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Kim JH, Nagaraja R, Ogurtsov AY, Noskov VN, Liskovykh M, Lee HS, Hori Y, Kobayashi T, Hunter K, Schlessinger D, Kouprina N, Shabalina SA, Larionov V. Comparative analysis and classification of highly divergent mouse rDNA units based on their intergenic spacer (IGS) variability. NAR Genom Bioinform 2024; 6:lqae070. [PMID: 38881577 PMCID: PMC11177557 DOI: 10.1093/nargab/lqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/20/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Ribosomal DNA (rDNA) repeat units are organized into tandem clusters in eukaryotic cells. In mice, these clusters are located on at least eight chromosomes and show extensive variation in the number of repeats between mouse genomes. To analyze intra- and inter-genomic variation of mouse rDNA repeats, we selectively isolated 25 individual rDNA units using Transformation-Associated Recombination (TAR) cloning. Long-read sequencing and subsequent comparative sequence analysis revealed that each full-length unit comprises an intergenic spacer (IGS) and a ∼13.4 kb long transcribed region encoding the three rRNAs, but with substantial variability in rDNA unit size, ranging from ∼35 to ∼46 kb. Within the transcribed regions of rDNA units, we found 209 variants, 70 of which are in external transcribed spacers (ETSs); but the rDNA size differences are driven primarily by IGS size heterogeneity, due to indels containing repetitive elements and some functional signals such as enhancers. Further evolutionary analysis categorized rDNA units into distinct clusters with characteristic IGS lengths; numbers of enhancers; and presence/absence of two common SNPs in promoter regions, one of which is located within promoter (p)RNA and may influence pRNA folding stability. These characteristic features of IGSs also correlated significantly with 5'ETS variant patterns described previously and associated with differential expression of rDNA units. Our results suggest that variant rDNA units are differentially regulated and open a route to investigate the role of rDNA variation on nucleolar formation and possible associations with pathology.
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Affiliation(s)
- Jung-Hyun Kim
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Ramaiah Nagaraja
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Alexey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir N Noskov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Mikhail Liskovykh
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Hee-Sheung Lee
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Yutaro Hori
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Takehiko Kobayashi
- The University of Tokyo, Laboratory of Genome Regeneration, Tokyo 113-0032, Japan
| | - Kent Hunter
- National Cancer Institute, Laboratory of Cancer Biology and Genetics, Bethesda, MD, USA
| | - David Schlessinger
- National Institute of Aging, Laboratory of Genetics and Genomics, Baltimore, MD, USA
| | - Natalay Kouprina
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Vladimir Larionov
- National Cancer Institute, Developmental Therapeutics Branch, Bethesda, MD, USA
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2
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Liskovykh M, Petrov NS, Noskov VN, Masumoto H, Earnshaw WC, Schlessinger D, Shabalina SA, Larionov V, Kouprina N. Actively transcribed rDNA and distal junction (DJ) sequence are involved in association of NORs with nucleoli. Cell Mol Life Sci 2023; 80:121. [PMID: 37043028 PMCID: PMC10097779 DOI: 10.1007/s00018-023-04770-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/13/2023]
Abstract
Although they are organelles without a limiting membrane, nucleoli have an exclusive structure, built upon the rDNA-rich acrocentric short arms of five human chromosomes (nucleolar organizer regions or NORs). This has raised the question: what are the structural features of a chromosome required for its inclusion in a nucleolus? Previous work has suggested that sequences adjacent to the tandemly repeated rDNA repeat units (DJ, distal junction sequence) may be involved, and we have extended such studies by addressing several issues related to the requirements for the association of NORs with nucleoli. We exploited both a set of somatic cell hybrids containing individual human acrocentric chromosomes and a set of Human Artificial Chromosomes (HACs) carrying different parts of a NOR, including an rDNA unit or DJ or PJ (proximal junction) sequence. Association of NORs with nucleoli was increased when constituent rDNA was transcribed and may be also affected by the status of heterochromatin blocks formed next to the rDNA arrays. Furthermore, our data suggest that a relatively small size DJ region, highly conserved in evolution, is also involved, along with the rDNA repeats, in the localization of p-arms of acrocentric chromosomes in nucleoli. Thus, we infer a cooperative action of rDNA sequence-stimulated by its activity-and sequences distal to rDNA contributing to incorporation into nucleoli. Analysis of NOR sequences also identified LncRNA_038958 in the DJ, a candidate transcript with the region of the suggested promoter that is located close to the DJ/rDNA boundary and contains CTCF binding sites. This LncRNA may affect RNA Polymerase I and/or nucleolar activity. Our findings provide the basis for future studies to determine which RNAs and proteins interact critically with NOR sequences to organize the higher-order structure of nucleoli and their function in normal cells and pathological states.
