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Cecalev D, Viçoso B, Galupa R. Compensation of gene dosage on the mammalian X. Development 2024; 151:dev202891. [PMID: 39140247 PMCID: PMC11361640 DOI: 10.1242/dev.202891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show 'natural' differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species.
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Affiliation(s)
- Daniela Cecalev
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Beatriz Viçoso
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Rafael Galupa
- Molecular, Cellular and Developmental Biology (MCD) Unit, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062, Toulouse, France
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2
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Wang Z, Wang Y, Zhou T, Chen S, Morris D, Magalhães RDM, Li M, Wang S, Wang H, Xie Y, McSwiggin H, Oliver D, Yuan S, Zheng H, Mohammed J, Lai EC, McCarrey JR, Yan W. The rapidly evolving X-linked MIR-506 family fine-tunes spermatogenesis to enhance sperm competition. eLife 2024; 13:RP90203. [PMID: 38639482 PMCID: PMC11031087 DOI: 10.7554/elife.90203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Despite rapid evolution across eutherian mammals, the X-linked MIR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (SLITRK2 and FMR1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked MIR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernible defects, but simultaneous ablation of five clusters containing 19 members of the MIR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility, and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked MIR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the MIR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.
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Affiliation(s)
- Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Sheng Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Dayton Morris
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | | | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Shawn Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Hetan Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Jaaved Mohammed
- Developmental Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San AntonioSan AntonioUnited States
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
- Department of Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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3
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Wang Y, Tang X, Lu J. Convergent and divergent evolution of microRNA-mediated regulation in metazoans. Biol Rev Camb Philos Soc 2024; 99:525-545. [PMID: 37987240 DOI: 10.1111/brv.13033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.
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Affiliation(s)
- Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha, 410082, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing, 100871, China
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4
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Geleta U, Prajapati P, Bachstetter A, Nelson PT, Wang WX. Sex-Biased Expression and Response of microRNAs in Neurological Diseases and Neurotrauma. Int J Mol Sci 2024; 25:2648. [PMID: 38473893 PMCID: PMC10931569 DOI: 10.3390/ijms25052648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Neurological diseases and neurotrauma manifest significant sex differences in prevalence, progression, outcome, and therapeutic responses. Genetic predisposition, sex hormones, inflammation, and environmental exposures are among many physiological and pathological factors that impact the sex disparity in neurological diseases. MicroRNAs (miRNAs) are a powerful class of gene expression regulator that are extensively involved in mediating biological pathways. Emerging evidence demonstrates that miRNAs play a crucial role in the sex dimorphism observed in various human diseases, including neurological diseases. Understanding the sex differences in miRNA expression and response is believed to have important implications for assessing the risk of neurological disease, defining therapeutic intervention strategies, and advancing both basic research and clinical investigations. However, there is limited research exploring the extent to which miRNAs contribute to the sex disparities observed in various neurological diseases. Here, we review the current state of knowledge related to the sexual dimorphism in miRNAs in neurological diseases and neurotrauma research. We also discuss how sex chromosomes may contribute to the miRNA sexual dimorphism phenomenon. We attempt to emphasize the significance of sexual dimorphism in miRNA biology in human diseases and to advocate a gender/sex-balanced science.
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Affiliation(s)
- Urim Geleta
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Paresh Prajapati
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
| | - Adam Bachstetter
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Neuroscience, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging, College of Medicine, University of Kentucky, Lexington, KY 40536, USA; (U.G.); (P.P.); (A.B.); (P.T.N.)
- Spinal Cord and Brain Injury Research Center, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
- Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
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5
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Wang Z, Wang Y, Zhou T, Chen S, Morris D, Magalhães RDM, Li M, Wang S, Wang H, Xie Y, McSwiggin H, Oliver D, Yuan S, Zheng H, Mohammed J, Lai EC, McCarrey JR, Yan W. The Rapidly Evolving X-linked miR-506 Family Finetunes Spermatogenesis to Enhance Sperm Competition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.14.544876. [PMID: 37398484 PMCID: PMC10312769 DOI: 10.1101/2023.06.14.544876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite rapid evolution across eutherian mammals, the X-linked miR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (Slitrk2 and Fmr1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked miR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernable defects, but simultaneous ablation of five clusters containing nineteen members of the miR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked miR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the miR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.
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Affiliation(s)
- Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Sheng Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Dayton Morris
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | | | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shawn Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hetan Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jaaved Mohammed
- Department of Developmental Biology, Memorial Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Eric C. Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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6
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Mönttinen HAM, Frilander MJ, Löytynoja A. Generation of de novo miRNAs from template switching during DNA replication. Proc Natl Acad Sci U S A 2023; 120:e2310752120. [PMID: 38019864 PMCID: PMC10710096 DOI: 10.1073/pnas.2310752120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
The mechanisms generating novel genes and genetic information are poorly known, even for microRNA (miRNA) genes with an extremely constrained design. All miRNA primary transcripts need to fold into a stem-loop structure to yield short gene products ([Formula: see text]22 nt) that bind and repress their mRNA targets. While a substantial number of miRNA genes are ancient and highly conserved, short secondary structures coding for entirely novel miRNA genes have been shown to emerge in a lineage-specific manner. Template switching is a DNA-replication-related mutation mechanism that can introduce complex changes and generate perfect base pairing for entire hairpin structures in a single event. Here, we show that the template-switching mutations (TSMs) have participated in the emergence of over 6,000 suitable hairpin structures in the primate lineage to yield at least 18 new human miRNA genes, that is 26% of the miRNAs inferred to have arisen since the origin of primates. While the mechanism appears random, the TSM-generated miRNAs are enriched in introns where they can be expressed with their host genes. The high frequency of TSM events provides raw material for evolution. Being orders of magnitude faster than other mechanisms proposed for de novo creation of genes, TSM-generated miRNAs enable near-instant rewiring of genetic information and rapid adaptation to changing environments.
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Affiliation(s)
- Heli A. M. Mönttinen
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
| | - Mikko J. Frilander
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, HelsinkiFI-000, Finland
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Zabihi MR, Norouzkhani N, Karkhah S, Akhoondian M. Identification of a valuable gene network for the diagnosis and treatment of non-obstructive azoospermia: in-silico analyses - experimental research. Ann Med Surg (Lond) 2023; 85:5941-5951. [PMID: 38098601 PMCID: PMC10718319 DOI: 10.1097/ms9.0000000000001358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 09/17/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Non-obstructive azoospermia (NOA) is an etiology of infertility in men. NOA may have various classifications; however, hypogonadotropic hypogonadism can be regarded as a class of NOA associated with genetic factors. Former studies have shown that noncoding RNA (ncRNA) plays an essential role in NOA incidence, but few studies have been performed on the NOA-related ncRNA interaction network. In the current study, genes, NOA-related microRNA (miRNA), and circular RNA (circRNA) were found by bioinformatics methods to offer a new perspective on NOA treatment. Methods The gonadotropin-releasing hormone receptor (GnRHR)-related protein-protein interaction (PPI) network was extracted by searching in 'string-database'. GO, KEGG, and Enrichr databases were used to identify pathways, molecular function, and biological processing. Four databases, including TargetScan, mirDIP, miRmap, and miRWalk, were used to extract miRNAs. At last, the circ2GO, circBase, and literature were used to identify circRNAs and their genes. Results The current study identified the four proteins associated with the GnRHR signaling; eight shared miRNAs that affect the expression of found proteins and 25 circRNAs and their origin genes that regulate the miRNAs' function. Conclusion The two miRNAs, hsa-miR-134-3p and hsa-miR-513C-3p, the three genes, VCAN, NFATC3, and PRDM5, and their associated circRNAs can perform as a valuable gene network in the diagnosis and treatment of NOA pathogenesis.
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Affiliation(s)
- Mohammad Reza Zabihi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran
| | - Narges Norouzkhani
- Department of Medical Informatics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad
| | - Samad Karkhah
- Department of Medical-Surgical Nursing, School of Nursing and Midwifery
- Burn and Regenerative Medicine Research Center
| | - Mohammad Akhoondian
- Department of Physiology, School of Medicine, Cellular and The Molecular Research Center, Guilan University of Medical Science, Rasht, Iran
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8
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Voss G, Rosenthal JJC. High-level RNA editing diversifies the coleoid cephalopod brain proteome. Brief Funct Genomics 2023; 22:525-532. [PMID: 37981860 DOI: 10.1093/bfgp/elad034] [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: 06/11/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 11/21/2023] Open
Abstract
Coleoid cephalopods (octopus, squid and cuttlefish) have unusually complex nervous systems. The coleoid nervous system is also the only one currently known to recode the majority of expressed proteins through A-to-I RNA editing. The deamination of adenosine by adenosine deaminase acting on RNA (ADAR) enzymes produces inosine, which is interpreted as guanosine during translation. If this occurs in an open reading frame, which is the case for tens of thousands of editing sites in coleoids, it can recode the encoded protein. Here, we describe recent findings aimed at deciphering the mechanisms underlying high-level recoding and its adaptive potential. We describe the complement of ADAR enzymes in cephalopods, including a recently discovered novel domain in sqADAR1. We further summarize current evidence supporting an adaptive role of high-level RNA recoding in coleoids, and review recent studies showing that a large proportion of recoding sites is temperature-sensitive. Despite these new findings, the mechanisms governing the high level of RNA recoding in coleoid cephalopods remain poorly understood. Recent advances using genome editing in squid may provide useful tools to further study A-to-I RNA editing in these animals.
