1
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Schreiber S, Daum P, Danzer H, Hauke M, Jäck HM, Wittmann J. Identification of miR-128 Target mRNAs That Are Expressed in B Cells Using a Modified Dual Luciferase Vector. Biomolecules 2023; 13:1517. [PMID: 37892199 PMCID: PMC10605364 DOI: 10.3390/biom13101517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
MicroRNAs (miRNAs) are 21-25 nucleotide long non-coding ribonucleic acids that modulate gene expression by degrading transcripts or inhibiting translation. The miRNA miR-128, originally thought to be brain-specific, was later also found in immune cells. To identify a valuable immune cell model system to modulate endogenous miR-128 amounts and to validate predicted miR-128 target mRNAs in B cells, we first investigated miR-128 expression using Northern blot analysis in several cell lines representing different stages of B cell development. The results showed that only primary brain cells showed significant levels of mature miR-128. To study the function of miR-128 in immune cells, we modified dual luciferase vectors to allow easy transfer of 3' UTR fragments with predicted miR-128 binding sites from widely used single to dual luciferase vectors. Comparison of in silico predicted miR-128-regulated mRNAs in single and dual luciferase constructs yielded similar results, validating the dual luciferase vector for miRNA target analysis. Furthermore, we confirmed miR-128-regulated mRNAs identified in silico and in vivo using the Ago HITS-CLIP technique and known to be expressed in B cells using the dual luciferase assay. In conclusion, this study provides new insights into the expression and function of miR-128 by validating novel target mRNAs expressed in B cells and identifying additional pathways likely controlled by this miRNA in the immune system.
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Affiliation(s)
| | | | | | | | | | - Jürgen Wittmann
- Division of Molecular Immunology, Department of Internal Medicine III, Nikolaus-Fiebiger-Center of Molecular Medicine (NFZ), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Glückstraße 6, D-91054 Erlangen, Germany
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2
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Le Sage V, Kanarek JP, Lakdawala SS, Lee N. Local changes in viral RNA sequence drive global changes in influenza nucleoprotein binding. J Med Virol 2023; 95:e28896. [PMID: 37386887 PMCID: PMC10878429 DOI: 10.1002/jmv.28896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/03/2023] [Indexed: 07/01/2023]
Abstract
The genome of influenza A viruses (IAV) consists of eight negative-sense RNA segments that are coated by viral nucleoprotein (NP). Until recently, it was assumed that NP binds viral genomic RNA (vRNA) uniformly along the entire segment. However, genome-wide studies have revised the original model in that NP instead binds preferentially to certain regions of vRNA, while others are depleted for NP binding. Even strains with high sequence similarity exhibit distinct NP-binding profiles. Thus, it remains unknown how NP-binding specificity to vRNA is established. Here we introduced nucleotide changes to vRNA to examine whether primary sequence can affect NP binding. Our findings demonstrate that NP binding is indeed susceptible to sequence alterations, as NP peaks can be lost or appear de novo at mutated sites. Unexpectedly, nucleotide changes not only affect NP binding locally at the site of mutation, but also impact NP binding at distal regions that have not been modified. Taken together, our results suggest that NP binding is not regulated by primary sequence alone, but that a network formed by multiple segments governs the deposition of NP on vRNA.
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Affiliation(s)
- Valerie Le Sage
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Jack P. Kanarek
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Seema S. Lakdawala
- Emory University School of Medicine, Department of Microbiology and Immunology, 1510 Clifton Rd., Atlanta, GA 30322
| | - Nara Lee
- University of Pittsburgh School of Medicine, Department of Microbiology and Molecular Genetics, 450 Technology Drive, Pittsburgh, PA 15219, USA
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3
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Cavallin I, Bartosovic M, Skalicky T, Rengaraj P, Demko M, Schmidt-Dengler MC, Drino A, Helm M, Vanacova S. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA 2022; 28:1568-1581. [PMID: 36192131 PMCID: PMC9670814 DOI: 10.1261/rna.079421.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
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Affiliation(s)
- Ivana Cavallin
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Marek Bartosovic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Praveenkumar Rengaraj
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin Demko
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Aleksej Drino
- Medical University of Vienna, Center for Anatomy and Cell Biology, 1090 Vienna, Austria
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS), D-55128 Mainz, Germany
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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4
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Zhou Y, Sotcheff SL, Routh AL. Next-generation sequencing: A new avenue to understand viral RNA-protein interactions. J Biol Chem 2022; 298:101924. [PMID: 35413291 PMCID: PMC8994257 DOI: 10.1016/j.jbc.2022.101924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/02/2022] [Indexed: 10/25/2022] Open
Abstract
The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA-protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA-protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA-protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA-protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.
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Affiliation(s)
- Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA.
| | - Stephanea L Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, Texas, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
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5
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Shawky AEM, Dondeti M, Mourelatos Z, Vourekas A. Solid-Support Directional (SSD) RNA-Seq as a Companion Method to CLIP-Seq. Methods Mol Biol 2022; 2509:251-268. [PMID: 35796968 DOI: 10.1007/978-1-0716-2380-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CLIP-Seq (Deep Sequencing after in vivo Crosslinking and Immunoprecipitation, HITS-CLIP) has emerged as a key method for the study of RNA-binding proteins (RBPs), as it can scrutinize the RNAs bound by an RBP in vivo, with minimum manipulation of biological samples. CLIP-Seq is best used to reveal changes of the RNA cargo of an RBP and differences on binding patterns of the bound RNAs in living cells in different genetic backgrounds or after experimental treatment, rather than simply identifying RNA species. It is therefore crucial that a reference of the steady state levels of the RNAs present in the samples used for the CLIP-Seq experiment is included in the bioinformatic analysis. A simple directional RNA-Seq method was developed that uses the same oligonucleotides and the same PCR amplification steps as our CLIP-Seq method, which therefore can be analyzed using the same bioinformatic pipeline as the CLIP-Seq data. This greatly simplifies and streamlines the analysis process, and at the same time reduces the chances of protocol-specific artifacts and biases interfering with data interpretation. Some considerations on ways to integrate CLIP-Seq and RNA-Seq analyses are also provided herein.
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Affiliation(s)
- Abd-El Monsif Shawky
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Mahmoud Dondeti
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Zissimos Mourelatos
- Division of Neuropathology, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA.
