1
|
Yan X, Xu K, Xu Z, Shi C, Lai B, Wu H, Yang S, Sheng L, Wang K, Zheng Y, Ouyang G, Yang D. GLYR1 transcriptionally regulates PER3 expression to promote the proliferation and migration of multiple myeloma. Genomics 2024; 116:110846. [PMID: 38642856 DOI: 10.1016/j.ygeno.2024.110846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 04/06/2024] [Accepted: 04/11/2024] [Indexed: 04/22/2024]
Abstract
Period circadian regulator 3 (PER3) functions as a tumor suppressor in various cancers. However, the role of PER3 in multiple myeloma (MM) has not been reported yet. Through this study, we aimed to investigate the potential role of PER3 in MM and the underlying mechanisms. RT-qPCR and western blotting were used to determine the mRNA and protein expression levels of PER3. Glyoxylate reductase 1 homolog (GLYR1) was predicted to be a transcription factor of PER3. The binding sites of GLYR1 on the promoter region of PER3 were analyzed using UCSC and confirmed using luciferase and chromatin immunoprecipitation assays. Viability, apoptosis, and metathesis were determined using CCK-8, colony formation, TUNEL, and transwell assays. We found that PER3 expression decreased in MM. Low PER3 levels may predict poor survival rates; PER3 overexpression suppresses the viability and migration of MM cells and promotes apoptosis. Moreover, GLYR1 transcriptionally activates PER3, and the knockdown of PER3 alleviates the effects of GLYR1 and induces its malignant behavior in MM cells. To conclude, GLYR1 upregulates PER3 and suppresses the aggressive behavior of MM cells, suggesting that GLYR1/PER3 signaling may be a potential therapeutic target for MM.
Collapse
Affiliation(s)
- Xiao Yan
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China.
| | - Kaihong Xu
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China
| | - Zhijuan Xu
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China
| | - Cong Shi
- Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China; Laboratory of Stem Cell Transplantation, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China
| | - Binbin Lai
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China
| | - Hao Wu
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China
| | - Shujun Yang
- Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China; Laboratory of Stem Cell Transplantation, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China
| | - Lixia Sheng
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China
| | - Keting Wang
- Health Science Center, Ningbo University, Ningbo 315000, China
| | - Yuhan Zheng
- Health Science Center, Ningbo University, Ningbo 315000, China
| | - Guifang Ouyang
- Department of Haematology, The First Affiliated Hospital of Ningbo University, Ningbo 315000, China; Ningbo Clinical Research Center for Hematologic malignancies, Ningbo 315000, China.
| | - Di Yang
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
| |
Collapse
|
2
|
Slow growing behavior in African trypanosomes during adipose tissue colonization. Nat Commun 2022; 13:7548. [PMID: 36481558 PMCID: PMC9732351 DOI: 10.1038/s41467-022-34622-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
When Trypanosoma brucei parasites, the causative agent of sleeping sickness, colonize the adipose tissue, they rewire gene expression. Whether this adaptation affects population behavior and disease treatment remained unknown. By using a mathematical model, we estimate that the population of adipose tissue forms (ATFs) proliferates slower than blood parasites. Analysis of the ATFs proteome, measurement of protein synthesis and proliferation rates confirm that the ATFs divide on average every 12 h, instead of 6 h in the blood. Importantly, the population of ATFs is heterogeneous with parasites doubling times ranging between 5 h and 35 h. Slow-proliferating parasites remain capable of reverting to the fast proliferation profile in blood conditions. Intravital imaging shows that ATFs are refractory to drug treatment. We propose that in adipose tissue, a subpopulation of T. brucei parasites acquire a slow growing behavior, which contributes to disease chronicity and treatment failure.