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Affiliation(s)
- Gjendine Voss
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, 7 MBL Street, Woods Hole MA 02543, United States
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Regmi R, Newman TE, Khentry Y, Kamphuis LG, Derbyshire MC. Genome-wide identification of Sclerotinia sclerotiorum small RNAs and their endogenous targets. BMC Genomics 2023; 24:582. [PMID: 37784009 PMCID: PMC10544508 DOI: 10.1186/s12864-023-09686-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Several phytopathogens produce small non-coding RNAs of approximately 18-30 nucleotides (nt) which post-transcriptionally regulate gene expression. Commonly called small RNAs (sRNAs), these small molecules were also reported to be present in the necrotrophic pathogen Sclerotinia sclerotiorum. S. sclerotiorum causes diseases in more than 400 plant species, including the important oilseed crop Brassica napus. sRNAs can further be classified as microRNAs (miRNAs) and short interfering RNAs (siRNAs). Certain miRNAs can activate loci that produce further sRNAs; these secondary sRNA-producing loci are called 'phased siRNA' (PHAS) loci and have only been described in plants. To date, very few studies have characterized sRNAs and their endogenous targets in S. sclerotiorum. RESULTS We used Illumina sequencing to characterize sRNAs from fungal mycelial mats of S. sclerotiorum spread over B. napus leaves. In total, eight sRNA libraries were prepared from in vitro, 12 h post-inoculation (HPI), and 24 HPI mycelial mat samples. Cluster analysis identified 354 abundant sRNA clusters with reads of more than 100 Reads Per Million (RPM). Differential expression analysis revealed upregulation of 34 and 57 loci at 12 and 24 HPI, respectively, in comparison to in vitro samples. Among these, 25 loci were commonly upregulated. Altogether, 343 endogenous targets were identified from the major RNAs of 25 loci. Almost 88% of these targets were annotated as repeat element genes, while the remaining targets were non-repeat element genes. Fungal degradome reads confirmed cleavage of two transposable elements by one upregulated sRNA. Altogether, 24 milRNA loci were predicted with both mature and milRNA* (star) sequences; these are both criteria associated previously with experimentally verified miRNAs. Degradome sequencing data confirmed the cleavage of 14 targets. These targets were related to repeat element genes, phosphate acetyltransferases, RNA-binding factor, and exchange factor. A PHAS gene prediction tool identified 26 possible phased interfering loci with 147 phasiRNAs from the S. sclerotiorum genome, suggesting this pathogen might produce sRNAs that function similarly to miRNAs in higher eukaryotes. CONCLUSIONS Our results provide new insights into sRNA populations and add a new resource for the study of sRNAs in S. sclerotiorum.
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Affiliation(s)
- Roshan Regmi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
- Present address: Microbiome for One Systems Health, CSIRO, Urrbrae, South Australia, Australia
| | - Toby E Newman
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Floreat, WA, 6014, Australia
| | - Mark C Derbyshire
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102, Australia.
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10
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Li Z, Duan Y, Yan S, Zhang Y, Wu Y. The miR-302/367 cluster: Aging, inflammation, and cancer. Cell Biochem Funct 2023; 41:752-766. [PMID: 37555645 DOI: 10.1002/cbf.3836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 07/25/2023] [Indexed: 08/10/2023]
Abstract
MicroRNAs (miRNAs) are a class of noncoding RNAs that occupy a significant role in biological processes as important regulators of intracellular homeostasis. First, we will discuss the biological genesis and functions of the miR-302/367 cluster, including miR-302a, miR-302b, miR-302c, miR-302d, and miR-367, as well as their roles in physiologically healthy tissues. The second section of this study reviews the progress of the miR-302/367 cluster in the treatment of cancer, inflammation, and diseases associated with aging. This cluster's aberrant expression in cells and/or tissues exhibits similar or different effects in various diseases through molecular mechanisms such as proliferation, apoptosis, cycling, drug resistance, and invasion. This article also discusses the upstream and downstream regulatory networks of miR-302/367 clusters and their related mechanisms. Particularly because studies on the upstream regulatory molecules of miR-302/367 clusters, which include age-related macular degeneration, myocardial infarction, and cancer, have become more prevalent in recent years. MiR-302/367 cluster can be an important therapeutic target and the use of miRNAs in combination with other molecular markers may improve diagnostic or therapeutic capabilities, providing unique insights and a more dynamic view of various diseases. It is noted that miRNAs can be an important bio-diagnostic target and offer a promising method for illness diagnosis, prevention, and treatment.
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Affiliation(s)
- Zhou Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yan Duan
- Department of Stomatology, Shanxi Provincial People's Hospital, Taiyuan, Shanxi Province, China
| | - Shaofu Yan
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yao Zhang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
| | - Yunxia Wu
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi Province, China
- Department of Stomatology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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11
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Wu Y, Weng Z, Yan H, Yao Z, Li Z, Sun Y, Ma K, Hull JJ, Zhang D, Ma W, Hua H, Lin Y. The microRNA-7322-5p/p38/Hsp19 axis modulates Chilo suppressalis cell-defences against Cry1Ca: an effective target for a stacked transgenic rice approach. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1827-1838. [PMID: 37353991 PMCID: PMC10440986 DOI: 10.1111/pbi.14095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/08/2023] [Accepted: 05/16/2023] [Indexed: 06/25/2023]
Abstract
Bacillus thuringiensis (Bt)-secreted crystal (Cry) toxins form oligomeric pores in host cell membranes and are a common element in generating insect-resistant transgenic crops. Although Cry toxin function has been well documented, cellular defences against pore-formation have not been as well developed. Elucidation of the processes underlying this defence, however, could contribute to the development of enhanced Bt crops. Here, we demonstrate that Cry1Ca-mediated downregulation of microRNA-7322-5p (miR-7322-5p), which binds to the 3' untranslated region of p38, negatively regulates the susceptibility of Chilo suppressalis to Cry1Ca. Moreover, Cry1Ca exposure enhanced phosphorylation of Hsp19, and hsp19 downregulation increased susceptibility to Cry1Ca. Further, Hsp19 phosphorylation occurs downstream of p38, and pull-down assays confirmed the interactions between Hsp19 and Cry1Ca, suggesting that activation of Hsp19 by the miR-7322-5p/p38/Hsp19 pathway promotes Cry1Ca sequestration. To assess the efficacy of targeting this pathway in planta, double-stranded RNA (dsRNA) targeting C. suppressalis p38 (dsp38) was introduced into a previously generated cry1Ca-expressing rice line (1CH1-2) to yield a single-copy cry1Ca/dsp38 rice line (p38-rice). Feeding on this rice line triggered a significant reduction in C. suppressalis p38 expression and the line was more resistant to C. suppressalis than 1CH1-2 in both short term (7-day) and continuous feeding bioassays as well as field trials. These findings provide new insights into invertebrate epithelium cellular defences and demonstrate a potential new pyramiding strategy for Bt crops.
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Affiliation(s)
- Yan Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zijin Weng
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Haixia Yan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhuotian Yao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Zhenzhen Li
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yajie Sun
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Kangsheng Ma
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - J. Joe Hull
- U.S. Arid Land Agricultural Research Center, Department of AgricultureU.S. Agricultural Research ServiceMaricopaArizonaUSA
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hongxia Hua
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubeiChina
- College of Life Science and TechnologyHuazhong Agricultural UniversityWuhanHubeiChina
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12
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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13
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Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023; 51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still no comprehensive picture of how miRNAs and their associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline for the targeted search of miRNA orthologs in unannotated genome sequences. ncOrtho matches miRNA annotations from multi-tissue transcriptomes in precision, while scaling to the analysis of hundreds of custom-selected species. The presence-absence pattern of orthologs to 266 human miRNA families across 402 vertebrate species reveals four bursts of miRNA acquisition, of which the most recent event occurred in the last common ancestor of higher primates. miRNA families are rarely modified or lost, but notable exceptions for both events exist. miRNA co-ortholog numbers faithfully indicate lineage-specific whole genome duplications, and miRNAs are powerful markers for phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable to resolve clades where the phylogenetic signal is blurred by incomplete lineage sorting of ancestral alleles. In summary, ncOrtho allows to routinely consider miRNAs in evolutionary analyses that were thus far reserved to protein-coding genes.
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Affiliation(s)
- Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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14
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Kumar P, Courtes M, Lemmers C, Le Digarcher A, Coku I, Monteil A, Hong C, Varrault A, Liu R, Wang L, Bouschet T. Functional mapping of microRNA promoters with dCas9 fused to transcriptional regulators. Front Genet 2023; 14:1147222. [PMID: 37214422 PMCID: PMC10196145 DOI: 10.3389/fgene.2023.1147222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
MicroRNAs are small non-coding RNAs that control gene expression during development, physiology, and disease. Transcription is a key factor in microRNA abundance and tissue-specific expression. Many databases predict the location of microRNA transcription start sites and promoters. However, these candidate regions require functional validation. Here, dCas9 fused to transcriptional activators or repressors - CRISPR activation (CRISPRa) and inhibition (CRISPRi)- were targeted to the candidate promoters of two intronic microRNAs, mmu-miR-335 and hsa-miR-3662, including the promoters of their respective host genes Mest and HBS1L. We report that in mouse embryonic stem cells and brain organoids, miR-335 was downregulated upon CRISPRi of its host gene Mest. Reciprocally, CRISPRa of Mest promoter upregulated miR-335. By contrast, CRISPRa of the predicted miR-335-specific promoter (located in an intron of Mest) did not affect miR-335 levels. Thus, the expression of miR-335 only depends on the promoter activity of its host gene Mest. By contrast, miR-3662 was CRISPR activatable both by the promoter of its host gene HBS1L and an intronic sequence in HEK-293T cells. Thus, CRISPRa and CRISPRi are powerful tools to evaluate the relevance of endogenous regulatory sequences involved in microRNA transcription in defined cell types.