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6
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Koshre GR, Shaji F, Mohanan NK, Mohan N, Ali J, Laishram RS. Star-PAP RNA Binding Landscape Reveals Novel Role of Star-PAP in mRNA Metabolism That Requires RBM10-RNA Association. Int J Mol Sci 2021; 22:9980. [PMID: 34576144 PMCID: PMC8469156 DOI: 10.3390/ijms22189980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/08/2021] [Accepted: 08/19/2021] [Indexed: 11/17/2022] Open
Abstract
Star-PAP is a non-canonical poly(A) polymerase that selects mRNA targets for polyadenylation. Yet, genome-wide direct Star-PAP targets or the mechanism of specific mRNA recognition is still vague. Here, we employ HITS-CLIP to map the cellular Star-PAP binding landscape and the mechanism of global Star-PAP mRNA association. We show a transcriptome-wide association of Star-PAP that is diminished on Star-PAP depletion. Consistent with its role in the 3'-UTR processing, we observed a high association of Star-PAP at the 3'-UTR region. Strikingly, there is an enrichment of Star-PAP at the coding region exons (CDS) in 42% of target mRNAs. We demonstrate that Star-PAP binding de-stabilises these mRNAs indicating a new role of Star-PAP in mRNA metabolism. Comparison with earlier microarray data reveals that while UTR-associated transcripts are down-regulated, CDS-associated mRNAs are largely up-regulated on Star-PAP depletion. Strikingly, the knockdown of a Star-PAP coregulator RBM10 resulted in a global loss of Star-PAP association on target mRNAs. Consistently, RBM10 depletion compromises 3'-end processing of a set of Star-PAP target mRNAs, while regulating stability/turnover of a different set of mRNAs. Our results establish a global profile of Star-PAP mRNA association and a novel role of Star-PAP in the mRNA metabolism that requires RBM10-mRNA association in the cell.
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Affiliation(s)
- Ganesh R. Koshre
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Feba Shaji
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Regional Centre for Biotechnology, Faridabad 121001, India
| | - Neeraja K. Mohanan
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
- Manipal Academy of Higher Education, Manipal 576104, India
| | - Nimmy Mohan
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
| | - Jamshaid Ali
- Bioinformatics Facility, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695585, India;
| | - Rakesh S. Laishram
- Cardiovascular Diseases & Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum 695014, India; (G.R.K.); (F.S.); (N.K.M.); (N.M.)
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7
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Chu-Tan JA, Cioanca AV, Feng ZP, Wooff Y, Schumann U, Aggio-Bruce R, Patel H, Rutar M, Hannan K, Panov K, Provis J, Natoli R. Functional microRNA targetome undergoes degeneration-induced shift in the retina. Mol Neurodegener 2021; 16:60. [PMID: 34465369 PMCID: PMC8406976 DOI: 10.1186/s13024-021-00478-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/03/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases including age-related macular degeneration (AMD), acting as post-transcriptional gene suppressors through their association with argonaute 2 (AGO2) - a key member of the RNA Induced Silencing Complex (RISC). Identifying the retinal miRNA/mRNA interactions in health and disease will provide important insight into the key pathways miRNA regulate in disease pathogenesis and may lead to potential therapeutic targets to mediate retinal degeneration. METHODS To identify the active miRnome targetome interactions in the healthy and degenerating retina, AGO2 HITS-CLIP was performed using a rodent model of photoreceptor degeneration. Analysis of publicly available single-cell RNA sequencing (scRNAseq) data was performed to identify the cellular location of AGO2 and key members of the microRNA targetome in the retina. AGO2 findings were verified by in situ hybridization (RNA) and immunohistochemistry (protein). RESULTS Analysis revealed a similar miRnome between healthy and damaged retinas, however, a shift in the active targetome was observed with an enrichment of miRNA involvement in inflammatory pathways. This shift was further demonstrated by a change in the seed binding regions of miR-124-3p, the most abundant retinal AGO2-bound miRNA, and has known roles in regulating retinal inflammation. Additionally, photoreceptor cluster miR-183/96/182 were all among the most highly abundant miRNA bound to AGO2. Following damage, AGO2 expression was localized to the inner retinal layers and more in the OLM than in healthy retinas, indicating a locational miRNA response to retinal damage. CONCLUSIONS This study provides important insight into the alteration of miRNA regulatory activity that occurs as a response to retinal degeneration and explores the miRNA-mRNA targetome as a consequence of retinal degenerations. Further characterisation of these miRNA/mRNA interactions in the context of the degenerating retina may provide an important insight into the active role these miRNA may play in diseases such as AMD.
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Affiliation(s)
- Joshua A. Chu-Tan
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Adrian V. Cioanca
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Zhi-Ping Feng
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Yvette Wooff
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Ulrike Schumann
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Riemke Aggio-Bruce
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Hardip Patel
- The ANU Bioinformatics Consultancy, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Matt Rutar
- School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria 3010 Australia
- Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617 Australia
| | - Katherine Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
| | - Konstantin Panov
- School of Biological Sciences Queen’s University Belfast, Belfast, BT9 5DL Northern Ireland
| | - Jan Provis
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
| | - Riccardo Natoli
- Eccles Institute of Neuroscience, The John Curtin School of Medical Research, College of Health and Medicine, The Australian National University, Acton, Canberra, ACT 2601 Australia
- The Australian National University Medical School, College of Health and Medicine, Canberra, ACT 2601 Australia
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8
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O'Connor S, Murphy EA, Szwed SK, Kanke M, Marchildon F, Sethupathy P, Darnell RB, Cohen P. AGO HITS-CLIP reveals distinct miRNA regulation of white and brown adipose tissue identity. Genes Dev 2021; 35:771-781. [PMID: 33832988 PMCID: PMC8091975 DOI: 10.1101/gad.345447.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are short, noncoding RNAs that associate with Argonaute (AGO) to influence mRNA stability and translation, thereby regulating cellular determination and phenotype. While several individual miRNAs have been shown to control adipocyte function, including energy storage in white fat and energy dissipation in brown fat, a comprehensive analysis of miRNA activity in these tissues has not been performed. We used high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to comprehensively characterize the network of high-confidence, in vivo mRNA:miRNA interactions across white and brown fat, revealing >20,000 unique AGO binding sites. When coupled with miRNA and mRNA sequencing, we found an inverse correlation between depot-enriched miRNAs and their targets. To illustrate the functionality of our HITS-CLIP data set in identifying specific miRNA:mRNA interactions, we show that miR-29 is a novel regulator of leptin, an adipocyte-derived hormone that coordinates food intake and energy homeostasis. Two independent miR-29 binding sites in the leptin 3' UTR were validated using luciferase assays, and miR-29 gain and loss of function modulated leptin mRNA and protein secretion in primary adipocytes. This work represents the only experimentally generated miRNA targetome in adipose tissue and identifies multiple regulatory pathways that may specify the unique identities of white and brown fat.