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Affiliation(s)
- Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Nikolai S Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir N Noskov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Hiroshi Masumoto
- Laboratory of Chromosome Engineering, Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, Scotland, UK
| | - David Schlessinger
- National Institute on Aging, Laboratory of Genetics and Genomics, NIH, Baltimore, MD, 21224, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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3
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Liu X, Zang C, Wu Y, Meng R, Chen Y, Jiang T, Wang C, Yang X, Guo Y, Situ C, Hu Z, Zhang J, Guo X. Homeodomain-interacting protein kinase HIPK4 regulates phosphorylation of manchette protein RIMBP3 during spermiogenesis. J Biol Chem 2022; 298:102327. [PMID: 35931115 PMCID: PMC9440445 DOI: 10.1016/j.jbc.2022.102327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
Nonobstructive azoospermia (NOA) is the most serious form of spermatogenesis abnormalities in male infertility. Genetic factors are important to consider as elements leading to NOA. Although many pathogenic genes have been reported, the causative genes of NOA for many patients are still unknown. In this study, we found ten point mutations in the gene encoding homeodomain-interacting protein kinase 4 (HIPK4) in patients with NOA, and using in vitro studies, we determined a premature termination point mutation (p. Lys490∗, c.1468A>T) that can cause decreased expression of HIPK4. Our phosphoproteomic analysis of Hipk4−/− testes revealed phosphorylation of multiple proteins regulated by HIPK4 during spermiogenesis. We also confirmed that a substrate of HIPK4 with four downregulated phosphorylation sites matching the xSPx motif is the known manchette-related protein RIMS-binding protein 3, which is required for sperm head morphogenesis. Therefore, we conclude HIPK4 regulates the phosphorylation of manchette protein RIMS-binding protein 3 and plays essential roles in sperm head shaping and male fertility.
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Affiliation(s)
- Xiaofei Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Chunyan Zang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ru Meng
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Yu Chen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyu Yang
- Center of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China.
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4
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Wooding SP, Ramirez VA, Behrens M. Bitter taste receptors: Genes, evolution and health. Evol Med Public Health 2022; 9:431-447. [PMID: 35154779 PMCID: PMC8830313 DOI: 10.1093/emph/eoab031] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/05/2021] [Indexed: 02/01/2023] Open
Abstract
Bitter taste perception plays vital roles in animal behavior and fitness. By signaling the presence of toxins in foods, particularly noxious defense compounds found in plants, it enables animals to avoid exposure. In vertebrates, bitter perception is initiated by TAS2Rs, a family of G protein-coupled receptors expressed on the surface of taste buds. There, oriented toward the interior of the mouth, they monitor the contents of foods, drinks and other substances as they are ingested. When bitter compounds are encountered, TAS2Rs respond by triggering neural pathways leading to sensation. The importance of this role placed TAS2Rs under selective pressures in the course of their evolution, leaving signatures in patterns of gene gain and loss, sequence polymorphism, and population structure consistent with vertebrates' diverse feeding ecologies. The protective value of bitter taste is reduced in modern humans because contemporary food supplies are safe and abundant. However, this is not always the case. Some crops, particularly in the developing world, retain surprisingly high toxicity and bitterness remains an important measure of safety. Bitter perception also shapes health through its influence on preference driven behaviors such as diet choice, alcohol intake and tobacco use. Further, allelic variation in TAS2Rs is extensive, leading to individual differences in taste sensitivity that drive these behaviors, shaping susceptibility to disease. Thus, bitter taste perception occupies a critical intersection between ancient evolutionary processes and modern human health.