Collapse
|
3
|
CHAMP1-POGZ counteracts the inhibitory effect of 53BP1 on homologous recombination and affects PARP inhibitor resistance. Oncogene 2022; 41:2706-2718. [PMID: 35393543 DOI: 10.1038/s41388-022-02299-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 12/15/2022]
Abstract
DNA double-strand break (DSB) repair-pathway choice regulated by 53BP1 and BRCA1 contributes to genome stability. 53BP1 cooperates with the REV7-Shieldin complex and inhibits DNA end resection to block homologous recombination (HR) and affects the sensitivity to inhibitors for poly (ADP-ribose) polymerases (PARPs) in BRCA1-deficient cells. Here, we show that a REV7 binding protein, CHAMP1 (chromosome alignment-maintaining phosphoprotein 1), has an opposite function of REV7 in DSB repair and promotes HR through DNA end resection together with POGZ (POGO transposable element with ZNF domain). CHAMP1 was recruited to laser-micro-irradiation-induced DSB sites and promotes HR, but not NHEJ. CHAMP1 depletion suppressed the recruitment of BRCA1, but not the recruitment of 53BP1, suggesting that CHAMP1 regulates DSB repair pathway in favor of HR. Depletion of either CHAMP1 or POGZ impaired the recruitment of phosphorylated RPA2 and CtIP (CtBP-interacting protein) at DSB sites, implying that CHAMP1, in complex with POGZ, promotes DNA end resection for HR. Furthermore, loss of CHAMP1 and POGZ restored the sensitivity to a PARP inhibitor in cells depleted of 53BP1 together with BRCA1. These data suggest that CHAMP1and POGZ counteract the inhibitory effect of 53BP1 on HR by promoting DNA end resection and affect the resistance to PARP inhibitors.
Collapse
|
4
|
Deng L, Mojica-Perez SP, Azaria RD, Schultz M, Parent JM, Niu W. Loss of POGZ alters neural differentiation of human embryonic stem cells. Mol Cell Neurosci 2022; 120:103727. [PMID: 35367590 PMCID: PMC9549529 DOI: 10.1016/j.mcn.2022.103727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/21/2022] [Accepted: 03/28/2022] [Indexed: 11/26/2022] Open
Abstract
POGZ is a pogo transposable element derived protein with multiple zinc finger domains. Many de novo loss-of-function (LoF) variants of the POGZ gene are associated with autism and other neurodevelopmental disorders. However, the role of POGZ in human cortical development remains poorly understood. Here we generated multiple POGZ LoF lines in H9 human embryonic stem cells (hESCs) using CRISPR/CAS9 genome editing. These lines were then differentiated into neural structures, similar to those found in early to mid-fetal human brain, a critical developmental stage for studying disease mechanisms of neurodevelopmental disorders. We found that the loss of POGZ reduced neural stem cell proliferation in excitatory cortex-patterned neural rosettes, structures analogous to the cortical ventricular zone in human fetal brain. As a result, fewer intermediate progenitor cells and early born neurons were generated. In addition, neuronal migration from the apical center to the basal surface of neural rosettes was perturbed due to the loss of POGZ. Furthermore, cortical-like excitatory neurons derived from multiple POGZ homozygous knockout lines exhibited a more simplified dendritic architecture compared to wild type lines. Our findings demonstrate how POGZ regulates early neurodevelopment in the context of human cells, and provide further understanding of the cellular pathogenesis of neurodevelopmental disorders associated with POGZ variants.
Collapse
|
5
|
Membrane-associated cytoplasmic granules carrying the Argonaute protein WAGO-3 enable paternal epigenetic inheritance in Caenorhabditis elegans. Nat Cell Biol 2022; 24:217-229. [PMID: 35132225 PMCID: PMC9973253 DOI: 10.1038/s41556-021-00827-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 01/04/2023]
Abstract
Epigenetic inheritance describes the transmission of gene regulatory information across generations without altering DNA sequences, enabling offspring to adapt to environmental conditions. Small RNAs have been implicated in this, through both the oocyte and the sperm. However, as much of the cellular content is extruded during spermatogenesis, it is unclear whether cytoplasmic small RNAs can contribute to epigenetic inheritance through sperm. Here we identify a sperm-specific germ granule, termed the paternal epigenetic inheritance (PEI) granule, that mediates paternal epigenetic inheritance by retaining the cytoplasmic Argonaute protein WAGO-3 during spermatogenesis in Caenorhabditis elegans. We identify the PEI granule proteins PEI-1 and PEI-2, which have distinct functions in this process: granule formation, Argonaute selectivity and subcellular localization. We show that PEI granule segregation is coupled to the transport of sperm-specific secretory vesicles through PEI-2 in an S-palmitoylation-dependent manner. PEI-like proteins are found in humans, suggesting that the identified mechanism may be conserved.