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Affiliation(s)
- Pradeep Kumar
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Mathilde Courtes
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Céline Lemmers
- Plateforme de Vectorologie de Montpellier (PVM), BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Anne Le Digarcher
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Ilda Coku
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Arnaud Monteil
- Plateforme de Vectorologie de Montpellier (PVM), BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Charles Hong
- Vanderbilt University School of Medicine Nashville, Nashville, TN, United States
| | - Annie Varrault
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Runhua Liu
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Lizhong Wang
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
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15
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Son S, Kim B, Yang J, Kim VN. Role of the proline-rich disordered domain of DROSHA in intronic microRNA processing. Genes Dev 2023; 37:383-397. [PMID: 37236670 PMCID: PMC10270192 DOI: 10.1101/gad.350275.122] [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: 11/22/2022] [Accepted: 04/24/2023] [Indexed: 05/28/2023]
Abstract
DROSHA serves as a gatekeeper of the microRNA (miRNA) pathway by processing primary transcripts (pri-miRNAs). While the functions of structured domains of DROSHA have been well documented, the contribution of N-terminal proline-rich disordered domain (PRD) remains elusive. Here we show that the PRD promotes the processing of miRNA hairpins located within introns. We identified a DROSHA isoform (p140) lacking the PRD, which is produced by proteolytic cleavage. Small RNA sequencing revealed that p140 is significantly impaired in the maturation of intronic miRNAs. Consistently, our minigene constructs demonstrated that PRD enhances the processing of intronic hairpins, but not those in exons. Splice site mutations did not affect the PRD's enhancing effect on intronic constructs, suggesting that the PRD acts independently of splicing reaction by interacting with sequences residing within introns. The N-terminal regions from zebrafish and Xenopus DROSHA can replace the human counterpart, indicating functional conservation despite poor sequence alignment. Moreover, we found that rapidly evolving intronic miRNAs are generally more dependent on PRD than conserved ones, suggesting a role of PRD in miRNA evolution. Our study reveals a new layer of miRNA regulation mediated by a low-complexity disordered domain that senses the genomic contexts of miRNA loci.
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Affiliation(s)
- Soomin Son
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Baekgyu Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea;
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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16
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Niu H, Pang Y, Xie L, Yu Q, Shen Y, Li J, Xu X. Clustering pattern and evolution characteristic of microRNAs in grass carp (Ctenopharyngodon idella). BMC Genomics 2023; 24:73. [PMID: 36782132 PMCID: PMC9926789 DOI: 10.1186/s12864-023-09159-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND A considerable fraction of microRNAs (miRNAs) are highly conserved, and certain miRNAs correspond to genomic clusters. The clustering of miRNAs can be advantageous, possibly by allowing coordinated expression. However, little is known about the evolutionary forces responsible for the loss and acquisition of miRNA and miRNA clusters. RESULTS The results demonstrated that several novel miRNAs arose throughout grass carp evolution. Duplication and de novo production were critical strategies for miRNA cluster formation. Duplicates accounted for a smaller fraction of the expansion in the grass carp miRNA than de novo creation. Clustered miRNAs are more conserved and change slower, whereas unique miRNAs usually have high evolution rates and low expression levels. The expression level of miRNA expression in clusters is strongly correlated. CONCLUSIONS This study examines the genomic distribution, evolutionary background, and expression regulation of grass carp miRNAs. Our findings provide novel insights into the genesis and development of miRNA clusters in teleost.
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Affiliation(s)
- Huiqin Niu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yifan Pang
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Lingli Xie
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Qiaozhen Yu
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Yubang Shen
- grid.412514.70000 0000 9833 2433Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China ,grid.412514.70000 0000 9833 2433Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
| | - Xiaoyan Xu
- Key Laboratory of Freshwater Aquatic Genetic Resources Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, China. .,National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China. .,Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai, China.
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17
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Murat F, Mbengue N, Winge SB, Trefzer T, Leushkin E, Sepp M, Cardoso-Moreira M, Schmidt J, Schneider C, Mößinger K, Brüning T, Lamanna F, Belles MR, Conrad C, Kondova I, Bontrop R, Behr R, Khaitovich P, Pääbo S, Marques-Bonet T, Grützner F, Almstrup K, Schierup MH, Kaessmann H. The molecular evolution of spermatogenesis across mammals. Nature 2023; 613:308-316. [PMID: 36544022 PMCID: PMC9834047 DOI: 10.1038/s41586-022-05547-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022]
Abstract
The testis produces gametes through spermatogenesis and evolves rapidly at both the morphological and molecular level in mammals1-6, probably owing to the evolutionary pressure on males to be reproductively successful7. However, the molecular evolution of individual spermatogenic cell types across mammals remains largely uncharacterized. Here we report evolutionary analyses of single-nucleus transcriptome data for testes from 11 species that cover the three main mammalian lineages (eutherians, marsupials and monotremes) and birds (the evolutionary outgroup), and include seven primates. We find that the rapid evolution of the testis was driven by accelerated fixation rates of gene expression changes, amino acid substitutions and new genes in late spermatogenic stages, probably facilitated by reduced pleiotropic constraints, haploid selection and transcriptionally permissive chromatin. We identify temporal expression changes of individual genes across species and conserved expression programs controlling ancestral spermatogenic processes. Genes predominantly expressed in spermatogonia (germ cells fuelling spermatogenesis) and Sertoli (somatic support) cells accumulated on X chromosomes during evolution, presumably owing to male-beneficial selective forces. Further work identified transcriptomal differences between X- and Y-bearing spermatids and uncovered that meiotic sex-chromosome inactivation (MSCI) also occurs in monotremes and hence is common to mammalian sex-chromosome systems. Thus, the mechanism of meiotic silencing of unsynapsed chromatin, which underlies MSCI, is an ancestral mammalian feature. Our study illuminates the molecular evolution of spermatogenesis and associated selective forces, and provides a resource for investigating the biology of the testis across mammals.
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Affiliation(s)
- Florent Murat
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany. .,INRAE, LPGP, Rennes, France.
| | - Noe Mbengue
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
| | - Sofia Boeg Winge
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Timo Trefzer
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Mari Sepp
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Julia Schmidt
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Celine Schneider
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Katharina Mößinger
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Thoomke Brüning
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Francesco Lamanna
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | | | - Christian Conrad
- Berlin Institute of Health at Charité, University of Medicine Berlin, Corporate Member of the Free University of Berlin, Humboldt-University of Berlin, Berlin, Germany
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, the Netherlands
| | - Rüdiger Behr
- German Primate Center (DPZ), Platform Degenerative Diseases, Göttingen, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Miquel Crusafont Catalan Institute of Paleontology, Autonomous University of Barcelona, Barcelona, Spain
| | - Frank Grützner
- The Robinson Research Institute, School of Biological Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Henrik Kaessmann
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.
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18
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Structural and functional basis of mammalian microRNA biogenesis by Dicer. Mol Cell 2022; 82:4064-4079.e13. [DOI: 10.1016/j.molcel.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/21/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022]
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19
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First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species. Genes (Basel) 2022; 13:genes13091569. [PMID: 36140737 PMCID: PMC9498476 DOI: 10.3390/genes13091569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/22/2022] Open
Abstract
The extant reptiles are one of the most diverse clades among terrestrial vertebrates and one of a few groups with instances of parthenogenesis. Due to the hybrid origin of parthenogenetic species, reference genomes of the parental species as well as of the parthenogenetic progeny are indispensable to explore the genetic foundations of parthenogenetic reproduction. Here, we report on the first genome assembly of rock lizard Darevskia valentini, a paternal species for several parthenogenetic lineages. The novel genome was used in the reconstruction of the comprehensive phylogeny of Squamata inferred independently from 7369 trees of single-copy orthologs and a supermatrix of 378 conserved proteins. We also investigated Hox clusters, the loci that are often regarded as playing an important role in the speciation of animal groups with drastically diverse morphology. We demonstrated that Hox clusters of D. valentini are invaded with transposons and contain the HoxC1 gene that has been considered to be lost in the amniote ancestor. This study provides confirmation for previous works and releases new genomic data that will contribute to future discoveries on the mechanisms of parthenogenesis as well as support comparative studies among reptiles.
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20
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Abstract
"De novo" genes evolve from previously non-genic DNA. This strikes many of us as remarkable, because it seems extraordinarily unlikely that random sequence would produce a functional gene. How is this possible? In this two-part review, I first summarize what is known about the origins and molecular functions of the small number of de novo genes for which such information is available. I then speculate on what these examples may tell us about how de novo genes manage to emerge despite what seem like enormous opposing odds.
