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López-Pérez M, Aguirre-Garrido F, Herrera-Zúñiga L, Fernández FJ. Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version. Biosystems 2023; 234:105060. [PMID: 37844827 DOI: 10.1016/j.biosystems.2023.105060] [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: 04/27/2023] [Revised: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare model, in which two tendencies converge, one focused on rapid adaptation to achieve survival, and the other that prevents an over-adaptation effect. In this context, a revision of the gene concept must be made, which must include these new mechanisms and approaches. In this paper, we propose a new conception of the idea of a gene that moves from a static and defined version of hereditary information to a dynamic idea that preponderates gene interaction (circumscribed to that established between protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid) and the selection it exerts, as the irreducible element that works in a coordinated way in a genomic regulatory network (GRN).
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Affiliation(s)
- Marcos López-Pérez
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico.
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico
| | - Leonardo Herrera-Zúñiga
- Chemistry Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico
| | - Francisco J Fernández
- Biotechnology Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico.
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2
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Evolutionary honing in and mutational replacement: how long-term directed mutational responses to specific environmental pressures are possible. Theory Biosci 2023; 142:87-105. [PMID: 36899155 DOI: 10.1007/s12064-023-00387-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/13/2023] [Indexed: 03/12/2023]
Abstract
Recent results have shown that the human malaria-resistant hemoglobin S mutation originates de novo more frequently in the gene and in the population where it is of adaptive significance, namely, in the hemoglobin subunit beta gene compared to the nonresistant but otherwise identical 20A[Formula: see text]T mutation in the hemoglobin subunit delta gene, and in sub-Saharan Africans, who have been subject to intense malarial pressure for many generations, compared to northern Europeans, who have not. This finding raises a fundamental challenge to the traditional notion of accidental mutation. Here, we address this finding with the replacement hypothesis, according to which preexisting genetic interactions can lead directly and mechanistically to mutations that simplify and replace them. Thus, an evolutionary process under selection can gradually hone in on interactions of importance for the currently evolving adaptations, from which large-effect mutations follow that are relevant to these adaptations. We exemplify this hypothesis using multiple types of mutation, including gene fusion mutations, gene duplication mutations, A[Formula: see text]G mutations in RNA-edited sites and transcription-associated mutations, and place it in the broader context of a system-level view of mutation origination called interaction-based evolution. Potential consequences include that similarity of mutation pressures may contribute to parallel evolution in genetically related species, that the evolution of genome organization may be driven by mutational mechanisms, that transposable element movements may also be explained by replacement, and that long-term directed mutational responses to specific environmental pressures are possible. Such mutational phenomena need to be further tested by future studies in natural and artificial settings.
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3
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Li JT, Wang Q, Huang Yang MD, Li QS, Cui MS, Dong ZJ, Wang HW, Yu JH, Zhao YJ, Yang CR, Wang YX, Sun XQ, Zhang Y, Zhao R, Jia ZY, Wang XY. Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish. Nat Genet 2021; 53:1493-1503. [PMID: 34594040 PMCID: PMC8492472 DOI: 10.1038/s41588-021-00933-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
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Affiliation(s)
- Jiong-Tang Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China.