Collapse
|
6
|
Placentino M, de Jesus Domingues AM, Schreier J, Dietz S, Hellmann S, de Albuquerque BFM, Butter F, Ketting RF. Intrinsically disordered protein PID-2 modulates Z granules and is required for heritable piRNA-induced silencing in the Caenorhabditis elegans embryo. EMBO J 2021; 40:e105280. [PMID: 33231880 PMCID: PMC7849312 DOI: 10.15252/embj.2020105280] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 09/25/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
In Caenorhabditis elegans, the piRNA (21U RNA) pathway is required to establish proper gene regulation and an immortal germline. To achieve this, PRG-1-bound 21U RNAs trigger silencing mechanisms mediated by RNA-dependent RNA polymerase (RdRP)-synthetized 22G RNAs. This silencing can become PRG-1-independent and heritable over many generations, a state termed RNA-induced epigenetic gene silencing (RNAe). How and when RNAe is established, and how it is maintained, is not known. We show that maternally provided 21U RNAs can be sufficient for triggering RNAe in embryos. Additionally, we identify PID-2, a protein containing intrinsically disordered regions (IDRs), as a factor required for establishing and maintaining RNAe. PID-2 interacts with two newly identified and partially redundant eTudor domain-containing proteins, PID-4 and PID-5. PID-5 has an additional domain related to the X-prolyl aminopeptidase APP-1, and binds APP-1, implicating potential N-terminal proteolysis in RNAe. All three proteins are required for germline immortality, localize to perinuclear foci, affect size and appearance of RNA inheritance-linked Z granules, and are required for balancing of 22G RNA populations. Overall, our study identifies three new proteins with crucial functions in C. elegans small RNA silencing.
Collapse
Affiliation(s)
- Maria Placentino
- Biology of Non‐coding RNA GroupInstitute of Molecular Biology (IMB)MainzGermany
- International PhD Programme on Gene Regulation, Epigenetics & Genome StabilityMainzGermany
| | | | - Jan Schreier
- Biology of Non‐coding RNA GroupInstitute of Molecular Biology (IMB)MainzGermany
- International PhD Programme on Gene Regulation, Epigenetics & Genome StabilityMainzGermany
| | - Sabrina Dietz
- International PhD Programme on Gene Regulation, Epigenetics & Genome StabilityMainzGermany
- Quantitative Proteomics GroupInstitute of Molecular Biology (IMB)MainzGermany
| | - Svenja Hellmann
- Biology of Non‐coding RNA GroupInstitute of Molecular Biology (IMB)MainzGermany
| | - Bruno FM de Albuquerque
- Biology of Non‐coding RNA GroupInstitute of Molecular Biology (IMB)MainzGermany
- Graduate Program in Areas of Basic and Applied BiologyUniversity of PortoPortoPortugal
| | - Falk Butter
- Quantitative Proteomics GroupInstitute of Molecular Biology (IMB)MainzGermany
| | - René F Ketting
- Biology of Non‐coding RNA GroupInstitute of Molecular Biology (IMB)MainzGermany
- Institute of Developmental Biology and NeurobiologyJohannses Gutenberg UniversityMainzGermany
| |
Collapse
|
7
|
Peng Y, Markov Y, Goncearenco A, Landsman D, Panchenko AR. Human Histone Interaction Networks: An Old Concept, New Trends. J Mol Biol 2020; 433:166684. [PMID: 33098859 DOI: 10.1016/j.jmb.2020.10.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022]
Abstract
To elucidate the properties of human histone interactions on the large scale, we perform a comprehensive mapping of human histone interaction networks by using data from structural, chemical cross-linking and various high-throughput studies. Histone interactomes derived from different data sources show limited overlap and complement each other. It inspires us to integrate these data into the combined histone global interaction network which includes 5308 proteins and 10,330 interactions. The analysis of topological properties of the human histone interactome reveals its scale free behavior and high modularity. Our study of histone binding interfaces uncovers a remarkably high number of residues involved in interactions between histones and non-histone proteins, 80-90% of residues in histones H3 and H4 have at least one binding partner. Two types of histone binding modes are detected: interfaces conserved in most histone variants and variant specific interfaces. Finally, different types of chromatin factors recognize histones in nucleosomes via distinct binding modes, and many of these interfaces utilize acidic patches among other sites. Interaction networks are available at https://github.com/Panchenko-Lab/Human-histone-interactome.