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Affiliation(s)
- Caroline M Weisman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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21
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Tomasello U, Klingler E, Niquille M, Mule N, Santinha AJ, de Vevey L, Prados J, Platt RJ, Borrell V, Jabaudon D, Dayer A. miR-137 and miR-122, two outer subventricular zone non-coding RNAs, regulate basal progenitor expansion and neuronal differentiation. Cell Rep 2022; 38:110381. [PMID: 35172154 PMCID: PMC8864305 DOI: 10.1016/j.celrep.2022.110381] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/22/2021] [Accepted: 01/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cortical expansion in primate brains relies on enlargement of germinal zones during a prolonged developmental period. Although most mammals have two cortical germinal zones, the ventricular zone (VZ) and subventricular zone (SVZ), gyrencephalic species display an additional germinal zone, the outer subventricular zone (oSVZ), which increases the number and diversity of neurons generated during corticogenesis. How the oSVZ emerged during evolution is poorly understood, but recent studies suggest a role for non-coding RNAs, which allow tight genetic program regulation during development. Here, using in vivo functional genetics, single-cell RNA sequencing, live imaging, and electrophysiology to assess progenitor and neuronal properties in mice, we identify two oSVZ-expressed microRNAs (miRNAs), miR-137 and miR-122, which regulate key cellular features of cortical expansion. miR-137 promotes basal progenitor self-replication and superficial layer neuron fate, whereas miR-122 decreases the pace of neuronal differentiation. These findings support a cell-type-specific role of miRNA-mediated gene expression in cortical expansion. oSVZ-expressed microRNAs 137 and 122 promote superficial layer identity of neurons miR-137 promotes basal progenitor proliferation and layer 2/3 neuron generation miR-122 slows down neuronal differentiation pace
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Affiliation(s)
- Ugo Tomasello
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, 03550 Alacant, Spain
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Mathieu Niquille
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Nandkishor Mule
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Antonio J Santinha
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Laura de Vevey
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland
| | - Julien Prados
- Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Victor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, 03550 Alacant, Spain
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Clinic of Neurology, Geneva University Hospital, 1205 Geneva, Switzerland.
| | - Alexandre Dayer
- Department of Basic Neurosciences, University of Geneva, 1205 Geneva, Switzerland; Department of Psychiatry, Geneva University Hospital, 1205 Geneva, Switzerland
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22
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Cheuquemán C, Maldonado R. Non-coding RNAs and chromatin: key epigenetic factors from spermatogenesis to transgenerational inheritance. Biol Res 2021; 54:41. [PMID: 34930477 PMCID: PMC8686607 DOI: 10.1186/s40659-021-00364-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/07/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular fate and gene expression patterns are modulated by different epigenetic factors including non-coding RNAs (ncRNAs) and chromatin organization. Both factors are dynamic throughout male germ cell differentiation on the seminiferous tubule, despite the transcriptional inactivation in the last stages of spermatogenesis. Sperm maturation during the caput-to-cauda transit on the epididymis involves changes in chromatin organization and the soma-to-germ line transference of ncRNAs that are essential to obtain a functional sperm for fertilization and embryo development. Here, the male environment (diseases, drugs, mental stress) is crucial to modulate these epigenetic factors throughout sperm maturation, affecting the corresponding offspring. Paternal transgenerational inheritance has been directly related to sperm epigenetic changes, most of them associated with variations in the ncRNA content and chromatin marks. Our aim is to give an overview about how epigenetics, focused on ncRNAs and chromatin, is pivotal to understand spermatogenesis and sperm maturation, and how the male environment impacts the sperm epigenome modulating the offspring gene expression pattern.
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Affiliation(s)
- Carolina Cheuquemán
- Núcleo de Ciencias Biológicas, Dirección de Núcleos Transversales, Facultad de estudios Interdisciplinarios, Universidad Mayor, Temuco, Chile
| | - Rodrigo Maldonado
- Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.
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23
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Demystifying the long noncoding RNA landscape of small EVs derived from human mesenchymal stromal cells. J Adv Res 2021; 39:73-88. [PMID: 35777918 PMCID: PMC9263655 DOI: 10.1016/j.jare.2021.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/01/2021] [Accepted: 11/07/2021] [Indexed: 11/24/2022] Open
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24
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Stitz M, Chaparro C, Lu Z, Olzog VJ, Weinberg CE, Blom J, Goesmann A, Grunau C, Grevelding CG. Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni. Genome Biol Evol 2021; 13:6361599. [PMID: 34469545 PMCID: PMC8490949 DOI: 10.1093/gbe/evab204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2021] [Indexed: 12/17/2022] Open
Abstract
A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. We investigated satellite-DNA elements of the platyhelminth Schistosoma mansoni, a parasite with remarkable biological features. Schistosoma mansoni lives in the vasculature of humans causing schistosomiasis, a disease of worldwide importance. Schistosomes are the only trematodes that have evolved separate sexes, and the sexual maturation of the female depends on constant pairing with the male. The schistosome karyotype comprises eight chromosome pairs, males are homogametic (ZZ) and females are heterogametic (ZW). Part of the repetitive DNA of S. mansoni are W-elements (WEs), originally discovered as female-specific satellite DNAs in the heterochromatic block of the W-chromosome. Based on new genome and transcriptome data, we performed a reanalysis of the W-element families (WEFs). Besides a new classification of 19 WEFs, we provide first evidence for stage-, sex-, pairing-, gonad-, and strain-specific/preferential transcription of WEs as well as their mobile nature, deduced from autosomal copies of full-length and partial WEs. Structural analyses suggested roles as sources of noncoding RNA-like hammerhead ribozymes, for which we obtained functional evidence. Finally, the variable WEF occurrence in different schistosome species revealed remarkable divergence. From these results, we propose that WEs potentially exert enduring influence on the biology of S. mansoni. Their variable occurrence in different strains, isolates, and species suggests that schistosome WEs may represent genetic factors taking effect on variability and evolution of the family Schistosomatidae.
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Affiliation(s)
- Maria Stitz
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | - Cristian Chaparro
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
| | - Zhigang Lu
- Institute of Parasitology, BFS, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | - Christoph Grunau
- IHPE, CNRS, IFREMER, UPVD, University Montpellier, Perpignan, France
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25
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Evolution and Phylogeny of MicroRNAs - Protocols, Pitfalls, and Problems. Methods Mol Biol 2021. [PMID: 34432281 DOI: 10.1007/978-1-0716-1170-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.
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26
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Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. Clustering genomic organization of sea cucumber miRNAs impacts their evolution and expression. Genomics 2021; 113:3544-3555. [PMID: 34371099 DOI: 10.1016/j.ygeno.2021.08.003] [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: 10/12/2020] [Revised: 07/08/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
Echinoderms are marine deuterostomes with fascinating adaptation features such as aestivation and organ regeneration. However, post-transcriptional gene regulation by microRNAs (miRNAs) underlying these features are largely unexplored. Here, using homology-based and de novo approaches supported by expression data, we provided a comprehensive annotation of miRNA genes in the sea cucumber Apostichopus japonicus. By linkage and phylogenic analyses, we characterized miRNA genomic organization, evolutionary history and expression regulation. The results showed that sea cucumbers evolved a large number of new miRNAs, which tended to form polycistronic clusters via tandem duplication that had been especially active in the echinoderms. Most new miRNAs were weakly expressed, but miRNA clustering increased the expression level of clustered new miRNAs. The most abundantly expressed new miRNAs were organized in a single tandem cluster (cluster n2), which was activated during aestivation and intestine regeneration. Overall, our analyses suggest that clustering of miRNAs is important for their evolutionary origin, expression control, and functional cooperation.
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Affiliation(s)
- Chengzhang Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jianbo Yuan
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaojun Zhang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Songjun Jin
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Fuhua Li
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jianhai Xiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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27
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Desvignes T, Sydes J, Montfort J, Bobe J, Postlethwait JH. Evolution after Whole-Genome Duplication: Teleost MicroRNAs. Mol Biol Evol 2021; 38:3308-3331. [PMID: 33871629 PMCID: PMC8321539 DOI: 10.1093/molbev/msab105] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene expression regulators implicated in many biological processes, but we lack a global understanding of how miRNA genes evolve and contribute to developmental canalization and phenotypic diversification. Whole-genome duplication events likely provide a substrate for species divergence and phenotypic change by increasing gene numbers and relaxing evolutionary pressures. To understand the consequences of genome duplication on miRNA evolution, we studied miRNA genes following the teleost genome duplication (TGD). Analysis of miRNA genes in four teleosts and in spotted gar, whose lineage diverged before the TGD, revealed that miRNA genes were retained in ohnologous pairs more frequently than protein-coding genes, and that gene losses occurred rapidly after the TGD. Genomic context influenced retention rates, with clustered miRNA genes retained more often than nonclustered miRNA genes and intergenic miRNA genes retained more frequently than intragenic miRNA genes, which often shared the evolutionary fate of their protein-coding host. Expression analyses revealed both conserved and divergent expression patterns across species in line with miRNA functions in phenotypic canalization and diversification, respectively. Finally, major strands of miRNA genes experienced stronger purifying selection, especially in their seeds and 3'-complementary regions, compared with minor strands, which nonetheless also displayed evolutionary features compatible with constrained function. This study provides the first genome-wide, multispecies analysis of the mechanisms influencing metazoan miRNA evolution after whole-genome duplication.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Jason Sydes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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28
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Jin L, Tang Q, Hu S, Chen Z, Zhou X, Zeng B, Wang Y, He M, Li Y, Gui L, Shen L, Long K, Ma J, Wang X, Chen Z, Jiang Y, Tang G, Zhu L, Liu F, Zhang B, Huang Z, Li G, Li D, Gladyshev VN, Yin J, Gu Y, Li X, Li M. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription. Nat Commun 2021; 12:3715. [PMID: 34140474 PMCID: PMC8211698 DOI: 10.1038/s41467-021-23560-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits. A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.
