Institute of Biochemistry, Justus Liebig University, Giessen 35392, Germany
| |
Collapse
|
15
|
Abstract
Diabetes and obesity are the two notorious metabolic disorders in today's world. Both diabetes and obesity are interlinked with each other and often referred to as 'Diabesity'. It is a complex and multi-organ failure disorder. Thus, many researches and tremendous efforts have been made toward prevention, treatment as well as early detection of diabesity. However, and still, there is a large gap in understanding the etiology as well as treatment of diabesity. Various animal models are also used to decipher the mechanism underlying diabesity. Among all the model organism, recently Drosophila melanogaster is gaining its importance to study diabetes, obesity, and other metabolic disorder. Various experimental methods like histological, biochemical, developmental, and behavioral assays are described in this study to detect diabetes as well as obesity in the fly model.
Collapse
Affiliation(s)
- Nibedita Nayak
- Neural Developmental Biology Lab, Department of Life Science, National Institute of Technology , Rourkela , India
| | - Monalisa Mishra
- Neural Developmental Biology Lab, Department of Life Science, National Institute of Technology , Rourkela , India
| |
Collapse
|
16
|
Kwasnieski JC, Orr-Weaver TL, Bartel DP. Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns. Genome Res 2019; 29:1188-1197. [PMID: 31235656 PMCID: PMC6633261 DOI: 10.1101/gr.242164.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 05/08/2019] [Indexed: 01/02/2023]
Abstract
Control of metazoan embryogenesis shifts from maternal to zygotic gene products as the zygotic genome becomes transcriptionally activated. In Drosophila, zygotic genome activation (ZGA) has been thought to occur in two phases, starting with a minor wave, in which a small number of genes become expressed, and progressing to the major wave, in which many more genes are activated. However, technical challenges have hampered the identification of early transcripts or obscured the onset of their transcription. Here, we develop an approach to isolate transcribed mRNAs and apply it over the course of Drosophila early genome activation. Our results increase by 10-fold the genes reported to be activated during what has been thought of as the minor wave and show that early genome activation is continuous and gradual. Transposable-element mRNAs are also produced, but discontinuously. Genes transcribed in the early and middle part of ZGA are short with few if any introns, and their transcripts are frequently aborted and tend to have retained introns, suggesting that inefficient splicing as well as rapid cell divisions constrain the lengths of early transcripts.
Collapse
Affiliation(s)
- Jamie C Kwasnieski
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - Terry L Orr-Weaver
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| | - David P Bartel
- Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
| |
Collapse
|
17
|
Zhou X, Zhang Y, Michal JJ, Qu L, Zhang S, Wildung MR, Du W, Pouchnik DJ, Zhao H, Xia Y, Shi H, Ji G, Davis JF, Smith GD, Griswold MD, Harland RM, Jiang Z. Alternative polyadenylation coordinates embryonic development, sexual dimorphism and longitudinal growth in Xenopus tropicalis. Cell Mol Life Sci 2019; 76:2185-2198. [PMID: 30729254 PMCID: PMC6597005 DOI: 10.1007/s00018-019-03036-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 12/27/2022]
Abstract
RNA alternative polyadenylation contributes to the complexity of information transfer from genome to phenome, thus amplifying gene function. Here, we report the first X. tropicalis resource with 127,914 alternative polyadenylation (APA) sites derived from embryos and adults. Overall, APA networks play central roles in coordinating the maternal-zygotic transition (MZT) in embryos, sexual dimorphism in adults and longitudinal growth from embryos to adults. APA sites coordinate reprogramming in embryos before the MZT, but developmental events after the MZT due to zygotic genome activation. The APA transcriptomes of young adults are more variable than growing adults and male frog APA transcriptomes are more divergent than females. The APA profiles of young females were similar to embryos before the MZT. Enriched pathways in developing embryos were distinct across the MZT and noticeably segregated from adults. Briefly, our results suggest that the minimal functional units in genomes are alternative transcripts as opposed to genes.
Collapse
Affiliation(s)
- Xiang Zhou
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
- College of Animal Sciences and Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yangzi Zhang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Jennifer J Michal
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Lujiang Qu
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
- College of Animal Sciences and Technology, China Agricultural University, Beijing, China
| | - Shuwen Zhang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA
| | - Mark R Wildung
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Weiwei Du
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Derek J Pouchnik
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Hui Zhao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Yin Xia
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Honghua Shi
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, Shanghai, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China
| | - Jon F Davis
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
| | - Gary D Smith
- Departments of OB/GYN, Physiology, and Urology, University of Michigan, Ann Arbor, MI, USA
| | - Michael D Griswold
- Laboratory for Biotechnology and Bioanalysis, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, 99164-7620, USA.