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Affiliation(s)
- Stephen P Wooding
- Department of Anthropology and Health Sciences Research Institute, University of California, Merced, CA, USA
| | - Vicente A Ramirez
- Department of Public Health, University of California, Merced, CA, USA
| | - Maik Behrens
- Maik Behrens, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
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5
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Piltonen M, Krokhotin A, Parisien M, Bérubé P, Djambazian H, Sladek R, Dokholyan NV, Shabalina SA, Diatchenko L. Alternative Splicing of Opioid Receptor Genes Shows a Conserved Pattern for 6TM Receptor Variants. Cell Mol Neurobiol 2021; 41:1039-1055. [PMID: 33010019 PMCID: PMC8159799 DOI: 10.1007/s10571-020-00971-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/23/2020] [Indexed: 11/18/2022]
Abstract
The opioid receptor (OPR) family comprises the mu-, delta-, and kappa-opioid, and nociceptin receptors that belong to the superfamily of 7-transmembrane spanning G protein-coupled receptors (GPCRs). The mu-opioid receptor is the main target for clinically used opioid analgesics, and its biology has been extensively studied. The N-terminally truncated 6TM receptors isoform produced through alternative splicing of the OPRM1 gene displays unique signaling and analgesic properties, but it is unclear if other OPRs have the same ability. In this study, we have built a comprehensive map of alternative splicing events that produce 6TM receptor variants in all the OPRs and demonstrated their evolutionary conservation. We then obtained evidence for their translation through ribosomal footprint analysis. We discovered that N-terminally truncated 6TM GPCRs are rare in the human genome and OPRs are overrepresented in this group. Finally, we also observed a significant enrichment of 6TM GPCR genes among genes associated with pain, psychiatric disorders, and addiction. Understanding the biology of 6TM receptors and leveraging this knowledge for drug development should pave the way for novel therapies.
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Affiliation(s)
- Marjo Piltonen
- School of Dentistry, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
- Department of Anesthesia, School of Medicine, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
| | - Andrey Krokhotin
- Departments of Pathology, Genetics and Developmental Biology, Stanford Medical School, Howard Hughes Medical Institute, Palo Alto, CA, 94305, USA
| | - Marc Parisien
- School of Dentistry, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
- Department of Anesthesia, School of Medicine, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
- Alan Edwards Centre for Research on Pain, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada
| | - Pierre Bérubé
- Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
| | - Haig Djambazian
- Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, H3A 0G1, Canada
| | - Rob Sladek
- Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, Quebec, H3A 0G1, Canada
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, H3A 0G1, Canada
| | - Nikolay V Dokholyan
- Departments of Pharmacology, and Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA
- Departments of Chemistry, and Biomedical Engineering, Penn State, University Park, PA, 16802, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, Room S604, 8600 Rockville Pike MSC 3830, Bethesda, MD, 20894-6075, USA.
| | - Luda Diatchenko
- School of Dentistry, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada.
- Department of Anesthesia, School of Medicine, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada.
- Alan Edwards Centre for Research on Pain, McGill University, Genome Building, Room 2201, 740 Dr. Penfield Avenue, Montreal, Quebec, H3A 0G1, Canada.
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6
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Auslander N, Wolf YI, Shabalina SA, Koonin EV. A unique insert in the genomes of high-risk human papillomaviruses with a predicted dual role in conferring oncogenic risk. F1000Res 2019; 8:1000. [PMID: 31448109 PMCID: PMC6685453 DOI: 10.12688/f1000research.19590.2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/17/2019] [Indexed: 12/12/2022] Open
Abstract
The differences between high risk and low risk human papillomaviruses (HR-HPV and LR-HPV, respectively) that contribute to the tumorigenic potential of HR-HPV are not well understood but can be expected to involve the HPV oncoproteins, E6 and E7. We combine genome comparison and machine learning techniques to identify a previously unnoticed insert near the 3’-end of the E6 oncoprotein gene that is unique to HR-HPV. Analysis of the insert sequence suggests that it exerts a dual effect, by creating a PDZ domain-binding motif at the C-terminus of E6, as well as eliminating the overlap between the E6 and E7 coding regions in HR-HPV. We show that, as a result, the insert might enable coupled termination-reinitiation of the E6 and E7 genes, supported by motifs complementary to the human 18S rRNA. We hypothesize that the added functionality of E6 and positive regulation of E7 expression jointly account for the tumorigenic potential of HR-HPV.