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Mei-Di Huang Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Qing-Song Li
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ming-Shu Cui
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zai-Jie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Hong-Wei Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ju-Hua Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Yu-Jie Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Chen-Ru Yang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ya-Xin Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Xiao-Qing Sun
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Ran Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zhi-Ying Jia
- Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Xi-Yin Wang
- North China University of Science and Technology, Tangshan, China
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4
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Kotwica-Rolinska J, Krištofová L, Chvalová D, Pauchová L, Provazník J, Hejníková M, Sehadová H, Lichý M, Vaněčková H, Doležel D. Functional analysis and localisation of a thyrotropin-releasing hormone-type neuropeptide (EFLa) in hemipteran insects. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 122:103376. [PMID: 32339620 PMCID: PMC7294237 DOI: 10.1016/j.ibmb.2020.103376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 03/20/2020] [Accepted: 03/31/2020] [Indexed: 05/07/2023]
Abstract
EFLamide (EFLa) is a neuropeptide known for a long time from crustaceans, chelicerates and myriapods. Recently, EFLa-encoding genes were identified in the genomes of apterygote hexapods including basal insect species. In pterygote insects, however, evidence of EFLa was limited to partial sequences in the bed bug (Cimex), migratory locust and a few phasmid species. Here we present identification of a full length EFLa-encoding transcript in the linden bug, Pyrrhocoris apterus (Heteroptera). We created complete null mutants allowing unambiguous anatomical location of this peptide in the central nervous system. Only 2-3 EFLa-expressing cells are located very close to each other near to the surface of the lateral protocerebrum with dense neuronal arborization. Homozygous null EFLa mutants are fully viable and do not have any visible defect in development, reproduction, lifespan, diapause induction or circadian rhythmicity. Phylogenetic analysis revealed that EFLa-encoding transcripts are produced by alternative splicing of a gene that also produces Prohormone-4. However, this Proh-4/EFLa connection is found only in Hemiptera and Locusta, whereas EFLa-encoding transcripts in apterygote hexapods, chelicerates and crustaceans are clearly distinct from Proh-4 genes. The exact mechanism leading to the fused Proh-4/EFLa transcript is not yet determined, and might be a result of canonical cis-splicing, cis-splicing of adjacent genes (cis-SAG), or trans-splicing.
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Affiliation(s)
- Joanna Kotwica-Rolinska
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Lucie Krištofová
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Daniela Chvalová
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Lucie Pauchová
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Jan Provazník
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Markéta Hejníková
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia in Ceske Budejovice, 37005, Ceske Budejovice, Czech Republic
| | - Hana Sehadová
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Martin Lichý
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - Hana Vaněčková
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic
| | - David Doležel
- Biology Center of the Academy of Sciences of the Czech Republic, Institute of Entomology, 37005, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia in Ceske Budejovice, 37005, Ceske Budejovice, Czech Republic.
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5
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Chen L, Li W, Li Y, Feng X, Du K, Wang G, Zhao L. Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE. PLANT MOLECULAR BIOLOGY 2019; 100:647-658. [PMID: 31154655 DOI: 10.1007/s11103-019-00886-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/24/2019] [Indexed: 05/28/2023]
Abstract
Found a trans-splicing of PHYTOENE SYNTHASE 1 alters tomato fruit color by map-based cloning, functional complementation and RACE providing an insight into fruit color development. Color is an important fruit quality trait and a major determinant of the economic value of tomato (Solanum lycopersicum). Fruit color inheritance in a yellow-fruited cherry tomato (cv. No. 22), named yellow-fruited tomato 2 (yft2), was shown to be controlled by a single recessive gene, YFT2. The YFT2 gene was mapped in a 95.7 kb region on chromosome 3, and the candidate gene, PHYTOENE SYNTHASE 1 (PSY1), was confirmed by functional complementation analysis. Constitutive over expression of PSY1 in yft2 increased the accumulation of carotenoids and resulted in a red fruit color, while no causal mutation was detected in the YFT2 allele of yft2, compared with red-fruited SL1995 cherry tomato or cultivated variety (cv. M82). Expression of YFT2 3' region in yft2 was significantly lower than in SL1995, and further studies revealed a difference in YFT2 post-transcriptional processing in yft2 compared with SL1995 and cv. M82, resulting in a longer YFT2 transcript. The alternatively trans-spliced allele of YFT2 in yft2 is predicted to encode a novel LT-YFT2 protein of 432 amino acid (AA) residues, compared to the 412 AA YFT2 protein of SL1995. The trans-spliced event also resulted in significantly down regulated expression of YFT2 in yft2 tomato, and the YFT2 allele suppressed expression of the downstream genes involved in the carotenoid biosynthesis pathway and carotenoids synthesis by a mechanism of the feed-forward regulation. In conclusion, we found that trans-splicing of YFT2 alters tomato fruit color, providing new insights into fruit color development.