| |
Collapse
|
18
|
Co-expression network analysis identifies gonad- and embryo-associated protein modules in the sentinel species Gammarus fossarum. Sci Rep 2019; 9:7862. [PMID: 31133674 PMCID: PMC6536538 DOI: 10.1038/s41598-019-44203-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 05/10/2019] [Indexed: 12/12/2022] Open
Abstract
Next generation sequencing and mass spectrometry technologies have recently expanded the availability of whole transcriptomes and proteomes beyond classical model organisms in molecular biology, even in absence of an annotated genome. However, the fragmented nature of transcriptomic and proteomic data reduces the ability to interpret the data, notably in non-model organisms. Network-based approaches may help extracting important biological information from -omics datasets. The reproductive cycle of the freshwater crustacean Gammarus fossarum.provides an excellent case study to test the relevance of a network analysis in non-model organisms. Here, we illustrated how the use of a co-expression network analysis (based on Weighted Gene Co-expression Network Analysis algorithm, WGCNA) allowed identifying protein modules whose expression profiles described germ cell maturation and embryonic development in the freshwater crustacean Gammarus fossarum. Proteome datasets included testes, ovaries or embryos samples at different maturation or developmental stages, respectively. We identified an embryonic module correlated with mid-developmental stages corresponding to the organogenesis and it was characterized by enrichment in proteins involved in RNA editing and splicing. An ovarian module was enriched in vitellogenin-like proteins and clottable proteins, confirming the diversity of proteins belonging to the large lipid transfer family involved in oocytes maturations in this freshwater amphipod. Moreover, our results found evidence of a fine-tuned regulation between energy production by glycolysis and actin-myosin-dependent events in G. fossarum spermatogenesis. This study illustrates the importance of applying systems biology approaches to emergent animal models to improve the understanding of the molecular mechanisms regulating important physiological events with ecological relevance.
Collapse
|
19
|
Gomulski LM, Mariconti M, Di Cosimo A, Scolari F, Manni M, Savini G, Malacrida AR, Gasperi G. The Nix locus on the male-specific homologue of chromosome 1 in Aedes albopictus is a strong candidate for a male-determining factor. Parasit Vectors 2018; 11:647. [PMID: 30583734 PMCID: PMC6304787 DOI: 10.1186/s13071-018-3215-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Global concern over the rapid expansion of the Asian tiger mosquito, Aedes albopictus, and its vector competence has highlighted an urgent need to improve currently available population control methods, like the Sterile Insect Technique. Knowledge of the sex determination cascade is a prerequisite for the development of early-stage sexing systems. To this end, we have characterised the putative sex determination gene, Nix, in this species. In Aedes species the chromosome complement consists of three pairs of chromosomes. The sex determination alleles are linked to the smallest homomorphic chromosome. Results We identified the male-specific chromosome 1 of Ae. albopictus that carries the putative male-determining gene Nix. We have also characterised the complete genomic sequence of the Nix gene which is composed of two exons and a short intron. The gene displays different levels of intron retention during development. Comparison of DNA sequences covering most of the Nix gene from individuals across the species range revealed no polymorphism. Conclusions Our characterisation of the Nix gene in Ae. albopictus represents an initial step in the analysis of the sex determination cascade in this species. We found evidence of intron retention (IR) in Nix. IR might play a role in regulating the expression of Nix during development. Our results provide the basis for the development of new genetic control strategies. Electronic supplementary material The online version of this article (10.1186/s13071-018-3215-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ludvik M Gomulski
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Marina Mariconti
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Alessandro Di Cosimo
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Francesca Scolari
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Mosè Manni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.,Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Grazia Savini
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Anna R Malacrida
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Giuliano Gasperi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.
| |
Collapse
|
20
|
Hamm DC, Harrison MM. Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster. Open Biol 2018; 8:180183. [PMID: 30977698 PMCID: PMC6303782 DOI: 10.1098/rsob.180183] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
The onset of metazoan development requires that two terminally differentiated germ cells, a sperm and an oocyte, become reprogrammed to the totipotent embryo, which can subsequently give rise to all the cell types of the adult organism. In nearly all animals, maternal gene products regulate the initial events of embryogenesis while the zygotic genome remains transcriptionally silent. Developmental control is then passed from mother to zygote through a process known as the maternal-to-zygotic transition (MZT). The MZT comprises an intimately connected set of molecular events that mediate degradation of maternally deposited mRNAs and transcriptional activation of the zygotic genome. This essential developmental transition is conserved among metazoans but is perhaps best understood in the fruit fly, Drosophila melanogaster. In this article, we will review our understanding of the events that drive the MZT in Drosophila embryos and highlight parallel mechanisms driving this transition in other animals.