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Affiliation(s)
- Noam Auslander
- National Center for Biotechnology Information, National Institutes of Health, USA, Bethesda, Maryland, 20814, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Institutes of Health, USA, Bethesda, Maryland, 20814, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Institutes of Health, USA, Bethesda, Maryland, 20814, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Institutes of Health, USA, Bethesda, Maryland, 20814, USA
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7
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Ameri M, Aghakhani K, Memarian A, Ameri E. Epidemiology of sport trauma: a prospective study. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2018. [DOI: 10.23736/s0393-3660.18.03685-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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8
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Alternative Splicing of the Delta-Opioid Receptor Gene Suggests Existence of New Functional Isoforms. Mol Neurobiol 2018; 56:2855-2869. [PMID: 30066306 DOI: 10.1007/s12035-018-1253-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/17/2018] [Indexed: 12/26/2022]
Abstract
The delta-opioid receptor (DOPr) participates in mediating the effects of opioid analgesics. However, no selective agonists have entered clinical care despite potential to ameliorate many neurological and psychiatric disorders. In an effort to address the drug development challenges, the functional contribution of receptor isoforms created by alternative splicing of the three-exonic coding gene, OPRD1, has been overlooked. We report that the gene is transcriptionally more diverse than previously demonstrated, producing novel protein isoforms in humans and mice. We provide support for the functional relevance of splice variants through context-dependent expression profiling (tissues, disease model) and conservation of the transcriptional landscape in closely related vertebrates. The conserved alternative transcriptional events have two distinct patterns. First, cassette exon inclusions between exons 1 and 2 interrupt the reading frame, producing truncated receptor fragments comprising only the first transmembrane (TM) domain, despite the lack of exact exon orthologues between distant species. Second, a novel promoter and transcriptional start site upstream of exon 2 produces a transcript of an N-terminally truncated 6TM isoform. However, a fundamental difference in the exonic landscaping as well as translation and translation products poses limits for modelling the human DOPr receptor system in mice.
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9
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Matveeva OV, Ogurtsov AY, Nazipova NN, Shabalina SA. Sequence characteristics define trade-offs between on-target and genome-wide off-target hybridization of oligoprobes. PLoS One 2018; 13:e0199162. [PMID: 29928000 PMCID: PMC6013149 DOI: 10.1371/journal.pone.0199162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/02/2018] [Indexed: 12/20/2022] Open
Abstract
Off-target oligoprobe's interaction with partially complementary nucleotide sequences represents a problem for many bio-techniques. The goal of the study was to identify oligoprobe sequence characteristics that control the ratio between on-target and off-target hybridization. To understand the complex interplay between specific and genome-wide off-target (cross-hybridization) signals, we analyzed a database derived from genomic comparison hybridization experiments performed with an Affymetrix tiling array. The database included two types of probes with signals derived from (i) a combination of specific signal and cross-hybridization and (ii) genomic cross-hybridization only. All probes from the database were grouped into bins according to their sequence characteristics, where both hybridization signals were averaged separately. For selection of specific probes, we analyzed the following sequence characteristics: vulnerability to self-folding, nucleotide composition bias, numbers of G nucleotides and GGG-blocks, and occurrence of probe's k-mers in the human genome. Increases in bin ranges for these characteristics are simultaneously accompanied by a decrease in hybridization specificity-the ratio between specific and cross-hybridization signals. However, both averaged hybridization signals exhibit growing trends along with an increase of probes' binding energy, where the hybridization specific signal increases significantly faster in comparison to the cross-hybridization. The same trend is evident for the S function, which serves as a combined evaluation of probe binding energy and occurrence of probe's k-mers in the genome. Application of S allows extracting a larger number of specific probes, as compared to using only binding energy. Thus, we showed that high values of specific and cross-hybridization signals are not mutually exclusive for probes with high values of binding energy and S. In this study, the application of a new set of sequence characteristics allows detection of probes that are highly specific to their targets for array design and other bio-techniques that require selection of specific probes.