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Affiliation(s)
- Sean O'Connor
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Elisabeth A Murphy
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
| | - Sarah K Szwed
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA.,Weill-Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York 10065, USA
| | - Matt Kanke
- Department of Biomedical Sciences, Cornell University, Ithaca, New York 14853, USA
| | - François Marchildon
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, New York 14853, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York 10065, USA
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9
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Rozen-Gagnon K, Gu M, Luna JM, Luo JD, Yi S, Novack S, Jacobson E, Wang W, Paul MR, Scheel TKH, Carroll T, Rice CM. Argonaute-CLIP delineates versatile, functional RNAi networks in Aedes aegypti, a major vector of human viruses. Cell Host Microbe 2021; 29:834-848.e13. [PMID: 33794184 DOI: 10.1016/j.chom.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/20/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Argonaute (AGO) proteins bind small RNAs to silence complementary RNA transcripts, and they are central to RNA interference (RNAi). RNAi is critical for regulation of gene expression and antiviral defense in Aedes aegypti mosquitoes, which transmit Zika, chikungunya, dengue, and yellow fever viruses. In mosquitoes, AGO1 mediates miRNA interactions, while AGO2 mediates siRNA interactions. We applied AGO-crosslinking immunoprecipitation (AGO-CLIP) for both AGO1 and AGO2, and we developed a universal software package for CLIP analysis (CLIPflexR), identifying 230 small RNAs and 5,447 small RNA targets that comprise a comprehensive RNAi network map in mosquitoes. RNAi network maps predicted expression levels of small RNA targets in specific tissues. Additionally, this resource identified unexpected, context-dependent AGO2 target preferences, including endogenous viral elements and 3'UTRs. Finally, contrary to current thinking, mosquito AGO2 repressed imperfect targets. These findings expand our understanding of small RNA networks and have broad implications for the study of antiviral RNAi.
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Affiliation(s)
- Kathryn Rozen-Gagnon
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
| | - Meigang Gu
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Soon Yi
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Sasha Novack
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Eliana Jacobson
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA
| | - Wei Wang
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Troels K H Scheel
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA; Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark; Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Thomas Carroll
- Bioinformatics Resource Center, the Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, the Rockefeller University, New York, NY 10065, USA.
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10
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Qiu C, Zhang Y, Fan YJ, Pang TL, Su Y, Zhan S, Xu YZ. HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila. J Mol Cell Biol 2020; 11:170-181. [PMID: 29750417 DOI: 10.1093/jmcb/mjy029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 03/20/2018] [Accepted: 05/07/2018] [Indexed: 12/27/2022] Open
Abstract
Serine/arginine (SR)-rich proteins are critical for the regulation of alternative splicing (AS), which generates multiple mRNA isoforms from one gene and provides protein diversity for cell differentiation and tissue development. Genetic evidence suggests that Drosophila genital-specific overexpression of SR-related nuclear matrix protein of 160 kDa (SRm160), an SR protein with a PWI RNA-binding motif, causes defective development only in male flies and results in abnormal male genital structures and abnormal testis. However, the molecular characterization of SRm160 is limited. Using the high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) method in two sex-specific embryonic cell lines, S2 from the male and Kc from the female, we first identified the genome-wide RNA-binding characteristics of SRm160, which preferred binding to the exonic tri-nucleotide repeats GCA and AAC. We then validated this binding through both in vitro gel-shift assay and in vivo splicing of minigenes and found that SRm160 level affects AS of many transcripts. Furthermore, we identified 492 differential binding sites (DBS) of SRm160 varying between the two sex-specific cell lines. Among these DBS-containing genes, splicing factors were highly enriched, including transformer, a key regulator in the sex determination cascade. Analyses of fly mutants demonstrated that the SRm160 level affects AS isoforms of transformer. These findings shed crucial light on SRm160's RNA-binding specificity and regulation of AS in Drosophila sex determination and development.
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Affiliation(s)
- Chen Qiu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yu-Jie Fan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Ting-Lin Pang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yan Su
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong-Zhen Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
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11
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Wang M, Yu L, Wang S, Yang F, Wang M, Li L, Wu X. LIN28A binds to meiotic gene transcripts and modulates their translation in male germ cells. J Cell Sci 2020; 133:jcs242701. [PMID: 32376786 DOI: 10.1242/jcs.242701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 11/20/2022] Open
Abstract
The RNA-binding protein LIN28A is required for maintaining tissue homeostasis, including in the reproductive system, but the underlying mechanisms on how LIN28A regulates germline progenitors remain unclear. Here, we dissected LIN28A-binding targets using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse testes. LIN28A preferentially binds to mRNA coding sequence (CDS) or 3'UTR regions at sites enriched with GGAG(A) sequences. Further investigation of Lin28a-null mouse testes indicated that meiosis-associated mRNAs bound by LIN28A were differentially expressed. Next, ribosome profiling revealed that the mRNA levels of these targets were significantly reduced in the polysome fractions, and their protein expression levels decreased, in Lin28a-null mouse testes, even when meiotic arrest in the null mouse testes was not apparent. Collectively, these findings provide a set of LIN28A-regulated target mRNAs, and show that LIN28A binding might be a mechanism through which LIN28A acts to regulate undifferentiated spermatogonia fates and male fertility in mammals.
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Affiliation(s)
- Mei Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
- Centre for Reproductive Medicine, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu 222000, China
| | - Luping Yu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Shu Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Fan Yang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Min Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Lufan Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Xin Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 210029, China
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12
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Hayakawa-Yano Y, Yano M. An RNA Switch of a Large Exon of Ninein Is Regulated by the Neural Stem Cell Specific-RNA Binding Protein, Qki5. Int J Mol Sci 2019; 20:E1010. [PMID: 30813567 DOI: 10.3390/ijms20051010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
A set of tissue-specific splicing factors are thought to govern alternative splicing events during neural progenitor cell (NPC)-to-neuron transition by regulating neuron-specific exons. Here, we propose one such factor, RNA-binding protein Quaking 5 (Qki5), which is specifically expressed in the early embryonic neural stem cells. We performed mRNA-SEQ (Sequence) analysis using mRNAs obtained by developing cerebral cortices in Qk (Quaking) conditional knockout (cKO) mice. As expected, we found a large number of alternative splicing changes between control and conditional knockouts relative to changes in transcript levels. DAVID (The Database for Annotation, Visualization and Integrated Discovery) and Metascape analyses suggested that the affected spliced genes are involved in axon development and microtubule-based processes. Among these, the mRNA coding for the Ninein protein is listed as one of Qki protein-dependent alternative splicing targets. Interestingly, this exon encodes a very long polypeptide (2121 nt), and has been previously defined as a dynamic RNA switch during the NPC-to-neuron transition. Additionally, we validated that the regulation of this large exon is consistent with the Qki5-dependent alternative exon inclusion mode suggested by our previous Qki5 HITS-CLIP (high throughput sequencing-cross linking immunoprecipitation) analysis. Taken together, these data suggest that Qki5 is an important factor for alternative splicing in the NPC-to-neuron transition.