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Affiliation(s)
- Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Xuming Zhou
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuhao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan, China
| | - Linyuan Shen
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhengli Chen
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yanzhi Jiang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Guoqing Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Fei Liu
- Information and Educational Technology Center, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Zhang
- Ya'an Digital Economy Operation Company, Ya'an, Sichuan, China
| | - Zhiqing Huang
- Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guisen Li
- Renal Department and Nephrology Institute, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingdong Yin
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
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29
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Kumar S, Ashraf MU, Kumar A, Bae YS. Therapeutic Potential of microRNA Against Th2-associated Immune Disorders. Curr Top Med Chem 2021; 21:753-766. [PMID: 33655864 DOI: 10.2174/1568026621666210303150235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/17/2020] [Accepted: 11/28/2020] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are short ~18-22 nucleotide, single-stranded, non-coding RNA molecules playing a crucial role in regulating diverse biological processes and are frequently dysregulated during disease pathogenesis. Thus, targeting miRNA could be a potential candidate for therapeutic invention. This systemic review aims to summarize our current understanding regarding the role of miRNAs associated with Th2-mediated immune disorders and strategies for therapeutic drug development and current clinical trials.
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Affiliation(s)
- Sunil Kumar
- Department of Biological Sciences, Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do 16419, South Korea
| | - Muhammad Umer Ashraf
- Department of Biological Sciences, Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do 16419, South Korea
| | - Anil Kumar
- Amity Institute of Biotechnology, Amity University Haryana, Amity Education Valley, Gurugram-122413, India
| | - Yong-Soo Bae
- Department of Biological Sciences, Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon, Gyeonggi-do 16419, South Korea
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30
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Abstract
Hundreds of microRNAs (miRNAs) are expressed in distinct spatial and temporal patterns during embryonic and postnatal mouse development. The loss of all miRNAs through the deletion of critical miRNA biogenesis factors results in early lethality. The function of each miRNA stems from their cumulative negative regulation of multiple mRNA targets expressed in a particular cell type. During development, miRNAs often coordinate the timing and direction of cell fate transitions. In adults, miRNAs frequently contribute to organismal fitness through homeostatic roles in physiology. Here, we review how the recent dissection of miRNA-knockout phenotypes in mice as well as advances related to their targets, dosage, and interactions have collectively informed our understanding of the roles of miRNAs in mammalian development and adaptive responses.
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31
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Ma X, He K, Shi Z, Li M, Li F, Chen XX. Large-Scale Annotation and Evolution Analysis of MiRNA in Insects. Genome Biol Evol 2021; 13:6255746. [PMID: 33905491 PMCID: PMC8126727 DOI: 10.1093/gbe/evab083] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/22/2022] Open
Abstract
Insects are among the most diverse and successful groups of animals and exhibit great morphological diversity and complexity. The innovation of wings and metamorphosis are some examples of the fascinating biological evolution of insects. Most microRNAs (miRNAs) contribute to canalization by conferring robustness to gene networks and thus increase the heritability of important phenotypes. Though previous studies have demonstrated how miRNAs regulate important phenotypes, little is still known about miRNA evolution in insects. Here, we used both small RNA-seq data and homology searching methods to annotate the miRNA repertoires of 152 arthropod species, including 135 insects and 17 noninsect arthropods. We identified 16,212 miRNA genes, and classified them into highly conserved (62), insect-conserved (90), and lineage-specific (354) miRNA families. The phylogenetic relationship of miRNA binary presence/absence dynamics implies that homoplastic loss of conserved miRNA families tends to occur in far-related morphologically simplified taxa, including scale insects (Coccoidea) and twisted-wing insects (Strepsiptera), leading to inconsistent phylogenetic tree reconstruction. The common ancestor of Insecta shares 62 conserved miRNA families, of which five were rapidly gained in the early winged-insects (Pterygota). We also detected extensive miRNA losses in Paraneoptera that are correlated with morphological reduction, and miRNA gains in early Endopterygota around the time holometabolous metamorphosis appeared. This was followed by abundant miRNA gains in Hymenoptera and Lepidoptera. In summary, we provide a comprehensive data set and a detailed evolutionary analysis of miRNAs in insects. These data will be important for future studies on miRNA functions associated with insect morphological innovation and trait biodiversity.
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Affiliation(s)
- Xingzhou Ma
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Plant Protection, Nanjing Agricultural University, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmin Shi
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Meizhen Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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32
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Zhao Y, Lu GA, Yang H, Lin P, Liufu Z, Tang T, Xu J. Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. Mol Biol Evol 2021; 38:1544-1553. [PMID: 33306129 PMCID: PMC8042761 DOI: 10.1093/molbev/msaa317] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Red Queen hypothesis depicts evolution as the continual struggle to adapt. According to this hypothesis, new genes, especially those originating from nongenic sequences (i.e., de novo genes), are eliminated unless they evolve continually in adaptation to a changing environment. Here, we analyze two Drosophila de novo miRNAs that are expressed in a testis-specific manner with very high rates of evolution in their DNA sequence. We knocked out these miRNAs in two sibling species and investigated their contributions to different fitness components. We observed that the fitness contributions of miR-975 in Drosophila simulans seem positive, in contrast to its neutral contributions in D. melanogaster, whereas miR-983 appears to have negative contributions in both species, as the fitness of the knockout mutant increases. As predicted by the Red Queen hypothesis, the fitness difference of these de novo miRNAs indicates their different fates.
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Affiliation(s)
- Yixin Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guang-An Lu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Hao Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Pei Lin
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhongqi Liufu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Jin Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, China
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33
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Nachtigall PG, Bovolenta LA, Patton JG, Fromm B, Lemke N, Pinhal D. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics 2021; 22:153. [PMID: 33663371 PMCID: PMC7931589 DOI: 10.1186/s12864-021-07441-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency, blood pressure, and cardiac output volume. Despite these differences, the heart developmental process is guided by a core gene set conserved across vertebrates. Nonetheless, the regulatory mechanisms controlling the expression of genes involved in heart development and maintenance are largely uncharted. MicroRNAs (miRNAs) have been described as important regulatory elements in several biological processes, including heart biology. These small RNA molecules are broadly conserved in sequence and genomic context in metazoans. Mutations may occur in miRNAs and/or genes that contribute to the establishment of distinct repertoires of miRNA-target interactions, thereby favoring the differential control of gene expression and, consequently, the origin of novel phenotypes. In fact, several studies showed that miRNAs are integrated into genetic regulatory networks (GRNs) governing specific developmental programs and diseases. However, studies integrating miRNAs in vertebrate heart GRNs under an evolutionary perspective are still scarce. RESULTS We comprehensively examined and compared the heart miRNome of 20 species representatives of the five major vertebrate groups. We found 54 miRNA families with conserved expression and a variable number of miRNA families with group-specific expression in fishes, amphibians, reptiles, birds, and mammals. We also detected that conserved miRNAs present higher expression levels and a higher number of targets, whereas the group-specific miRNAs present lower expression levels and few targets. CONCLUSIONS Both the conserved and group-specific miRNAs can be considered modulators orchestrating the core and peripheral genes of heart GRNs of vertebrates, which can be related to the morphophysiological differences and similarities existing in the heart of distinct vertebrate groups. We propose a hypothesis to explain evolutionary differences in the putative functional roles of miRNAs in the heart GRNs analyzed. Furthermore, we present new insights into the molecular mechanisms that could be helping modulate the diversity of morphophysiology in the heart organ of vertebrate species.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório Especial de Toxinologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, Brazil. .,Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University, Stockholm, Sweden
| | - Ney Lemke
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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34
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Ray A, Kunhiraman H, Perera RJ. The Paradoxical Behavior of microRNA-211 in Melanomas and Other Human Cancers. Front Oncol 2021; 10:628367. [PMID: 33628737 PMCID: PMC7897698 DOI: 10.3389/fonc.2020.628367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 12/21/2020] [Indexed: 01/27/2023] Open
Abstract
Cancer initiation, progression, and metastasis leverage many regulatory agents, such as signaling molecules, transcription factors, and regulatory RNA molecules. Among these, regulatory non-coding RNAs have emerged as molecules that control multiple cancer types and their pathologic properties. The human microRNA-211 (MIR211) is one such molecule, which affects several cancer types, including melanoma, glioblastoma, lung adenocarcinomas, breast, ovarian, prostate, and colorectal carcinoma. Previous studies suggested that in certain tumors MIR211 acts as a tumor suppressor while in others it behaves as an oncogenic regulator. Here we summarize the known molecular genetic mechanisms that regulate MIR211 gene expression and molecular pathways that are in turn controlled by MIR211 itself. We discuss how cellular and epigenetic contexts modulate the biological effects of MIR211, which exhibit pleiotropic effects. For example, up-regulation of MIR211 expression down-regulates Warburg effect in melanoma tumor cells associated with an inhibition of the growth of human melanoma cells in vitro, and yet these conditions robustly increase tumor growth in xenografted mice. Signaling through the DUSP6-ERK5 pathway is modulated by MIR211 in BRAFV600E driven melanoma tumors, and this function is involved in the resistance of tumor cells to the BRAF inhibitor, Vemurafenib. We discuss several alternate but testable models, involving stochastic cell-to-cell expression heterogeneity due to multiple equilibria involving feedback circuits, intracellular communication, and genetic variation at miRNA target sties, to reconcile the paradoxical effects of MIR211 on tumorigenesis. Understanding the precise role of this miRNA is crucial to understanding the genetic basis of melanoma as well as the other cancer types where this regulatory molecule has important influences. We hope this review will inspire novel directions in this field.
