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Takenaka R, Simmerman SM, Schmidt CA, Albanese EH, Rieder LE, Malik HS. The Drosophila maternal-effect gene abnormal oocyte ( ao) does not repress histone gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613536. [PMID: 39345629 PMCID: PMC11429765 DOI: 10.1101/2024.09.17.613536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
The abnormal oocyte (ao) gene of Drosophila melanogaster is a maternal-effect lethal gene previously identified as encoding a transcriptional regulator of core histones. However, background genetic mutations in existing ao mutant strains could compromise their utility in manipulating histone levels. To distinguish the true ao phenotype from background effects, we created two new ao reagents: a CRISPR/Cas9-mediated knockout of the ao allele for genetic and molecular analyses and an epitope-tagged ao allele for cytological experiments. Using these reagents, we confirm previous findings that ao exhibits maternal-effect lethality, which can be rescued by either a decrease in the histone gene copy number or by Y chromosome heterochromatin. We also confirm that the Ao protein localizes to the histone locus bodies in ovaries. Our data also suggest that ao genetically interacts with the histone genes and heterochromatin, as previously suggested. However, contrary to prior findings, we find that ao does not repress core histone transcript levels. Thus, the molecular basis for ao-associated maternal-effect lethality remains unknown.
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Affiliation(s)
- Risa Takenaka
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle WA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle WA 98109
| | | | - Casey A. Schmidt
- Department of Biology, Emory University, Atlanta GA 30322
- Biology Department, Lafayette College, Easton PA 18042
| | | | | | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle WA 98109
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle WA 98109
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2
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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of the Drosophila context-dependent transcription factor CLAMP. Genetics 2024; 227:iyae060. [PMID: 38775472 DOI: 10.1093/genetics/iyae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/19/2024] [Indexed: 06/04/2024] Open
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor (TF) often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent TF chromatin-linked adaptor for male-specific lethal proteins (CLAMP) targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, locus-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Casey A Schmidt
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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3
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Terradas M, Schubert SA, Viana-Errasti J, Ruano D, Aiza G, Nielsen M, Marciel P, Tops CM, Parra G, Morreau H, Torrents D, van Leerdam ME, Capellá G, de Miranda NFCC, Valle L, van Wezel T. Germline NPAT inactivating variants as cause of hereditary colorectal cancer. Eur J Hum Genet 2024; 32:871-875. [PMID: 38778081 PMCID: PMC11219789 DOI: 10.1038/s41431-024-01625-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Two independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene that encodes a cyclin E/CDK2 effector required for S phase entry and a coactivator of histone transcription, in two families with multiple members affected with colorectal cancer. Enrichment of loss-of-function and predicted deleterious NPAT variants was identified in familial/early-onset colorectal cancer patients compared to non-cancer gnomAD individuals, further supporting the association with the disease. Previous studies in Drosophila models showed that NPAT abrogation results in chromosomal instability, increase of double strand breaks, and induction of tumour formation. In line with these results, colorectal cancers with NPAT somatic variants and no DNA repair defects have significantly higher aneuploidy levels than NPAT-wildtype colorectal cancers. In conclusion, our findings suggest that constitutional inactivating NPAT variants predispose to mismatch repair-proficient nonpolyposis colorectal cancer.
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Affiliation(s)
- Mariona Terradas
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Stephanie A Schubert
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Julen Viana-Errasti
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Gemma Aiza
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Paula Marciel
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Carli M Tops
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Genís Parra
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - David Torrents
- Life Sciences Department, Barcelona Supercomputing Centre (BSC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Monique E van Leerdam
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gabriel Capellá
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Laura Valle
- Hereditary Cancer Programme, Catalan Institute of Oncology; Oncobell Programme, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands.
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
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4
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Hannon CE, Eisen MB. Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors. eLife 2024; 12:RP88221. [PMID: 38275292 PMCID: PMC10945700 DOI: 10.7554/elife.88221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
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Affiliation(s)
- Colleen E Hannon
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
| | - Michael B Eisen
- Howard Hughes Medical Institute, University of CaliforniaBerkeleyUnited States
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5
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O'Haren T, Aoki T, Rieder LE. Zelda is dispensable for Drosophila melanogaster histone gene regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.19.572383. [PMID: 38187550 PMCID: PMC10769256 DOI: 10.1101/2023.12.19.572383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
To ensure that the embryo can package exponentially increasing amounts of DNA, replication-dependent histones are some of the earliest transcribed genes from the zygotic genome. However, how the histone genes are identified is not known. The pioneer factors Zelda and CLAMP collaborate at a subset of genes to regulate zygotic genome activation in Drosophila melanogaster and target early activated genes to induce transcription. CLAMP also regulates the embryonic histone genes and helps establish the histone locus body, a suite of factors that controls histone mRNA biosynthesis. The relationship between Zelda and CLAMP led us to hypothesize that Zelda helps identify histone genes for early embryonic expression. We found that Zelda targets the histone locus early during embryogenesis, prior to histone gene expression. However, depletion of zelda in the early embryo does not affect histone mRNA levels or histone locus body formation. While surprising, these results concur with other investigations into Zelda's role in the early embryo, suggesting the earliest factors responsible for specifying the zygotic histone genes remain undiscovered.
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Affiliation(s)
- Tommy O'Haren
- Emory University Department of Biology, Atlanta, GA 30322, USA
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E Rieder
- Emory University Department of Biology, Atlanta, GA 30322, USA
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6
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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of a Drosophila context-dependent transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570650. [PMID: 38106168 PMCID: PMC10723421 DOI: 10.1101/2023.12.07.570650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent transcription factor CLAMP targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J. Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322 USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322 USA
| | | | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E. Rieder
- Department of Biology Emory University, Atlanta, GA 30322 USA
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7
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Geisler MS, Kemp JP, Duronio RJ. Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression. Nucleus 2023; 14:2293604. [PMID: 38095604 PMCID: PMC10730174 DOI: 10.1080/19491034.2023.2293604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/07/2023] [Indexed: 12/18/2023] Open
Abstract
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and instead end in a conserved 3' stem loop critical for coordinated production of histone proteins during S phase of the cell cycle. Several evolutionarily conserved factors necessary for synthesis of RD histone mRNAs concentrate only in the HLB. Moreover, because HLBs are present throughout the cell cycle even though RD histone genes are only expressed during S phase, changes in HLB composition during cell cycle progression drive much of the cell cycle regulation of RD histone gene expression. Thus, HLBs provide a powerful opportunity to determine the cause-and-effect relationships between nuclear body formation and cell cycle regulated gene expression. In this review, we focus on progress during the last five years that has advanced our understanding of HLB biology.
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Affiliation(s)
- Mark S. Geisler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - James P. Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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8
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Chaubal A, Waldern JM, Taylor C, Laederach A, Marzluff WF, Duronio RJ. Coordinated expression of replication-dependent histone genes from multiple loci promotes histone homeostasis in Drosophila. Mol Biol Cell 2023; 34:ar118. [PMID: 37647143 PMCID: PMC10846616 DOI: 10.1091/mbc.e22-11-0532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 08/07/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Production of large amounts of histone proteins during S phase is critical for proper chromatin formation and genome integrity. This process is achieved in part by the presence of multiple copies of replication dependent (RD) histone genes that occur in one or more clusters in metazoan genomes. In addition, RD histone gene clusters are associated with a specialized nuclear body, the histone locus body (HLB), which facilitates efficient transcription and 3' end-processing of RD histone mRNA. How all five RD histone genes within these clusters are coordinately regulated such that neither too few nor too many histones are produced, a process referred to as histone homeostasis, is not fully understood. Here, we explored the mechanisms of coordinate regulation between multiple RD histone loci in Drosophila melanogaster and Drosophila virilis. We provide evidence for functional competition between endogenous and ectopic transgenic histone arrays located at different chromosomal locations in D. melanogaster that helps maintain proper histone mRNA levels. Consistent with this model, in both species we found that individual histone gene arrays can independently assemble an HLB that results in active histone transcription. Our findings suggest a role for HLB assembly in coordinating RD histone gene expression to maintain histone homeostasis.
