1
|
Yang Y, Shi L, Xu X, Wen J, Xie T, Li H, Li X, Chen M, Dou X, Yuan C, Song H, Xie B, Tao Y. Spermidine Synthase and Saccharopine Reductase Have Co-Expression Patterns Both in Basidiomycetes with Fusion Form and Ascomycetes with Separate Form. J Fungi (Basel) 2023; 9:jof9030352. [PMID: 36983520 PMCID: PMC10051792 DOI: 10.3390/jof9030352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
Gene fusion is a process through which two or more distinct genes are fused into a single chimeric gene. Unlike most harmful fusion genes in cancer cells, in this study, we first found that spermidine synthetase- (SPDS, catalyst of spermidine biosynthesis) and saccharopine reductase- (SR, catalyst of the penultimate step of lysine biosynthesis) encoding genes form a natural chimeric gene, FfSpdsSr, in Flammulina filiformis. Through the cloning of full-length ORFs in different strains and the analysis of alternative splicing in developmental stages, FfSpdsSr has only one copy and unique transcript encoding chimeric SPDS-SR in F. filiformis. By an orthologous gene search of SpdsSr in more than 80 fungi, we found that the chimeric SpdsSr exists in basidiomycetes, while the two separate Spds and Sr independently exist in ascomycetes, chytridiomycetes, and oomycetes. Further, the transcript level of FfSpdsSr was investigated in different developmental stages and under some common environmental factors and stresses by RT-qPCR. The results showed that FfSpdsSr mainly up-regulated in the elongation stage and pileus development of F. filiformis, as well as under blue light, high temperature, H2O2, and MeJA treatments. Moreover, a total of 15 sets of RNA-Seq data, including 218 samples of Neurospora crassa, were downloaded from the GEO database and used to analyze the expression correlation of NcSpds and NcSr. The results showed that the separate NcSpds and NcSr shared highly similar co-expression patterns in the samples with different strains and different nutritional and environmental condition treatments. The chimeric SpdsSr in basidiomycetes and the co-expression pattern of the Spds and Sr in N. crassa indicate the special link of spermidine and lysine in fungi, which may play an important role in the growth and development of fruiting body and in response to the multiple environmental factors and abiotic stresses.
Collapse
Affiliation(s)
- Yayong Yang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lei Shi
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jin Wen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tianyue Xie
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hui Li
- Institute of Cash Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
| | - Xiaoyu Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengyu Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyi Dou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chengjin Yuan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hanbing Song
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baogui Xie
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongxin Tao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Mycological Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: ; Tel.: +86-0591-83789281
| |
Collapse
|
2
|
Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
Collapse
Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
| |
Collapse
|
3
|
Liu D, Xia J, Yang Z, Zhao X, Li J, Hao W, Yang X. Identification of Chimeric RNAs in Pig Skeletal Muscle and Transcriptomic Analysis of Chimeric RNA TNNI2-ACTA1 V1. Front Vet Sci 2021; 8:742593. [PMID: 34778431 PMCID: PMC8578878 DOI: 10.3389/fvets.2021.742593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/27/2021] [Indexed: 12/11/2022] Open
Abstract
Chimeric RNA was considered a special marker of cancer. However, recent studies have demonstrated that chimeric RNAs also exist in non-cancerous cells and tissues. Here, we analyzed and predicted jointly 49 chimeric RNAs by Star-Fusion and FusionMap. One chimeric RNA, we named TNNI2-ACTA1, and its eight transcript variants were identified by reverse transcriptase–polymerase chain reaction. The overexpression of TNNI2-ACTA1 V1 inhibited the proliferation of porcine skeletal muscle satellite cells through down-regulating the mRNA expression levels of cell cycle–related genes cyclinD1. However, as parental genes, there is no such effect in the TNNI2 and ACTA1. To explore the underlying mechanism for this phenomenon, we used RNA-seq to profile the transcriptomes of PSCs with overexpression. Compared with the negative control group, 1,592 differentially expressed genes (DEGs) were upregulated and 1,077 DEGs downregulated in TNNI2 group; 1,226 DEGs were upregulated and 902 DEGs downregulated in ACTA1 group; and 13 DEGs were upregulated and 16 DEGs downregulated in TNNI2-ACTA1 V1 group, respectively. Compared with the parental gene groups, three specific genes were enriched in the TNNI2-ACTA1 V1 group (NCOA3, Radixin, and DDR2). These three genes may be the key to TNNI2-ACTA1 V1 regulating cell proliferation. Taken together, our study explores the role of chimeric RNAs in normal tissues. In addition, our study as the first research provides the foundation for the mechanism of chimeric RNAs regulating porcine skeletal muscle growth.