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Affiliation(s)
- Olga V. Matveeva
- Biopolymer Design LLC, Acton, Massachusetts, United States of America
- * E-mail: (OVM); (SAS)
| | - Aleksey Y. Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nafisa N. Nazipova
- Institute of Mathematical Problems of Biology, RAS – the Branch of Keldysh Institute of Applied Mathematics of Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Svetlana A. Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (OVM); (SAS)
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10
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Andisheh-Tadbir A, Ashraf MJ, Jeiroodi N. Expression of CDK6 in Oral Squamous Cell Carcinomas. Asian Pac J Cancer Prev 2018; 19:1013-1016. [PMID: 29693970 PMCID: PMC6031802 DOI: 10.22034/apjcp.2018.19.4.1013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: CDK6 is the key factor in regulation of the cell cycle and essential for passage into the G1 phase. It
also plays an important role in the development of various tumors. In this cross-sectional study expression of the CDK6
protein in oral squamous cell carcinoma (OSCC) and healthy oral mucosa of controls was assessed to determine relations
with malignant transformation and clinicopathologic factors. Method: A total of 60 samples, 45 from OSCCs and 15
from healthy tissue, underwent immunohistochemistry for CDK6. Nuclear and cytoplasmic staining of keratinocytes
was considered as positive and the percentages of positive cells were calculated. Results: Expression of CDK6 was
detected in 55.6% of OSCC samples (25 cases) and 13.3% of controls (2 cases), the difference being significant. Mean
percentage of CDK6 stained cells was 24.2±29.3 in the OSCC cases and 4.33±2.1 in the control group, again statistically
significant. No relationship was detected between CDK6 expression and clinicopathologic factors. Conclusion:
Overexpression of CDK6 observed in OSCC points to a role for this protein in oral carcinogenesis.
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Affiliation(s)
- Azadeh Andisheh-Tadbir
- Oral and Dental Disease Research Center, Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, Shiraz University of Medical Sciences, Shiraz, Iran.
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11
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Kaushik K, Sivadas A, Vellarikkal SK, Verma A, Jayarajan R, Pandey S, Sethi T, Maiti S, Scaria V, Sivasubbu S. RNA secondary structure profiling in zebrafish reveals unique regulatory features. BMC Genomics 2018; 19:147. [PMID: 29448945 PMCID: PMC5815192 DOI: 10.1186/s12864-018-4497-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 01/28/2018] [Indexed: 01/08/2023] Open
Abstract
Background RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure. Results We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented. We identified RNA secondary structural features embedded in functional units of zebrafish mRNAs. Translation start and stop sites were demarcated by weak structural signals. The coding regions were characterized by the three-nucleotide periodicity of secondary structure and display a codon base specific structural constrain. The splice sites of transcripts were also delineated by distinct signature signals. Relatively higher structural signals were observed at 3’ Untranslated Regions (UTRs) compared to Coding DNA Sequence (CDS) and 5’ UTRs. The 3′ ends of transcripts were also marked by unique structure signals. Secondary structural signals in long non-coding RNAs were also explored to better understand their molecular function. Conclusions Our study presents the first PARS-enabled transcriptome-wide secondary structure map of zebrafish, which documents pairing probability of RNA at single nucleotide precision. Our findings open avenues for exploring structural features in zebrafish RNAs and their influence on gene expression. Electronic supplementary material The online version of this article (10.1186/s12864-018-4497-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kriti Kaushik
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ambily Sivadas
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Satyaprakash Pandey
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Tavprithesh Sethi
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Souvik Maiti
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Vinod Scaria
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
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12
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Matveeva OV, Nechipurenko YD, Riabenko E, Ragan C, Nazipova NN, Ogurtsov AY, Shabalina SA. Optimization of signal-to-noise ratio for efficient microarray probe design. Bioinformatics 2017; 32:i552-i558. [PMID: 27587674 DOI: 10.1093/bioinformatics/btw451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Target-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis. RESULTS In this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization. A microarray database, derived from the Genomic Comparison Hybridization (GCH) experiment and performed using the Affymetrix platform, contains two different types of probes. The first type of oligo-probes does not have a specific target on the genome and their hybridization signals are derived from genome-wide cross-hybridization alone. The second type includes oligonucleotides that have a specific target