Collapse
Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yaroslav Markov
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA; Computational Biology and Bioinformatics, Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT 06520, USA
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA; VantAI, New York, NY 10003, USA
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON K7L 3N6, Canada.
| |
Collapse
|
8
|
Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 2020; 21:e49443. [PMID: 32350990 DOI: 10.15252/embr.201949443] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently emerged as an important layer of gene regulation. N6-methyladenosine (m6 A) is the most prominent modification on eukaryotic messenger RNA and has also been found on noncoding RNA, including ribosomal and small nuclear RNA. Recently, several m6 A methyltransferases were identified, uncovering the specificity of m6 A deposition by structurally distinct enzymes. In order to discover additional m6 A enzymes, we performed an RNAi screen to deplete annotated orthologs of human methyltransferase-like proteins (METTLs) in Drosophila cells and identified CG9666, the ortholog of human METTL5. We show that CG9666 is required for specific deposition of m6 A on 18S ribosomal RNA via direct interaction with the Drosophila ortholog of human TRMT112, CG12975. Depletion of CG9666 yields a subsequent loss of the 18S rRNA m6 A modification, which lies in the vicinity of the ribosome decoding center; however, this does not compromise rRNA maturation. Instead, a loss of CG9666-mediated m6 A impacts fly behavior, providing an underlying molecular mechanism for the reported human phenotype in intellectual disability. Thus, our work expands the repertoire of m6 A methyltransferases, demonstrates the specialization of these enzymes, and further addresses the significance of ribosomal RNA modifications in gene expression and animal behavior.
Collapse
Affiliation(s)
| | | | | | - Ludivine Wacheul
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Minh Anh Vu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Pablo Mier
- Faculty of Biology, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Marc Graille
- BIOC, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Denis Lj Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Mainz, Germany.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
9
|
Warncke JD, Passecker A, Kipfer E, Brand F, Pérez-Martínez L, Proellochs NI, Kooij TWA, Butter F, Voss TS, Beck HP. The PHIST protein GEXP02 targets the host cytoskeleton during sexual development of Plasmodium falciparum. Cell Microbiol 2019; 22:e13123. [PMID: 31652487 DOI: 10.1111/cmi.13123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 09/11/2019] [Accepted: 09/23/2019] [Indexed: 11/27/2022]
Abstract
A hallmark of the biology of Plasmodium falciparum blood stage parasites is their extensive host cell remodelling, facilitated by parasite proteins that are exported into the erythrocyte. Although this area has received extensive attention, only a few exported parasite proteins have been analysed in detail, and much of this remodelling process remains unknown, particularly for gametocyte development. Recent advances to induce high rates of sexual commitment enable the production of large numbers of gametocytes. We used this approach to study the Plasmodium helical interspersed subtelomeric (PHIST) protein GEXP02, which is expressed during sexual development. We show by immunofluorescence that GEXP02 is exported to the gametocyte-infected host cell periphery. Co-immunoprecipitation revealed potential interactions between GEXP02 and components of the erythrocyte cytoskeleton as well as other exported parasite proteins. This indicates that GEXP02 targets the erythrocyte cytoskeleton and is likely involved in its remodelling. GEXP02 knock-out parasites show no obvious phenotype during gametocyte maturation, transmission through mosquitoes, and hepatocyte infection, suggesting auxiliary or redundant functions for this protein. In summary, we performed a detailed cellular and biochemical analysis of a sexual stage-specific exported parasite protein using a novel experimental approach that is broadly applicable to study the biology of P. falciparum gametocytes.
Collapse
Affiliation(s)
- Jan D Warncke
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Armin Passecker
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Enja Kipfer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Françoise Brand
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lara Pérez-Martínez
- Proteomics Core Facility, Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Nicholas I Proellochs
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Taco W A Kooij
- Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Falk Butter
- Proteomics Core Facility, Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Till S Voss
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Hans-Peter Beck
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| |
Collapse
|
10
|
Goos C, Dejung M, Wehman AM, M-Natus E, Schmidt J, Sunter J, Engstler M, Butter F, Kramer S. Trypanosomes can initiate nuclear export co-transcriptionally. Nucleic Acids Res 2019; 47:266-282. [PMID: 30418648 PMCID: PMC6326799 DOI: 10.1093/nar/gky1136] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/25/2018] [Indexed: 02/03/2023] Open
Abstract
The nuclear envelope serves as important messenger RNA (mRNA) surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualized nuclear export in trypanosomes by intra- and intermolecular multi-colour single molecule FISH. We found that, in striking contrast to other eukaryotes, the initiation of nuclear export requires neither the completion of transcription nor splicing. Nevertheless, we show that unspliced mRNAs are mostly prevented from reaching the nucleus-distant cytoplasm and instead accumulate at the nuclear periphery in cytoplasmic nuclear periphery granules (NPGs). Further characterization of NPGs by electron microscopy and proteomics revealed that the granules are located at the cytoplasmic site of the nuclear pores and contain most cytoplasmic RNA-binding proteins but none of the major translation initiation factors, consistent with a function in preventing faulty mRNAs from reaching translation. Our data indicate that trypanosomes regulate the completion of nuclear export, rather than the initiation. Nuclear export control remains poorly understood, in any organism, and the described way of control may not be restricted to trypanosomes.