Collapse
Affiliation(s)
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| |
Collapse
|
21
|
Pellacani C, Bucciarelli E, Renda F, Hayward D, Palena A, Chen J, Bonaccorsi S, Wakefield JG, Gatti M, Somma MP. Splicing factors Sf3A2 and Prp31 have direct roles in mitotic chromosome segregation. eLife 2018; 7:40325. [PMID: 30475206 PMCID: PMC6287947 DOI: 10.7554/elife.40325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 11/14/2018] [Indexed: 12/26/2022] Open
Abstract
Several studies have shown that RNAi-mediated depletion of splicing factors (SFs) results in mitotic abnormalities. However, it is currently unclear whether these abnormalities reflect defective splicing of specific pre-mRNAs or a direct role of the SFs in mitosis. Here, we show that two highly conserved SFs, Sf3A2 and Prp31, are required for chromosome segregation in both Drosophila and human cells. Injections of anti-Sf3A2 and anti-Prp31 antibodies into Drosophila embryos disrupt mitotic division within 1 min, arguing strongly against a splicing-related mitotic function of these factors. We demonstrate that both SFs bind spindle microtubules (MTs) and the Ndc80 complex, which in Sf3A2- and Prp31-depleted cells is not tightly associated with the kinetochores; in HeLa cells the Ndc80/HEC1-SF interaction is restricted to the M phase. These results indicate that Sf3A2 and Prp31 directly regulate interactions among kinetochores, spindle microtubules and the Ndc80 complex in both Drosophila and human cells.
Collapse
Affiliation(s)
- Claudia Pellacani
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Elisabetta Bucciarelli
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Fioranna Renda
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Daniel Hayward
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Antonella Palena
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| | - Jack Chen
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Silvia Bonaccorsi
- Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - James G Wakefield
- Biosciences/Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Maurizio Gatti
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy.,Dipartimento di Biologia e Biotecnologie "C. Darwin", Sapienza Università di Roma, Roma, Italy
| | - Maria Patrizia Somma
- Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, Roma, Italy
| |
Collapse
|
22
|
Prudêncio P, Guilgur LG, Sobral J, Becker JD, Martinho RG, Navarro-Costa P. The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization. EMBO Rep 2018; 19:e45728. [PMID: 30037897 PMCID: PMC6073209 DOI: 10.15252/embr.201845728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 06/27/2018] [Accepted: 07/02/2018] [Indexed: 12/25/2022] Open
Abstract
The transition from fertilized oocyte to totipotent embryo relies on maternal factors that are synthetized and accumulated during oocyte development. Yet, it is unclear how oocytes regulate the expression of maternal genes within the transcriptional program of oogenesis. Here, we report that the Drosophila Trithorax group protein dMLL3/4 (also known as Trr) is essential for the transition to embryo fate at fertilization. In the absence of dMLL3/4, oocytes develop normally but fail to initiate the embryo mitotic divisions after fertilization. This incapability results from defects in paternal genome reprogramming and maternal meiotic completion. The methyltransferase activity of dMLL3/4 is dispensable for both these processes. We further show that dMLL3/4 promotes the expression of a functionally coherent gene subset that is required for the initiation of post-fertilization development. Accordingly, we identify the evolutionarily conserved IDGF4 glycoprotein (known as oviductin in mammals) as a new oocyte-to-embryo transition gene under direct dMLL3/4 transcriptional control. Based on these observations, we propose that dMLL3/4 plays an instructive role in the oocyte-to-embryo transition that is functionally uncoupled from the requirements of oogenesis.
Collapse
Affiliation(s)
- Pedro Prudêncio
- Center for Biomedical Research and Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | | | - João Sobral
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | - Rui Gonçalo Martinho
- Center for Biomedical Research and Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Institute of Biomedicine - iBiMED and Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal
| | - Paulo Navarro-Costa
- Center for Biomedical Research and Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Faro, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| |
Collapse
|
23
|
Splicing dysfunction and disease: The case of granulopoiesis. Semin Cell Dev Biol 2018; 75:23-39. [DOI: 10.1016/j.semcdb.2017.08.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022]
|
24
|
Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins. Nat Commun 2017; 8:1721. [PMID: 29167427 PMCID: PMC5700196 DOI: 10.1038/s41467-017-01927-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Bivalve molluscs are descendants of an early-Cambrian lineage superbly adapted to benthic filter feeding. Adaptations in form and behavior are well recognized, but the underlying molecular mechanisms are largely unknown. Here, we investigate the genome, various transcriptomes, and proteomes of the scallop Chlamys farreri, a semi-sessile bivalve with well-developed adductor muscle, sophisticated eyes, and remarkable neurotoxin resistance. The scallop's large striated muscle is energy-dynamic but not fully differentiated from smooth muscle. Its eyes are supported by highly diverse, intronless opsins expanded by retroposition for broadened spectral sensitivity. Rapid byssal secretion is enabled by a specialized foot and multiple proteins including expanded tyrosinases. The scallop uses hepatopancreas to accumulate neurotoxins and kidney to transform to high-toxicity forms through expanded sulfotransferases, probably as deterrence against predation, while it achieves neurotoxin resistance through point mutations in sodium channels. These findings suggest that expansion and mutation of those genes may have profound effects on scallop's phenotype and adaptation.