on the genomic DNA and their signals are derived from specific and cross-hybridization components combined together in a total signal. A comparative analysis of hybridization specificity of oligo-probes, as well as their nucleotide sequences and thermodynamic features was performed on the database. The comparison has revealed that hybridization specificity was negatively affected by low stability of the fully-paired oligo-target duplex, stable probe self-folding, G-rich content, including GGG motifs, low sequence complexity and nucleotide composition symmetry. CONCLUSION Filtering out the probes with defined 'negative' characteristics significantly increases specific hybridization and dramatically decreasing genome-wide cross-hybridization. Selected oligo-probes have two times higher hybridization specificity on average, compared to the probes that were filtered from the analysis by applying suggested cutoff thresholds to the described parameters. A new approach for efficient oligo-probe design is described in our study. CONTACT shabalin@ncbi.nlm.nih.gov or olga.matveeva@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Olga V Matveeva
- Biopolymer Design LLC, Acton, MA 01721, USA Engelhardt Institute of Molecular Biology, Moscow 119991, Russia
| | | | - Evgeniy Riabenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Chikako Ragan
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Nafisa N Nazipova
- Institute of Mathematical Problems of Biology, Pushchino, Moscow Region, 142290, Russia
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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13
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Shabalina SA, Ogurtsov AY, Spiridonov NA, Koonin EV. Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals. Nucleic Acids Res 2014; 42:7132-44. [PMID: 24792168 PMCID: PMC4066770 DOI: 10.1093/nar/gku342] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Alternative splicing (AS), alternative transcription initiation (ATI) and alternative transcription termination (ATT) create the extraordinary complexity of transcriptomes and make key contributions to the structural and functional diversity of mammalian proteomes. Analysis of mammalian genomic and transcriptomic data shows that contrary to the traditional view, the joint contribution of ATI and ATT to the transcriptome and proteome diversity is quantitatively greater than the contribution of AS. Although the mean numbers of protein-coding constitutive and alternative nucleotides in gene loci are nearly identical, their distribution along the transcripts is highly non-uniform. On average, coding exons in the variable 5' and 3' transcript ends that are created by ATI and ATT contain approximately four times more alternative nucleotides than core protein-coding regions that diversify exclusively via AS. Short upstream exons that encompass alternative 5'-untranslated regions and N-termini of proteins evolve under strong nucleotide-level selection whereas in 3'-terminal exons that encode protein C-termini, protein-level selection is significantly stronger. The groups of genes that are subject to ATI and ATT show major differences in biological roles, expression and selection patterns.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
| | - Nikolay A Spiridonov
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, US Food and Drug Administration, Bethesda, MD 20892, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
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14
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Jha KN, Coleman AR, Wong L, Salicioni AM, Howcroft E, Johnson GR. Heat shock protein 90 functions to stabilize and activate the testis-specific serine/threonine kinases, a family of kinases essential for male fertility. J Biol Chem 2013; 288:16308-16320. [PMID: 23599433 DOI: 10.1074/jbc.m112.400978] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Spermiogenesis is characterized by a profound morphological differentiation of the haploid spermatid into spermatozoa. The testis-specific serine/threonine kinases (TSSKs) comprise a family of post-meiotic kinases expressed in spermatids, are critical to spermiogenesis, and are required for male fertility in mammals. To explore the role of heat shock protein 90 (HSP90) in regulation of TSSKs, the stability and catalytic activity of epitope-tagged murine TSSKs were assessed in 293T and COS-7 cells. TSSK1, -2, -4, and -6 (small serine/threonine kinase) were all found to associate with HSP90, and pharmacological inhibition of HSP90 function using the highly specific drugs 17-AAG, SNX-5422, or NVP-AUY922 reduced TSSK protein levels in cells. The attenuation of HSP90 function abolished the catalytic activities of TSSK4 and -6 but did not significantly alter the specific activities of TSSK1 and -2. Inhibition of HSP90 resulted in increased TSSK ubiquitination and proteasomal degradation, indicating that HSP90 acts to control ubiquitin-mediated catabolism of the TSSKs. To study HSP90 and TSSKs in germ cells, a mouse primary spermatid culture model was developed and characterized. Using specific antibodies against murine TSSK2 and -6, it was demonstrated that HSP90 inhibition resulted in a marked decrease of the endogenous kinases in spermatids. Together, our findings demonstrate that HSP90 plays a broad and critical role in stabilization and activation of the TSSK family of protein kinases.