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Affiliation(s)
- Lulu Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenzhen Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yongpeng Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuechao Feng
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Keyu Du
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ge Wang
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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6
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Chuang TJ, Chen YJ, Chen CY, Mai TL, Wang YD, Yeh CS, Yang MY, Hsiao YT, Chang TH, Kuo TC, Cho HH, Shen CN, Kuo HC, Lu MY, Chen YH, Hsieh SC, Chiang TW. Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. Nucleic Acids Res 2019; 46:3671-3691. [PMID: 29385530 PMCID: PMC6283421 DOI: 10.1093/nar/gky032] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/13/2018] [Indexed: 01/16/2023] Open
Abstract
Transcriptionally non-co-linear (NCL) transcripts can originate from trans-splicing (trans-spliced RNA; 'tsRNA') or cis-backsplicing (circular RNA; 'circRNA'). While numerous circRNAs have been detected in various species, tsRNAs remain largely uninvestigated. Here, we utilize integrative transcriptome sequencing of poly(A)- and non-poly(A)-selected RNA-seq data from diverse human cell lines to distinguish between tsRNAs and circRNAs. We identified 24,498 NCL events and found that a considerable proportion (20-35%) of them arise from both tsRNAs and circRNAs, representing extensive alternative trans-splicing and cis-backsplicing in human cells. We show that sequence generalities of exon circularization are also observed in tsRNAs. Recapitulation of NCL RNAs further shows that inverted Alu repeats can simultaneously promote the formation of tsRNAs and circRNAs. However, tsRNAs and circRNAs exhibit quite different, or even opposite, expression patterns, in terms of correlation with the expression of their co-linear counterparts, expression breadth/abundance, transcript stability, and subcellular localization preference. These results indicate that tsRNAs and circRNAs may play different regulatory roles and analysis of NCL events should take the joint effects of different NCL-splicing types and joint effects of multiple NCL events into consideration. This study describes the first transcriptome-wide analysis of trans-splicing and cis-backsplicing, expanding our understanding of the complexity of the human transcriptome.
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Affiliation(s)
- Trees-Juen Chuang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617 & Academia Sinica, Taipei 11529, Taiwan
| | - Yen-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University, Taipei 10617 & Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Te-Lun Mai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Da Wang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Min-Yu Yang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ting Hsiao
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | | | - Tzu-Chien Kuo
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Hua Cho
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ning Shen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mei-Yeh Lu
- High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hua Chen
- High Throughput Genomics Core, Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Shan-Chi Hsieh
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Tai-Wei Chiang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
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7
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Tikhonov M, Utkina M, Maksimenko O, Georgiev P. Conserved sequences in the Drosophila mod(mdg4) intron promote poly(A)-independent transcription termination and trans-splicing. Nucleic Acids Res 2019; 46:10608-10618. [PMID: 30102331 PMCID: PMC6237743 DOI: 10.1093/nar/gky716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/26/2018] [Indexed: 11/15/2022] Open
Abstract
Alternative splicing (AS) is a regulatory mechanism of gene expression that greatly expands the coding capacities of genomes by allowing the generation of multiple mRNAs from a single gene. In Drosophila, the mod(mdg4) locus is an extreme example of AS that produces more than 30 different mRNAs via trans-splicing that joins together the common exons and the 3′ variable exons generated from alternative promoters. To map the regions required for trans-splicing, we have developed an assay for measuring trans-splicing events and identified a 73-bp region in the last common intron that is critical for trans-splicing of three pre-mRNAs synthesized from different DNA strands. We have also found that conserved sequences in the distal part of the last common intron induce polyadenylation-independent transcription termination and are enriched by paused RNA polymerase II (RNAP II). These results suggest that all mod(mdg4) mRNAs are formed by joining in trans the 5′ splice site in the last common exon with the 3′ splice site in one of the alternative exons.