Collapse
|
25
|
Ketosugbo KF, Bushnell HL, Johnson RI. A screen for E3 ubiquitination ligases that genetically interact with the adaptor protein Cindr during Drosophila eye patterning. PLoS One 2017; 12:e0187571. [PMID: 29117266 PMCID: PMC5678704 DOI: 10.1371/journal.pone.0187571] [Citation(s) in RCA: 10] [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: 06/27/2017] [Accepted: 10/23/2017] [Indexed: 01/12/2023] Open
Abstract
Ubiquitination is a crucial post-translational modification that can target proteins for degradation. The E3 ubiquitin ligases are responsible for recognizing substrate proteins for ubiquitination, hence providing specificity to the process of protein degradation. Here, we describe a genetic modifier screen that identified E3 ligases that modified the rough-eye phenotype generated by expression of cindrRNAi transgenes during Drosophila eye development. In total, we identified 36 E3 ligases, as well as 4 Cullins, that modified the mild cindrRNA mis-patterning phenotype. This indicates possible roles for these E3s/Cullins in processes that require Cindr function, including cytoskeletal regulation, cell adhesion, cell signaling and cell survival. Three E3 ligases identified in our screen had previously been linked to regulating JNK signaling.
Collapse
Affiliation(s)
- Kwami F. Ketosugbo
- Biology Department, Wesleyan University, Middletown, Connecticut, United States of America
| | - Henry L. Bushnell
- Biology Department, Wesleyan University, Middletown, Connecticut, United States of America
| | - Ruth I. Johnson
- Biology Department, Wesleyan University, Middletown, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
26
|
Exploring the Impact of Cleavage and Polyadenylation Factors on Pre-mRNA Splicing Across Eukaryotes. G3-GENES GENOMES GENETICS 2017; 7:2107-2114. [PMID: 28500052 PMCID: PMC5499120 DOI: 10.1534/g3.117.041483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In human, mouse, and Drosophila, the spliceosomal complex U1 snRNP (U1) protects transcripts from premature cleavage and polyadenylation at proximal intronic polyadenylation signals (PAS). These U1-mediated effects preserve transcription integrity, and are known as telescripting. The watchtower role of U1 throughout transcription is clear. What is less clear is whether cleavage and polyadenylation factors (CPFs) are simply patrolled or if they might actively antagonize U1 recruitment. In addressing this question, we found that, in the introns of human, mouse, and Drosophila, and of 14 other eukaryotes, including multi- and single-celled species, the conserved AATAAA PAS—a major target for CPFs—is selected against. This selective pressure, approximated using DNA strand asymmetry, is detected for peripheral and internal introns alike. Surprisingly, it is more pronounced within—rather than outside—the action range of telescripting, and particularly intense in the vicinity of weak 5′ splice sites. Our study uncovers a novel feature of eukaryotic genes: that the AATAAA PAS is universally counter-selected in spliceosomal introns. This pattern implies that CPFs may attempt to access introns at any time during transcription. However, natural selection operates to minimize this access. By corroborating and extending previous work, our study further indicates that CPF access to intronic PASs might perturb the recruitment of U1 to the adjacent 5′ splice sites. These results open the possibility that CPFs may impact the splicing process across eukaryotes.
