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Jiang X, Wen J, Paver E, Wu YH, Sun G, Bullman A, Dahlstrom JE, Tremethick DJ, Soboleva TA. H2A.B is a cancer/testis factor involved in the activation of ribosome biogenesis in Hodgkin lymphoma. EMBO Rep 2021; 22:e52462. [PMID: 34350706 DOI: 10.15252/embr.202152462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 12/12/2022] Open
Abstract
Testis-specific regulators of chromatin function are commonly ectopically expressed in human cancers, but their roles are poorly understood. Examination of 81 primary Hodgkin lymphoma (HL) samples showed that the ectopic expression of the eutherian testis-specific histone variant H2A.B is an inherent feature of HL. In experiments using two HL cell lines derived from different subtypes of HL, H2A.B knockdown inhibited cell proliferation. H2A.B was enriched in both nucleoli of these HL cell lines and primary HL samples. We found that H2A.B enhanced ribosomal DNA (rDNA) transcription, was enriched at the rDNA promoter and transcribed regions, and interacted with RNA Pol I. Depletion of H2A.B caused the loss of RNA Pol I from rDNA chromatin. Remarkably, H2A.B was also required for high levels of ribosomal protein gene expression being located at the transcriptional start site and within the gene body. H2A.B knockdown reduced gene body chromatin accessibility of active RNA Pol II genes concurrent with a decrease in transcription. Taken together, our data show that in HL H2A.B has acquired a new function, the ability to increase ribosome biogenesis.
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Affiliation(s)
- Xuanzhao Jiang
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Jiayu Wen
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Elizabeth Paver
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Yu-Huan Wu
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Gege Sun
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Amanda Bullman
- Department of Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra, ACT, Australia
| | - Jane E Dahlstrom
- Department of Anatomical Pathology, ACT Pathology, The Canberra Hospital, Canberra, ACT, Australia.,Australian National University Medical School, The Australian National University, Canberra, ACT, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Tatiana A Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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Gao W, Jones TA, Rivas E. Discovery of 17 conserved structural RNAs in fungi. Nucleic Acids Res 2021; 49:6128-6143. [PMID: 34086938 PMCID: PMC8216456 DOI: 10.1093/nar/gkab355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/25/2021] [Accepted: 04/21/2021] [Indexed: 11/13/2022] Open
Abstract
Many non-coding RNAs with known functions are structurally conserved: their intramolecular secondary and tertiary interactions are maintained across evolutionary time. Consequently, the presence of conserved structure in multiple sequence alignments can be used to identify candidate functional non-coding RNAs. Here, we present a bioinformatics method that couples iterative homology search with covariation analysis to assess whether a genomic region has evidence of conserved RNA structure. We used this method to examine all unannotated regions of five well-studied fungal genomes (Saccharomyces cerevisiae, Candida albicans, Neurospora crassa, Aspergillus fumigatus, and Schizosaccharomyces pombe). We identified 17 novel structurally conserved non-coding RNA candidates, which include four H/ACA box small nucleolar RNAs, four intergenic RNAs and nine RNA structures located within the introns and untranslated regions (UTRs) of mRNAs. For the two structures in the 3' UTRs of the metabolic genes GLY1 and MET13, we performed experiments that provide evidence against them being eukaryotic riboswitches.
