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Zhang J, Xu X, Deng H, Liu L, Xiang Y, Feng J. Overcoming cancer drug-resistance calls for novel strategies targeting abnormal alternative splicing. Pharmacol Ther 2024; 261:108697. [PMID: 39025436 DOI: 10.1016/j.pharmthera.2024.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 05/12/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Abnormal gene alternative splicing (AS) events are strongly associated with cancer progression. Here, we summarize AS events that contribute to the development of drug resistance and classify them into three categories: alternative cis-splicing (ACS), alternative trans-splicing (ATS), and alternative back-splicing (ABS). The regulatory mechanisms underlying AS processes through cis-acting regulatory elements and trans-acting factors are comprehensively described, and the distinct functions of spliced variants, including linear spliced variants derived from ACS, chimeric spliced variants arising from ATS, and circRNAs generated through ABS, are discussed. The identification of dysregulated spliced variants, which contribute to drug resistance and hinder effective cancer treatment, suggests that abnormal AS processes may together serve as a precise regulatory mechanism enabling drug-resistant cancer cell survival or, alternatively, represent an evolutionary pathway for cancer cells to adapt to changes in the external environment. Moreover, this review summarizes recent advancements in treatment approaches targeting AS-associated drug resistance, focusing on cis-acting regulatory elements, trans-acting factors, and specific spliced variants. Collectively, gaining an in-depth understanding of the mechanisms underlying aberrant alternative splicing events and developing strategies to target this process hold great promise for overcoming cancer drug resistance.
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Affiliation(s)
- Ji Zhang
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Xinyu Xu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Hongwei Deng
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Li Liu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China
| | - Yuancai Xiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou city, Sichuan 646000, China.
| | - Jianguo Feng
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan Province 646000, China; Nucleic Acid Medicine of Luzhou Key Laboratory, Southwest Medical University, Luzhou, Sichuan Province 646000, China.
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2
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Shen A, Hencel K, Parker M, Scott R, Skukan R, Adesina A, Metheringham C, Miska E, Nam Y, Haerty W, Simpson G, Akay A. U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Res 2024; 52:9139-9160. [PMID: 38808663 PMCID: PMC11347140 DOI: 10.1093/nar/gkae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 05/30/2024] Open
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that the conserved U6 snRNA m6A methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of METT-10 in C. elegans and METTL16 in humans primarily leads to alternative splicing at 5' splice sites with an adenosine at +4 position. In addition, METT-10 is required for splicing of weak 3' cis- and trans-splice sites. We identified a significant overlap between METT-10 and the conserved splicing factor SNRNP27K in regulating 5' splice sites with +4A. Finally, we show that editing endogenous 5' splice site +4A positions to +4U restores splicing to wild-type positions in a mett-10 mutant background, supporting a direct role for U6 snRNA m6A modification in 5' splice site recognition. We conclude that the U6 snRNA m6A modification is important for accurate and efficient pre-mRNA splicing.
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Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robyn Scott
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberta Skukan
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
| | | | | | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge CB2 1QN, UK
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wilfried Haerty
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Alper Akay
- School of Biological Sciences, University of East Anglia, NR4 7TJ Norwich, UK
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3
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Eijlers P, Al-Khafaji M, Soto-Martin E, Fasimoye R, Stead D, Wenzel M, Müller B, Pettitt J. A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs. Nucleic Acids Res 2024; 52:7245-7260. [PMID: 38676950 PMCID: PMC11229312 DOI: 10.1093/nar/gkae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5' ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5' ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
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Affiliation(s)
- Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Mohammed Al-Khafaji
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Rotimi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - David Stead
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Rowett Institute, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
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4
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Gao P, Zhao Y, Xu G, Zhong Y, Sun C. Unique features of conventional and nonconventional introns in Euglena gracilis. BMC Genomics 2024; 25:595. [PMID: 38872102 PMCID: PMC11170887 DOI: 10.1186/s12864-024-10495-9] [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: 03/05/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Nuclear introns in Euglenida have been understudied. This study aimed to investigate nuclear introns in Euglenida by identifying a large number of introns in Euglena gracilis (E. gracilis), including cis-spliced conventional and nonconventional introns, as well as trans-spliced outrons. We also examined the sequence characteristics of these introns. RESULTS A total of 28,337 introns and 11,921 outrons were identified. Conventional and nonconventional introns have distinct splice site features; the former harbour canonical GT/C-AG splice sites, whereas the latter are capable of forming structured motifs with their terminal sequences. We observed that short introns had a preference for canonical GT-AG introns. Notably, conventional introns and outrons in E. gracilis exhibited a distinct cytidine-rich polypyrimidine tract, in contrast to the thymidine-rich tracts observed in other organisms. Furthermore, the SL-RNAs in E. gracilis, as well as in other trans-splicing species, can form a recently discovered motif called the extended U6/5' ss duplex with the respective U6s. We also describe a novel type of alternative splicing pattern in E. gracilis. The tandem repeat sequences of introns in this protist were determined, and their contents were comparable to those in humans. CONCLUSIONS Our findings highlight the unique features of E. gracilis introns and provide insights into the splicing mechanism of these introns, as well as the genomics and evolution of Euglenida.
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Affiliation(s)
- Pingwei Gao
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Yali Zhao
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Guangjie Xu
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China
| | - Yujie Zhong
- Clinical Laboratory Department, Zigong Hospital of Women's and Children's Healthcare, Zigong, 643002, China.
| | - Chengfu Sun
- Scientific Research Center, Chengdu Medical College, Chengdu, 610500, China.
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5
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Fingerhut JM, Lannes R, Whitfield TW, Thiru P, Yamashita YM. Co-transcriptional splicing facilitates transcription of gigantic genes. PLoS Genet 2024; 20:e1011241. [PMID: 38870220 PMCID: PMC11207136 DOI: 10.1371/journal.pgen.1011241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/26/2024] [Accepted: 05/31/2024] [Indexed: 06/15/2024] Open
Abstract
Although introns are typically tens to thousands of nucleotides, there are notable exceptions. In flies as well as humans, a small number of genes contain introns that are more than 1000 times larger than typical introns, exceeding hundreds of kilobases (kb) to megabases (Mb). It remains unknown why gigantic introns exist and how cells overcome the challenges associated with their transcription and RNA processing. The Drosophila Y chromosome contains some of the largest genes identified to date: multiple genes exceed 4Mb, with introns accounting for over 99% of the gene span. Here we demonstrate that co-transcriptional splicing of these gigantic Y-linked genes is important to ensure successful transcription: perturbation of splicing led to the attenuation of transcription, leading to a failure to produce mature mRNA. Cytologically, defective splicing of the Y-linked gigantic genes resulted in disorganization of transcripts within the nucleus suggestive of entanglement of transcripts, likely resulting from unspliced long RNAs. We propose that co-transcriptional splicing maintains the length of nascent transcripts of gigantic genes under a critical threshold, preventing their entanglement and ensuring proper gene expression. Our study reveals a novel biological significance of co-transcriptional splicing.
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Affiliation(s)
- Jaclyn M. Fingerhut
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
| | - Romain Lannes
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Troy W. Whitfield
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Prathapan Thiru
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Yukiko M. Yamashita
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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6
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Yokomori R, Kusakabe TG, Nakai K. Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing. NAR Genom Bioinform 2024; 6:lqae067. [PMID: 38846348 PMCID: PMC11155486 DOI: 10.1093/nargab/lqae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
Trans-splicing is a post-transcriptional processing event that joins exons from separate RNAs to produce a chimeric RNA. However, the detailed mechanism of trans-splicing remains poorly understood. Here, we characterize trans-spliced genes and provide insights into the mechanism of trans-splicing in the tunicate Ciona. Tunicates are the closest invertebrates to humans, and their genes frequently undergo trans-splicing. Our analysis revealed that, in genes that give rise to both trans-spliced and non-trans-spliced messenger RNAs, trans-splice acceptor sites were preferentially located at the first functional acceptor site, and their paired donor sites were weak in both Ciona and humans. Additionally, we found that Ciona trans-spliced genes had GU- and AU-rich 5' transcribed regions. Our data and findings not only are useful for Ciona research community, but may also aid in a better understanding of the trans-splicing mechanism, potentially advancing the development of gene therapy based on trans-splicing.
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Affiliation(s)
- Rui Yokomori
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takehiro G Kusakabe
- Institute for Integrative Neurobiology, Graduate School of Natural Science, Konan University, Kobe 658-8501, Japan
- Department of Biology, Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan
| | - Kenta Nakai
- Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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7
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Speakman E, Gunaratne GH. On a kneading theory for gene-splicing. CHAOS (WOODBURY, N.Y.) 2024; 34:043125. [PMID: 38579148 DOI: 10.1063/5.0199364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/05/2024] [Indexed: 04/07/2024]
Abstract
Two well-known facets in protein synthesis in eukaryotic cells are transcription of DNA to pre-RNA in the nucleus and the translation of messenger-RNA (mRNA) to proteins in the cytoplasm. A critical intermediate step is the removal of segments (introns) containing ∼97% of the nucleic-acid sites in pre-RNA and sequential alignment of the retained segments (exons) to form mRNA through a process referred to as splicing. Alternative forms of splicing enrich the proteome while abnormal splicing can enhance the likelihood of a cell developing cancer or other diseases. Mechanisms for splicing and origins of splicing errors are only partially deciphered. Our goal is to determine if rules on splicing can be inferred from data analytics on nucleic-acid sequences. Toward that end, we represent a nucleic-acid site as a point in a plane defined in terms of the anterior and posterior sub-sequences of the site. The "point-set" representation expands analytical approaches, including the use of statistical tools, to characterize genome sequences. It is found that point-sets for exons and introns are visually different, and that the differences can be quantified using a family of generalized moments. We design a machine-learning algorithm that can recognize individual exons or introns with 91% accuracy. Point-set distributions and generalized moments are found to differ between organisms.