Collapse
Affiliation(s)
- Dongyu Liu
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Jiqiao Xia
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Zewei Yang
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Xuelian Zhao
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Jiaxin Li
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Wanjun Hao
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| | - Xiuqin Yang
- College of Animal Sciences and Technology, Northeast Agricultural University, Harbin, China
| |
Collapse
|
4
|
Li P, Li Y, Ma L. Potential role of chimeric genes in pathway-related gene co-expression modules. World J Surg Oncol 2021; 19:149. [PMID: 33980272 PMCID: PMC8117532 DOI: 10.1186/s12957-021-02248-9] [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] [Received: 12/20/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Gene fusion has epigenetic modification functions. The novel proteins encoded by gene fusion products play a role in cancer development. Therefore, a better understanding of the novel protein products may provide insights into the pathogenesis of tumors. However, the characteristics of chimeric genes are rarely studied. Here, we used weighted co-expression network analysis to investigate the biological roles and underlying mechanisms of chimeric genes. Methods Download the pig transcriptome data, we screened chimeric genes and parental genes from 688 sequences and 153 samples, predict their domains, and analyze their associations. We constructed a co-expression network of chimeric genes in pigs and conducted Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis on the generated modules using DAVID to identify key networks and modules related to chimeric genes. Results Our findings showed that most of the protein domains of chimeric genes were derived from fused pre-genes. Chimeric genes were enriched in modules involved in the negative regulation of cell proliferation and protein localization to centrosomes. In addition, the chimeric genes were related to the growth factor-β superfamily, which regulates cell growth and differentiation. Furthermore, in helper T cells, chimeric genes regulate the specific recognition of T cell receptors, implying that chimeric genes play a key role in the regulation pathway of T cells. Chimeric genes can produce new domains, and some chimeric genes are a key role involved in pathway-related function. Conclusions Most chimeric genes show binding activity. Domains of chimeric genes are derived from several combinations of parent genes. Chimeric genes play a key role in the regulation of several cellular pathways. Our findings may provide new directions to explore the roles of chimeric genes in tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-021-02248-9.
Collapse
Affiliation(s)
- Piaopiao Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Yingxia Li
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Lei Ma
- College of Life Science, Shihezi University, Shihezi, Xinjiang, 832000, China.
| |
Collapse
|
5
|
Landscape of Chimeric RNAs in Non-Cancerous Cells. Genes (Basel) 2021; 12:genes12040466. [PMID: 33805149 PMCID: PMC8064075 DOI: 10.3390/genes12040466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/21/2022] Open
Abstract
Gene fusions and their products (RNA and protein) have been traditionally recognized as unique features of cancer cells and are used as ideal biomarkers and drug targets for multiple cancer types. However, recent studies have demonstrated that chimeric RNAs generated by intergenic alternative splicing can also be found in normal cells and tissues. In this study, we aim to identify chimeric RNAs in different non-neoplastic cell lines and investigate the landscape and expression of these novel candidate chimeric RNAs. To do so, we used HEK-293T, HUVEC, and LO2 cell lines as models, performed paired-end RNA sequencing, and conducted analyses for chimeric RNA profiles. Several filtering criteria were applied, and the landscape of chimeric RNAs was characterized at multiple levels and from various angles. Further, we experimentally validated 17 chimeric RNAs from different classifications. Finally, we examined a number of validated chimeric RNAs in different cancer and non-cancer cells, including blood from healthy donors, and demonstrated their ubiquitous expression pattern.
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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 .
Collapse
Affiliation(s)
- Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | | |
Collapse
|
8
|
It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research. Int J Mol Sci 2017; 18:ijms18040714. [PMID: 28350330 PMCID: PMC5412300 DOI: 10.3390/ijms18040714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/27/2022] Open
Abstract
There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.
Collapse
|
9
|
Yang Y, Tang Z, Fan X, Xu K, Mu Y, Zhou R, Li K. Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle. Sci Rep 2016; 6:29039. [PMID: 27352850 PMCID: PMC4926253 DOI: 10.1038/srep29039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/14/2016] [Indexed: 01/28/2023] Open
Abstract
Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.