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Affiliation(s)
- William Gao
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
| | - Thomas A Jones
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, USA
| | - Elena Rivas
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, USA
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Prakash C, Pandey M, Talwar S, Singh Y, Kanojiya S, Pandey AK, Kumar N. Extra-ribosomal functions of Mtb RpsB in imparting stress resilience and drug tolerance to mycobacteria. Biochimie 2020; 177:87-97. [PMID: 32828823 DOI: 10.1016/j.biochi.2020.08.007] [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: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 01/21/2023]
Abstract
Emerging observations suggest that ribosomal proteins (RPs) play important extra-ribosomal roles in maintenance of cellular homeostasis. However, the mechanistic insights into these processes have not been extensively explored, especially in pathogenic bacteria. Here, we present our findings on potential extra-ribosomal functions of Mycobacterium tuberculosis (Mtb) RPs. We observed that Mtb RpsB and RpsQ are differentially localized to cell wall fraction in M. tuberculosis (H37Rv), while their M. smegmatis (Msm) homologs are primarily cytosolic. Cellular fractionation of ectopically expressed Mtb RPs in surrogate host (M. smegmatis) also shows their association with cell membrane/cell wall without any gross changes in cell morphology. M. smegmatis expressing Mtb RpsB exhibited altered redox homeostasis, decreased drug-induced ROS, reduced cell wall permeability and increased tolerance to various proteotoxic stress (oxidative stress, SDS and starvation). Mtb RpsB expression was also associated with increased resistance specifically towards Isoniazid, Ethionamide and Streptomycin. The enhanced drug tolerance was specific to Mtb RpsB and not observed upon ectopic expression of M. smegmatis homolog (Msm RpsB). Interestingly, C-terminus deletion in Mtb RpsB affected its localization and reversed the stress-resilient phenotypes. We also observed that M. tuberculosis (H37Rv) with upregulated RpsB levels had higher intracellular survival in macrophage. All these observations hint towards existence of moonlighting roles of Mtb RpsB in imparting stress resilience to mycobacteria. This work open avenues for further exploration of alternative pathways associated with fitness and drug tolerance in mycobacteria.
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Affiliation(s)
- Chetan Prakash
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Manitosh Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India; Department of Life Sciences, ITM University, Gwalior 475001, Madhya Pradesh, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yatendra Singh
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Sanjeev Kanojiya
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Amit Kumar Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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Li S, Breaker RR. Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics. BMC Genomics 2017; 18:785. [PMID: 29029611 PMCID: PMC5640933 DOI: 10.1186/s12864-017-4171-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 10/05/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies. RESULTS We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements. CONCLUSIONS Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs. Although initial examinations of several motifs provide evidence for their likely functions, other motifs will require more in-depth analysis to reveal their functions.
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Affiliation(s)
- Sanshu Li
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 China
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103 USA
| | - Ronald R. Breaker
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103 USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103 USA
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Kraushar ML, Popovitchenko T, Volk NL, Rasin MR. The frontier of RNA metamorphosis and ribosome signature in neocortical development. Int J Dev Neurosci 2016; 55:131-139. [PMID: 27241046 PMCID: PMC5124555 DOI: 10.1016/j.ijdevneu.2016.02.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/26/2016] [Accepted: 02/28/2016] [Indexed: 12/14/2022] Open
Abstract
More than a passive effector of gene expression, mRNA translation (protein synthesis) by the ribosome is a rapidly tunable and dynamic molecular mechanism. Neurodevelopmental disorders are associated with abnormalities in mRNA translation, protein synthesis, and neocortical development; yet, we know little about the molecular mechanisms underlying these abnormalities. Furthermore, our understanding of regulation of the ribosome and mRNA translation during normal brain development is only in its early stages. mRNA translation is emerging as a key driver of the rapid and timed regulation of spatiotemporal gene expression in the developing nervous system, including the neocortex. In this review, we focus on the regulatory role of the ribosome in neocortical development, and construct a current understanding of how ribosomal complex specificity may contribute to the development of the neocortex. We also present a microarray analysis of ribosomal protein-coding mRNAs across the neurogenic phase of neocortical development, in addition to the dynamic enrichment of these mRNAs in actively translating neocortical polysomal ribosomes. Understanding the multivariate control of mRNA translation by ribosomal complex specificity will be critical to reveal the intricate mechanisms of normal brain development and pathologies of neurodevelopmental disorders.
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Affiliation(s)
- Matthew L Kraushar
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Tatiana Popovitchenko
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Nicole L Volk
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA.
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Ivanov AV, Malygin AA, Karpova GG. Common features in arrangements of ribosomal protein S26e binding sites on its pre-mRNA and 18S rRNA. Mol Biol 2014. [DOI: 10.1134/s002689331403008x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Graifer D, Malygin A, Zharkov DO, Karpova G. Eukaryotic ribosomal protein S3: A constituent of translational machinery and an extraribosomal player in various cellular processes. Biochimie 2014; 99:8-18. [DOI: 10.1016/j.biochi.2013.11.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/05/2013] [Indexed: 01/26/2023]
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Ivanov AV, Parakhnevitch NM, Malygin AA, Karpova GG. Human ribosomal protein S16 inhibits excision of the first intron from its own pre-mRNA. Mol Biol 2010. [DOI: 10.1134/s0026893310010115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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