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Affiliation(s)
- Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont, CA, United States
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Haritha Kunhiraman
- Cancer & Blood Disorder Institute, Johns Hopkins All Children’s Hospital, South, St. Petersburg, FL, United States
| | - Ranjan J. Perera
- Cancer & Blood Disorder Institute, Johns Hopkins All Children’s Hospital, South, St. Petersburg, FL, United States
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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35
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Weitzner EL, Fanter CE, Hindle AG. Pinniped Ontogeny as a Window into the Comparative Physiology and Genomics of Hypoxia Tolerance. Integr Comp Biol 2020; 60:1414-1424. [PMID: 32559283 DOI: 10.1093/icb/icaa083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Diving physiology has received considerable scientific attention as it is a central element of the extreme phenotype of marine mammals. Many scientific discoveries have illuminated physiological mechanisms supporting diving, such as massive, internally bound oxygen stores and dramatic cardiovascular regulation. However, the cellular and molecular mechanisms that support the diving phenotype remain mostly unexplored as logistic and legal restrictions limit the extent of scientific manipulation possible. With next-generation sequencing (NGS) tools becoming more widespread and cost-effective, there are new opportunities to explore the diving phenotype. Genomic investigations come with their own challenges, particularly those including cross-species comparisons. Studying the regulatory pathways that underlie diving mammal ontogeny could provide a window into the comparative physiology of hypoxia tolerance. Specifically, in pinnipeds, which shift from terrestrial pups to elite diving adults, there is potential to characterize the transcriptional, epigenetic, and posttranslational differences between contrasting phenotypes while leveraging a common genome. Here we review the current literature detailing the maturation of the diving phenotype in pinnipeds, which has primarily been explored via biomarkers of metabolic capability including antioxidants, muscle fiber typing, and key aerobic and anaerobic metabolic enzymes. We also discuss how NGS tools have been leveraged to study phenotypic shifts within species through ontogeny, and how this approach may be applied to investigate the biochemical and physiological mechanisms that develop as pups become elite diving adults. We conclude with a specific example of the Antarctic Weddell seal by overlapping protein biomarkers with gene regulatory microRNA datasets.
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Affiliation(s)
- Emma L Weitzner
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Cornelia E Fanter
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
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36
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Abstract
MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high Fst significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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37
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Kyrgiafini MA, Markantoni M, Sarafidou T, Chatziparasidou A, Christoforidis N, Mamuris Z. Genome-wide association study identifies candidate markers related to lincRNAs associated with male infertility in the Greek population. J Assist Reprod Genet 2020; 37:2869-2881. [PMID: 32880781 PMCID: PMC7642051 DOI: 10.1007/s10815-020-01937-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Male infertility is currently one of the most common problems faced by couples worldwide. We performed a GWAS on Greek population and gathered statistically significant SNPs in order to investigate whether they lie within or near lncRNA regions. OBJECTIVES The aim of this study was to investigate whether polymorphisms on or near lncRNAs affect interactions with miRNAs and can cause male infertility. MATERIALS AND METHODS In the present study, a GWAS was conducted, using samples from 159 individuals (83 normozoospermic individuals and 76 patients of known fertility issues). Standard procedures for quality controls and association testing were followed, based on case-control testing. RESULTS We detected six lncRNAs (LINC02231, LINC00347, LINC02134, NCRNA00157, LINC02493, Lnc-CASK-1) that are associated with male infertility through their interaction with miRNAs. Furthermore, we identified the genes targeted by those miRNAs and highlighted their functions in spermatogenesis and the fertilization process. DISCUSSION AND CONCLUSION lncRNAs are involved in spermatogenesis through their interaction with miRNAs. Thus, their study is very important, and it may contribute to the understanding of the molecular mechanisms underlying male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Maria Markantoni
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | - Theologia Sarafidou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece
| | | | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500, Larisa, Greece.
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38
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Rui T, Zhang X, Feng S, Huang H, Zhan S, Xie H, Zhou L, Ling Q, Zheng S. The Similar Effects of miR-512-3p and miR-519a-2-5p on the Promotion of Hepatocellular Carcinoma: Different Tunes Sung With Equal Skill. Front Oncol 2020; 10:1244. [PMID: 32850377 PMCID: PMC7427533 DOI: 10.3389/fonc.2020.01244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 06/16/2020] [Indexed: 01/27/2023] Open
Abstract
Although the therapeutic methods of hepatocellular carcinoma (HCC) have made great advances, the current situation is that HCC is the common malignancy. Our previous bioinformatic study presented that two members of C19MC (mir-512-1 and mir-519a-2) acted as crucial roles in the HCC progression. In this study, we first demonstrated that the miR-512-3p and miR-519a-2-5p, which were spliced from the mir-512-1 and mir-519a-2, were the functional mature miRNAs. Meanwhile, both miR-512-3p and miR-519a-2-5p were significantly upregulated in human HCC samples and HCC cell lines. The miR-512-3p and miR-519a-2-5p promoted the proliferation, invasion, and metastasis in vitro and in vivo. Moreover, the two miRNAs co-targeted the downstream tumor suppressors MAP3K2 and MAP2K4 and subsequently achieved the HCC progression. In the clinical cohort, high expression of miR-512-3p and miR-519a-2-5p acted as two risk factors for HCC recurrence and distinguished patients with poor tumor-free survival after radical resection. The integration of the two miRNAs into the AJCC staging system significantly improved the accuracy for the prediction of HCC recurrence. Our study suggests that miR-512-3p and miR-519a-2-5p have similar effects on the promotion of HCC progression. They can be robust markers for the prediction of HCC recurrence and therapy targets.
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Affiliation(s)
- Tao Rui
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Xueyou Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Shi Feng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Haitao Huang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Shaowei Zhan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Qi Ling
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, School of Medicine, First Affiliated Hospital, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center for the Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, China
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39
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Kang L, Han C, Yang G, Li H, Li T, Yang S, Liang N, Zhong R, Jia L, Zhu D, Zhang Y. miR-378 and its host gene Ppargc1β exhibit independent expression in mouse skeletal muscle. Acta Biochim Biophys Sin (Shanghai) 2020; 52:883-890. [PMID: 32602911 DOI: 10.1093/abbs/gmaa061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/12/2020] [Accepted: 03/29/2020] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are implicated in multiple biological processes in physiological and pathological settings. Nearly half of the known miRNAs are classified as 'intronic' miRNAs because they are embedded within the introns of protein-coding or noncoding genes. Such miRNAs were thought to be processed from primary host gene transcripts and share the promoter of their host. Recent analyses predicted that some intronic miRNAs might be transcribed and regulated as independent units, but there is little direct evidence for this in a specific biological context. Here, we focused on miR-378, which is located within the first intron of the peroxisome proliferator-activated receptor γ coactivator 1-beta (Ppargc1β) gene and critically regulates skeletal muscle cell differentiation and muscle regeneration. We demonstrate that miR-378 and Ppargc1β exhibit distinct expression patterns during skeletal muscle cell differentiation. In terminally differentiated adult skeletal muscle tissues of mice, miR-378 is predominantly expressed in glycolytic muscle, whereas Ppargc1β is mainly expressed in oxidative soleus muscle. Mechanistically, miR-378, but not Ppargc1β, is regulated by the transcription factor, MyoD, in muscle cells. Our findings identify a regulatory model of miR-378 expression, thereby helping us to understand its physiological function in skeletal muscle.
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Affiliation(s)
- Lin Kang
- Department of Endocrinology, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Chunmiao Han
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Guangyan Yang
- Department of Endocrinology, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Hu Li
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shu Yang
- Department of Endocrinology, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Na Liang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Ran Zhong
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Lijing Jia
- Department of Endocrinology, the Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen 518020, China
| | - Dahai Zhu
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510530, China
| | - Yong Zhang
- The State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
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40
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Guo M, Gan L, Si J, Zhang J, Liu Z, Zhao J, Gou Z, Zhang H. Role of miR-302/367 cluster in human physiology and pathophysiology. Acta Biochim Biophys Sin (Shanghai) 2020; 52:791-800. [PMID: 32785592 DOI: 10.1093/abbs/gmaa065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/22/2020] [Accepted: 12/26/2019] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate target mRNAs at the post-transcriptional level. Increasing evidence shows the involvement of miRNAs in diverse biological processes. miR-302/367 cluster is highly conserved among vertebrates and made up of five members, including miR-367, miR-302a, miR-302b, miR-302c and miR-302d. miR-302/367 cluster plays an important role in cell proliferation, differentiation and reprogramming, affecting the development of tumor, cardiovascular system, nervous system and immune system. In this review, we will summarize the role of miR-302/367 cluster in embryonic stem cells and induced pluripotent stem cells and try to point out its relationship with tumors, cardiovascular system, nervous system and immune system.