Collapse
|
27
|
Romney AL, Podrabsky JE. Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus. EvoDevo 2017; 8:6. [PMID: 28439397 PMCID: PMC5401559 DOI: 10.1186/s13227-017-0069-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause. Alternately, embryos can be programmed to “escape” from diapause and develop directly by both maternal factors and embryonic incubation conditions. Thus, maternally packaged gene products are hypothesized to regulate developmental trajectory and perhaps the other unique developmental characters in this species. Results Using high-throughput RNA sequencing, we generated transcriptomic profiles of mRNAs, long non-coding RNAs and small non-coding RNAs (sncRNAs) in 1–2 cell stage embryos of A. limnaeus. Transcriptomic analyses suggest maternal programming of embryos through alternatively spliced mRNAs and antisense sncRNAs. Comparison of these results to those of comparable studies on zebrafish and other fishes reveals a surprisingly high abundance of transcripts involved in the cellular response to stress and a relatively lower expression of genes required for rapid transition through the cell cycle. Conclusions Maternal programming of developmental trajectory is unlikely accomplished by differential expression of diapause-specific genes. Rather, evidence suggests a role for trajectory-specific splice variants of genes expressed in both phenotypes. In addition, based on comparative studies with zebrafish, the A. limnaeus 1–2 cell stage transcriptome is unique in ways that are consistent with their unique life history. These results not only impact our understanding of the genetic mechanisms that regulate entrance into diapause, but also provide insight into the epigenetic regulation of gene expression during development. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0069-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Amie L Romney
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
| | - Jason E Podrabsky
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207 USA
| |
Collapse
|
28
|
Sauerwald J, Soneson C, Robinson MD, Luschnig S. Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila. Development 2017; 144:657-663. [PMID: 28087625 DOI: 10.1242/dev.144535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/30/2016] [Indexed: 01/26/2023]
Abstract
Morphogenesis requires the dynamic regulation of gene expression, including transcription, mRNA maturation and translation. Dysfunction of the general mRNA splicing machinery can cause surprisingly specific cellular phenotypes, but the basis for these effects is not clear. Here, we show that the Drosophila faint sausage (fas) locus, which is implicated in epithelial morphogenesis and has previously been reported to encode a secreted immunoglobulin domain protein, in fact encodes a subunit of the spliceosome-activating Prp19 complex, which is essential for efficient pre-mRNA splicing. Loss of zygotic fas function globally impairs the efficiency of splicing, and is associated with widespread retention of introns in mRNAs and dramatic changes in gene expression. Surprisingly, despite these general effects, zygotic fas mutants show specific defects in tracheal cell migration during mid-embryogenesis when maternally supplied splicing factors have declined. We propose that tracheal branching, which relies on dynamic changes in gene expression, is particularly sensitive for efficient spliceosome function. Our results reveal an entry point to study requirements of the splicing machinery during organogenesis and provide a better understanding of disease phenotypes associated with mutations in general splicing factors.
Collapse
Affiliation(s)
- Julia Sauerwald
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany.,Cluster of Excellence EXC 1003, Cells in Motion (CiM), 48149 Münster, Germany.,Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Charlotte Soneson
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,SIB Swiss Institute of Bioinformatics, 8057 Zürich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,SIB Swiss Institute of Bioinformatics, 8057 Zürich, Switzerland
| | - Stefan Luschnig
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany .,Cluster of Excellence EXC 1003, Cells in Motion (CiM), 48149 Münster, Germany.,Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| |
Collapse
|
29
|
Ribeiro AL, Silva RD, Foyn H, Tiago MN, Rathore OS, Arnesen T, Martinho RG. Naa50/San-dependent N-terminal acetylation of Scc1 is potentially important for sister chromatid cohesion. Sci Rep 2016; 6:39118. [PMID: 27996020 PMCID: PMC5171793 DOI: 10.1038/srep39118] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/17/2016] [Indexed: 12/17/2022] Open
Abstract
The gene separation anxiety (san) encodes Naa50/San, a N-terminal acetyltransferase required for chromosome segregation during mitosis. Although highly conserved among higher eukaryotes, the mitotic function of this enzyme is still poorly understood. Naa50/San was originally proposed to be required for centromeric sister chromatid cohesion in Drosophila and human cells, yet, more recently, it was also suggested to be a negative regulator of microtubule polymerization through internal acetylation of beta Tubulin. We used genetic and biochemical approaches to clarify the function of Naa50/San during development. Our work suggests that Naa50/San is required during tissue proliferation for the correct interaction between the cohesin subunits Scc1 and Smc3. Our results also suggest a working model where Naa50/San N-terminally acetylates the nascent Scc1 polypeptide, and that this co-translational modification is subsequently required for the establishment and/or maintenance of sister chromatid cohesion.
Collapse
Affiliation(s)
- Ana Luisa Ribeiro
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Rui D Silva
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Håvard Foyn
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway
| | - Margarida N Tiago
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Om Singh Rathore
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
| | - Thomas Arnesen
- Department of Molecular Biology, University of Bergen, N-5020 Bergen, Norway.,Department of Surgery, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Rui Gonçalo Martinho
- Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.,Center for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal.,Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| |
Collapse
|
30
|
XAB2 functions in mitotic cell cycle progression via transcriptional regulation of CENPE. Cell Death Dis 2016; 7:e2409. [PMID: 27735937 PMCID: PMC5133980 DOI: 10.1038/cddis.2016.313] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/05/2016] [Accepted: 09/05/2016] [Indexed: 12/16/2022]
Abstract
Xeroderma pigmentosum group A (XPA)-binding protein 2 (XAB2) is a multi-functional protein that plays critical role in processes including transcription, transcription-coupled DNA repair, pre-mRNA splicing, homologous recombination and mRNA export. Microarray analysis on gene expression in XAB2 knockdown cells reveals that many genes with significant change in expression function in mitotic cell cycle regulation. Fluorescence-activated cell scanner analysis confirmed XAB2 depletion led to cell arrest in G2/M phase, mostly at prophase or prometaphase. Live cell imaging further disclosed that XAB2 knockdown induced severe mitotic defects including chromosome misalignment and defects in segregation, leading to mitotic arrest, mitotic catastrophe and subsequent cell death. Among top genes down-regulated by XAB2 depletion is mitotic motor protein centrosome-associated protein E (CENPE). Knockdown CENPE showed similar phenotypes to loss of XAB2, but CENPE knockdown followed by XAB2 depletion did not further enhance cell cycle arrest. Luciferase assay on CENPE promoter showed that overexpression of XAB2 increased luciferase activity, whereas XAB2 depletion resulted in striking reduction of luciferase activity. Further mapping revealed a region in CENPE promoter that is required for the transcriptional regulation by XAB2. Moreover, ChIP assay showed that XAB2 interacted with CENPE promoter. Together, these results support a novel function of XAB2 in mitotic cell cycle regulation, which is partially mediated by transcription regulation on CENPE.