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Affiliation(s)
- Ethan Speakman
- Department of Physics, University of Houston, Houston, Texas 77204, USA
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8
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Nayab DE, Din FU, Ali H, Kausar WA, Urooj S, Zafar M, Khan I, Shabbir K, Khan GM. Nano biomaterials based strategies for enhanced brain targeting in the treatment of neurodegenerative diseases: an up-to-date perspective. J Nanobiotechnology 2023; 21:477. [PMID: 38087359 PMCID: PMC10716964 DOI: 10.1186/s12951-023-02250-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
Neurons and their connecting axons gradually degenerate in neurodegenerative diseases (NDs), leading to dysfunctionality of the neuronal cells and eventually their death. Drug delivery for the treatment of effected nervous system is notoriously complicated because of the presence of natural barriers, i.e., the blood-brain barrier and the blood cerebrospinal fluid barrier. Palliative care is currently the standard care for many diseases. Therefore, treatment programs that target the disease's origin rather than its symptoms are recommended. Nanotechnology-based drug delivery platforms offer an innovative way to circumvent these obstacles and deliver medications directly to the central nervous system, thereby enabling treatment of several common neurological problems, i.e., Alzheimer's, Parkinson's, Huntington's, and amyotrophic lateral sclerosis. Interestingly, the combination of nanomedicine and gene therapy enables targeting of selective mutant genes responsible for the progression of NDs, which may provide a much-needed boost in the struggle against these diseases. Herein, we discussed various central nervous system delivery obstacles, followed by a detailed insight into the recently developed techniques to restore neurological function via the differentiation of neural stem cells. Moreover, a comprehensive background on the role of nanomedicine in controlling neurogenesis via differentiation of neural stem cells is explained. Additionally, numerous phytoconstituents with their neuroprotective properties and molecular targets in the identification and management of NDs are also deliberated. Furthermore, a detailed insight of the ongoing clinical trials and currently marketed products for the treatment of NDs is provided in this manuscript.
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Affiliation(s)
- Dur E Nayab
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fakhar Ud Din
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
- Nanomedicine Research Group, Department of Pharmacy, Faculty of Biological Sciences, Quaid- i-Azam University, Islamabad, 45320, Pakistan.
| | - Hussain Ali
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
| | - Warda Arooj Kausar
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shaiza Urooj
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Nanomedicine Research Group, Department of Pharmacy, Faculty of Biological Sciences, Quaid- i-Azam University, Islamabad, 45320, Pakistan
| | - Maryam Zafar
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Ibrahim Khan
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kanwal Shabbir
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Nanomedicine Research Group, Department of Pharmacy, Faculty of Biological Sciences, Quaid- i-Azam University, Islamabad, 45320, Pakistan
| | - Gul Majid Khan
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Nanomedicine Research Group, Department of Pharmacy, Faculty of Biological Sciences, Quaid- i-Azam University, Islamabad, 45320, Pakistan
- Islamia College University, Peshawar, Khyber Pakhtunkhwa, Pakistan
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9
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Pan J, Wei S, Qiu Q, Tong X, Shen Z, Zhu M, Hu X, Gong C. A novel chimeric RNA originating from BmCPV S4 and Bombyx mori HDAC11 transcripts regulates virus proliferation. PLoS Pathog 2023; 19:e1011184. [PMID: 38048361 PMCID: PMC10721177 DOI: 10.1371/journal.ppat.1011184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 12/14/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
Polymerases encoded by segmented negative-strand RNA viruses cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching") to generate chimeric RNA, and trans-splicing occurs between viral and cellular transcripts. Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), an RNA virus belonging to Reoviridae, is a major pathogen of silkworm (B. mori). The genome of BmCPV consists of 10 segmented double-stranded RNAs (S1-S10) from which viral RNAs encoding a protein are transcribed. In this study, chimeric silkworm-BmCPV RNAs, in which the sequence derived from the silkworm transcript could fuse with both the 5' end and the 3' end of viral RNA, were identified in the midgut of BmCPV-infected silkworms by RNA_seq and further confirmed by RT-PCR and Sanger sequencing. A novel chimeric RNA, HDAC11-S4 RNA 4, derived from silkworm histone deacetylase 11 (HDAC11) and the BmCPV S4 transcript encoding viral structural protein 4 (VP4), was selected for validation by in situ hybridization and Northern blotting. Interestingly, our results indicated that HDAC11-S4 RNA 4 was generated in a BmCPV RNA-dependent RNA polymerase (RdRp)-independent manner and could be translated into a truncated BmCPV VP4 with a silkworm HDAC11-derived N-terminal extension. Moreover, it was confirmed that HDAC11-S4 RNA 4 inhibited BmCPV proliferation, decreased the level of H3K9me3 and increased the level of H3K9ac. These results indicated that during infection with BmCPV, a novel mechanism, different from that described in previous reports, allows the genesis of chimeric silkworm-BmCPV RNAs with biological functions.
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Affiliation(s)
- Jun Pan
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Shulin Wei
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Qunnan Qiu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Xinyu Tong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Zeen Shen
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, People’s Republic of China
| | - Min Zhu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
| | - Xiaolong Hu
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, People’s Republic of China
| | - Chengliang Gong
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, Jiangsu, People’s Republic of China
- Agricultural Biotechnology Research Institute, Agricultural biotechnology and Ecological Research Institute, Soochow University, Suzhou, People’s Republic of China
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10
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Shen A, Hencel K, Parker MT, Scott R, Skukan R, Adesina AS, Metheringham CL, Miska EA, Nam Y, Haerty W, Simpson GG, Akay A. U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegans mRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558044. [PMID: 37745402 PMCID: PMC10516052 DOI: 10.1101/2023.09.16.558044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
pre-mRNA splicing is a critical feature of eukaryotic gene expression. Many eukaryotes use cis-splicing to remove intronic sequences from pre-mRNAs. In addition to cis-splicing, many organisms use trans-splicing to replace the 5' ends of mRNAs with a non-coding spliced-leader RNA. Both cis- and trans-splicing rely on accurately recognising splice site sequences by spliceosomal U snRNAs and associated proteins. Spliceosomal snRNAs carry multiple RNA modifications with the potential to affect different stages of pre-mRNA splicing. Here, we show that m6A modification of U6 snRNA A43 by the RNA methyltransferase METT-10 is required for accurate and efficient cis- and trans-splicing of C. elegans pre-mRNAs. The absence of U6 snRNA m6A modification primarily leads to alternative splicing at 5' splice sites. Furthermore, weaker 5' splice site recognition by the unmodified U6 snRNA A43 affects splicing at 3' splice sites. U6 snRNA m6A43 and the splicing factor SNRNP27K function to recognise an overlapping set of 5' splice sites with an adenosine at +4 position. Finally, we show that U6 snRNA m6A43 is required for efficient SL trans-splicing at weak 3' trans-splice sites. We conclude that the U6 snRNA m6A modification is important for accurate and efficient cis- and trans-splicing in C. elegans.
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Affiliation(s)
- Aykut Shen
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
| | - Katarzyna Hencel
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
- These authors contributed equally
| | - Matthew T Parker
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- These authors contributed equally
| | - Robyn Scott
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roberta Skukan
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
| | | | | | - Eric A Miska
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QN, UK
| | - Yunsun Nam
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Wilfried Haerty
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Gordon G Simpson
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
- Cell & Molecular Sciences, James Hutton Institute, Invergowrie, DD2 5DA, UK
| | - Alper Akay
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich
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Wiberg RAW, Brand JN, Viktorin G, Mitchell JO, Beisel C, Schärer L. Genome assemblies of the simultaneously hermaphroditic flatworms Macrostomum cliftonense and Macrostomum hystrix. G3 (BETHESDA, MD.) 2023; 13:jkad149. [PMID: 37398989 PMCID: PMC10468722 DOI: 10.1093/g3journal/jkad149] [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: 04/28/2023] [Revised: 06/05/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
The free-living, simultaneously hermaphroditic flatworms of the genus Macrostomum are increasingly used as model systems in various contexts. In particular, Macrostomum lignano, the only species of this group with a published genome assembly, has emerged as a model for the study of regeneration, reproduction, and stem-cell function. However, challenges have emerged due to M. lignano being a hidden polyploid, having recently undergone whole-genome duplication and chromosome fusion events. This complex genome architecture presents a significant roadblock to the application of many modern genetic tools. Hence, additional genomic resources for this genus are needed. Here, we present such resources for Macrostomum cliftonense and Macrostomum hystrix, which represent the contrasting mating behaviors of reciprocal copulation and hypodermic insemination found in the genus. We use a combination of PacBio long-read sequencing and Illumina shot-gun sequencing, along with several RNA-Seq data sets, to assemble and annotate highly contiguous genomes for both species. The assemblies span ∼227 and ∼220 Mb and are represented by 399 and 42 contigs for M. cliftonense and M. hystrix, respectively. Furthermore, high BUSCO completeness (∼84-85%), low BUSCO duplication rates (8.3-6.2%), and low k-mer multiplicity indicate that these assemblies do not suffer from the same assembly ambiguities of the M. lignano genome assembly, which can be attributed to the complex karyology of this species. We also show that these resources, in combination with the prior resources from M. lignano, offer an excellent foundation for comparative genomic research in this group of organisms.
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Affiliation(s)
- R Axel W Wiberg
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jeremias N Brand
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Gudrun Viktorin
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Jack O Mitchell
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Lukas Schärer
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel 4051, Switzerland
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12
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Lyu M, Lai H, Wang Y, Zhou Y, Chen Y, Wu D, Chen J, Ying B. Roles of alternative splicing in infectious diseases: from hosts, pathogens to their interactions. Chin Med J (Engl) 2023; 136:767-779. [PMID: 36893312 PMCID: PMC10150853 DOI: 10.1097/cm9.0000000000002621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Indexed: 03/11/2023] Open
Abstract
ABSTRACT Alternative splicing (AS) is an evolutionarily conserved mechanism that removes introns and ligates exons to generate mature messenger RNAs (mRNAs), extremely improving the richness of transcriptome and proteome. Both mammal hosts and pathogens require AS to maintain their life activities, and inherent physiological heterogeneity between mammals and pathogens makes them adopt different ways to perform AS. Mammals and fungi conduct a two-step transesterification reaction by spliceosomes to splice each individual mRNA (named cis -splicing). Parasites also use spliceosomes to splice, but this splicing can occur among different mRNAs (named trans -splicing). Bacteria and viruses directly hijack the host's splicing machinery to accomplish this process. Infection-related changes are reflected in the spliceosome behaviors and the characteristics of various splicing regulators (abundance, modification, distribution, movement speed, and conformation), which further radiate to alterations in the global splicing profiles. Genes with splicing changes are enriched in immune-, growth-, or metabolism-related pathways, highlighting approaches through which hosts crosstalk with pathogens. Based on these infection-specific regulators or AS events, several targeted agents have been developed to fight against pathogens. Here, we summarized recent findings in the field of infection-related splicing, including splicing mechanisms of pathogens and hosts, splicing regulation and aberrant AS events, as well as emerging targeted drugs. We aimed to systemically decode host-pathogen interactions from a perspective of splicing. We further discussed the current strategies of drug development, detection methods, analysis algorithms, and database construction, facilitating the annotation of infection-related splicing and the integration of AS with disease phenotype.