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Affiliation(s)
- Ashlesha Chaubal
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - Justin M. Waldern
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Colin Taylor
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - William F. Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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9
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Hodkinson LJ, Smith C, Comstra HS, Ajani BA, Albanese EH, Arsalan K, Daisson AP, Forrest KB, Fox EH, Guerette MR, Khan S, Koenig MP, Lam S, Lewandowski AS, Mahoney LJ, Manai N, Miglay J, Miller BA, Milloway O, Ngo N, Ngo VD, Oey NF, Punjani TA, SiMa H, Zeng H, Schmidt CA, Rieder LE. A bioinformatics screen reveals hox and chromatin remodeling factors at the Drosophila histone locus. BMC Genom Data 2023; 24:54. [PMID: 37735352 PMCID: PMC10515271 DOI: 10.1186/s12863-023-01147-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/07/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. RESULTS To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets of 27 unique factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax (Ubx), Abdominal-A (Abd-A), and Abdominal-B (Abd-B), suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other factors that target the histone gene array: JIL-1, hormone-like receptor 78 (Hr78), the long isoform of female sterile homeotic (1) (fs(1)h) as well as the general transcription factors TBP associated factor 1 (TAF-1), Transcription Factor IIB (TFIIB), and Transcription Factor IIF (TFIIF). CONCLUSIONS Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology graduate program, Emory University, Atlanta, GA, 30322, USA
| | - Connor Smith
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - H Skye Comstra
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Bukola A Ajani
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Eric H Albanese
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Kawsar Arsalan
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Alvaro Perez Daisson
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Katherine B Forrest
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Elijah H Fox
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Matthew R Guerette
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Samia Khan
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Madeleine P Koenig
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Shivani Lam
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Ava S Lewandowski
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Lauren J Mahoney
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nasserallah Manai
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - JonCarlo Miglay
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Blake A Miller
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Olivia Milloway
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nhi Ngo
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Vu D Ngo
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Nicole F Oey
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Tanya A Punjani
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - HaoMin SiMa
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Hollis Zeng
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA
| | - Casey A Schmidt
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA.
| | - Leila E Rieder
- Department of Biology, Emory University, 1510 Clifton Road, Atlanta, GA, 30322, USA.
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10
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Gilbonio HE, Puckett GL, Nguyen E, Rieder LE. A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes. BMC Res Notes 2023; 16:197. [PMID: 37679799 PMCID: PMC10486132 DOI: 10.1186/s13104-023-06482-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023] Open
Abstract
OBJECTIVES Investigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF. RESULTS We developed a hybrid RNA FISH-IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.
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Affiliation(s)
| | - Gwyn L Puckett
- Piedmont Virginia Community College, Charlottesville, VA, USA
| | - Erica Nguyen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA, USA.
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11
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Armstrong C, Passanisi VJ, Ashraf HM, Spencer SL. Cyclin E/CDK2 and feedback from soluble histone protein regulate the S phase burst of histone biosynthesis. Cell Rep 2023; 42:112768. [PMID: 37428633 PMCID: PMC10440735 DOI: 10.1016/j.celrep.2023.112768] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 04/17/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
Faithful DNA replication requires that cells fine-tune their histone pool in coordination with cell-cycle progression. Replication-dependent histone biosynthesis is initiated at a low level upon cell-cycle commitment, followed by a burst at the G1/S transition, but it remains unclear how exactly the cell regulates this burst in histone biosynthesis as DNA replication begins. Here, we use single-cell time-lapse imaging to elucidate the mechanisms by which cells modulate histone production during different phases of the cell cycle. We find that CDK2-mediated phosphorylation of NPAT at the restriction point triggers histone transcription, which results in a burst of histone mRNA precisely at the G1/S phase boundary. Excess soluble histone protein further modulates histone abundance by promoting the degradation of histone mRNA for the duration of S phase. Thus, cells regulate their histone production in strict coordination with cell-cycle progression by two distinct mechanisms acting in concert.
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Affiliation(s)
- Claire Armstrong
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Victor J Passanisi
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Humza M Ashraf
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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12
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Schede HH, Natarajan P, Chakraborty AK, Shrinivas K. A model for organization and regulation of nuclear condensates by gene activity. Nat Commun 2023; 14:4152. [PMID: 37438363 DOI: 10.1038/s41467-023-39878-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 07/03/2023] [Indexed: 07/14/2023] Open
Abstract
Condensation by phase separation has recently emerged as a mechanism underlying many nuclear compartments essential for cellular functions. Nuclear condensates enrich nucleic acids and proteins, localize to specific genomic regions, and often promote gene expression. How diverse properties of nuclear condensates are shaped by gene organization and activity is poorly understood. Here, we develop a physics-based model to interrogate how spatially-varying transcription activity impacts condensate properties and dynamics. Our model predicts that spatial clustering of active genes can enable precise localization and de novo nucleation of condensates. Strong clustering and high activity results in aspherical condensate morphologies. Condensates can flow towards distant gene clusters and competition between multiple clusters lead to stretched morphologies and activity-dependent repositioning. Overall, our model predicts and recapitulates morphological and dynamical features of diverse nuclear condensates and offers a unified mechanistic framework to study the interplay between non-equilibrium processes, spatially-varying transcription, and multicomponent condensates in cell biology.
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Affiliation(s)
- Halima H Schede
- School of Life Sciences, École Polytechnique Fédérale Lausanne, CH-1015, Lausanne, Switzerland
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pradeep Natarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, MA, USA.
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13
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Gilbonio HE, Puckett GL, Nguyen E, Rieder LE. A hybrid RNA FISH immunofluorescence protocol on Drosophila polytene chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544616. [PMID: 37398336 PMCID: PMC10312655 DOI: 10.1101/2023.06.12.544616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Objectives Investigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF. Results We developed a hybrid RNA FISH and IF protocol for use on Drosophila melanogaster polytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi-sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level in Drosophila melanogaster polytene chromosomes.
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Affiliation(s)
| | - Gwyn L. Puckett
- Piedmont Virginia Community College, Charlottesville, VA, USA
| | - Erica Nguyen
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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14
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Hirose T, Ninomiya K, Nakagawa S, Yamazaki T. A guide to membraneless organelles and their various roles in gene regulation. Nat Rev Mol Cell Biol 2023; 24:288-304. [PMID: 36424481 DOI: 10.1038/s41580-022-00558-8] [Citation(s) in RCA: 129] [Impact Index Per Article: 129.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/25/2022]
Abstract
Membraneless organelles (MLOs) are detected in cells as dots of mesoscopic size. By undergoing phase separation into a liquid-like or gel-like phase, MLOs contribute to intracellular compartmentalization of specific biological functions. In eukaryotes, dozens of MLOs have been identified, including the nucleolus, Cajal bodies, nuclear speckles, paraspeckles, promyelocytic leukaemia protein (PML) nuclear bodies, nuclear stress bodies, processing bodies (P bodies) and stress granules. MLOs contain specific proteins, of which many possess intrinsically disordered regions (IDRs), and nucleic acids, mainly RNA. Many MLOs contribute to gene regulation by different mechanisms. Through sequestration of specific factors, MLOs promote biochemical reactions by simultaneously concentrating substrates and enzymes, and/or suppressing the activity of the sequestered factors elsewhere in the cell. Other MLOs construct inter-chromosomal hubs by associating with multiple loci, thereby contributing to the biogenesis of macromolecular machineries essential for gene expression, such as ribosomes and spliceosomes. The organization of many MLOs includes layers, which might have different biophysical properties and functions. MLOs are functionally interconnected and are involved in various diseases, prompting the emergence of therapeutics targeting them. In this Review, we introduce MLOs that are relevant to gene regulation and discuss their assembly, internal structure, gene-regulatory roles in transcription, RNA processing and translation, particularly in stress conditions, and their disease relevance.