Collapse
Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Ann M Wehman
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Elisabeth M-Natus
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Johannes Schmidt
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Jack Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Markus Engstler
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| |
Collapse
|
11
|
Cordeiro Rodrigues RJ, de Jesus Domingues AM, Hellmann S, Dietz S, de Albuquerque BFM, Renz C, Ulrich HD, Sarkies P, Butter F, Ketting RF. PETISCO is a novel protein complex required for 21U RNA biogenesis and embryonic viability. Genes Dev 2019; 33:857-870. [PMID: 31147388 PMCID: PMC6601512 DOI: 10.1101/gad.322446.118] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/26/2019] [Indexed: 01/05/2023]
Abstract
Piwi proteins are important for germ cell development in most animals. These proteins are guided to specific targets by small guide RNAs, referred to as piRNAs or 21U RNAs in Caenorhabditis elegans In this organism, even though genetic screens have uncovered 21U RNA biogenesis factors, little is known about how these factors interact or what they do. Based on the previously identified 21U biogenesis factor PID-1 (piRNA-induced silencing-defective 1), we here define a novel protein complex, PETISCO (PID-3, ERH-2, TOFU-6, and IFE-3 small RNA complex), that is required for 21U RNA biogenesis. PETISCO contains both potential 5' cap and 5' phosphate RNA-binding domains and interacts with capped 21U precursor RNA. We resolved the architecture of PETISCO and revealed a second function for PETISCO in embryonic development. This essential function of PETISCO is mediated not by PID-1 but by the novel protein TOST-1 (twenty-one U pathway antagonist). In contrast, TOST-1 is not essential for 21U RNA biogenesis. Both PID-1 and TOST-1 interact directly with ERH-2 using a conserved sequence motif. Finally, our data suggest a role for TOST-1:PETISCO in SL1 homeostasis in the early embryo. Our work describes a key complex for 21U RNA processing in C. elegans and strengthens the view that 21U RNA biogenesis is built on an snRNA-related pathway.
Collapse
Affiliation(s)
- Ricardo J Cordeiro Rodrigues
- Biology of Non-coding RNA Group, Institute of Molecular Biology, 55128 Mainz, Germany
- International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, 55128 Mainz, Germany
| | | | - Svenja Hellmann
- Biology of Non-coding RNA Group, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sabrina Dietz
- International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, 55128 Mainz, Germany
- Quantitative Proteomics Group, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Bruno F M de Albuquerque
- Biology of Non-coding RNA Group, Institute of Molecular Biology, 55128 Mainz, Germany
- Graduate Program in Areas of Basic and Applied Biology, University of Porto, 4099-003 Porto, Portugal
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom
- Institute of Clinical Sciences, Imperial College London, London W12 0NN, United Kingdom
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, 55128 Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, 55128 Mainz, Germany
| |
Collapse
|
12
|
Almeida MV, Dietz S, Redl S, Karaulanov E, Hildebrandt A, Renz C, Ulrich HD, König J, Butter F, Ketting RF. GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans. EMBO J 2018; 37:embj.201899325. [PMID: 29769402 DOI: 10.15252/embj.201899325] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/09/2022] Open
Abstract
Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.