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Affiliation(s)
- Mengyuan Lyu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongli Lai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yili Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dongsheng Wu
- Department of Thoracic Surgery and Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jie Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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13
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Liu S, Ni Y, Li J, Zhang X, Yang H, Chen H, Liu C. CPGView: A package for visualizing detailed chloroplast genome structures. Mol Ecol Resour 2023; 23:694-704. [PMID: 36587992 DOI: 10.1111/1755-0998.13729] [Citation(s) in RCA: 207] [Impact Index Per Article: 207.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 10/23/2022] [Accepted: 11/01/2022] [Indexed: 01/03/2023]
Abstract
Chloroplast genomes have been widely used in studying plant phylogeny and evolution. Several chloroplast genome visualization tools have been developed to display the distribution of genes on the genome. However, these tools do not draw features, such as exons, introns, repetitive elements, and variable sites, disallowing in-depth examination of the genome structures. Here, we developed and validated a software package called Chloroplast Genome Viewers (CPGView). CPGView can draw three maps showing (i) the distributions of genes, variable sites, and repetitive sequences, including microsatellites, tandem and dispersed repeats; (ii) the structure of the cis-splicing genes after adjusting the exon-intron boundary positions using a coordinate scaling algorithm, and (iii) the structure of the trans-splicing gene rps12. To test the accuracy of CPGView, we sequenced, assembled, and annotated 31 chloroplast genomes from 31 genera of 22 families. CPGView drew maps correctly for all the 31 chloroplast genomes. Lastly, we used CPGView to examine 5998 publicly released chloroplast genomes from 2513 genera of 553 families. CPGView succeeded in plotting maps for 5882 but failed to plot maps for 116 chloroplast genomes. Further examination showed that the annotations of these 116 genomes had various errors needing manual correction. The test on newly generated data and publicly available data demonstrated the ability of CPGView to identify errors in the annotations of chloroplast genomes. CPGView will become a widely used tool to study the detailed structure of chloroplast genomes. The web version of CPGView can be accessed from http://www.1kmpg.cn/cpgview.
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Affiliation(s)
- Shengyu Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Department of Medical Data Sharing, Institute of Medical Information & Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yang Ni
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jingling Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyi Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Heyu Yang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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14
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Martinez P, Ustyantsev K, Biryukov M, Mouton S, Glasenburg L, Sprecher SG, Bailly X, Berezikov E. Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on body plan evolution and photosymbiosis. G3 (BETHESDA, MD.) 2023; 13:jkac336. [PMID: 36542495 PMCID: PMC9911081 DOI: 10.1093/g3journal/jkac336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found, mostly, lying in large pools on the surface of sand at low tide. As a member of the Acoela it has been thought as a proxy for ancestral bilaterian animals; however, its phylogenetic position remains still debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic species S. roscoffensis. The size of this genome was measured to be in the range of 910-940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate it. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.
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Affiliation(s)
- Pedro Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona 08193, Spain
| | - Kirill Ustyantsev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Mikhail Biryukov
- Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
| | - Stijn Mouton
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Liza Glasenburg
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
| | - Simon G Sprecher
- Department of Biology, University of Fribourg, Chemin du Musee 10, 1700 Fribourg, Switzerland
| | - Xavier Bailly
- Station Biologique de Roscoff, Multicellular Marine Models (M3) team, FR2424, CNRS/Sorbonne Université—Place Georges Teissier, 29680 Roscoff, France
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen 9700AD, The Netherlands
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15
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Oliveira C, Holetz FB, Alves LR, Ávila AR. Modulation of Virulence Factors during Trypanosoma cruzi Differentiation. Pathogens 2022; 12:pathogens12010032. [PMID: 36678380 PMCID: PMC9865030 DOI: 10.3390/pathogens12010032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Chagas disease is a neglected tropical disease caused by Trypanosoma cruzi. This protozoan developed several mechanisms to infect, propagate, and survive in different hosts. The specific expression of proteins is responsible for morphological and metabolic changes in different parasite stages along the parasite life cycle. The virulence strategies at the cellular and molecular levels consist of molecules responsible for mediating resistance mechanisms to oxidative damage, cellular invasion, and immune evasion, performed mainly by surface proteins. Since parasite surface coat remodeling is crucial to invasion and infectivity, surface proteins are essential virulence elements. Understanding the factors involved in these processes improves the knowledge of parasite pathogenesis. Genome sequencing has opened the door to high-throughput technologies, allowing us to obtain a deeper understanding of gene reprogramming along the parasite life cycle and identify critical molecules for survival. This review therefore focuses on proteins regulated during differentiation into infective forms considered virulence factors and addresses the current known mechanisms acting in the modulation of gene expression, emphasizing mRNA signals, regulatory factors, and protein complexes.
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Affiliation(s)
- Camila Oliveira
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Centre de Recherche CERVO, Université Laval, Québec City, QC G1V 0A6, Canada
| | - Fabíola Barbieri Holetz
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
| | - Lysangela Ronalte Alves
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Research Center in Infectious Diseases, Division of Infectious Disease and Immunity CHU de Quebec Research Center, University Laval, Québec City, QC G1V 4G2, Canada
| | - Andréa Rodrigues Ávila
- Laboratório de Pesquisa em Apicomplexa, Instituto Carlos Chagas, Fiocruz Paraná, Curitiba 81350-010, Brazil
- Correspondence: ; Tel.: +55-41-33163230
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16
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Wang Q, Chen J, Singh S, Xie Z, Qin F, Shi X, Cornelison R, Li H, Huang H. Profile of chimeric RNAs and TMPRSS2-ERG e2e4 isoform in neuroendocrine prostate cancer. Cell Biosci 2022; 12:153. [PMID: 36088396 PMCID: PMC9463804 DOI: 10.1186/s13578-022-00893-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose Specific gene fusions and their fusion products (chimeric RNA and protein) have served as ideal diagnostic markers and therapeutic targets for cancer. However, few systematic studies for chimeric RNAs have been conducted in neuroendocrine prostate cancer (NEPC). In this study, we explored the landscape of chimeric RNAs in different types of prostate cancer (PCa) cell lines and aimed to identify chimeric RNAs specifically expressed in NEPC. Methods To do so, we employed the RNA-seq data of eight prostate related cell lines from Cancer Cell Line Encyclopedia (CCLE) for chimeric RNA identification. Multiple filtering criteria were used and the candidate chimeric RNAs were characterized at multiple levels and from various angles. We then performed experimental validation on all 80 candidates, and focused on the ones that are specific to NEPC. Lastly, we studied the clinical relevance and effect of one chimera in neuroendocrine process. Results Out of 80 candidates, 15 were confirmed to be expressed preferentially in NEPC lines. Among them, 13 of the 15 were found to be specifically expressed in NEPC, and four were further validated in another NEPC cell line. Importantly, in silico analysis showed that tumor malignancy may be correlated to the level of these chimeric RNAs. Clinically, the expression of TMPRSS2-ERG (e2e4) was elevated in tumor tissues and indicated poor clinical prognosis, whereas the parental wild type transcripts had no such association. Furthermore, compared to the most frequently detected TMPRSS2-ERG form (e1e4), e2e4 encodes 31 more amino acids and accelerated neuroendocrine process of prostate cancer. Conclusions In summary, these findings painted the landscape of chimeric RNA in NEPC and supported the idea that some chimeric RNAs may represent additional biomarkers and/or treatment targets independent of parental gene transcripts. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00893-5.
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17
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Alacid E, Irwin NAT, Smilansky V, Milner DS, Kilias ES, Leonard G, Richards TA. A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa. Open Biol 2022; 12:220126. [PMID: 36000319 PMCID: PMC9399869 DOI: 10.1098/rsob.220126] [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] [Indexed: 11/16/2022] Open
Abstract
Spliced-leader trans-splicing (SLTS) has been described in distantly related eukaryotes and acts to mark mRNAs with a short 5′ exon, giving different mRNAs identical 5′ sequence-signatures. The function of these systems is obscure. Perkinsozoa encompasses a diversity of parasitic protists that infect bivalves, toxic-tide dinoflagellates, fish and frog tadpoles. Here, we report considerable sequence variation in the SLTS-system across the Perkinsozoa and find that multiple variant SLTS-systems are encoded in parallel in the ecologically important Perkinsozoa parasite Parvilucifera sinerae. These results demonstrate that the transcriptome of P. sinerae is segregated based on the addition of different spliced-leader (SL) exons. This segregation marks different gene categories, suggesting that SL-segregation relates to functional differentiation of the transcriptome. By contrast, both sets of gene categories are present in the single SL-transcript type sampled from Maranthos, implying that the SL-segregation of the Parvilucifera transcriptome is a recent evolutionary innovation. Furthermore, we show that the SLTS-system marks a subsection of the transcriptome with increased mRNA abundance and includes genes that encode the spliceosome system necessary for SLTS-function. Collectively, these data provide a picture of how the SLTS-systems can vary within a major evolutionary group and identify how additional transcriptional-complexity can be achieved through SL-segregation.
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Affiliation(s)
- Elisabet Alacid
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Nicholas A T Irwin
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK.,Merton College, University of Oxford, Oxford, Oxfordshire OX1 4JD, UK
| | - Vanessa Smilansky
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - David S Milner
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Estelle S Kilias
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
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18
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Fasimoye RY, Spencer R, Soto-Martin E, Eijlers P, Elmassoudi H, Brivio S, Mangana C, Sabele V, Rechtorikova R, Wenzel M, Connolly B, Pettitt J, Müller B. A novel, essential trans-splicing protein connects the nematode SL1 snRNP to the CBC-ARS2 complex. Nucleic Acids Res 2022; 50:7591-7607. [PMID: 35736244 PMCID: PMC9303266 DOI: 10.1093/nar/gkac534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/29/2022] Open
Abstract
Spliced leader trans-splicing is essential for gene expression in many eukaryotes. To elucidate the molecular mechanism of this process, we characterise the molecules associated with the Caenorhabditis elegans major spliced leader snRNP (SL1 snRNP), which donates the spliced leader that replaces the 5' untranslated region of most pre-mRNAs. Using a GFP-tagged version of the SL1 snRNP protein SNA-1 created by CRISPR-mediated genome engineering, we immunoprecipitate and identify RNAs and protein components by RIP-Seq and mass spectrometry. This reveals the composition of the SL1 snRNP and identifies associations with spliceosome components PRP-8 and PRP-19. Significantly, we identify a novel, nematode-specific protein required for SL1 trans-splicing, which we designate SNA-3. SNA-3 is an essential, nuclear protein with three NADAR domains whose function is unknown. Mutation of key residues in NADAR domains inactivates the protein, indicating that domain function is required for activity. SNA-3 interacts with the CBC-ARS2 complex and other factors involved in RNA metabolism, including SUT-1 protein, through RNA or protein-mediated contacts revealed by yeast two-hybrid assays, localisation studies and immunoprecipitations. Our data are compatible with a role for SNA-3 in coordinating trans-splicing with target pre-mRNA transcription or in the processing of the Y-branch product of the trans-splicing reaction.