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13
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Abstract
In the last two decades noncoding RNAs have been the recipients of increasing scientific interest. In particular, miRNAs, short (~22 nts) noncoding transcripts, have been thoroughly investigated since their essential role in posttranscriptional gene expression regulation had been established in the early 2000s. With the advent and the advancements of high-throughput sequencing technologies in recent years, long noncoding RNAs have also started to emerge as important actors in cellular functions and processes. Such transcripts, on average longer than 200 nt, whose functions have yet to be fully characterized, have recently been identified as regulatory elements of the RNAi pathway, harboring several miRNA response elements, uncovering the phenomena of competing endogenous RNAs (ceRNAs), or "sponge RNAs." The present chapter aims to provide a brief update on the actual biomedical relevance of ceRNAs, together with a summary of resources, tools, and practical examples of their application to aid researchers in the discovery and further elucidation of lncRNA-miRNA interactions.
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Affiliation(s)
- Dario Veneziano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
| | - Gioacchino P Marceca
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | | | - Giovanni Nigita
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
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14
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Gay LA, Turner PC, Renne R. Contemporary Ribonomics Methods for Viral microRNA Target Analysis. Noncoding RNA 2018; 4:E31. [PMID: 30424002 DOI: 10.3390/ncrna4040031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022] Open
Abstract
Numerous cellular processes are regulated by microRNAs (miRNAs), both cellular and viral. Elucidating the targets of miRNAs has become an active area of research. An important method in this field is cross-linking and immunoprecipitation (CLIP), where cultured cells or tissues are UV-irradiated to cross-link protein and nucleic acid, the RNA binding protein of interest is immunoprecipitated, and the RNAs pulled down with the protein are isolated, reverse-transcribed, and analyzed by sequencing. CLIP using antibody against Argonaute (Ago), which binds to both miRNA and mRNA as they interact in RISC, has allowed researchers to uncover a large number of miRNA targets. Coupled with high-throughput sequencing, CLIP has been useful for revealing miRNA targetomes for the γ-herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). Variants on the CLIP protocol are described, with the benefits and drawbacks of each. In particular, the most recent methods involving RNA⁻RNA ligation to join the miRNA and its RNA target have aided in target identification. Lastly, data supporting biologically meaningful interactions between miRNAs and long non-coding RNAs (lncRNAs) are reviewed. In summary, ribonomics-based miRNA targetome analysis has expanded our understanding of miRNA targeting and has provided a rich resource for EBV and KSHV research with respect to pathogenesis and tumorigenesis.
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15
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Drewe-Boss P, Wessels HH, Ohler U. omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. Genome Biol 2018; 19:183. [PMID: 30384847 DOI: 10.1186/s13059-018-1521-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 09/03/2018] [Indexed: 12/04/2022] Open
Abstract
CLIP-seq methods allow the generation of genome-wide maps of RNA binding protein – RNA interaction sites. However, due to differences between different CLIP-seq assays, existing computational approaches to analyze the data can only be applied to a subset of assays. Here, we present a probabilistic model called omniCLIP that can detect regulatory elements in RNAs from data of all CLIP-seq assays. omniCLIP jointly models data across replicates and can integrate background information. Therefore, omniCLIP greatly simplifies the data analysis, increases the reliability of results and paves the way for integrative studies based on data from different assays.
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16
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Le Sage V, Nanni AV, Bhagwat AR, Snyder DJ, Cooper VS, Lakdawala SS, Lee N. Non-Uniform and Non-Random Binding of Nucleoprotein to Influenza A and B Viral RNA. Viruses 2018; 10:E522. [PMID: 30257455 DOI: 10.3390/v10100522] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/17/2018] [Accepted: 09/22/2018] [Indexed: 12/20/2022] Open
Abstract
The genomes of influenza A and B viruses have eight, single-stranded RNA segments that exist in the form of a viral ribonucleoprotein complex in association with nucleoprotein (NP) and an RNA-dependent RNA polymerase complex. We previously used high-throughput RNA sequencing coupled with crosslinking immunoprecipitation (HITS-CLIP) to examine where NP binds to the viral RNA (vRNA) and demonstrated for two H1N1 strains that NP binds vRNA in a non-uniform, non-random manner. In this study, we expand on those initial observations and describe the NP-vRNA binding profile for a seasonal H3N2 and influenza B virus. We show that, similar to H1N1 strains, NP binds vRNA in a non-uniform and non-random manner. Each viral gene segment has a unique NP binding profile with areas that are enriched for NP association as well as free of NP-binding. Interestingly, NP-vRNA binding profiles have some conservation between influenza A viruses, H1N1 and H3N2, but no correlation was observed between influenza A and B viruses. Our study demonstrates the conserved nature of non-uniform NP binding within influenza viruses. Mapping of the NP-bound vRNA segments provides information on the flexible NP regions that may be involved in facilitating assembly.
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17
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Shivram H, Iyer VR. Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies. RNA 2018; 24:1266-1274. [PMID: 29950518 PMCID: PMC6097653 DOI: 10.1261/rna.066217.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
The quality of RNA sequencing data relies on specific priming by the primer used for reverse transcription (RT-primer). Nonspecific annealing of the RT-primer to the RNA template can generate reads with incorrect cDNA ends and can cause misinterpretation of data (RT mispriming). This kind of artifact in RNA-seq based technologies is underappreciated and currently no adequate tools exist to computationally remove them from published data sets. We show that mispriming can occur with as little as two bases of complementarity at the 3' end of the primer followed by intermittent regions of complementarity. We also provide a computational pipeline that identifies cDNA reads produced from RT mispriming, allowing users to filter them out from any aligned data set. Using this analysis pipeline, we identify thousands of mispriming events in a dozen published data sets from diverse technologies including short RNA-seq, total/mRNA-seq, HITS-CLIP, and GRO-seq. We further show how RT mispriming can lead to misinterpretation of data. In addition to providing a solution to computationally remove RT-misprimed reads, we also propose an experimental solution to completely avoid RT-mispriming by performing RNA-seq using thermostable group II intron derived reverse transcriptase (TGIRT-seq).