Collapse
|
31
|
Navarro-Costa P, McCarthy A, Prudêncio P, Greer C, Guilgur LG, Becker JD, Secombe J, Rangan P, Martinho RG. Early programming of the oocyte epigenome temporally controls late prophase I transcription and chromatin remodelling. Nat Commun 2016; 7:12331. [PMID: 27507044 PMCID: PMC4987523 DOI: 10.1038/ncomms12331] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/22/2016] [Indexed: 12/12/2022] Open
Abstract
Oocytes are arrested for long periods of time in the prophase of the first meiotic division (prophase I). As chromosome condensation poses significant constraints to gene expression, the mechanisms regulating transcriptional activity in the prophase I-arrested oocyte are still not entirely understood. We hypothesized that gene expression during the prophase I arrest is primarily epigenetically regulated. Here we comprehensively define the Drosophila female germ line epigenome throughout oogenesis and show that the oocyte has a unique, dynamic and remarkably diversified epigenome characterized by the presence of both euchromatic and heterochromatic marks. We observed that the perturbation of the oocyte's epigenome in early oogenesis, through depletion of the dKDM5 histone demethylase, results in the temporal deregulation of meiotic transcription and affects female fertility. Taken together, our results indicate that the early programming of the oocyte epigenome primes meiotic chromatin for subsequent functions in late prophase I.
Collapse
Affiliation(s)
- Paulo Navarro-Costa
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Alicia McCarthy
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12222, USA
| | - Pedro Prudêncio
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Christina Greer
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Leonardo G. Guilgur
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Jörg D. Becker
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12222, USA
| | - Rui G. Martinho
- Departamento de Ciências Biomédicas e Medicina, and Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| |
Collapse
|
32
|
Onyango DO, Howard SM, Neherin K, Yanez DA, Stark JM. Tetratricopeptide repeat factor XAB2 mediates the end resection step of homologous recombination. Nucleic Acids Res 2016; 44:5702-16. [PMID: 27084940 PMCID: PMC4937314 DOI: 10.1093/nar/gkw275] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 04/05/2016] [Indexed: 12/15/2022] Open
Abstract
We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3′ ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR that require end resection as an intermediate step, end resection of camptothecin (Cpt)-induced DNA damage, and RAD51 recruitment to ionizing radiation induced foci (IRIF), which requires end resection. Furthermore, XAB2 mediates specific aspects of the DNA damage response associated with end resection proficiency: CtIP hyperphosphorylation induced by Cpt and BRCA1 IRIF. XAB2 also promotes histone acetylation events linked to HR proficiency. From truncation mutation analysis, the capacity for XAB2 to promote HR correlates with its ability to form a complex with ISY1 and PRP19, which show a similar influence as XAB2 on HR. This XAB2 complex localizes to punctate structures consistent with interchromatin granules that show a striking adjacent-localization to the DSB marker γH2AX. In summary, we suggest that the XAB2 complex mediates DNA damage response events important for the end resection step of HR, and speculate that its adjacent-localization relative to DSBs marked by γH2AX is important for this function.
Collapse
Affiliation(s)
- David O Onyango
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Sean M Howard
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Kashfia Neherin
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Department of Biology, California State University, San Bernardino, CA 92407 USA; current address University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Diana A Yanez
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, 1500 E Duarte Rd., Duarte, CA 91010, USA Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA 91010, USA
| |
Collapse
|
33
|
Rathore OS, Faustino A, Prudêncio P, Van Damme P, Cox CJ, Martinho RG. Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms. Sci Rep 2016; 6:21304. [PMID: 26861501 PMCID: PMC4748286 DOI: 10.1038/srep21304] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/18/2016] [Indexed: 11/09/2022] Open
Abstract
Protein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes.