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Affiliation(s)
- Rotimi Yemi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Rosie Elizabeth Barker Spencer
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Haitem Elmassoudi
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Sarah Brivio
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Carolina Mangana
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Viktorija Sabele
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Radoslava Rechtorikova
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Marius Wenzel
- Centre of Genome-Enabled Biology and Medicine, University of Aberdeen, 23 St Machar Drive, Aberdeen AB24 3RY, Scotland, UK
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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19
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Hou S, Li G, Xu B, Dong H, Zhang S, Fu Y, Shi J, Li L, Fu J, Shi F, Meng Y, Jin Y. Trans-splicing facilitated by RNA pairing greatly expands sDscam isoform diversity but not homophilic binding specificity. SCIENCE ADVANCES 2022; 8:eabn9458. [PMID: 35857463 PMCID: PMC9258826 DOI: 10.1126/sciadv.abn9458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
The Down syndrome cell adhesion molecule 1 (Dscam1) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for nervous and immune functions. Chelicerates generate approximately 50 to 100 shortened Dscam (sDscam) isoforms by alternative promoters, similar to mammalian protocadherins. Here, we reveal that trans-splicing markedly increases the repository of sDscamβ isoforms in Tetranychus urticae. Unexpectedly, every variable exon cassette engages in trans-splicing with constant exons from another cluster. Moreover, we provide evidence that competing RNA pairing not only governs alternative cis-splicing but also facilitates trans-splicing. Trans-spliced sDscam isoforms mediate cell adhesion ability but exhibit the same homophilic binding specificity as their cis-spliced counterparts. Thus, we reveal a single sDscam locus that generates diverse adhesion molecules through cis- and trans-splicing coupled with alternative promoters. These findings expand understanding of the mechanism underlying molecular diversity and have implications for the molecular control of neuronal and/or immune specificity.
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Affiliation(s)
- Shouqing Hou
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Guo Li
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Jiayan Fu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang ZJ310018, P. R. China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
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20
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Jhaveri N, van den Berg W, Hwang BJ, Muller HM, Sternberg PW, Gupta BP. Genome annotation of Caenorhabditis briggsae by TEC-RED identifies new exons, paralogs, and conserved and novel operons. G3 (BETHESDA, MD.) 2022; 12:jkac101. [PMID: 35485953 PMCID: PMC9258526 DOI: 10.1093/g3journal/jkac101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/14/2022] [Indexed: 11/14/2022]
Abstract
The nematode Caenorhabditis briggsae is routinely used in comparative and evolutionary studies involving its well-known cousin Caenorhabditis elegans. The C. briggsae genome sequence has accelerated research by facilitating the generation of new resources, tools, and functional studies of genes. While substantial progress has been made in predicting genes and start sites, experimental evidence is still lacking in many cases. Here, we report an improved annotation of the C. briggsae genome using the trans-spliced exon coupled RNA end determination technique. In addition to identifying the 5' ends of expressed genes, we have discovered operons and paralogs. In summary, our analysis yielded 10,243 unique 5' end sequence tags with matches in the C. briggsae genome. Of these, 6,395 were found to represent 4,252 unique genes along with 362 paralogs and 52 previously unknown exons. These genes included 14 that are exclusively trans-spliced in C. briggsae when compared with C. elegans orthologs. A major contribution of this study is the identification of 492 high confidence operons, of which two-thirds are fully supported by tags. In addition, 2 SL1-type operons were discovered. Interestingly, comparisons with C. elegans showed that only 40% of operons are conserved. Of the remaining operons, 73 are novel, including 12 that entirely lack orthologs in C. elegans. Further analysis revealed that 4 of the 12 novel operons are conserved in Caenorhabditis nigoni. Altogether, the work described here has significantly advanced our understanding of the C. briggsae system and serves as a rich resource to aid biological studies involving this species.
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Affiliation(s)
- Nikita Jhaveri
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | | | - Byung Joon Hwang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
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21
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Karaoglanoglu F, Chauve C, Hach F. Genion, an accurate tool to detect gene fusion from long transcriptomics reads. BMC Genomics 2022; 23:129. [PMID: 35164688 PMCID: PMC8842519 DOI: 10.1186/s12864-022-08339-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/27/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The advent of next-generation sequencing technologies empowered a wide variety of transcriptomics studies. A widely studied topic is gene fusion which is observed in many cancer types and suspected of having oncogenic properties. Gene fusions are the result of structural genomic events that bring two genes closely located and result in a fused transcript. This is different from fusion transcripts created during or after the transcription process. These chimeric transcripts are also known as read-through and trans-splicing transcripts. Gene fusion discovery with short reads is a well-studied problem, and many methods have been developed. But the sensitivity of these methods is limited by the technology, especially the short read length. Advances in long-read sequencing technologies allow the generation of long transcriptomics reads at a low cost. Transcriptomic long-read sequencing presents unique opportunities to overcome the shortcomings of short-read technologies for gene fusion detection while introducing new challenges. RESULTS We present Genion, a sensitive and fast gene fusion detection method that can also detect read-through events. We compare Genion against a recently introduced long-read gene fusion discovery method, LongGF, both on simulated and real datasets. On simulated data, Genion accurately identifies the gene fusions and its clustering accuracy for detecting fusion reads is better than LongGF. Furthermore, our results on the breast cancer cell line MCF-7 show that Genion correctly identifies all the experimentally validated gene fusions. CONCLUSIONS Genion is an accurate gene fusion caller. Genion is implemented in C++ and is available at https://github.com/vpc-ccg/genion .
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Affiliation(s)
- Fatih Karaoglanoglu
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada.,Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Cedric Chauve
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
| | - Faraz Hach
- Vancouver Prostate Centre, Vancouver, BC, Canada. .,Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada.
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22
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Ustyantsev KV, Berezikov EV. Computational analysis of spliced leader trans-splicing in the regenerative flatworm Macrostomum lignano reveals its prevalence in conserved and stem cell related genes. Vavilovskii Zhurnal Genet Selektsii 2021; 25:101-107. [PMID: 34901707 PMCID: PMC8629364 DOI: 10.18699/vj21.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 11/28/2022] Open
Abstract
In eukaryotes, trans-splicing is a process of nuclear pre-mRNA maturation where two different RNA molecules are joined together by the spliceosomal machinery utilizing mechanisms similar to cis-splicing. In diverse taxa of
lower eukaryotes, spliced leader (SL) trans-splicing is the most frequent type of trans-splicing, when the same sequence
derived from short small nuclear RNA molecules, called SL RNAs, is attached to the 5’ ends of different non-processed
pre-mRNAs. One of the functions of SL trans-splicing is processing polycistronic pre-mRNA molecules transcribed from
operons, when several genes are transcribed as one pre-mRNA molecule. However, only a fraction of trans-spliced
genes reside in operons, suggesting that SL trans-splicing must also have some other, less understood functions. Regenerative flatworms are informative model organisms which hold the keys to understand the mechanism of stem
cell regulation and specialization during regeneration and homeostasis. Their ability to regenerate is fueled by the
division and differentiation of the adult somatic stem cell population called neoblasts. Macrostomum lignano is a flatworm model organism where substantial technological advances have been achieved in recent years, including the
development of transgenesis. Although a large fraction of genes in M. lignano were estimated to be SL trans-spliced,
SL trans-splicing was not studied in detail in M. lignano before. Here, we performed the first comprehensive study of
SL trans-splicing in M. lignano. By reanalyzing the existing genome and transcriptome data of M. lignano, we estimate
that 30 % of its genes are SL trans-spliced, 15 % are organized in operons, and almost 40 % are both SL trans-spliced
and in operons. We annotated and characterized the sequence of SL RNA and characterized conserved cis- and SL transsplicing motifs. Finally, we found that a majority of SL trans-spliced genes are evolutionarily conserved and significantly
over-represented in neoblast-specific genes. Our findings suggest an important role of SL trans-splicing in the regulation and maintenance of neoblasts in M. lignano.
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Affiliation(s)
- K V Ustyantsev
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Berezikov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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23
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Yang HP, Wenzel M, Hauser DA, Nelson JM, Xu X, Eliáš M, Li FW. Monodopsis and Vischeria Genomes Shed New Light on the Biology of Eustigmatophyte Algae. Genome Biol Evol 2021; 13:6402010. [PMID: 34665222 PMCID: PMC8570151 DOI: 10.1093/gbe/evab233] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2021] [Indexed: 11/12/2022] Open
Abstract
Members of eustigmatophyte algae, especially Nannochloropsis and Microchloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. Although extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis and Microchloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis strains C73 and C141 (60 Mb) and Vischeria strain C74 (106 Mb), which are the sister groups to Nannochloropsis and Microchloropsis in the order Eustigmatales. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis and Microchloropsis, long interspersed nuclear element repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and nonmevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis and Microchloropsis that have only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis and Microchloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
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Affiliation(s)
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | | | | | - Xia Xu
- Boyce Thompson Institute, Ithaca, New York, USA
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York, USA.,Plant Biology Section, Cornell University, USA
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24
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Chung S, Le TP, Vishwakarma V, Cheng YL, Andrew DJ. Isoform-specific roles of the Drosophila filamin-type protein Jitterbug (Jbug) during development. Genetics 2021; 219:iyab100. [PMID: 34173831 PMCID: PMC8860385 DOI: 10.1093/genetics/iyab100] [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: 05/11/2021] [Accepted: 06/20/2021] [Indexed: 11/14/2022] Open
Abstract
Filamins are highly conserved actin-crosslinking proteins that regulate organization of the actin cytoskeleton. As key components of versatile signaling scaffolds, filamins are implicated in developmental anomalies and cancer. Multiple isoforms of filamins exist, raising the possibility of distinct functions for each isoform during development and in disease. Here, we provide an initial characterization of jitterbug (jbug), which encodes one of the two filamin-type proteins in Drosophila. We generate Jbug antiserum that recognizes all of the spliced forms and reveals differential expression of different Jbug isoforms during development, and a significant maternal contribution of Jbug protein. To reveal the function of Jbug isoforms, we create new genetic tools, including a null allele that deletes all isoforms, hypomorphic alleles that affect only a subset, and UAS lines for Gal4-driven expression of the major isoforms. Using these tools, we demonstrate that Jbug is required for viability and that specific isoforms are required in the formation of actin-rich protrusions including thoracic bristles in adults and ventral denticles in the embryo. We also show that specific isoforms of Jbug show differential localization within epithelia and that maternal and zygotic loss of jbug disrupts Crumbs (Crb) localization in several epithelial cell types.