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Affiliation(s)
- Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
| | - Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Tomohiro Yamazaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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15
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [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: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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16
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Hodkinson LJ, Smith C, Comstra HS, Albanese EH, Ajani BA, Arsalan K, Daisson AP, Forrest KB, Fox EH, Guerette MR, Khan S, Koenig MP, Lam S, Lewandowski AS, Mahoney LJ, Manai N, Miglay J, Miller BA, Milloway O, Ngo VD, Oey NF, Punjani TA, SiMa H, Zeng H, Schmidt CA, Rieder LE. A bioinformatics screen reveals Hox and chromatin remodeling factors at the Drosophila histone locus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523008. [PMID: 36711759 PMCID: PMC9881919 DOI: 10.1101/2023.01.06.523008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cells orchestrate histone biogenesis with strict temporal and quantitative control. To efficiently regulate histone biogenesis, the repetitive Drosophila melanogaster replication-dependent histone genes are arrayed and clustered at a single locus. Regulatory factors concentrate in a nuclear body known as the histone locus body (HLB), which forms around the locus. Historically, HLB factors are largely discovered by chance, and few are known to interact directly with DNA. It is therefore unclear how the histone genes are specifically targeted for unique and coordinated regulation. To expand the list of known HLB factors, we performed a candidate-based screen by mapping 30 publicly available ChIP datasets and 27 factors to the Drosophila histone gene array. We identified novel transcription factor candidates, including the Drosophila Hox proteins Ultrabithorax, Abdominal-A and Abdominal-B, suggesting a new pathway for these factors in influencing body plan morphogenesis. Additionally, we identified six other transcription factors that target the histone gene array: JIL-1, Hr78, the long isoform of fs(1)h as well as the generalized transcription factors TAF-1, TFIIB, and TFIIF. Our foundational screen provides several candidates for future studies into factors that may influence histone biogenesis. Further, our study emphasizes the powerful reservoir of publicly available datasets, which can be mined as a primary screening technique.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology graduate program, Emory University, Atlanta, GA 30322, USA
| | - Connor Smith
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - H Skye Comstra
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Eric H Albanese
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Bukola A Ajani
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Kawsar Arsalan
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | | | - Katherine B Forrest
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Elijah H Fox
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Matthew R Guerette
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Samia Khan
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Madeleine P Koenig
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Shivani Lam
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Ava S Lewandowski
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Lauren J Mahoney
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Nasserallah Manai
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - JonCarlo Miglay
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Blake A Miller
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Olivia Milloway
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Vu D Ngo
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Nicole F Oey
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Tanya A Punjani
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - HaoMin SiMa
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Hollis Zeng
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Casey A Schmidt
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
| | - Leila E Rieder
- Department of Biology 1510 Clifton Road Atlanta, Emory University GA 30322, USA
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17
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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18
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Sang R, Wu C, Xie S, Xu X, Lou Y, Ge W, Xi Y, Yang X. Mxc, a Drosophila homolog of mental retardation-associated gene NPAT, maintains neural stem cell fate. Cell Biosci 2022; 12:78. [PMID: 35642004 PMCID: PMC9153134 DOI: 10.1186/s13578-022-00820-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
Background Mental retardation is a complex neurodevelopmental disorder. NPAT, a component of the histone locus body (HLB), has been implicated as a candidate gene for mental retardation, with a mechanism yet to be elucidated. Results We identified that mxc, the Drosophila ortholog of NPAT, is required for the development of nervous system. Knockdown of mxc resulted in a massive loss of neurons and locomotion dysfunction in adult flies. In the mxc mutant or RNAi knockdown larval brains, the neuroblast (NB, also known as neural stem cell) cell fate is prematurely terminated and its proliferation potential is impeded concurrent with the blocking of the differentiation process of ganglion mother cells (GMCs). A reduction of transcription levels of histone genes was shown in mxc knockdown larval brains, accompanied by DNA double-strand breaks (DSBs). The subsidence of histone transcription levels leads to prematurely termination of NB cell fate and blockage of the GMC differentiation process. Our data also show that the increase in autophagy induced by mxc knockdown in NBs could be a defense mechanism in response to abnormal HLB assembly and premature termination of NB cell fate. Conclusions Our study demonstrate that Mxc plays a critical role in maintaining neural stem cell fate and GMC differentiation in the Drosophila larval brain. This discovery may shed light on the understanding of the pathogenesis of NPAT-related mental retardation in humans. Supplementary information The online version contains supplementary material available at 10.1186/s13578-022-00820-8.
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19
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Suzuki H, Abe R, Shimada M, Hirose T, Hirose H, Noguchi K, Ike Y, Yasui N, Furugori K, Yamaguchi Y, Toyoda A, Suzuki Y, Yamamoto T, Saitoh N, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Takahashi H. The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies. Nat Commun 2022; 13:2905. [PMID: 35614107 PMCID: PMC9133132 DOI: 10.1038/s41467-022-30632-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Non-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3'-end processing factors for RDH genes are enriched; however, this association's role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs' association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)-Cap binding complex (CBC)-Negative elongation factor (NELF), components of CBs, interferes with CBs' association with HLBs and 3' Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator's involvement in CBs' association with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing of RDH genes by supplying 3'-end processing factors.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Miho Shimada
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hiroko Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Nanami Yasui
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa, 226-8501, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Shigeo Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Chieri Tomomori-Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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20
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Sundaria N, Upadhyay A, Prasad A, Prajapati VK, Poluri KM, Mishra A. Neurodegeneration & imperfect ageing: Technological limitations and challenges? Mech Ageing Dev 2021; 200:111574. [PMID: 34562507 DOI: 10.1016/j.mad.2021.111574] [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: 05/30/2021] [Revised: 08/29/2021] [Accepted: 09/21/2021] [Indexed: 11/18/2022]
Abstract
Cellular homeostasis is regulated by the protein quality control (PQC) machinery, comprising multiple chaperones and enzymes. Studies suggest that the loss of the PQC mechanisms in neurons may lead to the formation of abnormal inclusions that may lead to neurological disorders and defective aging. The questions could be raised how protein aggregate formation precisely engenders multifactorial molecular pathomechanism in neuronal cells and affects different brain regions? Such questions await thorough investigation that may help us understand how aberrant proteinaceous bodies lead to neurodegeneration and imperfect aging. However, these studies face multiple technological challenges in utilizing available tools for detailed characterizations of the protein aggregates or amyloids and developing new techniques to understand the biology and pathology of proteopathies. The lack of detection and analysis methods has decelerated the pace of the research in amyloid biology. Here, we address the significance of aggregation and inclusion formation, followed by exploring the evolutionary contribution of these structures. We also provide a detailed overview of current state-of-the-art techniques and advances in studying amyloids in the diseased brain. A comprehensive understanding of the structural, pathological, and clinical characteristics of different types of aggregates (inclusions, fibrils, plaques, etc.) will aid in developing future therapies.
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Affiliation(s)
- Naveen Sundaria
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH‑8 Bandarsindri, Ajmer, Rajasthan, 305817, India
| | - Krishna Mohan Poluri
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology, Jodhpur, Rajasthan, 342037, India.
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21
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Abstract
The current model of replication-dependent (RD) histone biosynthesis posits that RD histone gene expression is coupled to DNA replication, occurring only in S phase of the cell cycle once DNA synthesis has begun. However, several key factors in the RD histone biosynthesis pathway are up-regulated by E2F or phosphorylated by CDK2, suggesting these processes may instead begin much earlier, at the point of cell-cycle commitment. In this study, we use both fixed- and live-cell imaging of human cells to address this question, revealing a hybrid model in which RD histone biosynthesis is first initiated in G1, followed by a strong increase in histone production in S phase of the cell cycle. This suggests a mechanism by which cells that have committed to the cell cycle build up an initial small pool of RD histones to be available for the start of DNA replication, before producing most of the necessary histones required in S phase. Thus, a clear distinction exists at completion of mitosis between cells that are born with the intention of proceeding through the cell cycle and replicating their DNA and cells that have chosen to exit the cell cycle and have no immediate need for histone synthesis.
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22
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Child MB, Bateman JR, Jahangiri A, Reimer A, Lammers NC, Sabouni N, Villamarin D, McKenzie-Smith GC, Johnson JE, Jost D, Garcia HG. Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. eLife 2021; 10:64412. [PMID: 34100718 PMCID: PMC8294847 DOI: 10.7554/elife.64412] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Three-dimensional eukaryotic genome organization provides the structural basis for gene regulation. In Drosophila melanogaster, genome folding is characterized by somatic homolog pairing, where homologous chromosomes are intimately paired from end to end; however, how homologs identify one another and pair has remained mysterious. Recently, this process has been proposed to be driven by specifically interacting 'buttons' encoded along chromosomes. Here, we turned this hypothesis into a quantitative biophysical model to demonstrate that a button-based mechanism can lead to chromosome-wide pairing. We tested our model using live-imaging measurements of chromosomal loci tagged with the MS2 and PP7 nascent RNA labeling systems. We show solid agreement between model predictions and experiments in the pairing dynamics of individual homologous loci. Our results strongly support a button-based mechanism of somatic homolog pairing in Drosophila and provide a theoretical framework for revealing the molecular identity and regulation of buttons.