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Affiliation(s)
- Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
| | - Lu Gan
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Si
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinhua Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Liu
- School of Chemical Engineering, Northwest Minzu University, Lanzhou 730030, China
| | - Jin Zhao
- Medical College, Northwest Minzu University, Lanzhou 730030, China
| | - Zhong Gou
- Medical College, Northwest Minzu University, Lanzhou 730030, China
| | - Hong Zhang
- School of Pharmacy, Lanzhou University, Lanzhou 730000, China
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine, Chinese Academy of Sciences, Lanzhou 730000, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Huang X, Li S, Liu X, Huang S, Li S, Zhuo M. Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching. PeerJ 2020; 8:e9347. [PMID: 32728489 PMCID: PMC7357559 DOI: 10.7717/peerj.9347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 05/21/2020] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans.
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Affiliation(s)
- Xia Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shijia Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Xiaoming Liu
- Guangzhou Tulip Information Technologies Ltd., Guangzhou, Guangdong, China
| | - Shuting Huang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Shuang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Min Zhuo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong, China
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42
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Kapheim KM, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, Ben-Shahar Y. Brain microRNAs among social and solitary bees. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200517. [PMID: 32874647 PMCID: PMC7428247 DOI: 10.1098/rsos.200517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
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Affiliation(s)
- Karen M. Kapheim
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
- Author for correspondence: Karen M. Kapheim e-mail:
| | - Beryl M. Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eirik Søvik
- Department of Science and Mathematics, Volda University College, 6100 Volda, Norway
| | - Eckart Stolle
- Centre of Molecular Biodiversity Research, Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Guy Bloch
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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43
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Dexheimer PJ, Cochella L. MicroRNAs: From Mechanism to Organism. Front Cell Dev Biol 2020; 8:409. [PMID: 32582699 PMCID: PMC7283388 DOI: 10.3389/fcell.2020.00409] [Citation(s) in RCA: 197] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are short, regulatory RNAs that act as post-transcriptional repressors of gene expression in diverse biological contexts. The emergence of small RNA-mediated gene silencing preceded the onset of multicellularity and was followed by a drastic expansion of the miRNA repertoire in conjunction with the evolution of complexity in the plant and animal kingdoms. Along this process, miRNAs became an essential feature of animal development, as no higher metazoan lineage tolerated loss of miRNAs or their associated protein machinery. In fact, ablation of the miRNA biogenesis machinery or the effector silencing factors results in severe embryogenesis defects in every animal studied. In this review, we summarize recent mechanistic insight into miRNA biogenesis and function, while emphasizing features that have enabled multicellular organisms to harness the potential of this broad class of repressors. We first discuss how different mechanisms of regulation of miRNA biogenesis are used, not only to generate spatio-temporal specificity of miRNA production within an animal, but also to achieve the necessary levels and dynamics of expression. We then explore how evolution of the mechanism for small RNA-mediated repression resulted in a diversity of silencing complexes that cause different molecular effects on their targets. Multicellular organisms have taken advantage of this variability in the outcome of miRNA-mediated repression, with differential use in particular cell types or even distinct subcellular compartments. Finally, we present an overview of how the animal miRNA repertoire has evolved and diversified, emphasizing the emergence of miRNA families and the biological implications of miRNA sequence diversification. Overall, focusing on selected animal models and through the lens of evolution, we highlight canonical mechanisms in miRNA biology and their variations, providing updated insight that will ultimately help us understand the contribution of miRNAs to the development and physiology of multicellular organisms.
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Affiliation(s)
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
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44
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Wang Y, Liu B. Circular RNA in Diseased Heart. Cells 2020; 9:cells9051240. [PMID: 32429565 PMCID: PMC7290921 DOI: 10.3390/cells9051240] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/15/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
Heart disease remains the leading cause of death globally and leads to tremendous socio-economic burden. Despite advances in the field of cardiovascular research, novel theranostics are still in urgent need. Remarkable progress has been made in understanding aberrant protein interactions and signaling pathways in the diseased heart, but less is known regarding epigenetic regulation. Non-coding RNAs have emerged as important regulators of cardiac function and have been implicated in disease. While significant progress has been made in understanding the roles of microRNAs and long non-coding RNAs, the functional roles of circular RNAs are less explored. Recent studies have provided ample evidence supporting their roles in multiple physiological processes including regulating the function of the heart. Compared with other RNAs, circular RNAs exhibit higher stability and more versatile functional modes: including sponging microRNAs, scaffolding proteins, regulating transcription, and even encoding small regulatory peptides. These characteristics make circular RNAs promising candidates for the development of diagnostic tools and therapies for heart disease. In this review, we will discuss the biogenesis of circular RNAs and provide an update of their functional implications in heart disease, with an emphasis on heart failure and arrhythmias.
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Affiliation(s)
| | - Bin Liu
- Correspondence: (Y.W.); (B.L.)
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45
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Penso-Dolfin L, Haerty W, Hindle A, Di Palma F. microRNA profiling in the Weddell seal suggests novel regulatory mechanisms contributing to diving adaptation. BMC Genomics 2020; 21:303. [PMID: 32293246 PMCID: PMC7158035 DOI: 10.1186/s12864-020-6675-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving > 900 m deep and remaining underwater for more than 60 min. A number of key physiological specializations have been identified, including the low levels of aerobic, lipid-based metabolism under hypoxia, significant increase in oxygen storage in blood and muscle; high blood volume and extreme cardiovascular control. These adaptations have been linked to increased abundance of key proteins, suggesting an important, yet still understudied role for gene reprogramming. In this study, we investigate the possibility that post-transcriptional gene regulation by microRNAs (miRNAs) has contributed to the adaptive evolution of diving capacities in the Weddell Seal. Results Using small RNA data across 4 tissues (brain, heart, muscle and plasma), in 3 biological replicates, we generate the first miRNA annotation in this species, consisting of 559 high confidence, manually curated miRNA loci. Evolutionary analyses of miRNA gain and loss highlight a high number of Weddell seal specific miRNAs. Four hundred sixteen miRNAs were differentially expressed (DE) among tissues, whereas 80 miRNAs were differentially expressed (DE) across all tissues between pups and adults and age differences for specific tissues were detected in 188 miRNAs. mRNA targets of these altered miRNAs identify possible protective mechanisms in individual tissues, particularly relevant to hypoxia tolerance, anti-apoptotic pathways, and nitric oxide signal transduction. Novel, lineage-specific miRNAs associated with developmental changes target genes with roles in angiogenesis and vasoregulatory signaling. Conclusions Altogether, we provide an overview of miRNA composition and evolution in the Weddell seal, and the first insights into their possible role in the specialization to diving.
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Affiliation(s)
- Luca Penso-Dolfin
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK. .,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - Allyson Hindle
- Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA.,University of Nevada Las Vegas, 4505 S Maryland Pkwy, Las Vegas, NV, 89154, USA
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
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46
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LaRocca TJ, Seeger T, Prado M, Perea-Gil I, Neofytou E, Mecham BH, Ameen M, Chang ACY, Pandey G, Wu JC, Karakikes I. Pharmacological Silencing of MicroRNA-152 Prevents Pressure Overload-Induced Heart Failure. Circ Heart Fail 2020; 13:e006298. [PMID: 32160771 DOI: 10.1161/circheartfailure.119.006298] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND MicroRNAs are small, noncoding RNAs that play a key role in gene expression. Accumulating evidence suggests that aberrant microRNA expression contributes to the heart failure (HF) phenotype; however, the underlying molecular mechanisms are not well understood. A better understanding of the mechanisms of action of microRNAs could potentially lead to targeted therapies that could halt the progression or even reverse HF. METHODS AND RESULTS We found that microRNA-152 (miR-152) expression was upregulated in the failing human heart and experimental animal models of HF. Transgenic mice with cardiomyocyte-specific miR-152 overexpression developed systolic dysfunction (mean difference, -38.74% [95% CI, -45.73% to -31.74%]; P<0.001) and dilated cardiomyopathy. At the cellular level, miR-152 overexpression perturbed mitochondrial ultrastructure and dysregulated key genes involved in cardiomyocyte metabolism and inflammation. Mechanistically, we identified Glrx5 (glutaredoxin 5), a critical regulator of mitochondrial iron homeostasis and iron-sulfur cluster synthesis, as a direct miR-152 target. Finally, a proof-of-concept of the therapeutic efficacy of targeting miR-152 in vivo was obtained by utilizing a locked nucleic acid-based inhibitor of miR-152 (LNA 152) in a murine model of HF subjected to transverse aortic constriction. We demonstrated that animals treated with LNA-152 (n=10) showed preservation of systolic function when compared with locked nucleic acid-control treated animals (n=9; mean difference, 18.25% [95% CI, 25.10% to 11.39%]; P<0.001). CONCLUSIONS The upregulation of miR-152 expression in the failing myocardium contributes to HF pathophysiology. Preclinical evidence suggests that miR-152 inhibition preserves cardiac function in a model of pressure overload-induced HF. These findings offer new insights into the pathophysiology of HF and point to miR-152-Glrx5 axis as a potential novel therapeutic target.