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Affiliation(s)
- SeYeon Chung
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Thao Phuong Le
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vishakha Vishwakarma
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Yim Ling Cheng
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deborah J Andrew
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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25
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Yu E, Yamaji N, Mochida K, Galis I, Asaka K, Ma JF. LYSINE KETOGLUTARATE REDUCTASE TRANS-SPLICING RELATED 1 is involved in temperature-dependent root growth in rice. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6336-6349. [PMID: 34037776 DOI: 10.1093/jxb/erab240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Root length is an important root parameter directly related to the uptake of water and nutrients. However, the molecular mechanisms controlling root length are still not fully understood. Here, we isolated a short-root mutant of rice, dice2 (defective in cell elongation 2). The cell length and meristem size of the roots were decreased in dice2, but the root function in terms of mineral element uptake, root cell width, and root anatomy were hardly altered compared with wild-type (WT) rice. The root growth defect in dice2 could be partially rescued by high temperature. Map-based cloning combined with a complementation test revealed that the short-root phenotype was caused by a nonsense mutation in a gene which was annotated to encode Lysine Ketoglutarate Reductase Trans-Splicing related 1 (OsLKRT1). OsLKRT1, encoding a cytosol-localized protein, was expressed in all cells of the root tip and elongation region as well as the shoot. RNA-seq analysis showed that there was no difference between dice2 and the WT in the expression level of genes involved in root development identified so far. These results indicate that OsLKRT1 is involved in a novel pathway required for root cell elongation in rice, although its exact role remains to be further investigated.
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Affiliation(s)
- En Yu
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
| | - Naoki Yamaji
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
| | - Keiich Mochida
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Japan
| | - Ivan Galis
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
| | - Kanatani Asaka
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, Japan
| | - Jian Feng Ma
- Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki, Japan
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26
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Abstract
Historically, it has been understood that for gene expression in eukaryotes, each messenger RNA encodes a single protein. With the recent development of technologies to sequence full-length transcripts en masse, we have discovered hundreds of examples in two species of green algae where two, three, or more proteins are translated from a single transcript. These “polycistronic” transcripts are found in diverse species throughout the green algal lineage, which highlights their biological importance. We have leveraged these findings to coexpress pairs of genes on polycistronic transcripts in vitro, which should facilitate efforts to engineer algae for research and industrial applications. Polycistronic gene expression, common in prokaryotes, was thought to be extremely rare in eukaryotes. The development of long-read sequencing of full-length transcript isomers (Iso-Seq) has facilitated a reexamination of that dogma. Using Iso-Seq, we discovered hundreds of examples of polycistronic expression of nuclear genes in two divergent species of green algae: Chlamydomonas reinhardtii and Chromochloris zofingiensis. Here, we employ a range of independent approaches to validate that multiple proteins are translated from a common transcript for hundreds of loci. A chromatin immunoprecipitation analysis using trimethylation of lysine 4 on histone H3 marks confirmed that transcription begins exclusively at the upstream gene. Quantification of polyadenylated [poly(A)] tails and poly(A) signal sequences confirmed that transcription ends exclusively after the downstream gene. Coexpression analysis found nearly perfect correlation for open reading frames (ORFs) within polycistronic loci, consistent with expression in a shared transcript. For many polycistronic loci, terminal peptides from both ORFs were identified from proteomics datasets, consistent with independent translation. Synthetic polycistronic gene pairs were transcribed and translated in vitro to recapitulate the production of two distinct proteins from a common transcript. The relative abundance of these two proteins can be modified by altering the Kozak-like sequence of the upstream gene. Replacement of the ORFs with selectable markers or reporters allows production of such heterologous proteins, speaking to utility in synthetic biology approaches. Conservation of a significant number of polycistronic gene pairs between C. reinhardtii, C. zofingiensis, and five other species suggests that this mechanism may be evolutionarily ancient and biologically important in the green algal lineage.
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27
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Razin SV, Ioudinkova ES, Kantidze OL, Iarovaia OV. Co-Regulated Genes and Gene Clusters. Genes (Basel) 2021; 12:907. [PMID: 34208174 PMCID: PMC8230824 DOI: 10.3390/genes12060907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/27/2022] Open
Abstract
There are many co-regulated genes in eukaryotic cells. The coordinated activation or repression of such genes occurs at specific stages of differentiation, or under the influence of external stimuli. As a rule, co-regulated genes are dispersed in the genome. However, there are also gene clusters, which contain paralogous genes that encode proteins with similar functions. In this aspect, they differ significantly from bacterial operons containing functionally linked genes that are not paralogs. In this review, we discuss the reasons for the existence of gene clusters in vertebrate cells and propose that clustering is necessary to ensure the possibility of selective activation of one of several similar genes.
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Affiliation(s)
- Sergey V. Razin
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Elena S. Ioudinkova
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Omar L. Kantidze
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
| | - Olga V. Iarovaia
- Institute of Gene Biology Russian Academy of Sciences, 119334 Moscow, Russia; (E.S.I.); (O.L.K.); (O.V.I.)
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28
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Kanakis I, Alameddine M, Folkes L, Moxon S, Myrtziou I, Ozanne SE, Peffers MJ, Goljanek-Whysall K, Vasilaki A. Small-RNA Sequencing Reveals Altered Skeletal Muscle microRNAs and snoRNAs Signatures in Weanling Male Offspring from Mouse Dams Fed a Low Protein Diet during Lactation. Cells 2021; 10:cells10051166. [PMID: 34064819 PMCID: PMC8150574 DOI: 10.3390/cells10051166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/07/2021] [Accepted: 05/09/2021] [Indexed: 12/18/2022] Open
Abstract
Maternal diet during gestation and lactation affects the development of skeletal muscles in offspring and determines muscle health in later life. In this paper, we describe the association between maternal low protein diet-induced changes in offspring skeletal muscle and the differential expression (DE) of small non-coding RNAs (sncRNAs). We used a mouse model of maternal protein restriction, where dams were fed either a normal (N, 20%) or a low protein (L, 8%) diet during gestation and newborns were cross-fostered to N or L lactating dams, resulting in the generation of NN, NL and LN offspring groups. Total body and tibialis anterior (TA) weights were decreased in weanling NL male offspring but were not different in the LN group, as compared to NN. However, histological evaluation of TA muscle revealed reduced muscle fibre size in both groups at weaning. Small RNA-sequencing demonstrated DE of multiple miRs, snoRNAs and snRNAs. Bioinformatic analyses of miRs-15a, -34a, -122 and -199a, in combination with known myomiRs, confirmed their implication in key muscle-specific biological processes. This is the first comprehensive report for the DE of sncRNAs in nutrition-associated programming of skeletal muscle development, highlighting the need for further research to unravel the detailed molecular mechanisms.
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Affiliation(s)
- Ioannis Kanakis
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester CH2 1BR, UK;
- Correspondence: or
| | - Moussira Alameddine
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
| | - Leighton Folkes
- School of Biological Sciences, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, UK; (L.F.); (S.M.)
| | - Simon Moxon
- School of Biological Sciences, Faculty of Science, University of East Anglia, Norwich NR4 7TJ, UK; (L.F.); (S.M.)
| | - Ioanna Myrtziou
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester CH2 1BR, UK;
| | - Susan E. Ozanne
- Metabolic Research Laboratories, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK;
| | - Mandy J. Peffers
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
| | - Katarzyna Goljanek-Whysall
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
- Department of Physiology, School of Medicine and REMEDI, CMNHS, NUI Galway, Galway H91 TK33, Ireland
| | - Aphrodite Vasilaki
- Department of Musculoskeletal & Ageing Science, Institute of Life Course & Medical Sciences, Faculty of Health & Life Sciences, University of Liverpool, Liverpool L7 8TX, UK; (M.A.); (M.J.P.); (K.G.-W.); (A.V.)
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29
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Wenzel MA, Müller B, Pettitt J. SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data. BMC Bioinformatics 2021; 22:140. [PMID: 33752599 PMCID: PMC7986045 DOI: 10.1186/s12859-021-04009-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/08/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Spliced leader (SL) trans-splicing replaces the 5' end of pre-mRNAs with the spliced leader, an exon derived from a specialised non-coding RNA originating from elsewhere in the genome. This process is essential for resolving polycistronic pre-mRNAs produced by eukaryotic operons into monocistronic transcripts. SL trans-splicing and operons may have independently evolved multiple times throughout Eukarya, yet our understanding of these phenomena is limited to only a few well-characterised organisms, most notably C. elegans and trypanosomes. The primary barrier to systematic discovery and characterisation of SL trans-splicing and operons is the lack of computational tools for exploiting the surge of transcriptomic and genomic resources for a wide range of eukaryotes. RESULTS Here we present two novel pipelines that automate the discovery of SLs and the prediction of operons in eukaryotic genomes from RNA-Seq data. SLIDR assembles putative SLs from 5' read tails present after read alignment to a reference genome or transcriptome, which are then verified by interrogating corresponding SL RNA genes for sequence motifs expected in bona fide SL RNA molecules. SLOPPR identifies RNA-Seq reads that contain a given 5' SL sequence, quantifies genome-wide SL trans-splicing events and predicts operons via distinct patterns of SL trans-splicing events across adjacent genes. We tested both pipelines with organisms known to carry out SL trans-splicing and organise their genes into operons, and demonstrate that (1) SLIDR correctly detects expected SLs and often discovers novel SL variants; (2) SLOPPR correctly identifies functionally specialised SLs, correctly predicts known operons and detects plausible novel operons. CONCLUSIONS SLIDR and SLOPPR are flexible tools that will accelerate research into the evolutionary dynamics of SL trans-splicing and operons throughout Eukarya and improve gene discovery and annotation for a wide range of eukaryotic genomes. Both pipelines are implemented in Bash and R and are built upon readily available software commonly installed on most bioinformatics servers. Biological insight can be gleaned even from sparse, low-coverage datasets, implying that an untapped wealth of information can be retrieved from existing RNA-Seq datasets as well as from novel full-isoform sequencing protocols as they become more widely available.
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Affiliation(s)
- Marius A Wenzel
- School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen, AB24 2TZ, UK.
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
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30
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Wang L, Zhang W, Liu S, Tian Y, Liu X, Yan H, Cai Y, Teng X, Dong H, Chen R, Jiang X, Wang Y, Wan J. Rice FLOURY SHRUNKEN ENDOSPERM 5 Encodes a Putative Plant Organelle RNA Recognition Protein that Is Required for cis-Splicing of Mitochondrial nad4 Intron 1. RICE (NEW YORK, N.Y.) 2021; 14:29. [PMID: 33689034 PMCID: PMC7947098 DOI: 10.1186/s12284-021-00463-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The sequences of several important mitochondrion-encoded genes involved in respiration in higher plants are interrupted by introns. Many nuclear-encoded factors are involved in splicing these introns, but the mechanisms underlying this splicing remain unknown. RESULTS We isolated and characterized a rice mutant named floury shrunken endosperm 5 (fse5). In addition to having floury shrunken endosperm, the fse5 seeds either failed to germinate or produced seedlings which grew slowly and died ultimately. Fse5 encodes a putative plant organelle RNA recognition (PORR) protein targeted to mitochondria. Mutation of Fse5 hindered the splicing of the first intron of nad4, which encodes an essential subunit of mitochondrial NADH dehydrogenase complex I. The assembly and NADH dehydrogenase activity of complex I were subsequently disrupted by this mutation, and the structure of the mitochondria was abnormal in the fse5 mutant. The FSE5 protein was shown to interact with mitochondrial intron splicing factor 68 (MISF68), which is also a splicing factor for nad4 intron 1 identified previously via yeast two-hybrid (Y2H) assays. CONCLUSION Fse5 which encodes a PORR domain-containing protein, is essential for the splicing of nad4 intron 1, and loss of Fse5 function affects seed development and seedling growth.