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Affiliation(s)
- Haridha Shivram
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Vishwanath R Iyer
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA
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18
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Moore MJ, Blachere NE, Fak JJ, Park CY, Sawicka K, Parveen S, Zucker-Scharff I, Moltedo B, Rudensky AY, Darnell RB. ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity. eLife 2018; 7:33057. [PMID: 29848443 PMCID: PMC6033538 DOI: 10.7554/elife.33057] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/26/2018] [Indexed: 01/07/2023] Open
Abstract
Dynamic post-transcriptional control of RNA expression by RNA-binding proteins (RBPs) is critical during immune response. ZFP36 RBPs are prominent inflammatory regulators linked to autoimmunity and cancer, but functions in adaptive immunity are less clear. We used HITS-CLIP to define ZFP36 targets in mouse T cells, revealing unanticipated actions in regulating T-cell activation, proliferation, and effector functions. Transcriptome and ribosome profiling showed that ZFP36 represses mRNA target abundance and translation, notably through novel AU-rich sites in coding sequence. Functional studies revealed that ZFP36 regulates early T-cell activation kinetics cell autonomously, by attenuating activation marker expression, limiting T cell expansion, and promoting apoptosis. Strikingly, loss of ZFP36 in vivo accelerated T cell responses to acute viral infection and enhanced anti-viral immunity. These findings uncover a critical role for ZFP36 RBPs in restraining T cell expansion and effector functions, and suggest ZFP36 inhibition as a strategy to enhance immune-based therapies. The immune system must quickly respond to anything that may cause disease – from cancerous cells to viruses. For instance, a type of white blood cell called a T cell patrols the body, looking for potential threats. If a T cell identifies such a threat, it “activates” and undergoes various changes so that it can help to eliminate the problem. One way that T cells change is by switching on different genes to make specific proteins. The information in the genes is first used as a template to produce a molecule called a messenger RNA (mRNA), which is then translated to build proteins. So-called RNA-binding proteins help control events before, during and after the translation stage in the process. Previous studies have shown that one particular RNA-binding protein, called ZFP36, controls the translation of proteins that are important for how the immune system recognizes the body’s own tissue and deals with cancer cells. However, it was less clear if it also helped T cells to activate and defeat viruses. Now, using cutting-edge technology, Moore et al. have identified thousands of new mRNAs controlled by ZFP36 in mice, many of which did indeed make proteins that help T cells activate and spread throughout the body. Further experiments showed that mice that lack ZFP36 in the T cells were much quicker at responding to viruses than other mice. This suggests that ZFP36 actually restrains T cells and slows down the body’s immune system. Knowing more about how T cells work could lead to new treatments for diseases; it may, for example, allow scientists to engineer T cells to better attack cancer cells, However, other studies have shown that mice without ZFP36 often go on to develop autoimmune diseases, which result from the immune system attacking healthy cells by mistake. As such, it seems that there is a fine line between improving the body’s immune system and increasing the risk of autoimmune diseases, and that RNA-binding proteins play an important role in managing this delicate balance.
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Affiliation(s)
- Michael J Moore
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Nathalie E Blachere
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - John J Fak
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Christopher Y Park
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,New York Genome Center, New York, United States
| | - Kirsty Sawicka
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Salina Parveen
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Ilana Zucker-Scharff
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Bruno Moltedo
- Howard Hughes Medical Institute, Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, United States
| | - Alexander Y Rudensky
- Howard Hughes Medical Institute, Ludwig Center at Memorial Sloan Kettering Cancer Center, New York, United States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,New York Genome Center, New York, United States
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19
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Abstract
HITS-CLIP (High-Throughput Sequencing after in vivo Crosslinking and Immunoprecipitation, CLIP-Seq) libraries contain fragments of the RNA sequences bound in vivo by an RNA binding protein (RBP). Such fragments, especially if they represent RNA duplexes bound in vivo by the RBP, can occasionally be ligated together to form chimeric CLIP tags. Chimeric CLIP tags from Argonaute CLIP libraries can provide the exact base pairing profiles of small RNAs with their target RNA sequences, thus solving a critical problem in the field of post-transcriptional regulation. We recently reported an analysis of chimeric reads from the Drosophila Piwi protein Aubergine, which revealed a novel mechanism for mRNA entrapment within germ RNP granules. We term this novel approach chimeric CLIP (cCLIP) and present here the main steps that a researcher can take after the acquisition of the deep sequencing data, for the identification of candidate chimeric reads in Piwi CLIP libraries. Extending the scope beyond small-RNA binding proteins, we believe that cCLIP can be utilized to elucidate the in vivo functions of RNA-binding proteins in general, and especially those that modulate RNA secondary structures. We, therefore, also describe aspects of the generalized chimeric read identification problem, which can find use in the analysis of the CLIP libraries of any RNA-binding protein.
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20
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Hayakawa-Yano Y, Suyama S, Nogami M, Yugami M, Koya I, Furukawa T, Zhou L, Abe M, Sakimura K, Takebayashi H, Nakanishi A, Okano H, Yano M. An RNA-binding protein, Qki5, regulates embryonic neural stem cells through pre-mRNA processing in cell adhesion signaling. Genes Dev 2017; 31:1910-1925. [PMID: 29021239 PMCID: PMC5693031 DOI: 10.1101/gad.300822.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/14/2017] [Indexed: 01/07/2023]
Abstract
Cell type-specific transcriptomes are enabled by the action of multiple regulators, which are frequently expressed within restricted tissue regions. In the present study, we identify one such regulator, Quaking 5 (Qki5), as an RNA-binding protein (RNABP) that is expressed in early embryonic neural stem cells and subsequently down-regulated during neurogenesis. mRNA sequencing analysis in neural stem cell culture indicates that Qki proteins play supporting roles in the neural stem cell transcriptome and various forms of mRNA processing that may result from regionally restricted expression and subcellular localization. Also, our in utero electroporation gain-of-function study suggests that the nuclear-type Qki isoform Qki5 supports the neural stem cell state. We next performed in vivo transcriptome-wide protein-RNA interaction mapping to search for direct targets of Qki5 and elucidate how Qki5 regulates neural stem cell function. Combined with our transcriptome analysis, this mapping analysis yielded a bona fide map of Qki5-RNA interaction at single-nucleotide resolution, the identification of 892 Qki5 direct target genes, and an accurate Qki5-dependent alternative splicing rule in the developing brain. Last, our target gene list provides the first compelling evidence that Qki5 is associated with specific biological events; namely, cell-cell adhesion. This prediction was confirmed by histological analysis of mice in which Qki proteins were genetically ablated, which revealed disruption of the apical surface of the lateral wall in the developing brain. These data collectively indicate that Qki5 regulates communication between neural stem cells by mediating numerous RNA processing events and suggest new links between splicing regulation and neural stem cell states.
