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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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2
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Miao Z, Tidu A, Eriani G, Martin F. Secondary structure of the SARS-CoV-2 5'-UTR. RNA Biol 2021; 18:447-456. [PMID: 32965173 PMCID: PMC7544965 DOI: 10.1080/15476286.2020.1814556] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.
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Affiliation(s)
- Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, UK
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People’s Hospital Affiliated to Tongji University School of Medicine, Shanghai, China
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Antonin Tidu
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
| | - Gilbert Eriani
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
| | - Franck Martin
- Architecture Et Réactivité De l’ARN, Université De Strasbourg, Institut De Biologie Moléculaire Et Cellulaire Du CNRS, Strasbourg, France
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3
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Akay A, Craig A, Lehrbach N, Larance M, Pourkarimi E, Wright JE, Lamond A, Miska E, Gartner A. RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biol 2013; 3:130151. [PMID: 24258276 PMCID: PMC3843822 DOI: 10.1098/rsob.130151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Messenger RNA translation is regulated by RNA-binding proteins and small non-coding RNAs called microRNAs. Even though we know the majority of RNA-binding proteins and microRNAs that regulate messenger RNA expression, evidence of interactions between the two remain elusive. The role of the RNA-binding protein GLD-1 as a translational repressor is well studied during Caenorhabditis elegans germline development and maintenance. Possible functions of GLD-1 during somatic development and the mechanism of how GLD-1 acts as a translational repressor are not known. Its human homologue, quaking (QKI), is essential for embryonic development. Here, we report that the RNA-binding protein GLD-1 in C. elegans affects multiple microRNA pathways and interacts with proteins required for microRNA function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1, two known modulators of miRNA function, genetically interact with GLD-1. gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7 family mutants during somatic development. We used stable isotope labelling with amino acids in cell culture to globally analyse the changes in the proteome conferred by let-7 and gld-1 during animal development. We identified the histone mRNA-binding protein CDL-1 to be, in part, responsible for the phenotypes observed in let-7 and gld-1 mutants. The link between GLD-1 and miRNA-mediated gene regulation is further supported by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins implicated in miRNA regulation. Overall, we have uncovered genetic and biochemical interactions between GLD-1 and miRNA pathways.
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Affiliation(s)
- Alper Akay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
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Zhang M, Lam TT, Tonelli M, Marzluff WF, Thapar R. Interaction of the histone mRNA hairpin with stem-loop binding protein (SLBP) and regulation of the SLBP-RNA complex by phosphorylation and proline isomerization. Biochemistry 2012; 51:3215-31. [PMID: 22439849 DOI: 10.1021/bi2018255] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In metazoans, the majority of histone proteins are generated from replication-dependent histone mRNAs. These mRNAs are unique in that they are not polyadenylated but have a stem-loop structure in their 3' untranslated region. An early event in 3' end formation of histone mRNAs is the binding of stem-loop binding protein (SLBP) to the stem-loop structure. Here we provide insight into the mechanism by which SLBP contacts the histone mRNA. There are two binding sites in the SLBP RNA binding domain for the histone mRNA hairpin. The first binding site (Glu129-Val158) consists of a helix-turn-helix motif that likely recognizes the unpaired uridines in the loop of the histone hairpin and, upon binding, destabilizes the first G-C base pair at the base of the stem. The second binding site lies between residues Arg180 and Pro200, which appears to recognize the second G-C base pair from the base of the stem and possibly regions flanking the stem-loop structure. We show that the SLBP-histone mRNA complex is regulated by threonine phosphorylation and proline isomerization in a conserved TPNK sequence that lies between the two binding sites. Threonine phosphorylation increases the affinity of SLBP for histone mRNA by slowing the off rate for complex dissociation, whereas the adjacent proline acts as a critical hinge that may orient the second binding site for formation of a stable SLBP-histone mRNA complex. The nuclear magnetic resonance and kinetic studies presented here provide a framework for understanding how SLBP recognizes histone mRNA and highlight possible structural roles of phosphorylation and proline isomerization in RNA binding proteins in remodeling ribonucleoprotein complexes.
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Affiliation(s)
- Minyou Zhang
- Hauptman-Woodward Medical Research Institute, Buffalo, New York 14203, United States
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6
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Martin F, Barends S, Jaeger S, Schaeffer L, Prongidi-Fix L, Eriani G. Cap-assisted internal initiation of translation of histone H4. Mol Cell 2011; 41:197-209. [PMID: 21255730 DOI: 10.1016/j.molcel.2010.12.019] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 09/08/2010] [Accepted: 11/10/2010] [Indexed: 11/30/2022]
Abstract
In eukaryotes, a crucial step of translation initiation is the binding of the multifactor complex eIF4F to the 5' end of the mRNA, a prerequisite to recruitment of the activated small ribosomal 43S particle. Histone H4 mRNAs have short 5'UTRs, which do not conform to the conventional scanning-initiation model. Here we show that the ORF of histone mRNA contains two structural elements critical for translation initiation. One of the two structures binds eIF4E without the need of the cap. Ribosomal 43S particles become tethered to this site and directly loaded in the vicinity of the AUG. The other structure, 19 nucleotides downstream of the initiation codon, forms a three-way helix junction, which sequesters the m(7)G cap. This element facilitates direct positioning of the ribosome on the cognate start codon. This unusual translation initiation mode might be considered as a hybrid mechanism between the canonical and the IRES-driven translation initiation process.