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Affiliation(s)
- Liang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shijia Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunlu Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xi Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xuan Teng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Dong
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongbo Chen
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaokang Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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Ershov NI, Maslov DE, Bondar NP. Evaluation of various RNA-seq approaches for identification of gene outrons in the flatworm Opisthorchis felineus. Vavilovskii Zhurnal Genet Selektsii 2020; 24:897-904. [PMID: 35088003 PMCID: PMC8763715 DOI: 10.18699/vj20.688] [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: 03/21/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 11/19/2022] Open
Abstract
The parasitic flatworm Opisthorchis felineus is one of the causative agents of opisthorchiasis in humans.
Recently, we assembled the O. felineus genome, but the correct genome annotation by means of standard methods was hampered by the presence of spliced leader trans-splicing (SLTS). As a result of SLTS, the original 5’-end
(outron) of the transcripts is replaced by a short spliced leader sequence donated from a specialized SL RNA. SLTS
is involved in the RNA processing of more than half of O. felineus genes, making it hard to determine the structure
of outrons and bona fide transcription start sites of the corresponding genes and operons, being based solely on
mRNA-seq data. In the current study, we tested various experimental approaches for identifying the sequences of
outrons in O. felineus using massive parallel sequencing. Two of them were developed by us for targeted sequencing of already processed branched outrons. One was based on sequence-specific reverse transcription from the
SL intron toward the 5’-end of the Y-branched outron. The other used outron hybridization with an immobilized
single-stranded DNA probe complementary to the SL intron. Additionally, two approaches to the sequencing of
rRNA-depleted total RNA were used, allowing the identification of a wider range of transcripts compared to mRNAseq. One is based on the enzymatic elimination of overrepresented cDNAs, the other utilizes exonucleolytic degradation of uncapped RNA by Terminator enzyme. By using the outron-targeting methods, we were not able to
obtain the enrichment of RNA preparations by processed outrons, which is most likely indicative of a rapid turnover
of these trans-splicing intermediate products. Of the two rRNA depletion methods, a method based on the enzymatic normalization of cDNA (Zymo-Seq RiboFree) showed high efficiency. Compared to mRNA-seq, it provides an
approximately twofold increase in the fraction of reads originating from outrons and introns. The results suggest
that unprocessed nascent transcripts are the main source of outron sequences in the RNA pool of O. felineus.
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Affiliation(s)
- N. I. Ershov
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences
| | | | - N. P. Bondar
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences;
Novosibirsk State University
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Wenzel M, Johnston C, Müller B, Pettitt J, Connolly B. Resolution of polycistronic RNA by SL2 trans-splicing is a widely conserved nematode trait. RNA (NEW YORK, N.Y.) 2020; 26:1891-1904. [PMID: 32887788 PMCID: PMC7668243 DOI: 10.1261/rna.076414.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Spliced leader trans-splicing is essential for the processing and translation of polycistronic RNAs generated by eukaryotic operons. In C. elegans, a specialized spliced leader, SL2, provides the 5' end for uncapped pre-mRNAs derived from polycistronic RNAs. Studies of other nematodes suggested that SL2-type trans-splicing is a relatively recent innovation, confined to Rhabditina, the clade containing C. elegans and its close relatives. Here we conduct a survey of transcriptome-wide spliced leader trans-splicing in Trichinella spiralis, a distant relative of C. elegans with a particularly diverse repertoire of 15 spliced leaders. By systematically comparing the genomic context of trans-splicing events for each spliced leader, we identified a subset of T. spiralis spliced leaders that are specifically used to process polycistronic RNAs-the first examples of SL2-type spliced leaders outside of Rhabditina. These T. spiralis spliced leader RNAs possess a perfectly conserved stem-loop motif previously shown to be essential for SL2-type trans-splicing in C. elegans We show that genes trans-spliced to these SL2-type spliced leaders are organized in operonic fashion, with short intercistronic distances. A subset of T. spiralis operons show conservation of synteny with C. elegans operons. Our work substantially revises our understanding of nematode spliced leader trans-splicing, showing that SL2 trans-splicing is a major mechanism for nematode polycistronic RNA processing, which may have evolved prior to the radiation of the Nematoda. This work has important implications for the improvement of genome annotation pipelines in nematodes and other eukaryotes with operonic gene organization.
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Affiliation(s)
- Marius Wenzel
- Centre of Genome-Enabled Biology and Medicine, University of Aberdeen, Aberdeen AB24 3RY, United Kingdom
| | - Christopher Johnston
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
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Amaral MD. How to determine the mechanism of action of CFTR modulator compounds: A gateway to theranostics. Eur J Med Chem 2020; 210:112989. [PMID: 33190956 DOI: 10.1016/j.ejmech.2020.112989] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The greatest challenge of 21st century biology is to fully understand mechanisms of disease to drive new approaches and medical innovation. Parallel to this is the huge biomedical endeavour of treating people through personalized medicine. Until now all CFTR modulator drugs that have entered clinical trials have been genotype-dependent. An emerging alternative is personalized/precision medicine in CF, i.e., to determine whether rare CFTR mutations respond to existing (or novel) CFTR modulator drugs by pre-assessing them directly on patient's tissues ex vivo, an approach also now termed theranostics. To administer the right drug to the right person it is essential to understand how drugs work, i.e., to know their mechanism of action (MoA), so as to predict their applicability, not just in certain mutations but also possibly in other diseases that share the same defect/defective pathway. Moreover, an understanding the MoA of a drug before it is tested in clinical trials is the logical path to drug discovery and can increase its chance for success and hence also approval. In conclusion, the most powerful approach to determine the MoA of a compound is to understand the underlying biology. Novel large datasets of intervenients in most biological processes, namely those emerging from the post-genomic era tools, are available and should be used to help in this task.
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Affiliation(s)
- Margarida D Amaral
- BioISI - Biosystems & Integrative Sciences Institute, Lisboa, Faculty of Sciences, University of Lisboa, Portugal.
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35
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Cheng L, Zhang Y, Zhang Y, Chen T, Xu YZ, Rong YS. Loss of the RNA trimethylguanosine cap is compatible with nuclear accumulation of spliceosomal snRNAs but not pre-mRNA splicing or snRNA processing during animal development. PLoS Genet 2020; 16:e1009098. [PMID: 33085660 PMCID: PMC7605716 DOI: 10.1371/journal.pgen.1009098] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/02/2020] [Accepted: 09/07/2020] [Indexed: 12/31/2022] Open
Abstract
The 2,2,7-trimethylguanosine (TMG) cap is one of the first identified modifications on eukaryotic RNAs. TMG, synthesized by the conserved Tgs1 enzyme, is abundantly present on snRNAs essential for pre-mRNA splicing. Results from ex vivo experiments in vertebrate cells suggested that TMG ensures nuclear localization of snRNAs. Functional studies of TMG using tgs1 mutations in unicellular organisms yield results inconsistent with TMG being indispensable for either nuclear import or splicing. Utilizing a hypomorphic tgs1 mutation in Drosophila, we show that TMG reduction impairs germline development by disrupting the processing, particularly of introns with smaller sizes and weaker splice sites. Unexpectedly, loss of TMG does not disrupt snRNAs localization to the nucleus, disputing an essential role of TMG in snRNA transport. Tgs1 loss also leads to defective 3' processing of snRNAs. Remarkably, stronger tgs1 mutations cause lethality without severely disrupting splicing, likely due to the preponderance of TMG-capped snRNPs. Tgs1, a predominantly nucleolar protein in Drosophila, likely carries out splicing-independent functions indispensable for animal development. Taken together, our results suggest that nuclear import is not a conserved function of TMG. As a distinctive structure on RNA, particularly non-coding RNA, we suggest that TMG prevents spurious interactions detrimental to the function of RNAs that it modifies.
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Affiliation(s)
- Lin Cheng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yu Zhang
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States of America
| | - Tao Chen
- School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Hengyang College of Medicine, University of South China, Hengyang, China
| | - Yong-Zhen Xu
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yikang S. Rong
- Hengyang College of Medicine, University of South China, Hengyang, China
- * E-mail:
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36
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Calvelo J, Juan H, Musto H, Koziol U, Iriarte A. SLFinder, a pipeline for the novel identification of splice-leader sequences: a good enough solution for a complex problem. BMC Bioinformatics 2020; 21:293. [PMID: 32640978 PMCID: PMC7346339 DOI: 10.1186/s12859-020-03610-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Nevertheless, its study across the tree of life is severely hindered by the problem of identifying the SL sequences that are being trans-spliced. RESULTS In this paper we present SLFinder, a four-step pipeline meant to identify de novo candidate SL sequences making very few assumptions regarding the SL sequence properties. The pipeline takes transcriptomic de novo assemblies and a reference genome as input and allows the user intervention on several points to account for unexpected features of the dataset. The strategy and its implementation were tested on real RNAseq data from species with and without SL Trans-Splicing. CONCLUSIONS SLFinder is capable to identify SL candidates with good precision in a reasonable amount of time. It is especially suitable for species with unknown SL sequences, generating candidate sequences for further refining and experimental validation.
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Affiliation(s)
- Javier Calvelo
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Hernán Juan
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Héctor Musto
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Uriel Koziol
- Sección Biología Celular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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Liu C, Zhang Y, Li X, Jia Y, Li F, Li J, Zhang Z. Evidence of constraint in the 3D genome for trans-splicing in human cells. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1380-1393. [PMID: 32221814 DOI: 10.1007/s11427-019-1609-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/04/2019] [Indexed: 10/24/2022]
Abstract
Fusion transcripts are commonly found in eukaryotes, and many aberrant fusions are associated with severe diseases, including cancer. One class of fusion transcripts is generated by joining separate transcripts through trans-splicing. However, the mechanism of trans-splicing in mammals remains largely elusive. Here we showed evidence to support an intuitive hypothesis that attributes trans-sphcing to the spatial proximity between premature transcripts. A novel trans-splicing detection tool (TSD) was developed to reliably identify intra-chromosomal trans-splicing events (iTSEs) from RNA-seq data. TSD can maintain a remarkable balance between sensitivity and accuracy, thus distinguishing it from most state-of-the-art tools. The accuracy of TSD was experimentally demonstrated by excluding potential false discovery from mosaic genome or template switching during PCR. We showed that iTSEs identified by TSD were frequently found between genomic regulatory elements, which are known to be more prone to interact with each other. Moreover, iTSE sites may be more physically adjacent to each other than random control in the tested human lymphoblastoid cell line according to Hi-C data. Our results suggest that trans-splicing and 3D genome architecture may be coupled in mammals and that our pipeline, TSD, may facilitate investigations of trans-splicing on a systematic and accurate level previously thought impossible.