Collapse
Affiliation(s)
- Yalan Yang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Zhonglin Tang
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| | - Xinhao Fan
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Xu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Yulian Mu
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Rong Zhou
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
| | - Kui Li
- The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Babiceanu M, Qin F, Xie Z, Jia Y, Lopez K, Janus N, Facemire L, Kumar S, Pang Y, Qi Y, Lazar IM, Li H. Recurrent chimeric fusion RNAs in non-cancer tissues and cells. Nucleic Acids Res 2016; 44:2859-72. [PMID: 26837576 PMCID: PMC4824105 DOI: 10.1093/nar/gkw032] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Gene fusions and their products (RNA and protein) were once thought to be unique features to cancer. However, chimeric RNAs can also be found in normal cells. Here, we performed, curated and analyzed nearly 300 RNA-Seq libraries covering 30 different non-neoplastic human tissues and cells as well as 15 mouse tissues. A large number of fusion transcripts were found. Most fusions were detected only once, while 291 were seen in more than one sample. We focused on the recurrent fusions and performed RNA and protein level validations on a subset. We characterized these fusions based on various features of the fusions, and their parental genes. They tend to be expressed at higher levels relative to their parental genes than the non-recurrent ones. Over half of the recurrent fusions involve neighboring genes transcribing in the same direction. A few sequence motifs were found enriched close to the fusion junction sites. We performed functional analyses on a few widely expressed fusions, and found that silencing them resulted in dramatic reduction in normal cell growth and/or motility. Most chimeras use canonical splicing sites, thus are likely products of 'intergenic splicing'. We also explored the implications of these non-pathological fusions in cancer and in evolution.
Collapse
Affiliation(s)
- Mihaela Babiceanu
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuemeng Jia
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Kevin Lopez
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Nick Janus
- Department of Computer Science, University of Virginia, Charlottesville, VA 22908, USA
| | - Loryn Facemire
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Shailesh Kumar
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuwei Pang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA 22908, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
12
|
Chuang TJ, Wu CS, Chen CY, Hung LY, Chiang TW, Yang MY. NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res 2015; 44:e29. [PMID: 26442529 PMCID: PMC4756807 DOI: 10.1093/nar/gkv1013] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/24/2015] [Indexed: 12/19/2022] Open
Abstract
Analysis of RNA-seq data often detects numerous ‘non-co-linear’ (NCL) transcripts, which comprised sequence segments that are topologically inconsistent with their corresponding DNA sequences in the reference genome. However, detection of NCL transcripts involves two major challenges: removal of false positives arising from alignment artifacts and discrimination between different types of NCL transcripts (trans-spliced, circular or fusion transcripts). Here, we developed a new NCL-transcript-detecting method (‘NCLscan’), which utilized a stepwise alignment strategy to almost completely eliminate false calls (>98% precision) without sacrificing true positives, enabling NCLscan outperform 18 other publicly-available tools (including fusion- and circular-RNA-detecting tools) in terms of sensitivity and precision, regardless of the generation strategy of simulated dataset, type of intragenic or intergenic NCL event, read depth of coverage, read length or expression level of NCL transcript. With the high accuracy, NCLscan was applied to distinguishing between trans-spliced, circular and fusion transcripts on the basis of poly(A)- and nonpoly(A)-selected RNA-seq data. We showed that circular RNAs were expressed more ubiquitously, more abundantly and less cell type-specifically than trans-spliced and fusion transcripts. Our study thus describes a robust pipeline for the discovery of NCL transcripts, and sheds light on the fundamental biology of these non-canonical RNA events in human transcriptome.
Collapse
Affiliation(s)
- Trees-Juen Chuang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chan-Shuo Wu
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Chen
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yuan Hung
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Tai-Wei Chiang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Min-Yu Yang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
13
|
Lei MM, Wu SQ, Shao XB, Li XW, Chen Z, Ying SJ, Shi ZD. Creating leptin-like biofunctions by active immunization against chicken leptin receptor in growing chickens. Domest Anim Endocrinol 2015; 50:55-64. [PMID: 25447880 DOI: 10.1016/j.domaniend.2014.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 09/01/2014] [Accepted: 09/04/2014] [Indexed: 12/19/2022]
Abstract
In this study, immunization against chicken leptin receptor (cLEPR) extracellular domain (ECD) was applied to investigate leptin regulation and LEPR biofunction in growing chicken pullets. A recombinant protein (cLEPR ECD) based on the cLEPR complemenary DNA sequence corresponding to the 582nd to 796th amino acid residues of cLEPR mature peptide was prepared and used as antigen. Immunization against cLEPR ECD in growing chickens increased anti-cLEPR ECD antibody titers in blood, enhanced proportions of phosphorylated janus kinase 2 (JAK2) and served as signal transducer and activator of transcription 3 (STAT3) protein in liver tissue. Chicken live weight gain and abdominal fat mass were significantly decreased (P < 0.05), but feed intake was stimulated by cLEPR ECD immunization (P < 0.05). The treatment also upregulated the gene expression levels of lepR, AMP-activated protein kinase (AMPK), acetyl CoA carboxylase-2 (ACC2), and uncoupling protein 3 (UCP3) in liver, abdominal fat, and breast muscle (P < 0.05) but decreased fasn expression levels (P < 0.01). Apart from that of lepR, the expression of appetite-regulating genes, such as orexigenic genes, agouti-related peptide (AgRP) and neuropeptide Y (NPY), were upregulated (P < 0.01), whereas the anorexigenic gene proopiomelanocortin (POMC) was downregulated in the hypothalamic tissue of cLEPR-immunized pullets (P < 0.01). Blood concentrations of metabolic molecules, such as glucose, triglycerides, and very-low-density lipoprotein, were significantly decreased in cLEPR-immunized pullets but those of cholesterol, high-density lipoprotein, and low-density lipoprotein increased. These results demonstrate that antibodies to membrane proximal cLEPR ECD enhance cLEPR signal transduction, which stimulates metabolism and reduces fat deposition in chickens.