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Affiliation(s)
- Kula N Jha
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892.
| | - Alyssa R Coleman
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Lily Wong
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Ana M Salicioni
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts 01003
| | - Elizabeth Howcroft
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Gibbes R Johnson
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892.
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15
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Shabalina SA, Spiridonov NA, Kashina A. Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res 2013; 41:2073-94. [PMID: 23293005 PMCID: PMC3575835 DOI: 10.1093/nar/gks1205] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA.
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16
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Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV. Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol Evol 2011; 3:1390-404. [PMID: 22071789 PMCID: PMC3242500 DOI: 10.1093/gbe/evr116] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mammalian genomes contain numerous genes for long noncoding RNAs (lncRNAs). The functions of the lncRNAs remain largely unknown but their evolution appears to be constrained by purifying selection, albeit relatively weakly. To gain insights into the mode of evolution and the functional range of the lncRNA, they can be compared with much better characterized protein-coding genes. The evolutionary rate of the protein-coding genes shows a universal negative correlation with expression: highly expressed genes are on average more conserved during evolution than the genes with lower expression levels. This correlation was conceptualized in the misfolding-driven protein evolution hypothesis according to which misfolding is the principal cost incurred by protein expression. We sought to determine whether long intergenic ncRNAs (lincRNAs) follow the same evolutionary trend and indeed detected a moderate but statistically significant negative correlation between the evolutionary rate and expression level of human and mouse lincRNA genes. The magnitude of the correlation for the lincRNAs is similar to that for equal-sized sets of protein-coding genes with similar levels of sequence conservation. Additionally, the expression level of the lincRNAs is significantly and positively correlated with the predicted extent of lincRNA molecule folding (base-pairing), however, the contributions of evolutionary rates and folding to the expression level are independent. Thus, the anticorrelation between evolutionary rate and expression level appears to be a general feature of gene evolution that might be caused by similar deleterious effects of protein and RNA misfolding and/or other factors, for example, the number of interacting partners of the gene product.
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Affiliation(s)
- David Managadze
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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17
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Shabalina SA, Spiridonov AN, Spiridonov NA, Koonin EV. Connections between alternative transcription and alternative splicing in mammals. Genome Biol Evol 2010; 2:791-9. [PMID: 20889654 PMCID: PMC2975443 DOI: 10.1093/gbe/evq058] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The majority of mammalian genes produce multiple transcripts resulting from alternative splicing (AS) and/or alternative transcription initiation (ATI) and alternative transcription termination (ATT). Comparative analysis of the number of alternative nucleotides, isoforms, and introns per locus in genes with different types of alternative events suggests that ATI and ATT contribute to the diversity of human and mouse transcriptome even more than AS. There is a strong negative correlation between AS and ATI in 5′ untranslated regions (UTRs) and AS in coding sequences (CDSs) but an even stronger positive correlation between AS in CDSs and ATT in 3′ UTRs. These observations could reflect preferential regulation of distinct, large groups of genes by different mechanisms: 1) regulation at the level of transcription initiation and initiation of translation resulting from ATI and AS in 5′ UTRs and 2) posttranslational regulation by different protein isoforms. The tight linkage between AS in CDSs and ATT in 3′ UTRs suggests that variability of 3′ UTRs mediates differential translational regulation of alternative protein forms. Together, the results imply coordinate evolution of AS and alternative transcription, processes that occur concomitantly within gene expression factories.