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Affiliation(s)
- Myron Barber Child
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, United States
| | - Amir Jahangiri
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Armando Reimer
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - Nica Sabouni
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | | | | | | | - Daniel Jost
- Univ Grenoble Alpes CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France.,Université de Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratory of Biology and Modeling of the Cell, Lyon, France
| | - Hernan G Garcia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Physics, University of California, Berkeley, Berkeley, United States.,Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States.,Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States
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23
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Colgan DF, Goodfellow RX, Colgan JD. The transcriptional regulator GON4L is required for viability and hematopoiesis in mice. Exp Hematol 2021; 98:25-35. [PMID: 33864850 DOI: 10.1016/j.exphem.2021.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
The Gon4l gene encodes a putative transcriptional regulator implicated in the control of both cell differentiation and proliferation. Previously, we described a mutant mouse strain called Justy in which splicing of pre-mRNA generated from Gon4l is disrupted. This defect severely reduces, but does not abolish, GON4L protein expression and blocks the formation of early B-lineage progenitors, suggesting Gon4l is required for B-cell development in vertebrates. Yet, mutations that disable Gon4l in zebrafish impair several facets of embryogenesis that include the initiation of primitive hematopoiesis, arguing this gene is needed for multiple vertebrate developmental pathways. To better understand the importance of Gon4l in mammals, we created mice carrying an engineered version of Gon4l that can be completely inactivated by Cre-mediated recombination. Breeding mice heterozygous for the inactivated Gon4l allele failed to yield any homozygous-null offspring, indicating Gon4l is an essential gene in mammals. Consistent with this finding, as well previously published results, cell culture studies revealed that loss of Gon4l blocks cell proliferation and compromises viability, suggesting a fundamental role in the control of cell division and survival. Studies using mixed bone marrow chimeras confirmed Gon4l is required for B-cell development but also found it is needed to maintain definitive hematopoietic stem/progenitor cells that are the source of all hematopoietic cell lineages. Our findings reveal Gon4l is an essential gene in mammals that is required to form the entire hematopoietic system.
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Affiliation(s)
- Diana F Colgan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Renee X Goodfellow
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - John D Colgan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA; Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA; Interdisciplinary Graduate Program in Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA.
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24
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Kemp JP, Yang XC, Dominski Z, Marzluff WF, Duronio RJ. Superresolution light microscopy of the Drosophila histone locus body reveals a core-shell organization associated with expression of replication-dependent histone genes. Mol Biol Cell 2021; 32:942-955. [PMID: 33788585 PMCID: PMC8108526 DOI: 10.1091/mbc.e20-10-0645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of replication-dependent (RD) histone mRNAs, which are the only eukaryotic mRNAs lacking a poly-A tail. Many nuclear bodies contain distinct domains, but how internal organization is related to nuclear body function is not fully understood. Here, we demonstrate using structured illumination microscopy that Drosophila HLBs have a “core–shell” organization in which the internal core contains transcriptionally active RD histone genes. The N-terminus of Mxc, which contains a domain required for Mxc oligomerization, HLB assembly, and RD histone gene expression, is enriched in the HLB core. In contrast, the C-terminus of Mxc is enriched in the HLB outer shell as is FLASH, a component of the active U7 snRNP that cotranscriptionally cleaves RD histone pre-mRNA. Consistent with these results, we show biochemically that FLASH binds directly to the Mxc C-terminal region. In the rapid S-M nuclear cycles of syncytial blastoderm Drosophila embryos, the HLB disassembles at mitosis and reassembles the core–shell arrangement as histone gene transcription is activated immediately after mitosis. Thus, the core–shell organization is coupled to zygotic histone gene transcription, revealing a link between HLB internal organization and RD histone gene expression.
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Affiliation(s)
- James P Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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25
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Potter-Birriel JM, Gonsalvez GB, Marzluff WF. A region of SLBP outside the mRNA-processing domain is essential for deposition of histone mRNA into the Drosophila egg. J Cell Sci 2021; 134:jcs251728. [PMID: 33408246 PMCID: PMC7888719 DOI: 10.1242/jcs.251728] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023] Open
Abstract
Replication-dependent histone mRNAs are the only cellular mRNAs that are not polyadenylated, ending in a stemloop instead of a polyA tail, and are normally regulated coordinately with DNA replication. Stemloop-binding protein (SLBP) binds the 3' end of histone mRNA, and is required for processing and translation. During Drosophila oogenesis, large amounts of histone mRNAs and proteins are deposited in the developing oocyte. The maternally deposited histone mRNA is synthesized in stage 10B oocytes after the nurse cells complete endoreduplication. We report that in wild-type stage 10B oocytes, the histone locus bodies (HLBs), formed on the histone genes, produce histone mRNAs in the absence of phosphorylation of Mxc, which is normally required for histone gene expression in S-phase cells. Two mutants of SLBP, one with reduced expression and another with a 10-amino-acid deletion, fail to deposit sufficient histone mRNA in the oocyte, and do not transcribe the histone genes in stage 10B. Mutations in a putative SLBP nuclear localization sequence overlapping the deletion phenocopy the deletion. We conclude that a high concentration of SLBP in the nucleus of stage 10B oocytes is essential for histone gene transcription.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jennifer Michelle Potter-Birriel
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Interdisciplinary Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Graydon B Gonsalvez
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912 , USA
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Interdisciplinary Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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26
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Quiquand M, Rimesso G, Qiao N, Suo S, Zhao C, Slattery M, White KP, Han JJ, Baker NE. New regulators of Drosophila eye development identified from temporal transcriptome changes. Genetics 2021; 217:6117222. [PMID: 33681970 DOI: 10.1093/genetics/iyab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 12/28/2020] [Indexed: 11/12/2022] Open
Abstract
In the last larval instar, uncommitted progenitor cells in the Drosophila eye primordium start to adopt individual retinal cell fates, arrest their growth and proliferation, and initiate terminal differentiation into photoreceptor neurons and other retinal cell types. To explore the regulation of these processes, we have performed mRNA-Seq studies of the larval eye and antennal primordial at multiple developmental stages. A total of 10,893 fly genes were expressed during these stages and could be adaptively clustered into gene groups, some of whose expression increases or decreases in parallel with the cessation of proliferation and onset of differentiation. Using in situ hybridization of a sample of 98 genes to verify spatial and temporal expression patterns, we estimate that 534 genes or more are transcriptionally upregulated during retinal differentiation, and 1367 or more downregulated as progenitor cells differentiate. Each group of co-expressed genes is enriched for regulatory motifs recognized by co-expressed transcription factors, suggesting that they represent coherent transcriptional regulatory programs. Using available mutant strains, we describe novel roles for the transcription factors SoxNeuro (SoxN), H6-like homeobox (Hmx), CG10253, without children (woc), Structure specific recognition protein (Ssrp), and multisex combs (mxc).
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Affiliation(s)
- Manon Quiquand
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gerard Rimesso
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nan Qiao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shengbao Suo
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chunyu Zhao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Matthew Slattery
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Kevin P White
- Institute for Genomics & Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jackie J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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27
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Kurihara M, Takarada K, Inoue YH. Enhancement of leukemia-like phenotypes in Drosophila mxc mutant larvae due to activation of the RAS-MAP kinase cascade possibly via down-regulation of DE-cadherin. Genes Cells 2020; 25:757-769. [PMID: 33012036 DOI: 10.1111/gtc.12811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023]
Abstract
Loss of mxc gene function in mature hemocytes of Drosophila mxcmbn1 mutant results in malignant hyperplasia in larval hematopoietic tissues termed lymph glands (LGs) owing to over-proliferation of immature cells. This is a useful model for genetic analyses of leukemia progression. To identify other mutations that deteriorate the hyperplasia, we aimed to investigate whether hyper-activation of common signaling cascade enabled to enhance the phenotypes. Ectopic expression of the constitutively active forms of MAPK signaling factors in the mutant increased the hyperplasia and the number of circulating hemocytes, resulting in the production of LG fragments. The LG phenotype was related to the reduced DE-cadherin level in the mutants. Depletion of Drosophila MCRIP, involved in MAPK-induced silencing of cadherin gene expression, exhibited a similar enhancement of the mxcmbn1 phenotypes. Furthermore, expression of MMP1 proteinase that cleaves the extracellular matrix proteins increased in the mutant larvae harboring MAPK cascade activation. Depletion of Mmp1 and that of pnt (required for Mmp1 expression) suppressed the LG hyperplasia. Hence, we speculated that reduction in DE-cadherin level by either down-regulation of MCRIP or up-regulation of MMP1 was involved in the progression of the tumor phenotype. Our findings can contribute to understanding the mechanism underlying human leukemia progression.