Collapse
Affiliation(s)
- Om Singh Rathore
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,ProRegeM-PhD Program in Mechanisms of Disease and Regenerative Medicine, Faro, Portugal
| | - Alexandra Faustino
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal
| | - Pedro Prudêncio
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
| | - Petra Van Damme
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Cymon J Cox
- Center of Marine Sciences, University of Algarve, Faro, Portugal
| | - Rui Gonçalo Martinho
- Department of Biomedical Sciences and Medicine, Faro, Portugal.,Center for Biomedical Research (CBMR), Faro, Portugal.,Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, Oeiras 2781-901, Portugal
| |
Collapse
|
34
|
Liu J, Ma J. Modulation of temporal dynamics of gene transcription by activator potency in the Drosophila embryo. Development 2015; 142:3781-90. [PMID: 26395487 DOI: 10.1242/dev.126946] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/07/2015] [Indexed: 12/24/2022]
Abstract
The Drosophila embryo at the mid-blastula transition (MBT) concurrently experiences a receding first wave of zygotic transcription and the surge of a massive second wave. It is not well understood how genes in the first wave become turned off transcriptionally and how their precise timing may impact embryonic development. Here we perturb the timing of the shutdown of Bicoid (Bcd)-dependent hunchback (hb) transcription in the embryo through the use of a Bcd mutant that has heightened activating potency. A delayed shutdown specifically increases Bcd-activated hb levels, and this alters spatial characteristics of the patterning outcome and causes developmental defects. Our study thus documents a specific participation of maternal activator input strength in the timing of molecular events in precise accordance with MBT morphological progression.
Collapse
Affiliation(s)
- Junbo Liu
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Jun Ma
- Division of Biomedical Informatics, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| |
Collapse
|
35
|
Sharma R, Beer K, Iwanov K, Schmöhl F, Beckmann PI, Schröder R. The single fgf receptor gene in the beetle Tribolium castaneum codes for two isoforms that integrate FGF8- and Branchless-dependent signals. Dev Biol 2015; 402:264-75. [PMID: 25864412 DOI: 10.1016/j.ydbio.2015.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022]
Abstract
The precise regulation of cell-cell communication by numerous signal-transduction pathways is fundamental for many different processes during embryonic development. One important signalling pathway is the evolutionary conserved fibroblast-growth-factor (FGF)-pathway that controls processes like cell migration, axis specification and mesoderm formation in vertebrate and invertebrate animals. In the model insect Drosophila, the FGF ligand / receptor combinations of FGF8 (Pyramus and Thisbe) / Heartless (Htl) and Branchless (Bnl) / Breathless (Btl) are required for the migration of mesodermal cells and for the formation of the tracheal network respectively with both the receptors functioning independently of each other. However, only a single fgf-receptor gene (Tc-fgfr) has been identified in the genome of the beetle Tribolium. We therefore asked whether both the ligands Fgf8 and Bnl could transduce their signal through a common FGF-receptor in Tribolium. Indeed, we found that the function of the single Tc-fgfr gene is essential for mesoderm differentiation as well as for the formation of the tracheal network during early development. Ligand specific RNAi for Tc-fgf8 and Tc-bnl resulted in two distinct non-overlapping phenotypes of impaired mesoderm differentiation and abnormal formation of the tracheal network in Tc-fgf8- and Tc-bnl(RNAi) embryos respectively. We further show that the single Tc-fgfr gene encodes at least two different receptor isoforms that are generated through alternative splicing. We in addition demonstrate through exon-specific RNAi their distinct tissue-specific functions. Finally, we discuss the structure of the fgf-receptor gene from an evolutionary perspective.
Collapse
Affiliation(s)
- Rahul Sharma
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Katharina Beer
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Katharina Iwanov
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Felix Schmöhl
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Paula Indigo Beckmann
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany
| | - Reinhard Schröder
- University of Rostock, Biological Sciences, Department of Genetics, Albert-Einsteinstr. 3, 18059 Rostock, Germany.
| |
Collapse
|
36
|
Martinho RG, Guilgur LG, Prudêncio P. How gene expression in fast-proliferating cells keeps pace. Bioessays 2015; 37:514-24. [PMID: 25823409 DOI: 10.1002/bies.201400195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of living organisms requires a precise coordination of all basic cellular processes, in space and time. Early embryogenesis of most species with externally deposited eggs starts with a series of extremely fast cleavage cycles. These divisions have a strong influence on gene expression as mitosis represses transcription and pre-mRNA processing. In this review, we will describe the distinct adaptations for efficient gene expression and discuss the emerging role of the multifunctional NineTeen Complex (NTC) in gene expression and genomic stability during fast proliferation.