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Affiliation(s)
- Franck Martin
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg CEDEX, France
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7
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Farber LJ, Kort EJ, Wang P, Chen J, Teh BT. The tumor suppressor parafibromin is required for posttranscriptional processing of histone mRNA. Mol Carcinog 2010; 49:215-23. [PMID: 19908240 DOI: 10.1002/mc.20591] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Parafibromin, encoded by the gene HRPT2, is a tumor suppressor protein associated with the RNA polymerase II-associated complex, Paf1 complex. HRPT2 mutations were first identified in patients with the multiple endocrine neoplasia syndrome, hyperparathyroidism-jaw tumor (HPT-JT) syndrome, and have also been found in sporadic parathyroid and renal tumors. However, the mechanisms by which parafibromin suppresses tumor formation remain unknown. In this study, we identify a novel role of parafibromin in the regulation of replication-dependent histones. Both in vitro and in vivo analyses reveal a posttranscriptional role of parafibromin in histone mRNA processing. Downregulation of parafibromin through RNA interference or in vivo mutations lead to uncleaved histone mRNA with polyadenylated tails. These results indicate that parafibromin regulates the 3' processing of histone RNA, an essential component of the cell cycle.
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Affiliation(s)
- Leslie J Farber
- Laboratory of Cancer Genetics, Van Andel Research Institute, Grand Rapids, Michigan 49503, USA
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8
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Three proteins of the U7-specific Sm ring function as the molecular ruler to determine the site of 3'-end processing in mammalian histone pre-mRNA. Mol Cell Biol 2009; 29:4045-56. [PMID: 19470752 DOI: 10.1128/mcb.00296-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cleavage of histone pre-mRNAs at the 3' end is guided by the U7 snRNP, which is a component of a larger 3'-end processing complex. To identify other components of this complex, we isolated proteins that stably associate with a fragment of histone pre-mRNA containing all necessary processing elements and a biotin affinity tag at the 5' end. Among the isolated proteins, we identified three well-characterized processing factors: the stem-loop binding protein (SLBP), which interacts with the stem-loop structure upstream of the cleavage site, and both Lsm11 and SmB, which are components of the U7-specific Sm ring. We also identified 3'hExo/Eri-1, a multifunctional 3' exonuclease that is known to trim the 3' end of 5.8S rRNA. 3'hExo primarily binds to the downstream portion of the stem-loop structure in mature histone mRNA, with the upstream portion being occupied by SLBP. The two proteins bind their respective RNA sites in a cooperative manner, and 3'hExo can recruit SLBP to a mutant stem-loop that itself does not interact with SLBP. UV-cross-linking studies used to characterize interactions within the processing complex demonstrated that 3'hExo also interacts in a U7-dependent manner with unprocessed histone pre-mRNA. However, this interaction is not required for the cleavage reaction. The region between the cleavage site and the U7-binding site interacts with three low-molecular-weight proteins, which were identified as components of the U7-specific Sm core: SmB, SmD3, and Lsm10. These proteins likely rigidify the substrate and function as the molecular ruler in determining the site of cleavage.
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Zhang W, Poirier L, Diaz MM, Bordignon V, Clarke HJ. Maternally encoded stem-loop-binding protein is degraded in 2-cell mouse embryos by the co-ordinated activity of two separately regulated pathways. Dev Biol 2009; 328:140-7. [PMID: 19298784 DOI: 10.1016/j.ydbio.2009.01.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 01/09/2009] [Accepted: 01/12/2009] [Indexed: 01/05/2023]
Abstract
Oocytes accumulate mRNAs and proteins that direct early embryonic development. Although subsequent development requires the timely degradation of these maternal products, little is known of the underlying mechanisms. The stem-loop-binding protein (SLBP), which regulates the stability and translation of mRNAs encoding histones and is synthesized during S-phase and degraded during G2 in somatic cells, accumulates during oogenesis. Maternal SLBP is required for mouse embryos to develop beyond the 2-cell stage, but must be degraded to allow the cell-cycle-regulated expression of somatic cells to be established. We report that the quantity of maternal SLBP changes little following fertilization until 44-52 h post-hCG, corresponding to mid-/late G2 of the 2-cell stage, when it decreases by 75%. Efficient degradation requires two pathways. The first requires activity of cyclin-dependent kinases (cdk) and embryonic transcription, preferentially targets nuclear SLBP, and likely corresponds to the pathway that degrades SLBP at G2 in somatic cells. The second does not require cdk activity or transcription and becomes active at 44-52 h post-hCG independently of cell-cycle progression to mid-/late G2, but is not solely regulated by the time elapsed since hCG injection. Thus, the co-ordinated activity of two separately regulated pathways eliminates maternally encoded SLBP from early mouse embryos.
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Affiliation(s)
- Wenling Zhang
- Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
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