Collapse
Affiliation(s)
| | - Sabrina Dietz
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Emil Karaulanov
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany
| | - Andrea Hildebrandt
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Christian Renz
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Helle D Ulrich
- Maintenance of Genome Stability Group, Institute of Molecular Biology, Mainz, Germany
| | - Julian König
- Genomic Views of Splicing Regulation Group, Institute of Molecular Biology, Mainz, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| |
Collapse
|
13
|
Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m 6A machinery component Wtap/Fl(2)d. Genes Dev 2018. [PMID: 29535189 PMCID: PMC5900714 DOI: 10.1101/gad.309146.117] [Citation(s) in RCA: 384] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this study, Knuckles et al. identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. They show that Flacc promotes the recruitment of the methyltransferase to mRNA by bridging Fl(2)d to the mRNA-binding factor Nito, providing novel insights into the conservation and regulation of the m6A machinery. N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of methyltransferase-like 3 (Mettl3), which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 (zinc finger CCCH domain-containing protein 13)/Flacc [Fl(2)d-associated complex component] as a novel interactor of m6A methyltransferase complex components in Drosophila and mice. Like other components of this complex, Flacc controls m6A levels and is involved in sex determination in Drosophila. We demonstrate that Flacc promotes m6A deposition by bridging Fl(2)d to the mRNA-binding factor Nito. Altogether, our work advances the molecular understanding of conservation and regulation of the m6A machinery.
Collapse
Affiliation(s)
- Philip Knuckles
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Tina Lence
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Irmgard U Haussmann
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Dominik Jacob
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Nastasja Kreim
- Bioinformatics Core Facility, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Sarah H Carl
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel 4058, Switzerland
| | - Irene Masiello
- Institute of Molecular Biology, 55128 Mainz, Germany.,Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Tina Hares
- Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rodrigo Villaseñor
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, 55128 Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Animal Biology, University of Pavia, Pavia 27100, Italy
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Matthias Soller
- School of Life Science, Faculty of Health and Life Sciences, Coventry University, Coventry CV1 5FB, United Kingdom
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.,University of Basel, Basel 4002, Switzerland
| | | |
Collapse
|
14
|
Chitale S, Richly H. Nuclear organization of nucleotide excision repair is mediated by RING1B dependent H2A-ubiquitylation. Oncotarget 2018; 8:30870-30887. [PMID: 28416769 PMCID: PMC5458174 DOI: 10.18632/oncotarget.16142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/15/2017] [Indexed: 01/10/2023] Open
Abstract
One of the major cellular DNA repair pathways is nucleotide excision repair (NER). It is the primary pathway for repair of various DNA lesions caused by exposure to ultraviolet (UV) light, such as cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts. Although lesion-containing DNA associates with the nuclear matrix after UV irradiation it is still not understood how nuclear organization affects NER. Analyzing unscheduled DNA synthesis (UDS) indicates that NER preferentially occurs in specific nuclear areas, viz the nucleolus. Upon inducing localized damage, we observe migration of damaged DNA towards the nucleolus. Employing a LacR-based tethering system we demonstrate that H2A-ubiquitylation via the UV-RING1B complex localizes chromatin close to the nucleolus. We further show that the H2A-ubiquitin binding protein ZRF1 resides in the nucleolus, and that it anchors ubiquitylated chromatin along with XPC. Our data thus provide insight into the sub-nuclear organization of NER and reveal a novel role for histone H2A-ubiquitylation.
Collapse
Affiliation(s)
- Shalaka Chitale
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, Mainz, Germany, Ackermannweg, Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, Mainz, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, Mainz, Germany, Ackermannweg, Mainz, Germany
| |
Collapse
|
15
|
Anders F, Liu A, Mann C, Teister J, Lauzi J, Thanos S, Grus FH, Pfeiffer N, Prokosch V. The Small Heat Shock Protein α-Crystallin B Shows Neuroprotective Properties in a Glaucoma Animal Model. Int J Mol Sci 2017; 18:E2418. [PMID: 29135941 PMCID: PMC5713386 DOI: 10.3390/ijms18112418] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 11/10/2017] [Accepted: 11/12/2017] [Indexed: 11/29/2022] Open
Abstract
Glaucoma is a neurodegenerative disease that leads to irreversible retinal ganglion cell (RGC) loss and is one of the main causes of blindness worldwide. The pathogenesis of glaucoma remains unclear, and novel approaches for neuroprotective treatments are urgently needed. Previous studies have revealed significant down-regulation of α-crystallin B as an initial reaction to elevated intraocular pressure (IOP), followed by a clear but delayed up-regulation, suggesting that this small heat-shock protein plays a pathophysiological role in the disease. This study analyzed the neuroprotective effect of α-crystallin B in an experimental animal model of glaucoma. Significant IOP elevation induced by episcleral vein cauterization resulted in a considerable impairment of the RGCs and the retinal nerve fiber layer. An intravitreal injection of α-crystallin B at the time of the IOP increase was able to rescue the RGCs, as measured in a functional photopic electroretinogram, retinal nerve fiber layer thickness, and RGC counts. Mass-spectrometry-based proteomics and antibody-microarray measurements indicated that a α-crystallin injection distinctly up-regulated all of the subclasses (α, β, and γ) of the crystallin protein family. The creation of an interactive protein network revealed clear correlations between individual proteins, which showed a regulatory shift resulting from the crystallin injection. The neuroprotective properties of α-crystallin B further demonstrate the potential importance of crystallin proteins in developing therapeutic options for glaucoma.