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Affiliation(s)
- Masanori Kurihara
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Kazuki Takarada
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Yoshihiro H Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
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28
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Zhou Y, Pozo PN, Oh S, Stone HM, Cook JG. Distinct and sequential re-replication barriers ensure precise genome duplication. PLoS Genet 2020; 16:e1008988. [PMID: 32841231 PMCID: PMC7473519 DOI: 10.1371/journal.pgen.1008988] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/04/2020] [Accepted: 07/12/2020] [Indexed: 01/19/2023] Open
Abstract
Achieving complete and precise genome duplication requires that each genomic segment be replicated only once per cell division cycle. Protecting large eukaryotic genomes from re-replication requires an overlapping set of molecular mechanisms that prevent the first DNA replication step, the DNA loading of MCM helicase complexes to license replication origins, after S phase begins. Previous reports have defined many such origin licensing inhibition mechanisms, but the temporal relationships among them are not clear, particularly with respect to preventing re-replication in G2 and M phases. Using a combination of mutagenesis, biochemistry, and single cell analyses in human cells, we define a new mechanism that prevents re-replication through hyperphosphorylation of the essential MCM loading protein, Cdt1. We demonstrate that Cyclin A/CDK1 can hyperphosphorylate Cdt1 to inhibit MCM re-loading in G2 phase. The mechanism of inhibition is to block Cdt1 binding to MCM independently of other known Cdt1 inactivation mechanisms such as Cdt1 degradation during S phase or Geminin binding. Moreover, our findings suggest that Cdt1 dephosphorylation at the mitosis-to-G1 phase transition re-activates Cdt1. We propose that multiple distinct, non-redundant licensing inhibition mechanisms act in a series of sequential relays through each cell cycle phase to ensure precise genome duplication. The initial step of DNA replication is loading the DNA helicase, MCM, onto DNA during the first phase of the cell division cycle. If MCM loading occurs inappropriately onto DNA that has already been replicated, then cells risk DNA re-replication, a source of endogenous DNA damage and genome instability. How mammalian cells prevent any sections of their very large genomes from re-replicating is still not fully understood. We found that the Cdt1 protein, one of the critical MCM loading factors, is inhibited specifically in late cell cycle stages through a mechanism involving protein phosphorylation. This phosphorylation prevents Cdt1 from binding MCM; when Cdt1 cannot be phosphorylated MCM is inappropriately re-loaded onto DNA and cells are prone to re-replication. When cells divide and transition into G1 phase, Cdt1 is then dephosphorylated to re-activate it for MCM loading. Based on these findings we assert that the different mechanisms that cooperate to avoid re-replication are not redundant. Instead, different cell cycle phases are dominated by different re-replication control mechanisms. These findings have implications for understanding how genomes are duplicated precisely once per cell cycle and shed light on how that process is perturbed by changes in Cdt1 levels or phosphorylation activity.
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Affiliation(s)
- Yizhuo Zhou
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Pedro N. Pozo
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
| | - Seeun Oh
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute and the Research Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, United State of America
| | - Haley M. Stone
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United State of America
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- Lineberger Comprehensive Cancer, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United State of America
- * E-mail:
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29
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Bucholc K, Skrajna A, Adamska K, Yang XC, Krajewski K, Poznański J, Dadlez M, Domiński Z, Zhukov I. Structural Analysis of the SANT/Myb Domain of FLASH and YARP Proteins and Their Complex with the C-Terminal Fragment of NPAT by NMR Spectroscopy and Computer Simulations. Int J Mol Sci 2020; 21:ijms21155268. [PMID: 32722282 PMCID: PMC7432317 DOI: 10.3390/ijms21155268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/15/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
FLICE-associated huge protein (FLASH), Yin Yang 1-Associated Protein-Related Protein (YARP) and Nuclear Protein, Ataxia-Telangiectasia Locus (NPAT) localize to discrete nuclear structures called histone locus bodies (HLBs) where they control various steps in histone gene expression. Near the C-terminus, FLASH and YARP contain a highly homologous domain that interacts with the C-terminal region of NPAT. Structural aspects of the FLASH-NPAT and YARP-NPAT complexes and their role in histone gene expression remain largely unknown. In this study, we used multidimensional NMR spectroscopy and in silico modeling to analyze the C-terminal domain in FLASH and YARP in an unbound form and in a complex with the last 31 amino acids of NPAT. Our results demonstrate that FLASH and YARP domains share the same fold of a triple α -helical bundle that resembles the DNA binding domain of Myb transcriptional factors and the SANT domain found in chromatin-modifying and remodeling complexes. The NPAT peptide contains a single α -helix that makes multiple contacts with α -helices I and III of the FLASH and YARP domains. Surprisingly, in spite of sharing a significant amino acid similarity, each domain likely binds NPAT using a unique network of interactions, yielding two distinct complexes. In silico modeling suggests that both complexes are structurally compatible with DNA binding, raising the possibility that they may function in identifying specific sequences within histone gene clusters, hence initiating the assembly of HLBs and regulating histone gene expression during cell cycle progression.
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Affiliation(s)
- Katarzyna Bucholc
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Aleksandra Skrajna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Kinga Adamska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
| | - Zbigniew Domiński
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
| | - Igor Zhukov
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawińskiego 5a, 02-106 Warsaw, Poland; (K.B.); (A.S.); (K.A.); (J.P.); (M.D.)
- NanoBioMedical Centre, Adam Mickiewicz University, ul. Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
- Correspondence: (Z.D.); (I.Z.); Tel.: +48-22-592-2038 (I.Z.)
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30
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Hur W, Kemp JP, Tarzia M, Deneke VE, Marzluff WF, Duronio RJ, Di Talia S. CDK-Regulated Phase Separation Seeded by Histone Genes Ensures Precise Growth and Function of Histone Locus Bodies. Dev Cell 2020; 54:379-394.e6. [PMID: 32579968 DOI: 10.1016/j.devcel.2020.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/17/2020] [Accepted: 05/30/2020] [Indexed: 10/24/2022]
Abstract
Many membraneless organelles form through liquid-liquid phase separation, but how their size is controlled and whether size is linked to function remain poorly understood. The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of histone mRNAs. Here, we show that Drosophila HLBs form through phase separation. During embryogenesis, the size of HLBs is controlled in a precise and dynamic manner that is dependent on the cell cycle and zygotic histone gene activation. Control of HLB growth is achieved by a mechanism integrating nascent mRNAs at the histone locus, which facilitates phase separation, and the nuclear concentration of the scaffold protein multi-sex combs (Mxc), which is controlled by the activity of cyclin-dependent kinases. Reduced Cdk2 activity results in smaller HLBs and the appearance of nascent, misprocessed histone mRNAs. Thus, our experiments identify a mechanism linking nuclear body growth and size with gene expression.
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Affiliation(s)
- Woonyung Hur
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - James P Kemp
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marco Tarzia
- LPTMC, CNRS-UMR 7600, Sorbonne Université, 4 Pl. Jussieu, 75005 Paris, France
| | - Victoria E Deneke
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Department of Biology, Department of Genetics, Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27705, USA.
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31
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Koreski KP, Rieder LE, McLain LM, Chaubal A, Marzluff WF, Duronio RJ. Drosophila histone locus body assembly and function involves multiple interactions. Mol Biol Cell 2020; 31:1525-1537. [PMID: 32401666 PMCID: PMC7359574 DOI: 10.1091/mbc.e20-03-0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The histone locus body (HLB) assembles at replication-dependent (RD) histone loci and concentrates factors required for RD histone mRNA biosynthesis. The Drosophila melanogaster genome has a single locus comprised of ∼100 copies of a tandemly arrayed 5-kB repeat unit containing one copy of each of the 5 RD histone genes. To determine sequence elements required for D. melanogaster HLB formation and histone gene expression, we used transgenic gene arrays containing 12 copies of the histone repeat unit that functionally complement loss of the ∼200 endogenous RD histone genes. A 12x histone gene array in which all H3-H4 promoters were replaced with H2a-H2b promoters (12xPR) does not form an HLB or express high levels of RD histone mRNA in the presence of the endogenous histone genes. In contrast, this same transgenic array is active in HLB assembly and RD histone gene expression in the absence of the endogenous RD histone genes and rescues the lethality caused by homozygous deletion of the RD histone locus. The HLB formed in the absence of endogenous RD histone genes on the mutant 12x array contains all known factors present in the wild-type HLB including CLAMP, which normally binds to GAGA repeats in the H3-H4 promoter. These data suggest that multiple protein–protein and/or protein–DNA interactions contribute to HLB formation, and that the large number of endogenous RD histone gene copies sequester available factor(s) from attenuated transgenic arrays, thereby preventing HLB formation and gene expression on these arrays.