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Affiliation(s)
- Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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18
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Jha KN, Wong L, Zerfas PM, De Silva RS, Fan YX, Spiridonov NA, Johnson GR. Identification of a novel HSP70-binding cochaperone critical to HSP90-mediated activation of small serine/threonine kinase. J Biol Chem 2010; 285:35180-7. [PMID: 20829357 DOI: 10.1074/jbc.m110.134767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We previously reported the identification of small serine/threonine kinase (SSTK) that is expressed in postmeiotic germ cells, associates with HSP90, and is indispensable for male fertility. Sperm from SSTK-null mice cannot fertilize eggs in vitro and are incapable of fusing with eggs that lack zona pellucida. Here, using the yeast two-hybrid screen, we have discovered a novel SSTK-interacting protein (SIP) that is expressed exclusively in testis. The gene encoding SIP is restricted to mammals and encodes a 125-amino acid polypeptide with a predicted tetratricopeptide repeat domain. SIP is co-localized with SSTK in the cytoplasm of spermatids as they undergo restructuring and chromatin condensation, but unlike SSTK, is not retained in the mature sperm. SIP binds to SSTK with high affinity (K(d) ∼10 nM), and the proteins associate with each other when co-expressed in cells. In vitro, SIP inhibited SSTK kinase activity, whereas the presence of SIP in cells resulted in enzymatic activation of SSTK without affecting Akt or MAPK activity. SIP was found to be associated with cellular HSP70, and analyses with purified proteins revealed that SIP directly bound HSP70. Importantly, SSTK recruited SIP onto HSP90, and treatment of cells with the specific HSP90 inhibitor, 17-allylamino-17-demethoxygeldanamycin, completely abolished SSTK catalytic activity. Hence, these findings demonstrate that HSP90 is essential for functional maturation of the kinase and identify SIP as a cochaperone that is critical to the HSP90-mediated activation of SSTK.
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Affiliation(s)
- Kula N Jha
- Laboratory of Chemistry, Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892, USA
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Shabalina SA, Ogurtsov AY, Spiridonov AN, Novichkov PS, Spiridonov NA, Koonin EV. Distinct patterns of expression and evolution of intronless and intron-containing mammalian genes. Mol Biol Evol 2010; 27:1745-9. [PMID: 20360214 PMCID: PMC2908711 DOI: 10.1093/molbev/msq086] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Comparison of expression levels and breadth and evolutionary rates of intronless and intron-containing mammalian genes shows that intronless genes are expressed at lower levels, tend to be tissue specific, and evolve significantly faster than spliced genes. By contrast, monomorphic spliced genes that are not subject to detectable alternative splicing and polymorphic alternatively spliced genes show similar statistically indistinguishable patterns of expression and evolution. Alternative splicing is most common in ancient genes, whereas intronless genes appear to have relatively recent origins. These results imply tight coupling between different stages of gene expression, in particular, transcription, splicing, and nucleocytosolic transport of transcripts, and suggest that formation of intronless genes is an important route of evolution of novel tissue-specific functions in animals.
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Affiliation(s)
- Svetlana A. Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
- Corresponding author: E-mail: ;
| | - Aleksey Y. Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
| | | | | | - Nikolay A. Spiridonov
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, US Food and Drug Administration, Bethesda, MD
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
- Corresponding author: E-mail: ;
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Resch AM, Ogurtsov AY, Rogozin IB, Shabalina SA, Koonin EV. Evolution of alternative and constitutive regions of mammalian 5'UTRs. BMC Genomics 2009; 10:162. [PMID: 19371439 PMCID: PMC2674463 DOI: 10.1186/1471-2164-10-162] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2009] [Accepted: 04/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) in protein-coding sequences has emerged as an important mechanism of regulation and diversification of animal gene function. By contrast, the extent and roles of alternative events including AS and alternative transcription initiation (ATI) within the 5'-untranslated regions (5'UTRs) of mammalian genes are not well characterized. RESULTS We evaluated the abundance, conservation and evolution of putative regulatory control elements, namely, upstream start codons (uAUGs) and open reading frames (uORFs), in the 5'UTRs of human and mouse genes impacted by alternative events. For genes with alternative 5'UTRs, the fraction of alternative sequences (those present in a subset of the transcripts) is much greater than that in the corresponding coding sequence, conceivably, because 5'UTRs are not bound by constraints on protein structure that limit AS in coding regions. Alternative regions of mammalian 5'UTRs evolve faster and are subject to a weaker purifying selection than constitutive portions. This relatively weak selection results in over-abundance of uAUGs and uORFs in the alternative regions of 5'UTRs compared to constitutive regions. Nevertheless, even in alternative regions, uORFs evolve under a stronger selection than the rest of the sequences, indicating that some of the uORFs are conserved regulatory elements; some of the non-conserved uORFs could be involved in species-specific regulation. CONCLUSION The findings on the evolution and selection in alternative and constitutive regions presented here are consistent with the hypothesis that alternative events, namely, AS and ATI, in 5'UTRs of mammalian genes are likely to contribute to the regulation of translation.
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Affiliation(s)
- Alissa M Resch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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