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Affiliation(s)
- Yoshika Hayakawa-Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Satoshi Suyama
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masahiro Nogami
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Masato Yugami
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Ikuko Koya
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takako Furukawa
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Li Zhou
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Atsushi Nakanishi
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masato Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan.,Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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21
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Martin S, Bellora N, González-Vallinas J, Irimia M, Chebli K, de Toledo M, Raabe M, Eyras E, Urlaub H, Blencowe BJ, Tazi J. Preferential binding of a stable G3BP ribonucleoprotein complex to intron-retaining transcripts in mouse brain and modulation of their expression in the cerebellum. J Neurochem 2016; 139:349-368. [PMID: 27513819 DOI: 10.1111/jnc.13768] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 08/02/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022]
Abstract
Neuronal granules play an important role in the localization and transport of translationally silenced messenger ribonucleoproteins in neurons. Among the factors associated with these granules, the RNA-binding protein G3BP1 (stress-granules assembly factor) is involved in neuronal plasticity and is induced in Alzheimer's disease. We immunopurified a stable complex containing G3BP1 from mouse brain and performed high-throughput sequencing and cross-linking immunoprecipitation to identify the associated RNAs. The G3BP-complex contained the deubiquitinating protease USP10, CtBP1 and the RNA-binding proteins Caprin-1, G3BP2a and splicing factor proline and glutamine rich, or PSF. The G3BP-complex binds preferentially to transcripts that retain introns, and to non-coding sequences like 3'-untranslated region and long non-coding RNAs. Specific transcripts with retained introns appear to be enriched in the cerebellum compared to the rest of the brain and G3BP1 depletion decreased this intron retention in the cerebellum of G3BP1 knockout mice. Among the enriched transcripts, we found an overrepresentation of genes involved in synaptic transmission, especially glutamate-related neuronal transmission. Notably, G3BP1 seems to repress the expression of the mature Grm5 (metabotropic glutamate receptor 5) transcript, by promoting the retention of an intron in the immature transcript in the cerebellum. Our results suggest that G3BP is involved in a new functional mechanism to regulate non-coding RNAs including intron-retaining transcripts, and thus have broad implications for neuronal gene regulation, where intron retention is widespread.
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Affiliation(s)
- Sophie Martin
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Montpellier, France
| | - Nicolas Bellora
- Computational Genomics Group Universitat Pompeu Fabra PRBB, Barcelona, Spain.,Laboratorio de Microbiología Aplicada y Biotecnología, Instituto Andino-Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), CONICET - UNComahue, Bariloche, Argentina
| | | | - Manuel Irimia
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Karim Chebli
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Montpellier, France
| | - Marion de Toledo
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Montpellier, France
| | - Monika Raabe
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Eduardo Eyras
- Computational Genomics Group Universitat Pompeu Fabra PRBB, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, Barcelona, Spain
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ben J Blencowe
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jamal Tazi
- Institut de Génétique Moléculaire de Montpellier, CNRS UMR5535, Montpellier, France.
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22
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Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB. NOVA2-mediated RNA regulation is required for axonal pathfinding during development. eLife 2016; 5. [PMID: 27223325 PMCID: PMC4930328 DOI: 10.7554/elife.14371] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/23/2016] [Indexed: 01/13/2023] Open
Abstract
The neuron specific RNA-binding proteins NOVA1 and NOVA2 are highly homologous alternative splicing regulators. NOVA proteins regulate at least 700 alternative splicing events in vivo, yet relatively little is known about the biologic consequences of NOVA action and in particular about functional differences between NOVA1 and NOVA2. Transcriptome-wide searches for isoform-specific functions, using NOVA1 and NOVA2 specific HITS-CLIP and RNA-seq data from mouse cortex lacking either NOVA isoform, reveals that NOVA2 uniquely regulates alternative splicing events of a series of axon guidance related genes during cortical development. Corresponding axonal pathfinding defects were specific to NOVA2 deficiency: Nova2-/- but not Nova1-/- mice had agenesis of the corpus callosum, and axonal outgrowth defects specific to ventral motoneuron axons and efferent innervation of the cochlea. Thus we have discovered that NOVA2 uniquely regulates alternative splicing of a coordinate set of transcripts encoding key components in cortical, brainstem and spinal axon guidance/outgrowth pathways during neural differentiation, with severe functional consequences in vivo.
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Affiliation(s)
- Yuhki Saito
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Soledad Miranda-Rottmann
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Matteo Ruggiu
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | | | - John J Fak
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Ru Zhong
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Jeremy S Duncan
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, United States
| | - Brian A Fabella
- Laboratory of Sensory Neuroscience, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Harald J Junge
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, United States
| | - Zhe Chen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Boulder, United States
| | - Roberto Araya
- Department of Neurosciences, Faculty of Medicine, University of Montreal, Montreal, Canada
| | - Bernd Fritzsch
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, United States
| | - A J Hudspeth
- Laboratory of Sensory Neuroscience, Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,New York Genome Center, New York, United States
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Gillen AE, Yamamoto TM, Kline E, Hesselberth JR, Kabos P. Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts. BMC Genomics 2016; 17:338. [PMID: 27150721 DOI: 10.1186/s12864-016-2675-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/28/2016] [Indexed: 01/13/2023] Open
Abstract
Background High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) allows for high resolution, genome-wide mapping of RNA-binding proteins. This methodology is frequently used to validate predicted targets of microRNA binding, as well as direct targets of other RNA-binding proteins. Hence, the accuracy and sensitivity of binding site identification is critical. Results We found that substantial mispriming during reverse transcription results in the overrepresentation of sequences complementary to the primer used for reverse transcription. Up to 45 % of peaks in publicly available HITS-CLIP libraries are attributable to this mispriming artifact, and the majority of libraries have detectable levels of mispriming. We also found that standard techniques for validating microRNA-target interactions fail to differentiate between artifactual peaks and physiologically relevant peaks. Conclusions Here, we present a modification to the HITS-CLIP protocol that effectively eliminates this artifact and improves the sensitivity and complexity of resulting libraries. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2675-5) contains supplementary material, which is available to authorized users.
