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Sense-oriented AluYRa1 elements provide a lineage-specific transcription environment for polyadenylation. Sci Rep 2021; 11:3665. [PMID: 33574427 PMCID: PMC7878741 DOI: 10.1038/s41598-021-83360-4] [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: 10/15/2020] [Accepted: 01/29/2021] [Indexed: 11/08/2022] Open
Abstract
Transposable elements cause alternative splicing (AS) in different ways, contributing to transcript diversification. Alternative polyadenylation (APA), one of the AS events, is related to the generation of mRNA isoforms in 70% of human genes. In this study, we tried to investigate AluYRa1s located at the terminal region of cynomolgus monkey genes, utilizing both computational analysis and molecular experimentation. We found that ten genes had AluYRa1 at their 3' end, and nine of these AluYRa1s were sense-oriented. Furthermore, in seven genes, AluYRa1s were expected to have a similar consensus sequence for polyadenylation cleavage. Additional computational analysis using the annotation files from the UCSC database showed that AluYRa1 was more involved in polyadenylation than in open reading frame exon splicing. To examine the extent of AluYRa1 involvement in polyadenylation, RNA-seq data from 30 normal cynomolgus monkeys were analyzed using TAPAS, a recently devised software that detects all the promising polyadenylation sites including APA sites. We observed that approximately 74% of possible polyadenylation sites in the analyzed genes were provided by sense-oriented AluYRa1. In conclusion, AluYRa1 is an Old-World monkey-specific TE, and its sense-oriented insertion at the 3'UTR region tends to provide a favorable environment for polyadenylation, diversifying gene transcripts.
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Choe SH, Park SJ, Cho HM, Park HR, Lee JR, Kim YH, Huh JW. A single mutation in the ACTR8 gene associated with lineage-specific expression in primates. BMC Evol Biol 2020; 20:66. [PMID: 32503430 PMCID: PMC7275561 DOI: 10.1186/s12862-020-01620-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background Alternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey. Results We performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function. Conclusions The single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.
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Affiliation(s)
- Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
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3
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Cho HM, Park SJ, Choe SH, Lee JR, Kim SU, Jin YB, Kim JS, Lee SR, Kim YH, Huh JW. Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene. BMC Evol Biol 2019; 19:196. [PMID: 31666001 PMCID: PMC6822395 DOI: 10.1186/s12862-019-1530-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/18/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The BLOC1S2 gene encodes the multifunctional protein BLOS2, a shared subunit of two lysosomal trafficking complexes: i) biogenesis of lysosome-related organelles complex-1 and i) BLOC-1-related complex. In our previous study, we identified an intriguing unreported transcript of the BLOC1S2 gene that has a novel exon derived from two transposable elements (TEs), MIR and AluSp. To investigate the evolutionary footprint and molecular mechanism of action of this transcript, we performed PCR and RT-PCR experiments and sequencing analyses using genomic DNA and RNA samples from humans and various non-human primates. RESULTS The results showed that the MIR element had integrated into the genome of our common ancestor, specifically in the BLOC1S2 gene region, before the radiation of all primate lineages and that the AluSp element had integrated into the genome of our common ancestor, fortunately in the middle of the MIR sequences, after the divergence of Old World monkeys and New World monkeys. The combined MIR and AluSp sequences provide a 3' splice site (AG) and 5' splice site (GT), respectively, and generate the Old World monkey-specific transcripts. Moreover, branch point sequences for the intron removal process are provided by the MIR and AluSp combination. CONCLUSIONS We show for the first time that sequential integration into the same location and sequence divergence events of two different TEs generated lineage-specific transcripts through sequence collaboration during primate evolution.
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Affiliation(s)
- Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Sun-Uk Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.,Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Yeung-Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Ji-Su Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.,Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
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4
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Shin W, Mun S, Kim J, Lee W, Park DG, Choi S, Lee TY, Cha S, Han K. Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method. Mol Cells 2019; 42:87-95. [PMID: 30699287 PMCID: PMC6354063 DOI: 10.14348/molcells.2018.0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2018] [Accepted: 10/26/2018] [Indexed: 11/27/2022] Open
Abstract
Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.