Collapse
Affiliation(s)
- Rui G Martinho
- Departamento de Ciências Biomédicas e Medicina, Regenerative Medicine Program, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Center for Biomedical Research, Universidade do Algarve, Campus de Gambelas, Faro, Portugal; Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | | | | |
Collapse
|
37
|
Heyn P, Kalinka AT, Tomancak P, Neugebauer KM. Introns and gene expression: cellular constraints, transcriptional regulation, and evolutionary consequences. Bioessays 2014; 37:148-54. [PMID: 25400101 PMCID: PMC4654234 DOI: 10.1002/bies.201400138] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A gene's “expression profile” denotes the number of transcripts present relative to all other transcripts. The overall rate of transcript production is determined by transcription and RNA processing rates. While the speed of elongating RNA polymerase II has been characterized for many different genes and organisms, gene-architectural features – primarily the number and length of exons and introns – have recently emerged as important regulatory players. Several new studies indicate that rapidly cycling cells constrain gene-architecture toward short genes with a few introns, allowing efficient expression during short cell cycles. In contrast, longer genes with long introns exhibit delayed expression, which can serve as timing mechanisms for patterning processes. These findings indicate that cell cycle constraints drive the evolution of gene-architecture and shape the transcriptome of a given cell type. Furthermore, a tendency for short genes to be evolutionarily young hints at links between cellular constraints and the evolution of animal ontogeny.
Collapse
Affiliation(s)
- Patricia Heyn
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | | | | | | |
Collapse
|
38
|
Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J. Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 2014; 10:757. [PMID: 25358341 PMCID: PMC4299378 DOI: 10.15252/msb.20145625] [Citation(s) in RCA: 695] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In order to obtain a systems-level understanding of a complex biological system, detailed
proteome information is essential. Despite great progress in proteomics technologies, thorough
interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies
during processing. To address these challenges, here we introduce a novel protocol using
paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a
rapid and unbiased means of proteomic sample preparation in a single tube that facilitates
ultrasensitive analysis by outperforming existing protocols in terms of efficiency, scalability,
speed, throughput, and flexibility. To illustrate these benefits, characterization of 1,000 HeLa
cells and single Drosophila embryos is used to establish that SP3 provides an
enhanced platform for profiling proteomes derived from sub-microgram amounts of material. These data
present a first view of developmental stage-specific proteome dynamics in
Drosophila at a single-embryo resolution, permitting characterization of
inter-individual expression variation. Together, the findings of this work position SP3 as a
superior protocol that facilitates exciting new directions in multiple areas of proteomics ranging
from developmental biology to clinical applications.
Collapse
Affiliation(s)
| | - Sophia Foehr
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - David A Garfield
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Eileen E Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| |
Collapse
|
39
|
Lee MT, Bonneau AR, Giraldez AJ. Zygotic genome activation during the maternal-to-zygotic transition. Annu Rev Cell Dev Biol 2014; 30:581-613. [PMID: 25150012 DOI: 10.1146/annurev-cellbio-100913-013027] [Citation(s) in RCA: 385] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Embryogenesis depends on a highly coordinated cascade of genetically encoded events. In animals, maternal factors contributed by the egg cytoplasm initially control development, whereas the zygotic nuclear genome is quiescent. Subsequently, the genome is activated, embryonic gene products are mobilized, and maternal factors are cleared. This transfer of developmental control is called the maternal-to-zygotic transition (MZT). In this review, we discuss recent advances toward understanding the scope, timing, and mechanisms that underlie zygotic genome activation at the MZT in animals. We describe high-throughput techniques to measure the embryonic transcriptome and explore how regulation of the cell cycle, chromatin, and transcription factors together elicits specific patterns of embryonic gene expression. Finally, we illustrate the interplay between zygotic transcription and maternal clearance and show how these two activities combine to reprogram two terminally differentiated gametes into a totipotent embryo.
Collapse
Affiliation(s)
- Miler T Lee
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520; ,
| | | | | |
Collapse
|
40
|
Artieri CG, Fraser HB. Transcript length mediates developmental timing of gene expression across Drosophila. Mol Biol Evol 2014; 31:2879-89. [PMID: 25069653 PMCID: PMC4209130 DOI: 10.1093/molbev/msu226] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The time required to transcribe genes with long primary transcripts may limit their ability to be expressed in cells with short mitotic cycles, a phenomenon termed intron delay. As such short cycles are a hallmark of the earliest stages of insect development, we tested the impact of intron delay on the Drosophila developmental transcriptome. We find that long zygotically expressed genes show substantial delay in expression relative to their shorter counterparts, which is not observed for maternally deposited transcripts. Patterns of RNA-seq coverage along transcripts show that this delay is consistent with their inability to completely transcribe long transcripts, but not with transcriptional initiation-based regulatory control. We further show that highly expressed zygotic genes maintain compact transcribed regions across the Drosophila phylogeny, allowing conservation of embryonic expression patterns. We propose that the physical constraints of intron delay affect patterns of expression and the evolution of gene structure of a substantial portion of the Drosophila transcriptome.
Collapse
|