Collapse
Affiliation(s)
- Fabian Anders
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Aiwei Liu
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Carolina Mann
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Julia Teister
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Jasmin Lauzi
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Solon Thanos
- Department of Experimental Ophthalmology, School of Medicine, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany.
| | - Franz H Grus
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Norbert Pfeiffer
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| | - Verena Prokosch
- Experimental Ophthalmology, Department of Ophthalmology, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany.
| |
Collapse
|
16
|
Chitale S, Richly H. DICER and ZRF1 contribute to chromatin decondensation during nucleotide excision repair. Nucleic Acids Res 2017; 45:5901-5912. [PMID: 28402505 PMCID: PMC5449631 DOI: 10.1093/nar/gkx261] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/04/2017] [Indexed: 12/18/2022] Open
Abstract
Repair of damaged DNA relies on the recruitment of DNA repair factors in a well orchestrated manner. As a prerequisite, the chromatin needs to be decondensed by chromatin remodelers to allow for binding of repair factors and for DNA repair to occur. Recent studies have implicated members of the SWI/SNF and INO80 families as well as PARP1 in nucleotide excision repair (NER). In this study, we report that the endonuclease DICER is implicated in chromatin decondensation during NER. In response to UV irradiation, DICER is recruited to chromatin in a ZRF1-mediated manner. The H2A–ubiquitin binding protein ZRF1 and DICER together impact on the chromatin conformation via PARP1. Moreover, DICER-mediated chromatin decondensation is independent of its catalytic activity. Taken together, we describe a novel function of DICER at chromatin and its interaction with the ubiquitin signalling cascade during GG-NER.
Collapse
Affiliation(s)
- Shalaka Chitale
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.,Faculty of Biology, Johannes Gutenberg University, 55099 Mainz, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| |
Collapse
|
17
|
Goos C, Dejung M, Janzen CJ, Butter F, Kramer S. The nuclear proteome of Trypanosoma brucei. PLoS One 2017; 12:e0181884. [PMID: 28727848 PMCID: PMC5519215 DOI: 10.1371/journal.pone.0181884] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/07/2017] [Indexed: 12/14/2022] Open
Abstract
Trypanosoma brucei is a protozoan flagellate that is transmitted by tsetse flies into the mammalian bloodstream. The parasite has a huge impact on human health both directly by causing African sleeping sickness and indirectly, by infecting domestic cattle. The biology of trypanosomes involves some highly unusual, nuclear-localised processes. These include polycistronic transcription without classical promoters initiated from regions defined by histone variants, trans-splicing of all transcripts to the exon of a spliced leader RNA, transcription of some very abundant proteins by RNA polymerase I and antigenic variation, a switch in expression of the cell surface protein variants that allows the parasite to resist the immune system of its mammalian host. Here, we provide the nuclear proteome of procyclic Trypanosoma brucei, the stage that resides within the tsetse fly midgut. We have performed quantitative label-free mass spectrometry to score 764 significantly nuclear enriched proteins in comparison to whole cell lysates. A comparison with proteomes of several experimentally characterised nuclear and non-nuclear structures and pathways confirmed the high quality of the dataset: the proteome contains about 80% of all nuclear proteins and less than 2% false positives. Using motif enrichment, we found the amino acid sequence KRxR present in a large number of nuclear proteins. KRxR is a sub-motif of a classical eukaryotic monopartite nuclear localisation signal and could be responsible for nuclear localization of proteins in Kinetoplastida species. As a proof of principle, we have confirmed the nuclear localisation of six proteins with previously unknown localisation by expressing eYFP fusion proteins. While proteome data of several T. brucei organelles have been published, our nuclear proteome closes an important gap in knowledge to study trypanosome biology, in particular nuclear-related processes.