Collapse
Affiliation(s)
- M M Lei
- Laboratory of Animal Breed Improvement and Reproduction, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - S Q Wu
- College of Animal Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - X B Shao
- Institute of Guagndong Province Poultry Technology, Guangzhou, 510520, China
| | - X W Li
- College of Animal Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Z Chen
- Laboratory of Animal Breed Improvement and Reproduction, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - S J Ying
- Laboratory of Animal Breed Improvement and Reproduction, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Z D Shi
- Laboratory of Animal Breed Improvement and Reproduction, Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| |
Collapse
|
14
|
Yu CY, Liu HJ, Hung LY, Kuo HC, Chuang TJ. Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? Nucleic Acids Res 2014; 42:9410-23. [PMID: 25053845 PMCID: PMC4132752 DOI: 10.1093/nar/gku643] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Global transcriptome investigations often result in the detection of an enormous number of transcripts composed of non-co-linear sequence fragments. Such ‘aberrant’ transcript products may arise from post-transcriptional events or genetic rearrangements, or may otherwise be false positives (sequencing/alignment errors or in vitro artifacts). Moreover, post-transcriptionally non-co-linear (‘PtNcl’) transcripts can arise from trans-splicing or back-splicing in cis (to generate so-called ‘circular RNA’). Here, we collected previously-predicted human non-co-linear RNA candidates, and designed a validation procedure integrating in silico filters with multiple experimental validation steps to examine their authenticity. We showed that >50% of the tested candidates were in vitro artifacts, even though some had been previously validated by RT-PCR. After excluding the possibility of genetic rearrangements, we distinguished between trans-spliced and circular RNAs, and confirmed that these two splicing forms can share the same non-co-linear junction. Importantly, the experimentally-confirmed PtNcl RNA events and their corresponding PtNcl splicing types (i.e. trans-splicing, circular RNA, or both sharing the same junction) were all expressed in rhesus macaque, and some were even expressed in mouse. Our study thus describes an essential procedure for confirming PtNcl transcripts, and provides further insight into the evolutionary role of PtNcl RNA events, opening up this important, but understudied, class of post-transcriptional events for comprehensive characterization.
Collapse
Affiliation(s)
- Chun-Ying Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hsiao-Jung Liu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Li-Yuan Hung
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Trees-Juen Chuang
- Division of Physical and Computational Genomics, Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| |
Collapse
|
15
|
Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF. Atypical RNAs in the coelacanth transcriptome. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:342-51. [PMID: 24174405 DOI: 10.1002/jez.b.22542] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/22/2013] [Accepted: 08/16/2013] [Indexed: 01/15/2023]
Abstract
Circular and apparently trans-spliced RNAs have recently been reported as abundant types of transcripts in mammalian transcriptome data. Both types of non-colinear RNAs are also abundant in RNA-seq of different tissue from both the African and the Indonesian coelacanth. We observe more than 8,000 lincRNAs with normal gene structure and several thousands of circularized and trans-spliced products, showing that such atypical RNAs form a substantial contribution to the transcriptome. Surprisingly, the majority of the circularizing and trans-connecting splice junctions are unique to atypical forms, that is, are not used in normal isoforms.
Collapse
Affiliation(s)
- Anne Nitsche
- Department of Computer Science, Bioinformatics Group, University of Leipzig, Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | | | | | | | | | | | | | | | | | | |
Collapse
|