|
1
|
Hu Y, Yan S, Yan H, Su J, Cui Z, Li J, Wang S, Sun Y, Li W, Gao S. PacBio full-length transcriptome analysis reveals the role of tRNA-like structures in RNA processing. Cell Signal 2024; 125:111515. [PMID: 39571702 DOI: 10.1016/j.cellsig.2024.111515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 11/15/2024] [Accepted: 11/18/2024] [Indexed: 11/26/2024]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) and chloroplast DNA (cpDNA) are distinct from nuclear DNA (nuDNA) in a eukaryotic cell. Animal mitochondria transcribe a single primary transcript that carries all genes from a DNA strand; In contrast, plant mitochondria and chloroplasts produce multiple primary transcripts, with each transcript carrying several genes. How primary transcripts of plant mtDNA and cpDNA are processed into mature RNAs is still unknown. RESULTS In the present study, we employed PacBio's full-length transcriptome data to characterize the transcription of Arabidopsis thaliana mtDNA, providing a more comprehensive and precise understanding. The primary findings included 20 novel mitochondrial (mt) RNAs of A. thaliana, transcripts carrying single introns or exons, long mt and chloroplast (cp) tRNAs with intricate secondary structures, and the role of tRNA-like structures in RNA processing. The gene of No. 20 novel mt RNA and its paralog on chromosome 2 of A. thaliana were assigned locus IDs ATMG01335 and AT2G07811. CONCLUSIONS According to our upgraded "mitochondrial cleavage" model, tRNA-like structures serve as "punctuation" marks for RNA processing, akin to the role of tRNAs. Both tRNA-like structures and tRNAs collaborate for RNA processing in plant mitochondria and chloroplasts.
Collapse
Affiliation(s)
- Yanping Hu
- College of Life Sciences, Nankai University, Tianjin 300071, China; Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
| | - Shuangyong Yan
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Haohao Yan
- College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jingping Su
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Zhongqiu Cui
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Junling Li
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Shengjun Wang
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Yue Sun
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
| | - Wenjing Li
- Qinghai Key Laboratory of Qinghai-Tibet Plateau Biological Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| |
Collapse
|
|
2
|
Liao T, Zhang L, Wang Y, Guo L, Cao J, Liu G. Full-length transcriptome characterization of Platycladus orientalis based on the PacBio platform. Front Genet 2024; 15:1345039. [PMID: 38304337 PMCID: PMC10830785 DOI: 10.3389/fgene.2024.1345039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/10/2024] [Indexed: 02/03/2024] Open
Abstract
As a unique and native conifer in China, Platycladus orientalis is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of P. orientalis and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of P. orientalis offer a pioneering insight for future investigations into gene function and genetic breeding within Platycladus species.
Collapse
Affiliation(s)
| | | | | | | | | | - Guobin Liu
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|
|
3
|
Liang G, Mi D, Chang J, On Yau T, Xu G, Ruan J, Bu W, Gao S. Precise annotation of Drosophila mitochondrial genomes leads to insights into AT-rich regions. Mitochondrion 2022; 65:145-149. [PMID: 35779797 DOI: 10.1016/j.mito.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/24/2022] [Accepted: 06/26/2022] [Indexed: 11/16/2022]
Abstract
In the present study, we performed precise annotation of Drosophila melanogaster, D. simulans, D. grimshawi, Bactrocera oleae mitochondrial (mt) genomes using pan RNA-seq analysis. Using PacBio cDNA-seq data from D. simulans, we precisely annotated the Transcription Initiation Sites (TISs) of the mt Heavy and Light strands in Drosophila mt genomes and reported that the polyA(+) and polyA(-) motifs in the CRs are associated with TISs. The discovery of the conserved polyA(+) and polyA(-) motifs provides insights into many polyA and polyT sequences in CRs of insect mt genomes, leading to reveal the mt transcription and its regulation in invertebrates. Notably, we propose that: (1) polyA/polyT motifs in CRs function as signals to initiate mtDNA transcription; (2) the duplication, recombination or mutation of these polyA/polyT sequences formed the AT-rich regions during evolution; and (3) since CRs of many invertebrate species still contain many polyA/polyT sequences, there is a high probability that several TISs and TTSs exist in invertebrate mt genomes.
Collapse
Affiliation(s)
- Guangcai Liang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Dong Mi
- Department of Clinical Laboratory, Affiliated Maternity Hospital, Nankai University, Tianjin 300100, PR China
| | - Jia Chang
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Tung On Yau
- Department of Rural Land Use, Scotland's Rural College, Aberdeen AB21 9YA, United Kingdom
| | - Guofeng Xu
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Jishou Ruan
- School of Mathematical Sciences, Nankai University, Tianjin, Tianjin 300071, PR China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin 300071, PR China.