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Affiliation(s)
- Maxim Tikhonov
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Marina Utkina
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Oksana Maksimenko
- Group of Molecular Organization of Genome, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., Moscow 119334, Russia
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8
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Chen CY, Chuang TJ. Comment on "A comprehensive overview and evaluation of circular RNA detection tools". PLoS Comput Biol 2019; 15:e1006158. [PMID: 31150384 PMCID: PMC6544197 DOI: 10.1371/journal.pcbi.1006158] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/17/2018] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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9
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Chen CY, Chuang TJ. NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. BMC Bioinformatics 2019; 20:3. [PMID: 30606103 PMCID: PMC6318855 DOI: 10.1186/s12859-018-2589-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/21/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic fashion (fusion or intergenic trans-spliced RNAs). On the basis of RNA-seq data, numerous NCL event detectors have been developed and detected thousands of NCL events in diverse species. However, there are great discrepancies in the identification results among detectors, indicating a considerable proportion of false positives in the detected NCL events. Although several helpful guidelines for evaluating the performance of NCL event detectors have been provided, a systematic guideline for measurement of NCL events identified by existing tools has not been available. RESULTS We develop a software, NCLcomparator, for systematically post-screening the intragenic or intergenic NCL events identified by various NCL detectors. NCLcomparator first examine whether the input NCL events are potentially false positives derived from ambiguous alignments (i.e., the NCL events have an alternative co-linear explanation or multiple matches against the reference genome). To evaluate the reliability of the identified NCL events, we define the NCL score (NCLscore) based on the variation in the number of supporting NCL junction reads identified by the tools examined. Of the input NCL events, we show that the ambiguous alignment-derived events have relatively lower NCLscore values than the other events, indicating that an NCL event with a higher NCLscore has a higher level of reliability. To help selecting highly expressed NCL events, NCLcomparator also provides a series of useful measurements such as the expression levels of the detected NCL events and their corresponding host genes and the junction usage of the co-linear splice junctions at both NCL donor and acceptor sites. CONCLUSION NCLcomparator provides useful guidelines, with the input of identified NCL events from various detectors and the corresponding paired-end RNA-seq data only, to help users selecting potentially high-confidence NCL events for further functional investigation. The software thus helps to facilitate future studies into NCL events, shedding light on the fundamental biology of this important but understudied class of transcripts. NCLcomparator is freely accessible at https://github.com/TreesLab/NCLcomparator .
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Affiliation(s)
- Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan
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10
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Yu CY, Chuang CY, Kuo HC. Trans-spliced long non-coding RNA: an emerging regulator of pluripotency. Cell Mol Life Sci 2018; 75:3339-3351. [PMID: 29961157 PMCID: PMC11105688 DOI: 10.1007/s00018-018-2862-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/21/2018] [Accepted: 06/25/2018] [Indexed: 01/08/2023]
Abstract
With dual capacities for unlimited self-renewal and pluripotent differentiation, pluripotent stem cells (PSCs) give rise to many cell types in our body and PSC culture systems provide an unparalleled opportunity to study early human development and disease. Accumulating evidence indicates that the molecular mechanisms underlying pluripotency maintenance in PSCs involve many factors. Among these regulators, recent studies have shown that long non-coding RNAs (lncRNAs) can affect the pluripotency circuitry by cooperating with master pluripotency-associated factors. Additionally, trans-spliced RNAs, which are generated by combining two or more pre-mRNA transcripts to produce a chimeric RNA, have been identified as regulators of various biological processes, including human pluripotency. In this review, we summarize and discuss current knowledge about the roles of lncRNAs, including trans-spliced lncRNAs, in controlling pluripotency.
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Affiliation(s)
- Chun-Ying Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan
| | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan.
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
- College of Medicine, Graduate Institute of Medical Genomics and Proteomics, National Taiwan University, Taipei, Taiwan.