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Affiliation(s)
- Wonseok Shin
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Junse Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Dong-Guk Park
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Seungkyu Choi
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical Engineering, Chungnam National University, Daejeon 34134,
Korea
| | - Seunghee Cha
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610,
USA
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
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5
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Lee JR, Ryu DS, Park SJ, Choe SH, Cho HM, Lee SR, Kim SU, Kim YH, Huh JW. Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models. BMC Genomics 2018; 19:267. [PMID: 29669513 PMCID: PMC5907189 DOI: 10.1186/s12864-018-4666-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/12/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The characterization of genomic or epigenomic variation in human and animal models could provide important insight into pathophysiological mechanisms of various diseases, and lead to new developments in disease diagnosis and clinical intervention. The African green monkey (AGM; Chlorocebus aethiops) and cynomolgus monkey (CM; Macaca fascicularis) have long been considered important animal models in biomedical research. However, non-human primate-specific methods applicable to epigenomic analyses in AGM and CM are lacking. The recent development of methyl-capture sequencing (MC-seq) has an unprecedented advantage of cost-effectiveness, and further allows for extending the methylome coverage compared to conventional sequencing approaches. RESULTS Here, we used a human probe-designed MC-seq method to assay DNA methylation in DNA obtained from 13 CM and three AGM blood samples. To effectively adapt the human probe-designed target region for methylome analysis in non-human primates, we redefined the target regions, focusing on regulatory regions and intragenic regions with consideration of interspecific sequence homology and promoter region variation. Methyl-capture efficiency was controlled by the sequence identity between the captured probes based on the human reference genome and the AGM and CM genome sequences, respectively. Using reasonable guidelines, 56 and 62% of the human-based capture probes could be effectively mapped for DNA methylome profiling in the AGM and CM genome, respectively, according to numeric global statistics. In particular, our method could cover up to 89 and 87% of the regulatory regions of the AGM and CM genome, respectively. CONCLUSIONS Use of human-based MC-seq methods provides an attractive, cost-effective approach for the methylome profiling of non-human primates at the single-base resolution level.
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Affiliation(s)
- Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56216, Republic of Korea
| | - Dong-Sung Ryu
- Theragen Etex Bio Institute, Suwon, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sun-Uk Kim
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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6
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Domb K, Keidar D, Yaakov B, Khasdan V, Kashkush K. Transposable elements generate population-specific insertional patterns and allelic variation in genes of wild emmer wheat (Triticum turgidum ssp. dicoccoides). BMC PLANT BIOLOGY 2017; 17:175. [PMID: 29078757 PMCID: PMC5659041 DOI: 10.1186/s12870-017-1134-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 10/17/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes. RESULTS We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat. CONCLUSIONS For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.
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Affiliation(s)
- Katherine Domb
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Danielle Keidar
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Beery Yaakov
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Vadim Khasdan
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, 84105 Beer-Sheva, Israel
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7
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Identification and characterization of the tyrosinase gene (TYR) and its transcript variants (TYR_1 and TYR_2) in the crab-eating macaque (Macaca fascicularis). Gene 2017; 630:21-27. [PMID: 28756020 DOI: 10.1016/j.gene.2017.07.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/18/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
Tyrosinase is a copper-containing enzyme that regulates melanin biosynthesis and is encoded by the tyrosinase (TYR) gene. Previous studies demonstrated that mutations in TYR could lead to oculocutaneous albinism type 1 (OCA1) owing to the failure of melanin formation. Although a previous study found that albinism in the rhesus monkey was derived from a mutation in TYR, the identification and characterization of this gene in non-human primates has not been achieved thus far. Thus, using the rapid amplification of cDNA ends (RACE) and internal reverse transcription PCR (RT-PCR) we identified the full-length sequence of TYR in the crab-eating macaque, and two different transcript variants (TYR_1 and TYR_2). While TYR_1 comprised five exons and its coding sequence was highly similar to that of humans, TYR_2 comprised four exons and was generated by a third-exon-skipping event. Interestingly, these two transcripts were also present in the African green monkey (Old World monkey) and the common marmoset (New World monkey). Deduced amino acid sequence analyses revealed that TYR_2 had a shorter C-terminal region than TYR_1 owing to the exon-skipping event. Thus, the present study is the first to identify and characterize a full-length TYR gene in a non-human primate, while the further validation of the third-exon-skipping in TYR indicates that this event is well conserved in the primate lineage. Therefore, this study provides useful and important information for the study of albinism using non-human primate models.
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8
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Gim JA, Kim HS. Identification and Expression of Equine MER-Derived miRNAs. Mol Cells 2017; 40:262-270. [PMID: 28320202 PMCID: PMC5424272 DOI: 10.14348/molcells.2017.2295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 03/06/2017] [Accepted: 03/15/2017] [Indexed: 11/27/2022] Open
Abstract
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns. The MER5A1, MER53, and MER91C sequences obtained from RepeatMasker were matched with the eca-miR-544b, eca-miR-1302, and eca-miR-652 precursor sequences derived from Ensembl transcript database, respectively. Each precursor form was anticipated to yield two mature forms, and we confirmed miRNA expression in six different tissues (cerebrum, cerebellum, lung, spleen, adrenal gland, and duodenum) of one thorough-bred horse. MER5A1-derived miRNAs generally showed significantly higher expression in the lung than in other tissues. MER91C-derived miRNA-5p also showed significantly higher expression in the duodenum than in other tissues (cerebellum, lung, spleen, and adrenal gland). The MER117-overlapped expressed sequence tag generated polycistronic miRNAs, which showed higher expression in the duodenum than other tissues. These data indicate that horse MER transposons encode miR-NAs that are expressed in several tissues and are thought to have biological functions.