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Affiliation(s)
- Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322
| | - Lyndsey M McLain
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Ashlesha Chaubal
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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32
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Prieto-Sánchez S, Moreno-Castro C, Hernández-Munain C, Suñé C. Drosophila Prp40 localizes to the histone locus body and regulates gene transcription and development. J Cell Sci 2020; 133:jcs.239509. [PMID: 32094262 DOI: 10.1242/jcs.239509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/09/2020] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, a large amount of histones need to be synthesized during the S phase of the cell cycle to package newly synthesized DNA into chromatin. The transcription and 3' end processing of histone pre-mRNAs are controlled by the histone locus body (HLB), which is assembled on the shared promoter for H3 and H4 Here, we identified the Drosophila Prp40 pre-mRNA processing factor (dPrp40, annotated as CG3542) as a novel HLB component. We showed that dPrp40 is essential for Drosophila development, with functionally conserved activity in vertebrates and invertebrates. We observed that dPrp40 is fundamental in endocycling cells, highlighting a role for this factor in mediating replication efficiency in vivo The depletion of dPrp40 from fly cells inhibited the transcription, but not the 3' end processing, of histone mRNA in a H3- and H4-promoter-dependent manner. Our results establish that dPrp40 is an essential protein for Drosophila development that can localize to the HLB and might participate in histone mRNA biosynthesis.
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Affiliation(s)
- Silvia Prieto-Sánchez
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Moreno-Castro
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Cristina Hernández-Munain
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
| | - Carlos Suñé
- Department of Molecular Biology, Institute of Parasitology and Biomedicine "López-Neyra" (IPBLN-CSIC), PTS, 18016 Granada, Spain
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33
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Kurihara M, Komatsu K, Awane R, Inoue YH. Loss of Histone Locus Bodies in the Mature Hemocytes of Larval Lymph Gland Result in Hyperplasia of the Tissue in mxc Mutants of Drosophila. Int J Mol Sci 2020; 21:E1586. [PMID: 32111032 PMCID: PMC7084650 DOI: 10.3390/ijms21051586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/15/2020] [Accepted: 02/24/2020] [Indexed: 01/22/2023] Open
Abstract
Mutations in the multi sex combs (mxc) gene in Drosophila results in malignant hyperplasia in larval hematopoietic tissues, called lymph glands (LG). mxc encodes a component of the histone locus body (HLB) that is essential for cell cycle-dependent transcription and processing of histone mRNAs. The mammalian nuclear protein ataxia-telangiectasia (NPAT) gene, encoded by the responsible gene for ataxia telangiectasia, is a functional Mxc orthologue. However, their roles in tumorigenesis are unclear. Genetic analyses of the mxc mutants and larvae having LG-specific depletion revealed that a reduced activity of the gene resulted in the hyperplasia, which is caused by hyper-proliferation of immature LG cells. The depletion of mxc in mature hemocytes of the LG resulted in the hyperplasia. Furthermore, the inhibition of HLB formation was required for LG hyperplasia. In the mutant larvae, the total mRNA levels of the five canonical histones decreased, and abnormal forms of polyadenylated histone mRNAs, detected rarely in normal larvae, were generated. The ectopic expression of the polyadenylated mRNAs was sufficient for the reproduction of the hyperplasia. The loss of HLB function, especially 3-end processing of histone mRNAs, is critical for malignant LG hyperplasia in this leukemia model in Drosophila. We propose that mxc is involved in the activation to induce adenosine deaminase-related growth factor A (Adgf-A), which suppresses immature cell proliferation in LG.
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Affiliation(s)
| | | | | | - Yoshihiro H. Inoue
- Department of Insect Biomedical Research, Center for Advanced Insect Research Promotion, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-0962, Japan; (M.K.); (K.K.); (R.A.)
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34
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Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK. Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold Proteins in Drosophila S2 Cells-Transmission of Hallmarks of Nuclear Organization Through Mitosis. Mol Cell Proteomics 2018; 17:1965-1978. [PMID: 29991507 PMCID: PMC6166678 DOI: 10.1074/mcp.ra118.000591] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/07/2018] [Indexed: 01/08/2023] Open
Abstract
Chromatin condenses several folds to form mitotic chromosomes during cell division and decondenses post-mitotically to reoccupy their nuclear territory and regain their specific transcriptional profile in a precisely lineage specific manner. This necessitates that the features of nuclear architecture and DNA topology persist through mitosis. We compared the proteome of nuclease and high salt resistant fraction of interphase nucleus known as nuclear matrix (NuMat) and an equivalent biochemical fraction in the mitotic chromosome known as mitotic chromosome scaffold (MiCS). Our study elucidates that as much as 67% of the NuMat proteins are retained in the MiCS indicating that the features of nuclear architecture in interphase nucleus are retained on the mitotic chromosomes. Proteins of the NuMat/MiCS have large dynamic range of MS signal and were detected in sub-femtomolar amounts. Chromatin/RNA binding proteins with hydrolase and helicase activity are highly enriched in NuMat as well as MiCS. Although several transcription factors involved in functioning of interphase nucleus are present exclusively in NuMat, protein components responsible for assembly of membrane-less nuclear bodies are uniquely retained in MiCS. Our study clearly indicates that the features of nuclear architecture, in the structural context of NuMat, are retained in MiCS and possibly play an important role in maintenance of cell lineage specific transcriptional status during cell division and thereby, serve as components of cellular memory.
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Affiliation(s)
- Rahul Sureka
- From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Rashi Wadhwa
- From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Suman S Thakur
- From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Rashmi U Pathak
- From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
| | - Rakesh K Mishra
- From the Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad-500007, India
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35
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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36
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Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R. dCas9-targeted locus-specific protein isolation method identifies histone gene regulators. Proc Natl Acad Sci U S A 2018; 115:E2734-E2741. [PMID: 29507191 PMCID: PMC5866577 DOI: 10.1073/pnas.1718844115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic gene regulation is a complex process, often coordinated by the action of tens to hundreds of proteins. Although previous biochemical studies have identified many components of the basal machinery and various ancillary factors involved in gene regulation, numerous gene-specific regulators remain undiscovered. To comprehensively survey the proteome directing gene expression at a specific genomic locus of interest, we developed an in vitro nuclease-deficient Cas9 (dCas9)-targeted chromatin-based purification strategy, called "CLASP" (Cas9 locus-associated proteome), to identify and functionally test associated gene-regulatory factors. Our CLASP method, coupled to mass spectrometry and functional screens, can be efficiently adapted for isolating associated regulatory factors in an unbiased manner targeting multiple genomic loci across different cell types. Here, we applied our method to isolate the Drosophila melanogaster histone cluster in S2 cells to identify several factors including Vig and Vig2, two proteins that bind and regulate core histone H2A and H3 mRNA via interaction with their 3' UTRs.
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Affiliation(s)
- Chiahao Tsui
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Carla Inouye
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
| | - Michaella Levy
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Andrew Lu
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720
| | | | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California, Berkeley, CA 94720;
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720
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37
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Arias Escayola D, Neugebauer KM. Dynamics and Function of Nuclear Bodies during Embryogenesis. Biochemistry 2018; 57:2462-2469. [PMID: 29473743 DOI: 10.1021/acs.biochem.7b01262] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nuclear bodies are RNA-rich membraneless organelles in the cell nucleus that concentrate specific sets of nuclear proteins and RNA-protein complexes. Nuclear bodies such as the nucleolus, Cajal body (CB), and the histone locus body (HLB) concentrate factors required for nuclear steps of RNA processing. Formation of these nuclear bodies occurs on genomic loci and is frequently associated with active sites of transcription. Whether nuclear body formation is dependent on a particular gene element, an active process such as transcription, or the nascent RNA present at gene loci is a topic of debate. Recently, this question has been addressed through studies in model organisms and their embryos. The switch from maternally provided RNA and protein to zygotic gene products in early embryos has been well characterized in a variety of organisms. This process, termed maternal-to-zygotic transition, provides an excellent model for studying formation of nuclear bodies before, during, and after the transcriptional activation of the zygotic genome. Here, we review findings in embryos that reveal key principles in the study of the formation and function of nucleoli, CBs, and HLBs. We propose that while particular gene elements may contribute to formation of these nuclear bodies, active transcription promotes maturation of nuclear bodies and efficient RNA processing within them.