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11
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Huang Y, Cao Y, Li J, Liu Y, Zhong W, Li X, Chen C, Hao P. A survey on cellular RNA editing activity in response to Candida albicans infections. BMC Genomics 2018; 19:43. [PMID: 29363428 PMCID: PMC5780849 DOI: 10.1186/s12864-017-4374-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Adenosine-to-Inosine (A-to-I) RNA editing is catalyzed by the adenosine deaminase acting on RNA (ADAR) family of enzymes, which induces alterations in mRNA sequence. It has been shown that A-to-I RNA editing events are of significance in the cell’s innate immunity and cellular response to viral infections. However, whether RNA editing plays a role in cellular response to microorganism/fungi infection has not been determined. Candida albicans, one of the most prevalent human pathogenic fungi, usually act as a commensal on skin and superficial mucosal, but has been found to cause candidiasis in immunosuppression patients. Previously, we have revealed the up-regulation of A-to-I RNA editing activity in response to different types of influenza virus infections. The current work is designed to study the effect of microorganism/fungi infection on the activity of A-to-I RNA editing in infected hosts. Results We first detected and characterized the A-to-I RNA editing events in oral epithelial cells (OKF6) and primary human umbilical vein endothelial cells (HUVEC), under normal growth condition or with C. albicans infection. Eighty nine thousand six hundred forty eight and 60,872 A-to-I editing sites were detected in normal OKF6 and HUVEC cells, respectively. They were validated against the RNA editing databases, DARNED, RADAR, and REDIportal with 50, 80, and 80% success rates, respectively. While over 95% editing sites were detected in Alu regions, among the rest of the editing sites in non repetitive regions, the majority was located in introns and UTRs. The distributions of A-to-I editing activity and editing depth were analyzed during the course of C. albicans infection. While the normalized editing levels of common editing sites exhibited a significant increase, especially in Alu regions, no significant change in the expression of ADAR1 or ADAR2 was observed. Second, we performed further analysis on data from in vivo mouse study with C. albicans infection. One thousand one hundred thirty three and 955 A-to-I editing sites were identified in mouse tongue and kidney tissues, respectively. The number of A-to-I editing events was much smaller than in human epithelial or endothelial cells, due to the lack of Alu elements in mouse genome. Furthermore, during the course of C. albicans infection we observed stable level of A-to-I editing activity in 131 and 190 common editing sites in the mouse tongue and kidney tissues, and found no significant change in ADAR1 or ADAR2 expression (with the exception of ADAR2 displaying a significant increase at 12 h after infection in mouse kidney tissue before returning to normal). Conclusions This work represents the first comprehensive analysis of A-to-I RNA editome in human epithelial and endothelial cells. C. albicans infection of human epithelial and endothelial cells led to the up-regulation of A-to-I editing activities, through a mechanism different from that of viral infections in human hosts. However, the in vivo mouse model with C. albicans infection did not show significant changes in A-to-I editing activities in tongue and kidney tissues. The different results in the mouse model were likely due to the presence of more complex in vivo environments, e.g. circulation and mixed cell types. Electronic supplementary material The online version of this article (10.1186/s12864-017-4374-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaowei Huang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Yingying Cao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Jiarui Li
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100102, China.,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100102, China
| | - Yuanhua Liu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China
| | - Wu Zhong
- National Engineering Research Center For the Emergence Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 20032, China.
| | - Chen Chen
- Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, Beijing, 100102, China. .,Beijing Key Laboratory of Emerging Infectious Diseases, Beijing, 100102, China.
| | - Pei Hao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 20031, China.
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Jiang X, Hall AB, Biedler JK, Tu Z. Single molecule RNA sequencing uncovers trans-splicing and improves annotations in Anopheles stephensi. INSECT MOLECULAR BIOLOGY 2017; 26:298-307. [PMID: 28181326 PMCID: PMC5718059 DOI: 10.1111/imb.12294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single molecule real-time (SMRT) sequencing has recently been used to obtain full-length cDNA sequences that improve genome annotation and reveal RNA isoforms. Here, we used one such method called isoform sequencing from Pacific Biosciences (PacBio) to sequence a cDNA library from the Asian malaria mosquito Anopheles stephensi. More than 600 000 full-length cDNAs, referred to as reads of insert, were identified. Owing to the inherently high error rate of PacBio sequencing, we tested different approaches for error correction. We found that error correction using Illumina RNA sequencing (RNA-seq) generated more data than using the default SMRT pipeline. The full-length error-corrected PacBio reads greatly improved the gene annotation of Anopheles stephensi: 4867 gene models were updated and 1785 alternatively spliced isoforms were added to the annotation. In addition, six trans-splicing events, where exons from different primary transcripts were joined together, were identified in An. stephensi. All six trans-splicing events appear to be conserved in Culicidae, as they are also found in Anopheles gambiae and Aedes aegypti. The proteins encoded by trans-splicing events are also highly conserved and the orthologues of these proteins are cis-spliced in outgroup species, indicating that trans-splicing may arise as a mechanism to rescue genes that broke up during evolution.