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Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
- The Genomics Institute, Life Sciences Department, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919,
Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241,
Korea
- Genetic Engineering Institute, Pusan National University, Busan 46241,
Korea
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Lee JR, Park SJ, Kim YH, Choe SH, Cho HM, Lee SR, Kim SU, Kim JS, Sim BW, Song BS, Jeong KJ, Lee Y, Jin YB, Kang P, Huh JW, Chang KT. Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene. Mol Cells 2017; 40:100-108. [PMID: 28196413 PMCID: PMC5339500 DOI: 10.14348/molcells.2017.2204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 01/04/2017] [Accepted: 01/04/2017] [Indexed: 01/30/2023] Open
Abstract
Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crab-eating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3' splice site. Six transcript variants (V1-V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5' splice sites in the 5' and 3' flanking regions of CTSF_AluYRa1. Among them, V3-V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification.
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Affiliation(s)
- Ja-Rang Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Sun-Uk Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Ji-Su Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Bo-Woong Sim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Bong-Seok Song
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Kang-Jin Jeong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Youngjeon Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Yeung Bae Jin
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Philyong Kang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
| | - Kyu-Tae Chang
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
- University of Science & Technology (UST), National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116,
Korea
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10
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Identification of Alternative Variants and Insertion of the Novel Polymorphic AluYl17 in TSEN54 Gene during Primate Evolution. Int J Genomics 2016; 2016:1679574. [PMID: 28083540 PMCID: PMC5204098 DOI: 10.1155/2016/1679574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/30/2016] [Indexed: 11/24/2022] Open
Abstract
TSEN54 encodes a subunit of the tRNA-splicing endonuclease complex, which catalyzes the identification and cleavage of introns from precursor tRNAs. Previously, we identified an AluSx-derived alternative transcript in TSEN54 of cynomolgus monkey. Reverse transcription-polymerase chain reaction (RT-PCR) amplification and TSEN54 sequence analysis of primate and human samples identified five novel alternative transcripts, including the AluSx exonized transcript. Additionally, we performed comparative expression analysis via RT-qPCR in various cynomolgus, rhesus monkey, and human tissues. RT-qPCR amplification revealed differential expression patterns. Furthermore, genomic PCR amplification and sequencing of primate and human DNA samples revealed that AluSx elements were integrated in human and all of the primate samples tested. Intriguingly, in langur genomic DNA, an additional AluY element was inserted into AluSx of intron eight of TSEN54. The new AluY element showed polymorphic insertion. Using standardized nomenclature for Alu repeats, the polymorphic AluY of the langur TSEN54 was designated as being of the AluYl17 subfamily. Our results suggest that integration of the AluSx element in TSEN54 contributed to diversity in transcripts and induced lineage- or species-specific evolutionary events such as alternative splicing and polymorphic insertion during primate evolution.
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11
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Pancsa R, Tompa P. Coding Regions of Intrinsic Disorder Accommodate Parallel Functions. Trends Biochem Sci 2016; 41:898-906. [DOI: 10.1016/j.tibs.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 02/01/2023]
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12
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Seo J, Singh NN, Ottesen EW, Lee BM, Singh RN. A novel human-specific splice isoform alters the critical C-terminus of Survival Motor Neuron protein. Sci Rep 2016; 6:30778. [PMID: 27481219 PMCID: PMC4969610 DOI: 10.1038/srep30778] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022] Open
Abstract
Spinal muscular atrophy (SMA), a leading genetic disease of children and infants, is caused by mutations or deletions of Survival Motor Neuron 1 (SMN1) gene. SMN2, a nearly identical copy of SMN1, fails to compensate for the loss of SMN1 due to skipping of exon 7. SMN2 predominantly produces SMNΔ7, an unstable protein. Here we report exon 6B, a novel exon, generated by exonization of an intronic Alu-like sequence of SMN. We validate the expression of exon 6B-containing transcripts SMN6B and SMN6BΔ7 in human tissues and cell lines. We confirm generation of SMN6B transcripts from both SMN1 and SMN2. We detect expression of SMN6B protein using antibodies raised against a unique polypeptide encoded by exon 6B. We analyze RNA-Seq data to show that hnRNP C is a potential regulator of SMN6B expression and demonstrate that SMN6B is a substrate of nonsense-mediated decay. We show interaction of SMN6B with Gemin2, a critical SMN-interacting protein. We demonstrate that SMN6B is more stable than SMNΔ7 and localizes to both the nucleus and the cytoplasm. Our finding expands the diversity of transcripts generated from human SMN genes and reveals a novel protein isoform predicted to be stably expressed during conditions of stress.
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Affiliation(s)
- Joonbae Seo
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
| | - Natalia N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
| | - Eric W. Ottesen
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
| | - Brian M. Lee
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
- Center for Advanced Host Defenses, Immunobiotics & Translational Comparative Medicine (CAHDIT), Iowa State University, Ames, IA 50011, USA
| | - Ravindra N. Singh
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, USA
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