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Affiliation(s)
- Cong Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiqun Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoli Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Jia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feifei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, 100101, China. .,School of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
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39
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Kaur B, Záhonová K, Valach M, Faktorová D, Prokopchuk G, Burger G, Lukeš J. Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. Nucleic Acids Res 2020; 48:2694-2708. [PMID: 31919519 PMCID: PMC7049700 DOI: 10.1093/nar/gkz1215] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/14/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
Diplonemids are highly abundant heterotrophic marine protists. Previous studies showed that their strikingly bloated mitochondrial genome is unique because of systematic gene fragmentation and manifold RNA editing. Here we report a comparative study of mitochondrial genome architecture, gene structure and RNA editing of six recently isolated, phylogenetically diverse diplonemid species. Mitochondrial gene fragmentation and modes of RNA editing, which include cytidine-to-uridine (C-to-U) and adenosine-to-inosine (A-to-I) substitutions and 3' uridine additions (U-appendage), are conserved across diplonemids. Yet as we show here, all these features have been pushed to their extremes in the Hemistasiidae lineage. For example, Namystynia karyoxenos has its genes fragmented into more than twice as many modules than other diplonemids, with modules as short as four nucleotides. Furthermore, we detected in this group multiple A-appendage and guanosine-to-adenosine (G-to-A) substitution editing events not observed before in diplonemids and found very rarely elsewhere. With >1,000 sites, C-to-U and A-to-I editing in Namystynia is nearly 10 times more frequent than in other diplonemids. The editing density of 12% in coding regions makes Namystynia's the most extensively edited transcriptome described so far. Diplonemid mitochondrial genome architecture, gene structure and post-transcriptional processes display such high complexity that they challenge all other currently known systems.
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Affiliation(s)
- Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
- Faculty of Science, Charles University, BIOCEV, 25250 Vestec, Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, H3T 1J4 Montreal, Canada
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, H3T 1J4 Montreal, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
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40
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Li R, Ren X, Ding Q, Bi Y, Xie D, Zhao Z. Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development. Genome Res 2020; 30:287-298. [PMID: 32024662 PMCID: PMC7050527 DOI: 10.1101/gr.251512.119] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 12/18/2019] [Indexed: 01/08/2023]
Abstract
Massively parallel sequencing of the polyadenylated RNAs has played a key role in delineating transcriptome complexity, including alternative use of an exon, promoter, 5′ or 3′ splice site or polyadenylation site, and RNA modification. However, reads derived from the current RNA-seq technologies are usually short and deprived of information on modification, compromising their potential in defining transcriptome complexity. Here, we applied a direct RNA sequencing method with ultralong reads using Oxford Nanopore Technologies to study the transcriptome complexity in Caenorhabditis elegans. We generated approximately six million reads using native poly(A)-tailed mRNAs from three developmental stages, with average read lengths ranging from 900 to 1100 nt. Around half of the reads represent full-length transcripts. To utilize the full-length transcripts in defining transcriptome complexity, we devised a method to classify the long reads as the same as existing transcripts or as a novel transcript using sequence mapping tracks rather than existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. The sets of genes with differential expression versus differential isoform usage over development are largely different, implying a fine-tuned regulation at isoform level. We also observed an unexpected increase in putative RNA modification in all bases in the coding region relative to the UTR, suggesting their possible roles in translation. The RNA reads and the method for read classification are expected to deliver new insights into RNA processing and modification and their underlying biology in the future.
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Affiliation(s)
- Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.,State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, 999077, China
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41
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LaRoche-Johnston F, Monat C, Cousineau B. Detection of Group II Intron-Generated Chimeric mRNAs in Bacterial Cells. Methods Mol Biol 2020; 2079:95-107. [PMID: 31728964 DOI: 10.1007/978-1-4939-9904-0_7] [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] [Indexed: 06/10/2023]
Abstract
Chimeric RNAs are the transcripts composed of exons from two separate genes or transcripts. Although the presence of these joined RNA molecules have mainly been documented in a variety of eukaryotes, we recently demonstrated that the Ll.LtrB group II intron, from the gram-positive bacterium Lactococcus lactis, can generate chimeric mRNAs through a novel intergenic trans-splicing pathway. Here we describe the detailed experimental procedures to detect group II intron-generated mRNA-mRNA chimeras from total RNA extracts using stringent reverse transcription conditions along with a reverse splicing-deficient group II intron as a negative control.
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Affiliation(s)
| | - Caroline Monat
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Benoit Cousineau
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada.
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42
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Xiao MS, Wilusz JE. An improved method for circular RNA purification using RNase R that efficiently removes linear RNAs containing G-quadruplexes or structured 3' ends. Nucleic Acids Res 2019; 47:8755-8769. [PMID: 31269210 PMCID: PMC6895279 DOI: 10.1093/nar/gkz576] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/05/2019] [Accepted: 06/20/2019] [Indexed: 01/08/2023] Open
Abstract
Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3′-5′ exonuclease RNase R. Here, we demonstrate that standard protocols involving RNase R can fail to digest >20% of all highly expressed linear RNAs, but these shortcomings can largely be overcome. RNAs with highly structured 3′ ends, including snRNAs and histone mRNAs, are naturally resistant to RNase R, but can be efficiently degraded once a poly(A) tail has been added to their ends. In addition, RNase R stalls in the body of many polyadenylated mRNAs, especially at G-rich sequences that have been previously annotated as G-quadruplex (G4) structures. Upon replacing K+ (which stabilizes G4s) with Li+ in the reaction buffer, we find that RNase R is now able to proceed through these sequences and fully degrade the mRNAs in their entirety. In total, our results provide important improvements to the current methods used to isolate circular RNAs as well as a way to reveal RNA structures that may naturally inhibit degradation by cellular exonucleases.
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Affiliation(s)
- Mei-Sheng Xiao
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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Santos Pereira-Dutra F, Cancela M, Valandro Meneghetti B, Bunselmeyer Ferreira H, Mariante Monteiro K, Zaha A. Functional characterization of the translation initiation factor eIF4E of Echinococcus granulosus. Parasitol Res 2019; 118:2843-2855. [PMID: 31401657 DOI: 10.1007/s00436-019-06421-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/02/2019] [Indexed: 01/24/2023]
Abstract
The eukaryotic initiation factor 4E (eIF4E) specifically recognizes the 5' mRNA cap, a rate-limiting step in the translation initiation process. Although the 7-methylguanosine cap (MMGcap) is the most common 5' cap structure in eukaryotes, the trans-splicing process that occurs in several organism groups, including nematodes and flatworms, leads to the addition of a trimethylguanosine cap (TMGcap) to some RNA transcripts. In some helminths, eIF4E can have a dual capacity to bind both MMGcap and TMGcap. In the present work, we evaluated the distribution of eIF4E protein sequences in platyhelminths and we showed that only one gene coding for eIF4E is present in most parasitic flatworms. Based on this result, we cloned the Echinococcus granulosus cDNA sequence encoding eIF4E in Escherichia coli, expressed the recombinant eIF4E as a fusion protein to GST, and tested its ability to capture mRNAs through the 5' cap using pull-down assay and qPCR. Our results indicate that the recombinant eIF4E was able to bind preferentially 5'-capped mRNAs compared with rRNAs from total RNA preparations of E. granulosus. By qPCR, we observed an enrichment in MMG-capped mRNA compared with TMG-capped mRNAs among Eg-eIF4E-GST pull-down RNAs. Eg-eIF4E structural model using the Schistosoma mansoni eIF4E as template showed to be well preserved with only a few differences between chemically similar amino acid residues at the binding sites. These data showed that E. granulosus eIF4E can be used as a potential tool to study full-length 5'-capped mRNA, besides being a potential drug target against parasitic flatworms.
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Affiliation(s)
- Filipe Santos Pereira-Dutra
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Martin Cancela
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Bruna Valandro Meneghetti
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil
| | - Henrique Bunselmeyer Ferreira
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil.,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
| | - Karina Mariante Monteiro
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil.,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil.,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
| | - Arnaldo Zaha
- Laboratório de Biologia Molecular de Cestodeos, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Avenida Bento Gonçalves, 9500, Caixa Postal 15053, Porto Alegre, RS, CEP 91501-970, Brazil. .,Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, UFRGS, Porto Alegre, Brazil. .,Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil.
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Pandarakalam GC, Speake M, McElroy S, Alturkistani A, Philippe L, Pettitt J, Müller B, Connolly B. A high-throughput screen for the identification of compounds that inhibit nematode gene expression by targeting spliced leader trans-splicing. Int J Parasitol Drugs Drug Resist 2019; 10:28-37. [PMID: 31015150 PMCID: PMC6479105 DOI: 10.1016/j.ijpddr.2019.04.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 02/05/2023]
Abstract
Infections with parasitic nematodes are among the most significant of the neglected tropical diseases affecting about a billion people living mainly in tropical regions with low economic activity. The most effective current strategy to control nematode infections involves large scale treatment programs with anthelmintic drugs. This strategy is at risk from the emergence of drug resistant parasites. Parasitic nematodes also affect livestock, which are treated with the same limited group of anthelmintic drugs. Livestock parasites resistant to single drugs, and even multi-drug resistant parasites, are appearing in many areas. There is therefore a pressing need for new anthelmintic drugs. Here we use the nematode Caenorhabditis elegans as a model for parasitic nematodes and demonstrate that sinefungin, a competitive inhibitor of methyltransferases, causes a delay in development and reduced fecundity, and inhibits spliced leader trans-splicing. Spliced leader trans-splicing is an essential step in gene expression that does not occur in the hosts of parasitic nematodes, and is therefore a potential target for new anthelmintic drugs. We have exploited the ability of sinefungin to inhibit spliced leader trans-splicing to adapt a green fluorescent protein based reporter gene assay that monitors spliced leader trans-splicing for high-throughput screening for new anthelmintic compounds. We have established a protocol for robust high-throughput screening, combining mechanical dispensing of living C. elegans into 384- or 1536- well plates with addition of compounds using an acoustic liquid dispenser, and the detection of the inhibition of SL trans-splicing using a microplate reader. We have tested this protocol in a first pilot screen and envisage that this assay will be a valuable tool in the search for new anthelmintic drugs.
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Affiliation(s)
- George Cherian Pandarakalam
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Michael Speake
- European Screening Centre, University of Dundee, Biocity Scotland, Bo'ness Road, Newhouse, ML1 5UH, Scotland, UK
| | - Stuart McElroy
- European Screening Centre, University of Dundee, Biocity Scotland, Bo'ness Road, Newhouse, ML1 5UH, Scotland, UK
| | - Ammar Alturkistani
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Lucas Philippe
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK.