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24
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Maragkakis M, Alexiou P, Nakaya T, Mourelatos Z. CLIPSeqTools--a novel bioinformatics CLIP-seq analysis suite. RNA 2016; 22:1-9. [PMID: 26577377 PMCID: PMC4691824 DOI: 10.1261/rna.052167.115] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/18/2015] [Indexed: 05/22/2023]
Abstract
Immunoprecipitation of RNA binding proteins (RBPs) after in vivo crosslinking, coupled with sequencing of associated RNA footprints (HITS-CLIP, CLIP-seq), is a method of choice for the identification of RNA targets and binding sites for RBPs. Compared with RNA-seq, CLIP-seq analysis is widely diverse and depending on the RBPs that are analyzed, the approaches vary significantly, necessitating the development of flexible and efficient informatics tools. In this study, we present CLIPSeqTools, a novel, highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. It contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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Affiliation(s)
- Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tadashi Nakaya
- Laboratory of Neuroscience, Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA PENN Genome Frontiers Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Van Nostrand EL, Huelga SC, Yeo GW. Experimental and Computational Considerations in the Study of RNA-Binding Protein-RNA Interactions. Adv Exp Med Biol 2016; 907:1-28. [PMID: 27256380 DOI: 10.1007/978-3-319-29073-7_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
After an RNA is transcribed, it undergoes a variety of processing steps that can change the encoded protein sequence (through alternative splicing and RNA editing), regulate the stability of the RNA, and control subcellular localization, timing, and rate of translation. The recent explosion in genomics techniques has enabled transcriptome-wide profiling of RNA processing in an unbiased manner. However, it has also brought with it both experimental challenges in developing improved methods to probe distinct processing steps, as well as computational challenges in data storage, processing, and analysis tools to enable large-scale interpretation in the genomics era. In this chapter we review experimental techniques and challenges in profiling various aspects of RNA processing, as well as recent efforts to develop analyses integrating multiple data sources and techniques to infer RNA regulatory networks.
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26
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Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts usually longer than 200 nts that have recently emerged as one of the largest and significantly diverse RNA families. The biological role and functions of lncRNAs are still mostly uncharacterized. Their target-mimetic, sponge/decoy function on microRNAs was recently uncovered. miRNAs are a class of noncoding RNA species (~22 nts) that play a central role in posttranscriptional regulation of protein coding genes by mRNA cleavage, direct translational repression and/or mRNA destabilization. LncRNAs can act as miRNA sponges, reducing their regulatory effect on mRNAs. This function introduces an extra layer of complexity in the miRNA-target interaction network. This chapter focuses on the study of miRNA-lncRNA interactions with either in silico or experimentally supported analyses. The proposed methodologies can be appropriately adapted in order to become the backbone of advanced multistep functional miRNA analyses.
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Affiliation(s)
- Maria D Paraskevopoulou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Electrical & Computer Engineering, University of Thessaly, Volos, Greece.
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27
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Brooks L, Lyons SM, Mahoney JM, Welch JD, Liu Z, Marzluff WF, Whitfield ML. A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs. RNA 2015; 21:1943-65. [PMID: 26377992 PMCID: PMC4604434 DOI: 10.1261/rna.053389.115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/23/2015] [Indexed: 05/20/2023]
Abstract
The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem-loop (SL) structure. This SL structure interacts with the stem-loop binding protein (SLBP), which is involved in all aspects of RD-histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprecipitate (HITS-CLIP) to analyze the RNA-binding landscape of SLBP. SLBP was not bound to any RNAs other than histone mRNAs. We performed bioinformatic analyses of the HITS-CLIP data that included (i) clustering genes by sequencing read coverage using CVCA, (ii) mapping the bound RNA fragment termini, and (iii) mapping cross-linking induced mutation sites (CIMS) using CLIP-PyL software. These analyses allowed us to identify specific sites of molecular contact between SLBP and its RD-histone mRNA ligands. We performed in vitro crosslinking assays to refine the CIMS mapping and found that uracils one and three in the loop of the histone mRNA SL preferentially crosslink to SLBP, whereas uracil two in the loop preferentially crosslinks to a separate component, likely the 3'hExo. We also performed a secondary analysis of an iCLIP data set to map UPF1 occupancy across the RD-histone mRNAs and found that UPF1 is bound adjacent to the SLBP-binding site. Multiple proteins likely bind the 3' end of RD-histone mRNAs together with SLBP.
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Affiliation(s)
- Lionel Brooks
- Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA
| | - Shawn M Lyons
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - J Matthew Mahoney
- Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA
| | - Joshua D Welch
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Zhongle Liu
- Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Michael L Whitfield
- Department of Genetics, Dartmouth Geisel School of Medicine, Hanover, New Hampshire 03755, USA
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28
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Stefani G, Chen X, Zhao H, Slack FJ. A novel mechanism of LIN-28 regulation of let-7 microRNA expression revealed by in vivo HITS-CLIP in C. elegans. RNA 2015; 21:985-96. [PMID: 25805859 PMCID: PMC4408804 DOI: 10.1261/rna.045542.114] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 01/29/2015] [Indexed: 05/12/2023]
Abstract
The evolutionarily conserved gene lin-28 encodes an RNA-binding protein and is an important regulator of the proper temporal succession of several developmental events in both invertebrates and vertebrates. At the cellular level, LIN-28 promotes stemness and proliferation, and inhibits differentiation, a feature best illustrated by its ability to induce pluripotency when ectopically expressed in human fibroblasts in combination with NANOG, OCT4, and SOX2. Mammalian LIN28 functions in part by regulating processing of the let-7 microRNA through a GGAG binding site in the pre-let-7's distal loop region. However, many human and animal let-7 precursors lack the GGAG binding motif. In order to dissect the molecular mechanisms underlying its biological functions in a living animal, we identified a map of LIN-28 interactions with the transcriptome by in vivo HITS-CLIP in Caenorhabditis elegans. LIN-28 binds a large pool of messenger RNAs, and a substantial fraction of the bona fide LIN-28 targets are involved in aspects of animal development. Furthermore, our data show that LIN-28 regulates the expression of the let-7 microRNA by binding its primary transcript in a previously unknown region, revealing a novel regulatory mechanism.
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Affiliation(s)
- Giovanni Stefani
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06405, USA Centre for Integrative Biology (CIBIO), University of Trento, 38123 Povo (TN), Italy
| | - Xiaowei Chen
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06405, USA Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
| | - Hongyu Zhao
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06511, USA Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06405, USA
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Reyes-Herrera PH, Ficarra E. Computational Methods for CLIP-seq Data Processing. Bioinform Biol Insights 2014; 8:199-207. [PMID: 25336930 PMCID: PMC4196881 DOI: 10.4137/bbi.s16803] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/25/2022] Open
Abstract
RNA-binding proteins (RBPs) are at the core of post-transcriptional regulation and thus of gene expression control at the RNA level. One of the principal challenges in the field of gene expression regulation is to understand RBPs mechanism of action. As a result of recent evolution of experimental techniques, it is now possible to obtain the RNA regions recognized by RBPs on a transcriptome-wide scale. In fact, CLIP-seq protocols use the joint action of CLIP, crosslinking immunoprecipitation, and high-throughput sequencing to recover the transcriptome-wide set of interaction regions for a particular protein. Nevertheless, computational methods are necessary to process CLIP-seq experimental data and are a key to advancement in the understanding of gene regulatory mechanisms. Considering the importance of computational methods in this area, we present a review of the current status of computational approaches used and proposed for CLIP-seq data.