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Affiliation(s)
- Dahyana Arias Escayola
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
| | - Karla M Neugebauer
- Molecular Biophysics and Biochemistry , Yale University , New Haven , Connecticut 06520-8114 , United States
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38
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Sánchez-Hernández N, Prieto-Sánchez S, Moreno-Castro C, Muñoz-Cobo JP, El Yousfi Y, Boyero-Corral S, Suñé-Pou M, Hernández-Munain C, Suñé C. Targeting proteins to RNA transcription and processing sites within the nucleus. Int J Biochem Cell Biol 2017; 91:194-202. [DOI: 10.1016/j.biocel.2017.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/26/2022]
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39
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Marzluff WF, Koreski KP. Birth and Death of Histone mRNAs. Trends Genet 2017; 33:745-759. [PMID: 28867047 DOI: 10.1016/j.tig.2017.07.014] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022]
Abstract
In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73. Histone mRNAs are rapidly degraded when DNA replication is inhibited by a 3' to 5' pathway that requires extensive uridylation of mRNA decay intermediates.
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Affiliation(s)
- William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kaitlin P Koreski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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40
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Rieder LE, Koreski KP, Boltz KA, Kuzu G, Urban JA, Bowman SK, Zeidman A, Jordan WT, Tolstorukov MY, Marzluff WF, Duronio RJ, Larschan EN. Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP. Genes Dev 2017; 31:1494-1508. [PMID: 28838946 PMCID: PMC5588930 DOI: 10.1101/gad.300855.117] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/25/2017] [Indexed: 01/13/2023]
Abstract
Rieder et al. report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct histone locus body (HLB) formation in Drosophila. In addition, the CLAMP zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat cis elements within the bidirectional histone3–histone4 promoter direct HLB formation in Drosophila. In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We demonstrated previously that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X chromosome. Therefore, CLAMP binding to GA repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.
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Affiliation(s)
- Leila E Rieder
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kaitlin P Koreski
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Kara A Boltz
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jennifer A Urban
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Sarah K Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Anna Zeidman
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - William T Jordan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Michael Y Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William F Marzluff
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Biology, University of North Carolina at Chapel Hill, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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41
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Kassis JA, Kennison JA, Tamkun JW. Polycomb and Trithorax Group Genes in Drosophila. Genetics 2017; 206:1699-1725. [PMID: 28778878 PMCID: PMC5560782 DOI: 10.1534/genetics.115.185116] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/15/2017] [Indexed: 01/08/2023] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.
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Affiliation(s)
- Judith A Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - James A Kennison
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - John W Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
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42
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Duronio RJ, Marzluff WF. Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body. RNA Biol 2017; 14:726-738. [PMID: 28059623 DOI: 10.1080/15476286.2016.1265198] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing. These factors include the scaffolding protein NPAT, essential for histone gene transcription, and FLASH and U7 snRNP, both essential for histone pre-mRNA processing. Histone gene expression is activated by Cyclin E/Cdk2-mediated phosphorylation of NPAT at the G1-S transition. The concentration of factors within the HLB couples transcription with pre-mRNA processing, enhancing the efficiency of histone mRNA biosynthesis.
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Affiliation(s)
- Robert J Duronio
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,b Department of Genetics , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - William F Marzluff
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA.,e Department of Biochemistry and Biophysics , University of North Carolina , Chapel Hill , NC , USA
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43
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Musinova YR, Lisitsyna OM, Sorokin DV, Arifulin EA, Smirnova TA, Zinovkin RA, Potashnikova DM, Vassetzky YS, Sheval EV. RNA-dependent disassembly of nuclear bodies. J Cell Sci 2016; 129:4509-4520. [PMID: 27875271 DOI: 10.1242/jcs.189142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 11/02/2016] [Indexed: 12/17/2022] Open
Abstract
Nuclear bodies are membraneless organelles that play important roles in genome functioning. A specific type of nuclear bodies known as interphase prenucleolar bodies (iPNBs) are formed in the nucleoplasm after hypotonic stress from partially disassembled nucleoli. iPNBs are then disassembled, and the nucleoli are reformed simultaneously. Here, we show that diffusion of B23 molecules (also known as nucleophosmin, NPM1) from iPNBs, but not fusion of iPNBs with the nucleoli, contributes to the transfer of B23 from iPNBs to the nucleoli. Maturation of pre-ribosomal RNAs (rRNAs) and the subsequent outflow of mature rRNAs from iPNBs led to the disassembly of iPNBs. We found that B23 transfer was dependent on the synthesis of pre-rRNA molecules in nucleoli; these pre-rRNA molecules interacted with B23 and led to its accumulation within nucleoli. The transfer of B23 between iPNBs and nucleoli was accomplished through a nucleoplasmic pool of B23, and increased nucleoplasmic B23 content retarded disassembly, whereas B23 depletion accelerated disassembly. Our results suggest that iPNB disassembly and nucleolus assembly might be coupled through RNA-dependent exchange of nucleolar proteins, creating a highly dynamic system with long-distance correlations between spatially distinct processes.
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Affiliation(s)
- Yana R Musinova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France
| | - Olga M Lisitsyna
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Dmitry V Sorokin
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Botanická 68a, Brno 602 00, Czech Republic.,Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Eugene A Arifulin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Tatiana A Smirnova
- Department of Cell Biology and Histology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Roman A Zinovkin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Daria M Potashnikova
- Department of Cell Biology and Histology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yegor S Vassetzky
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France.,UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, Villejuif 94805, France
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia .,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France
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44
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Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Res 2016; 44:9190-9205. [PMID: 27402160 PMCID: PMC5100578 DOI: 10.1093/nar/gkw620] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 06/30/2016] [Indexed: 11/24/2022] Open
Abstract
Histone proteins are synthesized in large amounts during S-phase to package the newly replicated DNA, and are among the most stable proteins in the cell. The replication-dependent (RD)-histone mRNAs expressed during S-phase end in a conserved stem-loop rather than a polyA tail. In addition, there are replication-independent (RI)-histone genes that encode histone variants as polyadenylated mRNAs. Most variants have specific functions in chromatin, but H3.3 also serves as a replacement histone for damaged histones in long-lived terminally differentiated cells. There are no reported replacement histone genes for histones H2A, H2B or H4. We report that a subset of RD-histone genes are expressed in terminally differentiated tissues as polyadenylated mRNAs, likely serving as replacement histone genes in long-lived non-dividing cells. Expression of two genes, HIST2H2AA3 and HIST1H2BC, is conserved in mammals. They are expressed as polyadenylated mRNAs in fibroblasts differentiated in vitro, but not in serum starved fibroblasts, suggesting that their expression is part of the terminal differentiation program. There are two histone H4 genes and an H3 gene that encode mRNAs that are polyadenylated and expressed at 5- to 10-fold lower levels than the mRNAs from H2A and H2B genes, which may be replacement genes for the H3.1 and H4 proteins.
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Affiliation(s)
- Shawn M Lyons
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Clark H Cunningham
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joshua D Welch
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599
| | - Beezly Groh
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Andrew Y Guo
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Bruce Wei
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael L Whitfield
- Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, NH 03755, USA
| | - Yue Xiong
- Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - William F Marzluff
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA .,Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599.,Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
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Tatomer DC, Terzo E, Curry KP, Salzler H, Sabath I, Zapotoczny G, McKay DJ, Dominski Z, Marzluff WF, Duronio RJ. Concentrating pre-mRNA processing factors in the histone locus body facilitates efficient histone mRNA biogenesis. J Cell Biol 2016; 213:557-70. [PMID: 27241916 PMCID: PMC4896052 DOI: 10.1083/jcb.201504043] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 04/27/2016] [Indexed: 11/22/2022] Open
Abstract
The histone locus body (HLB) assembles at replication-dependent histone genes and concentrates factors required for histone messenger RNA (mRNA) biosynthesis. FLASH (Flice-associated huge protein) and U7 small nuclear RNP (snRNP) are HLB components that participate in 3' processing of the nonpolyadenylated histone mRNAs by recruiting the endonuclease CPSF-73 to histone pre-mRNA. Using transgenes to complement a FLASH mutant, we show that distinct domains of FLASH involved in U7 snRNP binding, histone pre-mRNA cleavage, and HLB localization are all required for proper FLASH function in vivo. By genetically manipulating HLB composition using mutations in FLASH, mutations in the HLB assembly factor Mxc, or depletion of the variant histone H2aV, we find that failure to concentrate FLASH and/or U7 snRNP in the HLB impairs histone pre-mRNA processing. This failure results in accumulation of small amounts of polyadenylated histone mRNA and nascent read-through transcripts at the histone locus. Thus, the HLB concentrates FLASH and U7 snRNP, promoting efficient histone mRNA biosynthesis and coupling 3' end processing with transcription termination.