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen, AB25 2ZD, UK
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45
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Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis. PLoS Genet 2019; 15:e1008028. [PMID: 31071079 PMCID: PMC6508621 DOI: 10.1371/journal.pgen.1008028] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/18/2019] [Indexed: 11/19/2022] Open
Abstract
Intron gigantism, where genes contain megabase-sized introns, is observed across species, yet little is known about its purpose or regulation. Here we identify a unique gene expression program utilized for the proper expression of genes with intron gigantism. We find that two Drosophila genes with intron gigantism, kl-3 and kl-5, are transcribed in a spatiotemporal manner over the course of spermatocyte differentiation, which spans ~90 hours. The introns of these genes contain megabases of simple satellite DNA repeats that comprise over 99% of the gene loci, and these satellite-DNA containing introns are transcribed. We identify two RNA-binding proteins that specifically localize to kl-3 and kl-5 transcripts and are needed for the successful transcription or processing of these genes. We propose that genes with intron gigantism require a unique gene expression program, which may serve as a platform to regulate gene expression during cellular differentiation. Introns are non-coding elements of eukaryotic genes, often containing important regulatory sequences. Curiously, some genes contain introns so large that more than 99% of the gene locus is non-coding. One of the best-studied large genes, Dystrophin, a causative gene for Duchenne Muscular Dystrophy, spans 2.2Mb, only 11kb of which is coding. This phenomenon, ‘intron gigantism’, is observed across species, yet little is known about its purpose or regulation. Here we identify a unique gene expression program utilized for the proper expression of genes with intron gigantism using Drosophila spermatogenic genes as a model system. We show that the gigantic introns of these genes are transcribed in line with the exons, likely as a single transcript. We identify two RNA-binding proteins that specifically localize to the site of transcription and are needed for the successful transcription or processing of these genes. We propose that genes with intron gigantism require a unique gene expression program, which may serve as a platform to regulate gene expression during cellular differentiation.
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46
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Gómez-Orte E, Sáenz-Narciso B, Zheleva A, Ezcurra B, de Toro M, López R, Gastaca I, Nilsen H, Sacristán MP, Schnabel R, Cabello J. Disruption of the Caenorhabditis elegans Integrator complex triggers a non-conventional transcriptional mechanism beyond snRNA genes. PLoS Genet 2019; 15:e1007981. [PMID: 30807579 PMCID: PMC6390993 DOI: 10.1371/journal.pgen.1007981] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 01/22/2019] [Indexed: 01/09/2023] Open
Abstract
Gene expression is generally regulated by recruitment of transcription factors and RNA polymerase II (RNAP II) to specific sequences in the gene promoter region. The Integrator complex mediates processing of small nuclear RNAs (snRNAs) as well as the initiation and release of paused RNAP II at specific genes in response to growth factors. Here we show that in C. elegans, disruption of the Integrator complex leads to transcription of genes located downstream of the snRNA loci via a non-conventional transcription mechanism based on the lack of processing of the snRNAs. RNAP II read-through generates long chimeric RNAs containing snRNA, the intergenic region and the mature mRNA of the downstream gene located in sense. These chimeric sn-mRNAs remain as untranslated long non-coding RNAs, in the case of U1- and U2-derived sn-mRNAs, but can be translated to proteins in the case of SL-derived sn-mRNAs. The transcriptional effect caused by disruption of the Integrator complex is not restricted to genes located downstream of the snRNA loci but also affects key regulators of signal transduction such as kinases and phosphatases. Our findings highlight that these transcriptional alterations may be behind the correlation between mutations in the Integrator complex and tumor transformation.
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Affiliation(s)
- Eva Gómez-Orte
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Beatriz Sáenz-Narciso
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Angelina Zheleva
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Begoña Ezcurra
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - María de Toro
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Rosario López
- Scientific Computing Group (GRUCACI), University of La Rioja, Logroño, La Rioja, Spain
| | - Irene Gastaca
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - María P. Sacristán
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Salamanca, Spain
| | - Ralf Schnabel
- Department of Developmental Genetics, Institute of Genetics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Juan Cabello
- Oncology Area, CIBIR (Center for Biomedical Research of La Rioja), Logroño, La Rioja, Spain
- * E-mail:
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Tang JX, Chen D, Deng SL, Li J, Li Y, Fu Z, Wang XX, Zhang Y, Chen SR, Liu YX. CRISPR/Cas9-mediated genome editing induces gene knockdown by altering the pre-mRNA splicing in mice. BMC Biotechnol 2018; 18:61. [PMID: 30285700 PMCID: PMC6171314 DOI: 10.1186/s12896-018-0472-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/20/2018] [Indexed: 11/18/2022] Open
Abstract
Background Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9 (CRISPR/Cas9) has been wildly used to generate gene knockout models through inducing indels causing frame-shift. However, there are few studies concerning the post-transcript effects caused by CRISPR-mediated genome editing. Results In the present study, we showed that gene knockdown model also could be generated using CRISPR-mediated gene editing by disrupting the boundary of exon and intron in mice (C57BL/6 J). CRISPR induced indel at the boundary of exon and intron (5′ splice site) caused alternative splicing and produced multiple different mRNAs, most of these mRNAs introduced premature termination codon causing down expression of the gene. Conclusions These results showed that alternative splicing mutants were able to generate through CRISPR-mediated genome editing by deleting the boundary of exon and intron causing disruption of 5′ splice site. Although alternative splicing was an unexpected outcome, this finding could be developed as a technology to generate gene knockdown models or to investigate pre-mRNA splicing. Electronic supplementary material The online version of this article (10.1186/s12896-018-0472-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ji-Xin Tang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Dafeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shou-Long Deng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanyuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheng Fu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiu-Xia Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Su-Ren Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yi-Xun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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48
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Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida KI, Inagaki Y, Obokata J. Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer. PLoS One 2018; 13:e0200961. [PMID: 30024971 PMCID: PMC6053224 DOI: 10.1371/journal.pone.0200961] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/04/2018] [Indexed: 02/04/2023] Open
Abstract
Paulinella micropora is a rhizarian thecate amoeba, belonging to a photosynthetic Paulinella species group that has a unique organelle termed chromatophore, whose cyanobacterial origin is distinct from that of plant and algal chloroplasts. Because acquisition of the chromatophore was quite a recent event compared with that of the chloroplast ancestor, the Paulinella species are thought to be model organisms for studying the early process of primary endosymbiosis. To obtain insight into how endosymbiotically transferred genes acquire expression competence in the host nucleus, here we analyzed the 5′ end sequences of the mRNAs of P. micropora MYN1 strain with the aid of a cap-trapper cDNA library. As a result, we found that mRNAs of 27 genes, including endosymbiotically transferred genes, possessed the common 5′ end sequence of 28–33 bases that were posttranscriptionally added by spliced leader (SL) trans-splicing. We also found two subtypes of SL RNA genes encoded by the P. micropora MYN1 genome. Differing from the other SL trans-splicing organisms that usually possess poly(A)-less SL RNAs, this amoeba has polyadenylated SL RNAs. In this study, we characterize the SL trans-splicing of this unique organism and discuss the putative merits of SL trans-splicing in functional gene transfer and genome evolution.
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Affiliation(s)
- Mitsuhiro Matsuo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Atsushi Katahata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Motomichi Matsuzaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mami Nomura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Ken-ichiro Ishida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
- * E-mail:
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Roy S, Jagus R, Morse D. Translation and Translational Control in Dinoflagellates. Microorganisms 2018; 6:microorganisms6020030. [PMID: 29642465 PMCID: PMC6027434 DOI: 10.3390/microorganisms6020030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/24/2022] Open
Abstract
Dinoflagellates are unicellular protists that feature a multitude of unusual nuclear features, including large genomes, packaging of DNA without histones, and multiple gene copies organized as tandem gene arrays. Furthermore, all dinoflagellate mRNAs experience trans-splicing with a common 22-nucleotide splice leader (SL) sequence. These features challenge some of the concepts and assumptions about the regulation of gene expression derived from work on model eukaryotes such as yeasts and mammals. Translational control in the dinoflagellates, based on extensive study of circadian bioluminescence and by more recent microarray and transcriptome analyses, is now understood to be a crucial element in regulating gene expression. A picture of the translation machinery of dinoflagellates is emerging from the recent availability of transcriptomes of multiple dinoflagellate species and the first complete genome sequences. The components comprising the translational control toolkit of dinoflagellates are beginning to take shape and are outlined here.
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Affiliation(s)
- Sougata Roy
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
| | - Rosemary Jagus
- Institute of Marine & Environmental Technology, University of Maryland Center for Environmental Science701 E. Pratt St., Baltimore, MD 21202, USA.
| | - David Morse
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke East, Montréal, QC H1X 2B2, Canada.
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Boroni M, Sammeth M, Gava SG, Jorge NAN, Macedo AM, Machado CR, Mourão MM, Franco GR. Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. Sci Rep 2018; 8:3877. [PMID: 29497070 PMCID: PMC5832876 DOI: 10.1038/s41598-018-22093-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 02/12/2018] [Indexed: 11/09/2022] Open
Abstract
Spliced leader dependent trans-splicing (SLTS) has been described as an important RNA regulatory process that occurs in different organisms, including the trematode Schistosoma mansoni. We identified more than seven thousand putative SLTS sites in the parasite, comprising genes with a wide spectrum of functional classes, which underlines the SLTS as a ubiquitous mechanism in the parasite. Also, SLTS gene expression levels span several orders of magnitude, showing that SLTS frequency is not determined by the expression level of the target gene, but by the presence of particular gene features facilitating or hindering the trans-splicing mechanism. Our in-depth investigation of SLTS events demonstrates widespread alternative trans-splicing (ATS) acceptor sites occurring in different regions along the entire gene body, highlighting another important role of SLTS generating alternative RNA isoforms in the parasite, besides the polycistron resolution. Particularly for introns where SLTS directly competes for the same acceptor substrate with cis-splicing, we identified for the first time additional and important features that might determine the type of splicing. Our study substantially extends the current knowledge of RNA processing by SLTS in S. mansoni, and provide basis for future studies on the trans-splicing mechanism in other eukaryotes.
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Affiliation(s)
- Mariana Boroni
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Michael Sammeth
- Bioinformatics in Transcriptomics and Functional Genomics (BITFUN), Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-901, Brazil
- Laboratório Nacional de Computação Científica, Petrópolis, 25651-075, Brazil
| | - Sandra Grossi Gava
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil
| | - Natasha Andressa Nogueira Jorge
- Laboratório de Bioinformática e Biologia Computacional, Coordenação de Pesquisa, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro, 20231-050, Brazil
| | - Andréa Mara Macedo
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Carlos Renato Machado
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Brazil.
| | - Glória Regina Franco
- Laboratório de Genética Bioquímica, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
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