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Affiliation(s)
- Paula H Reyes-Herrera
- Facultad de Ingeniería Electrónica y Biomédica, Universidad Antonio Nariño, Bogotá, Colombia
| | - Elisa Ficarra
- Department of Control and Computer Engineering, Politecnico di Torino, TO, Italy
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30
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Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB. NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. eLife 2013; 2:e00178. [PMID: 23359859 PMCID: PMC3552424 DOI: 10.7554/elife.00178] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/29/2012] [Indexed: 12/13/2022] Open
Abstract
The neuronal RNA binding protein NOVA regulates splicing, shuttles to the cytoplasm, and co-localizes with target transcripts in dendrites, suggesting links between splicing and local translation. Here we identified >200 transcripts showing NOVA-dependent changes in abundance, but, surprisingly, HITS-CLIP revealed NOVA binds these RNAs in introns rather than 3′ UTRs. This led us to discover NOVA-regulated splicing of cryptic exons within these introns. These exons triggered nonsense mediated decay (NMD), as UPF1 and protein synthesis were required for NOVA's effect on RNA levels. Their regulation was dynamic and physiologically relevant. The NMD exons were regulated by seizures, which also induced changes in Nova subcellular localization and mediated large changes in synaptic proteins, including proteins implicated in familial epilepsy. Moreover, Nova haploinsufficient mice had spontaneous epilepsy. The data reveal a hidden means of dynamic RNA regulation linking electrical activity to splicing and protein output, and of mediating homeostatic excitation/inhibition balance in neurons. DOI:http://dx.doi.org/10.7554/eLife.00178.001 After the DNA in a gene has been transcribed into messenger RNA, portions of the mRNA called introns are removed, and the remaining stretches of mRNA, which are known as exons, are spliced together. Within eukaryotic cells, a process known as alternative splicing allows a single gene to encode for multiple protein variants by ensuring that some exons are included in the final, modified mRNA, while other exons are excluded. This modified mRNA is then translated into proteins. Eukaryotic cells also contain proteins that bind to RNA to regulate alternative splicing. These RNA-binding proteins are often found in both the cytoplasm and nucleus of cells, and their involvement in splicing may be linked to other processes in the cell such as mRNA localization and translation. It has also become clear over the past two decades that certain types of RNA-binding proteins, including NOVA proteins, are only found in neurons, and that these proteins have been best characterized as alternative splicing regulators. Recent work has also suggested that they also have important roles in regulating neuronal activity and development, and that their actions in neuronal nuclei and cytoplasm might be coordinated. Now Eom et al. use the predictive power of a high throughput sequencing and crosslinking method termed HITS-CLIP to show that NOVA proteins can indirectly regulate cytoplasmic mRNA levels by regulating the process of alternative splicing in the nucleus to produce ‘cryptic’ exons in the brains of mice. The presence of these exons in the mRNA leads to the production of premature termination codons in the cytoplasm. These codons trigger a process called nonsense-mediated decay that involves identifying mRNA transcripts that contain nonsense mutations, and then degrading them. These cryptic exons were seen in mice missing the NOVA proteins, where they are expressed in abnormally high levels; in normal mice, these exons have not been seen before, hence they were termed ‘cryptic’. Eom et al. also show that these cryptic exons are physiologically relevant by inducing epileptic seizures in mice. Following the seizures, they find that the NOVA proteins up-regulate and down-regulate the levels of different cryptic exons, leading to changes in the levels of the proteins encoded by these mRNAs, including proteins that inhibit further seizures. Overall the results indicate that, by controlling the production of various proteins in neurons, these previously unknown cryptic exons have important roles in the workings of the brain. DOI:http://dx.doi.org/10.7554/eLife.00178.002
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Affiliation(s)
- Taesun Eom
- Laboratory of Molecular Neuro-Oncology , Rockefeller University , New York , United States
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31
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Abstract
By regulating the inclusion of ‘cryptic’ exons in messenger RNA in nerve cells, NOVA proteins are able to influence the abundance of the corresponding proteins.
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Affiliation(s)
- John A Calarco
- is at the FAS Center for Systems Biology , Harvard University , Cambridge , United States
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Racca C, Gardiol A, Eom T, Ule J, Triller A, Darnell RB. The Neuronal Splicing Factor Nova Co-Localizes with Target RNAs in the Dendrite. Front Neural Circuits 2010; 4:5. [PMID: 20407637 PMCID: PMC2856630 DOI: 10.3389/neuro.04.005.2010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 02/01/2010] [Indexed: 01/10/2023] Open
Abstract
Nova proteins are neuron-specific RNA binding proteins targeted by autoantibodies in a disorder manifest by failure of motor inhibition, and they regulate splicing and alternative 3' processing. Nova regulates splicing of RNAs encoding synaptic proteins, including the inhibitory glycine receptor alpha2 subunit (GlyRalpha2), and binds to others, including the GIRK2 channel. We found that Nova harbors functional NES and NLS elements, shuttles between the nucleus and cytoplasm, and that 50% of the protein localizes to the soma-dendritic compartment. Immunofluoresence and EM analysis of spinal cord motor neurons demonstrated that Nova co-localizes beneath synaptic contacts in dendrites with the same RNA, GlyRalpha2, whose splicing it regulates in the nucleus. HITS-CLIP identified intronic and 3' UTR sites where Nova binds to GlyRalpha2 and GIRK2 transcripts in the brain. This led directly to the identification of a 3' UTR localization element that mediates Nova-dependent localization of GIRK2 in primary neurons. These data demonstrate that HITS-CLIP can identify functional RNA localization elements, and they suggest new links between the regulation of nuclear RNA processing and mRNA localization.
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Affiliation(s)
- Claudia Racca
- Biologie Cellulaire de la Synapse Normale et Pathologique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale SupérieureParis, France
- Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Alejandra Gardiol
- Biologie Cellulaire de la Synapse Normale et Pathologique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale SupérieureParis, France
- The Wellcome Trust CR UK Gurdon Institute, University of CambridgeCambridge, UK
| | - Taesun Eom
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller UniversityNew York, NY, USA
| | - Jernej Ule
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller UniversityNew York, NY, USA
- Medical Research Council Laboratory of Molecular BiologyCambridge, UK
| | - Antoine Triller
- Biologie Cellulaire de la Synapse Normale et Pathologique, Institut National de la Santé et de la Recherche Médicale, Ecole Normale SupérieureParis, France
| | - Robert B. Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller UniversityNew York, NY, USA
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