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Affiliation(s)
- Deirdre C Tatomer
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Esteban Terzo
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Kaitlin P Curry
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Harmony Salzler
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Ivan Sabath
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Grzegorz Zapotoczny
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Daniel J McKay
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599
| | - William F Marzluff
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | - Robert J Duronio
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599 Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599 Department of Genetics, University of North Carolina, Chapel Hill, NC 27599
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Romeo V, Schümperli D. Cycling in the nucleus: regulation of RNA 3′ processing and nuclear organization of replication-dependent histone genes. Curr Opin Cell Biol 2016; 40:23-31. [DOI: 10.1016/j.ceb.2016.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 01/27/2016] [Accepted: 01/30/2016] [Indexed: 12/01/2022]
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Ozawa N, Furuhashi H, Masuko K, Numao E, Makino T, Yano T, Kurata S. Organ identity specification factor WGE localizes to the histone locus body and regulates histone expression to ensure genomic stability in Drosophila. Genes Cells 2016; 21:442-56. [PMID: 27145109 DOI: 10.1111/gtc.12354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/28/2016] [Indexed: 12/19/2022]
Abstract
Over-expression of Winged-Eye (WGE) in the Drosophila eye imaginal disc induces an eye-to-wing transformation. Endogenous WGE is required for organ development, and wge-deficient mutants exhibit growth arrest at the larval stage, suggesting that WGE is critical for normal growth. The function of WGE, however, remains unclear. Here, we analyzed the subcellular localization of WGE to gain insight into its endogenous function. Immunostaining showed that WGE localized to specific nuclear foci called the histone locus body (HLB), an evolutionarily conserved nuclear body required for S phase-specific histone mRNA production. Histone mRNA levels and protein levels in cytosolic fractions were aberrantly up-regulated in wge mutant larva, suggesting a role for WGE in regulating histone gene expression. Genetic analyses showed that wge suppresses position-effect variegation, and that WGE and a HLB component Mute appears to be synergistically involved in heterochromatin formation. Further supporting a role in chromatin regulation, wge-deficient mutants showed derepression of retrotransposons and increased γH2Av signals, a DNA damage marker. These findings suggest that WGE is a component of HLB in Drosophila with a role in heterochromatin formation and transposon silencing. We propose that WGE at HLB contributes to genomic stability and development by regulating heterochromatin structure via histone gene regulation.
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Affiliation(s)
- Nao Ozawa
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Keita Masuko
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Eriko Numao
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Tamaki Yano
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
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Abstract
In metazoan the 3′-end processing of histone mRNAs is a conserved process involving the concerted action of many protein factors and the non-coding U7 snRNA. Recently, we identified that the processing of histone pre-mRNAs is promoted by an additional ncRNA, the Y3-derived Y3** RNA. U7 modulates the association of the U7 snRNP whereas Y3** promotes recruitment of CPSF (cleavage and polyadenylation specific factor) proteins to nascent histone transcripts at histone locus bodies (HLBs) in mammals. This enhances the 3′-end cleavage of nascent histone pre-mRNAs and modulates HLB assembly. Here we discuss new insights in the role of ncRNAs in the spatiotemporal control of histone synthesis. We propose that ncRNAs scaffold the formation of functional protein-RNA complexes and their sequential deposition on nascent histone pre-mRNAs at HLBs. These findings add to the multiple roles of ncRNAs in controlling gene expression and may provide new avenues for targeting histone synthesis in cancer.
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Affiliation(s)
- Marcel Köhn
- a Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED , Halle , Germany
| | - Stefan Hüttelmaier
- a Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin-Luther-University Halle Wittenberg, ZAMED , Halle , Germany
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Skrajna A, Yang XC, Tarnowski K, Fituch K, Marzluff WF, Dominski Z, Dadlez M. Mapping the Interaction Network of Key Proteins Involved in Histone mRNA Generation: A Hydrogen/Deuterium Exchange Study. J Mol Biol 2016; 428:1180-1196. [PMID: 26860583 DOI: 10.1016/j.jmb.2016.01.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 01/27/2016] [Accepted: 01/30/2016] [Indexed: 10/22/2022]
Abstract
Histone pre-mRNAs are cleaved at the 3' end by a complex that contains U7 snRNP, the FLICE-associated huge protein (FLASH) and histone pre-mRNA cleavage complex (HCC) consisting of several polyadenylation factors. Within the complex, the N terminus of FLASH interacts with the N terminus of the U7 snRNP protein Lsm11, and together they recruit the HCC. FLASH through its distant C terminus independently interacts with the C-terminal SANT/Myb-like domain of nuclear protein, ataxia-telangiectasia locus (NPAT), a transcriptional co-activator required for expression of histone genes in S phase. To gain structural information on these interactions, we used mass spectrometry to monitor hydrogen/deuterium exchange in various regions of FLASH, Lsm11 and NPAT alone or in the presence of their respective binding partners. Our results indicate that the FLASH-interacting domain in Lsm11 is highly dynamic, while the more downstream region required for recruiting the HCC exchanges deuterium slowly and likely folds into a stable structure. In FLASH, a stable structure is adopted by the domain that interacts with Lsm11 and this domain is further stabilized by binding Lsm11. Notably, both hydrogen/deuterium exchange experiments and in vitro binding assays demonstrate that Lsm11, in addition to interacting with the N-terminal region of FLASH, also contacts the C-terminal SANT/Myb-like domain of FLASH, the same region that binds NPAT. However, while NPAT stabilizes this domain, Lsm11 causes its partial relaxation. These competing reactions may play a role in regulating histone gene expression in vivo.
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Affiliation(s)
- Aleksandra Skrajna
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiao-Cui Yang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Krzysztof Tarnowski
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kinga Fituch
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - William F Marzluff
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Zbigniew Dominski
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Michał Dadlez
- Department of Biophysics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
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50
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Köhn M, Ihling C, Sinz A, Krohn K, Hüttelmaier S. The Y3** ncRNA promotes the 3' end processing of histone mRNAs. Genes Dev 2016; 29:1998-2003. [PMID: 26443846 PMCID: PMC4604341 DOI: 10.1101/gad.266486.115] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In this study, Köhn et al. investigated how the cleavage and polyadenylation specificity factor (CPSF) is recruited to nascent histone pre-mRNAs during 3′ end processing of canonical histone mRNAs. They showed that the noncoding Y3/Y3** RNAs modulate the 3′ end processing of canonical histone mRNAs by binding to CPSF, thereby delineating a novel mechanism involved in the regulation of histone pre-mRNA processing. We demonstrate that the Y3/Y3** noncoding RNAs (ncRNAs) bind to the CPSF (cleavage and polyadenylation specificity factor) and that Y3** associates with the 3′ untranslated region (UTR) of histone pre-mRNAs. The depletion of Y3** impairs the 3′ end processing of histone pre-mRNAs as well as the formation and protein dynamics of histone locus bodies (HLBs), the site of histone mRNA synthesis and processing. HLB morphology is also disturbed by knockdown of the CPSF but not the U7-snRNP components. In conclusion, we propose that the Y3** ncRNA promotes the 3′ end processing of histone pre-mRNAs by enhancing the recruitment of the CPSF to histone pre-mRNAs at HLBs.
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Affiliation(s)
- Marcel Köhn
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Christian Ihling
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
| | - Knut Krohn
- Interdisziplinäres Zentrum für Klinische Forschung, Core Unit DNA-Technologies, University Leipzig, Saxony 04103, Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Martin-Luther-University Halle-Wittenberg, Saxony-Anhalt 06120, Germany
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