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Affiliation(s)
- X Jiang
- Program in Genetics Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - A B Hall
- Program in Genetics Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
| | - J K Biedler
- Program in Genetics Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
| | - Z Tu
- Program in Genetics Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA, USA
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
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Simplification, Innateness, and the Absorption of Meaning from Context: How Novelty Arises from Gradual Network Evolution. Evol Biol 2017; 44:145-189. [PMID: 28572690 PMCID: PMC5429377 DOI: 10.1007/s11692-017-9407-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/06/2017] [Indexed: 02/07/2023]
Abstract
How does new genetic information arise? Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift. There have been at least two fundamental conceptual problems with imagining an alternative. First, it seemed that the only alternative is a mutation that responds "smartly" to the immediate environment; but in complex multicellulars, it is hard to imagine how this could be implemented. Second, if there were mechanisms of mutation that "knew" what genetic changes would be favored in a given environment, this would have only begged the question of how they acquired that particular knowledge to begin with. This paper offers an alternative that avoids these problems. It holds that mutational mechanisms act on information that is in the genome, based on considerations of simplicity, parsimony, elegance, etc. (which are different than fitness considerations). This simplification process, under the performance pressure exerted by selection, not only leads to the improvement of adaptations but also creates elements that have the capacity to serve in new contexts they were not originally selected for. Novelty, then, arises at the system level from emergent interactions between such elements. Thus, mechanistically driven mutation neither requires Lamarckian transmission nor closes the door on novelty, because the changes it implements interact with one another globally in surprising and beneficial ways. Finally, I argue, for example, that genes used together are fused together; that simplification leads to complexity; and that evolution and learning are conceptually linked.
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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Lei Q, Li C, Zuo Z, Huang C, Cheng H, Zhou R. Evolutionary Insights into RNA trans-Splicing in Vertebrates. Genome Biol Evol 2016; 8:562-77. [PMID: 26966239 PMCID: PMC4824033 DOI: 10.1093/gbe/evw025] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pre-RNA splicing is an essential step in generating mature mRNA. RNA trans-splicing combines two separate pre-mRNA molecules to form a chimeric non-co-linear RNA, which may exert a function distinct from its original molecules. Trans-spliced RNAs may encode novel proteins or serve as noncoding or regulatory RNAs. These novel RNAs not only increase the complexity of the proteome but also provide new regulatory mechanisms for gene expression. An increasing amount of evidence indicates that trans-splicing occurs frequently in both physiological and pathological processes. In addition, mRNA reprogramming based on trans-splicing has been successfully applied in RNA-based therapies for human genetic diseases. Nevertheless, clarifying the extent and evolution of trans-splicing in vertebrates and developing detection methods for trans-splicing remain challenging. In this review, we summarize previous research, highlight recent advances in trans-splicing, and discuss possible splicing mechanisms and functions from an evolutionary viewpoint.
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Affiliation(s)
- Quan Lei
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Cong Li
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Zhixiang Zuo
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
| | - Chunhua Huang
- Department of Cell Biology, College of Life Sciences, Wuhan University, P.R. China
| | - Hanhua Cheng
- Department of Cell Biology, College of Life Sciences, Wuhan University, P.R. China
| | - Rongjia Zhou
- Department of Genetics, College of Life Sciences, Wuhan University, P.R. China
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