Collapse
Affiliation(s)
- Carina Goos
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Mario Dejung
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
| | - Christian J. Janzen
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, Germany
- * E-mail: (SK); (FB)
| | - Susanne Kramer
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Am Hubland, Würzburg, Germany
- * E-mail: (SK); (FB)
| |
Collapse
|
18
|
Lebedeva S, de Jesus Domingues AM, Butter F, Ketting RF. Characterization of genetic loss-of-function of Fus in zebrafish. RNA Biol 2017; 14:29-35. [PMID: 27898262 PMCID: PMC5270537 DOI: 10.1080/15476286.2016.1256532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/24/2016] [Accepted: 10/30/2016] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding protein FUS is implicated in transcription, alternative splicing of neuronal genes and DNA repair. Mutations in FUS have been linked to human neurodegenerative diseases such as ALS (amyotrophic lateral sclerosis). We genetically disrupted fus in zebrafish (Danio rerio) using the CRISPR-Cas9 system. The fus knockout animals are fertile and did not show any distinctive phenotype. Mutation of fus induces mild changes in gene expression on the transcriptome and proteome level in the adult brain. We observed a significant influence of genetic background on gene expression and 3'UTR usage, which could mask the effects of loss of Fus. Unlike published fus morphants, maternal zygotic fus mutants do not show motoneuronal degeneration and exhibit normal locomotor activity.
Collapse
Affiliation(s)
| | | | - Falk Butter
- Institute of Molecular Biology, Mainz, Germany
| | | |
Collapse
|
19
|
m6A modulates neuronal functions and sex determination in Drosophila. Nature 2016; 540:242-247. [DOI: 10.1038/nature20568] [Citation(s) in RCA: 324] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 10/21/2016] [Indexed: 12/28/2022]
|
20
|
Wierer M, Mann M. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 2016; 25:R106-R114. [PMID: 27402878 PMCID: PMC5036873 DOI: 10.1093/hmg/ddw208] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023] Open
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
Collapse
Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| |
Collapse
|
21
|
Gracheva E, Chitale S, Wilhelm T, Rapp A, Byrne J, Stadler J, Medina R, Cardoso MC, Richly H. ZRF1 mediates remodeling of E3 ligases at DNA lesion sites during nucleotide excision repair. J Cell Biol 2016; 213:185-200. [PMID: 27091446 PMCID: PMC5084270 DOI: 10.1083/jcb.201506099] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 03/16/2016] [Indexed: 01/26/2023] Open
Abstract
How ubiquitylation of multiple substrates, including repair proteins and histones, is regulated during nucleotide excision repair (NER) has been unclear. Gracheva et al. show that the histone H2A-ubiquitin binding factor ZRF1 is essential in NER as it mediates remodeling of the novel ubiquitin E3 complex responsible for monoubiquitylation of histone H2A at DNA lesion sites. Faithful DNA repair is essential to maintain genome integrity. Ultraviolet (UV) irradiation elicits both the recruitment of DNA repair factors and the deposition of histone marks such as monoubiquitylation of histone H2A at lesion sites. Here, we report how a ubiquitin E3 ligase complex specific to DNA repair is remodeled at lesion sites in the global genome nucleotide excision repair (GG-NER) pathway. Monoubiquitylation of histone H2A (H2A-ubiquitin) is catalyzed predominantly by a novel E3 ligase complex consisting of DDB2, DDB1, CUL4B, and RING1B (UV–RING1B complex) that acts early during lesion recognition. The H2A-ubiquitin binding protein ZRF1 mediates remodeling of this E3 ligase complex directly at the DNA lesion site, causing the assembly of the UV–DDB–CUL4A E3 ligase complex (DDB1–DDB2–CUL4A-RBX1). ZRF1 is an essential factor in GG-NER, and its function at damaged chromatin sites is linked to damage recognition factor XPC. Overall, the results shed light on the interplay between epigenetic and DNA repair recognition factors at DNA lesion sites.
Collapse
Affiliation(s)
- Ekaterina Gracheva
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Shalaka Chitale
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Thomas Wilhelm
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Alexander Rapp
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Jonathan Byrne
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Jens Stadler
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - Rebeca Medina
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| | - M Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Holger Richly
- Laboratory of Molecular Epigenetics, Institute of Molecular Biology, 55128 Mainz, Germany
| |
Collapse
|