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Affiliation(s)
- Thomas J LaRocca
- Division of Critical Care Medicine, Department of Pediatrics, Lucile Packard Children's Hospital (T.J.L.), Stanford University School of Medicine, CA
| | - Timon Seeger
- Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA
| | - Maricela Prado
- Department of Cardiothoracic Surgery (M.P., I.P.-G., I.K.), Stanford University School of Medicine, CA
| | - Isaac Perea-Gil
- Department of Cardiothoracic Surgery (M.P., I.P.-G., I.K.), Stanford University School of Medicine, CA.,Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA
| | - Evgenios Neofytou
- Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA
| | | | - Mohamed Ameen
- Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA
| | - Alex Chia Yu Chang
- Department of Cardiology and Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, China (A.C.Y.C.)
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY (G.P.)
| | - Joseph C Wu
- Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA.,Department of Radiology (J.C.W.), Stanford University School of Medicine, CA
| | - Ioannis Karakikes
- Department of Cardiothoracic Surgery (M.P., I.P.-G., I.K.), Stanford University School of Medicine, CA.,Stanford Cardiovascular Institute (T.S., I.P.-G., E.N., M.A., J.C.W., I.K.), Stanford University School of Medicine, CA
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47
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Konstantinidis AΟ, Pardali D, Adamama-Moraitou KK, Gazouli M, Dovas CI, Legaki E, Brellou GD, Savvas I, Jergens AE, Rallis TS, Allenspach K. Colonic mucosal and serum expression of microRNAs in canine large intestinal inflammatory bowel disease. BMC Vet Res 2020; 16:69. [PMID: 32087719 PMCID: PMC7035774 DOI: 10.1186/s12917-020-02287-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 02/13/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Canine inflammatory bowel disease (IBD) is a group of chronic gastrointestinal (GI) disorders of still largely unknown etiology. Canine IBD diagnosis is time-consuming and costly as other diseases with similar signs should be initially excluded. In human IBD microRNA (miR) expression changes have been reported in GI mucosa and blood. Thus, there is a possibility that miRs may provide insight into disease pathogenesis, diagnosis and even treatment of canine IBD. The aim of this study was to determine the colonic mucosal and serum relative expression of a miRs panel in dogs with large intestinal IBD and healthy control dogs. RESULTS Compared to healthy control dogs, dogs with large intestinal IBD showed significantly increased relative expression of miR-16, miR-21, miR-122 and miR-147 in the colonic mucosa and serum, while the relative expression of miR-185, miR-192 and miR-223 was significantly decreased. Relative expression of miR-146a was significantly increased only in the serum of dogs with large intestinal IBD. Furthermore, serum miR-192 and miR-223 relative expression correlated to disease activity and endoscopic score, respectively. CONCLUSION Our data suggest the existence of dysregulated miRs expression patterns in canine IBD and support the potential future use of serum miRs as useful noninvasive biomarkers.
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Affiliation(s)
- Alexandros Ο Konstantinidis
- Companion Animal Clinic (Medicine Unit), School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra Pardali
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Katerina K Adamama-Moraitou
- Companion Animal Clinic (Medicine Unit), School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Gazouli
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Chrysostomos I Dovas
- Diagnostic Laboratory, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evangelia Legaki
- Laboratory of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia D Brellou
- Laboratory of Pathology, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Savvas
- Companion Animal Clinic (Anesthesia and Intensive Care Unit), School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Albert E Jergens
- Departments of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, USA
| | - Timoleon S Rallis
- Companion Animal Clinic (Medicine Unit), School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Karin Allenspach
- Departments of Veterinary Clinical Sciences, Iowa State University College of Veterinary Medicine, Ames, IA, USA.
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48
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Murphy Schafer AR, Smith JL, Pryke KM, DeFilippis VR, Hirsch AJ. The E3 Ubiquitin Ligase SIAH1 Targets MyD88 for Proteasomal Degradation During Dengue Virus Infection. Front Microbiol 2020; 11:24. [PMID: 32117091 PMCID: PMC7033647 DOI: 10.3389/fmicb.2020.00024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/07/2020] [Indexed: 12/27/2022] Open
Abstract
The dengue virus presents a serious threat to human health globally and can cause severe, even life-threatening, illness. Dengue virus (DENV) is endemic on all continents except Antarctica, and it is estimated that more than 100 million people are infected each year. Herein, we further mine the data from a previously described screen for microRNAs (miRNAs) that block flavivirus replication. We use miR-424, a member of the miR-15/16 family, as a tool to further dissect the role of host cell proteins during DENV infection. We observed that miR-424 suppresses expression of the E3 ubiquitin ligase SIAH1, which is normally induced during dengue virus 2 (DENV2) infection through activation of the unfolded protein response (UPR). Specific siRNA-mediated knockdown of SIAH1 also results in inhibition of DENV replication, demonstrating that this target is at least partly responsible for the antiviral activity of miR-424. We further show that SIAH1 binds to and ubiquitinates the innate immune adaptor protein MyD88 and that the antiviral effect of SIAH1 knockdown is reduced in cells in which MyD88 has been deleted by CRISPR/Cas9 gene editing. Additionally, MyD88-dependent signaling, triggered either by DENV2 infection or the Toll-like receptor 7 (TLR7) ligand imiquimod, is increased in cells in which SIAH1 has been knocked down by miR-424 or a SIAH1-specific siRNA. These observations suggest an additional pathway by which DENV2 harnesses aspects of the UPR to dampen the host innate immune response and promote viral replication.
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Affiliation(s)
- Ashleigh R Murphy Schafer
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Jessica L Smith
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Kara M Pryke
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Victor R DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Alec J Hirsch
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
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49
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Simkin A, Geissler R, McIntyre ABR, Grimson A. Evolutionary dynamics of microRNA target sites across vertebrate evolution. PLoS Genet 2020; 16:e1008285. [PMID: 32012152 PMCID: PMC7018135 DOI: 10.1371/journal.pgen.1008285] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 02/13/2020] [Accepted: 01/02/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) control the abundance of the majority of the vertebrate transcriptome. The recognition sequences, or target sites, for bilaterian miRNAs are found predominantly in the 3' untranslated regions (3'UTRs) of mRNAs, and are amongst the most highly conserved motifs within 3'UTRs. However, little is known regarding the evolutionary pressures that lead to loss and gain of such target sites. Here, we quantify the selective pressures that act upon miRNA target sites. Notably, selective pressure extends beyond deeply conserved binding sites to those that have undergone recent substitutions. Our approach reveals that even amongst ancient animal miRNAs, which exert the strongest selective pressures on 3'UTR sequences, there are striking differences in patterns of target site evolution between miRNAs. Considering only ancient animal miRNAs, we find three distinct miRNA groups, each exhibiting characteristic rates of target site gain and loss during mammalian evolution. The first group both loses and gains sites rarely. The second group shows selection only against site loss, with site gains occurring at a neutral rate, whereas the third loses and gains sites at neutral or above expected rates. Furthermore, mutations that alter the strength of existing target sites are disfavored. Applying our approach to individual transcripts reveals variation in the distribution of selective pressure across the transcriptome and between miRNAs, ranging from strong selection acting on a small subset of targets of some miRNAs, to weak selection on many targets for other miRNAs. miR-20 and miR-30, and many other miRNAs, exhibit broad, deeply conserved targeting, while several other comparably ancient miRNAs show a lack of selective constraint, and a small number, including mir-146, exhibit evidence of rapidly evolving target sites. Our approach adds valuable perspective on the evolution of miRNAs and their targets, and can also be applied to characterize other 3'UTR regulatory motifs.
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Affiliation(s)
- Alfred Simkin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Biology, Elon University, Elon, North Carolina, United States of America
| | - Rene Geissler
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Alexa B. R. McIntyre
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, United States of America
| | - Andrew Grimson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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50
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Thornlow BP, Armstrong J, Holmes AD, Howard JM, Corbett-Detig RB, Lowe TM. Predicting transfer RNA gene activity from sequence and genome context. Genome Res 2020; 30:85-94. [PMID: 31857444 PMCID: PMC6961574 DOI: 10.1101/gr.256164.119] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/12/2019] [Indexed: 01/25/2023]
Abstract
Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined with difficulty in measuring transcript abundance and high sequence identity across transcripts, has severely limited our collective understanding of tRNA gene expression regulation and evolution. We establish sequence-based correlates to tRNA gene expression and develop a tRNA gene classification method that does not require, but benefits from, comparative genomic information and achieves accuracy comparable to molecular assays. We observe that guanine + cytosine (G + C) content and CpG density surrounding tRNA loci is exceptionally well correlated with tRNA gene activity, supporting a prominent regulatory role of the local genomic context in combination with internal sequence features. We use our tRNA gene activity predictions in conjunction with a comprehensive tRNA gene ortholog set spanning 29 placental mammals to estimate the evolutionary rate of functional changes among orthologs. Our method adds a new dimension to large-scale tRNA functional prediction and will help prioritize characterization of functional tRNA variants. Its simplicity and robustness should enable development of similar approaches for other clades, as well as exploration of functional diversification of members of large gene families.
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Affiliation(s)
- Bryan P Thornlow
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Joel Armstrong
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Andrew D Holmes
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Jonathan M Howard
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Russell B Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, California 95064, USA
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