| |
Collapse
|
|
4
|
Ebrahimie E, Rahimirad S, Tahsili M, Mohammadi-Dehcheshmeh M. Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis. World J Stem Cells 2021; 13:1394-1416. [PMID: 34786151 PMCID: PMC8567453 DOI: 10.4252/wjsc.v13.i10.1394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/21/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
Collapse
Affiliation(s)
- Esmaeil Ebrahimie
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide 5005, South Australia, Australia
- La Trobe Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne 3086, Australia
- School of Biosciences, The University of Melbourne, Melbourne 3010, Australia,
| | - Samira Rahimirad
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology, Tehran 1497716316, Iran
- Division of Urology, Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montreal H4A 3J1, Quebec, Canada
| | | | | |
Collapse
|
|
5
|
Chen Z, Xuan Y, Liang G, Yang X, Yu Z, Barker SC, Kelava S, Bu W, Liu J, Gao S. Precise annotation of tick mitochondrial genomes reveals multiple copy number variation of short tandem repeats and one transposon-like element. BMC Genomics 2020; 21:488. [PMID: 32680454 PMCID: PMC7367389 DOI: 10.1186/s12864-020-06906-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background In the present study, we used long-PCR amplification coupled with Next-Generation Sequencing (NGS) to obtain complete mitochondrial (mt) genomes of individual ticks and unprecedently performed precise annotation of these mt genomes. We aimed to: (1) develop a simple, cost-effective and accurate method for the study of extremely high AT-content mt genomes within an individual animal (e.g. Dermacentor silvarum) containing miniscule DNA; (2) provide a high-quality reference genome for D. silvarum with precise annotation and also for future studies of other tick mt genomes; and (3) detect and analyze mt DNA variation within an individual tick. Results These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Moreover, two new and important findings were reported for the first time, contributing fundamental knowledge to mt biology. The first was the discovery of a transposon-like element that may eventually reveal much about mechanisms of gene rearrangements in mt genomes. Another finding was that Copy Number Variation (CNV) of Short Tandem Repeats (STRs) account for mitochondrial sequence diversity (heterogeneity) within an individual tick, insect, mouse or human, whereas SNPs were not detected. The CNV of STRs in the protein-coding genes resulted in frameshift mutations in the proteins, which can cause deleterious effects. Mitochondria containing these deleterious STR mutations accumulate in cells and can produce deleterious proteins. Conclusions We proposed that the accumulation of CNV of STRs in mitochondria may cause aging or diseases. Future tests of the CNV of STRs hypothesis help to ultimately reveal the genetic basis of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will lead to the reconsideration of the importance of STRs and a unified study of CNV of STRs with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mt genomes.
Collapse
Affiliation(s)
- Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Yibo Xuan
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.,College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Guangcai Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, Tianjin, 300350, P. R. China
| | - Xiaolong Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Samuel Kelava
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, P. R. China.
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, Tianjin, 300071, P. R. China. .,School of Statistics and Data Science, Nankai University, Tianjin, Tianjin, 300071, P. R. China.
| |
Collapse
|
|
6
|
Jin X, Cheng Z, Wang B, Yau TO, Chen Z, Barker SC, Chen D, Bu W, Sun D, Gao S. Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals. RNA Biol 2020; 17:395-402. [PMID: 31905034 DOI: 10.1080/15476286.2019.1709746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.
Collapse
Affiliation(s)
- Xiufeng Jin
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Zhi Cheng
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Bo Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Tung On Yau
- John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Ze Chen
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, P.R. China
| | - Stephen C Barker
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Defu Chen
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Wenjun Bu
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, P.R.China
| | - Shan Gao
- College of Life Sciences, Nankai University, Tianjin, P.R.China
| |
Collapse
|
|
7
|
Ji H, Xu X, Jin X, Yin H, Luo J, Liu G, Zhao Q, Chen Z, Bu W, Gao S. Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region. RNA Biol 2019; 16:830-837. [PMID: 30870076 DOI: 10.1080/15476286.2019.1591035] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. The high-resolution annotations cover both entire strands of the mitochondrial genome without any gaps or overlaps. Most of the new annotations were consistent with the previous annotations which had been obtained using PacBio full-length transcripts. Two important findings were that animals transcribe both entire strands of mitochondrial genomes and the tandem repeats in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the heavy strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, suggesting that mitochondrial DNA recombination occurs in an individual. In conclusion, the sRNA-seq based method uses 5' and 3' end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution, and can be used to identify new steady RNAs, particularly long non-coding RNAs (lncRNAs). The high-resolution annotations of mitochondrial genomes can also be used to study the molecular phylogenetics and evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics. The complete mitochondrial genome sequence of E. fullo with the new annotations using the sRNA-seq based method is available at the NCBI GenBank database under the accession number MK374364. We publish our theories, methods, the high quality sRNA-seq and RNA-seq data (SRA: SRP174926) for extensive use.
Collapse
Affiliation(s)
- Haishuo Ji
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Xiaofeng Xu
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Xiufeng Jin
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Hong Yin
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China.,c Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonose , Yangzhou , P.R.China
| | - Jianxun Luo
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Guangyuan Liu
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Qiang Zhao
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Ze Chen
- b State Key Laboratory of Veterinary Etiological Biology and Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute , Chinese Academy of Agricultural Science , Lanzhou , P.R.China
| | - Wenjun Bu
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| | - Shan Gao
- a College of Life Sciences , Nankai University , Tianjin , P.R.China
| |
Collapse
|
|
8
|
Two novel lncRNAs discovered in human mitochondrial DNA using PacBio full-length transcriptome data. Mitochondrion 2017; 38:41-47. [PMID: 28802668 DOI: 10.1016/j.mito.2017.08.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 06/11/2017] [Accepted: 08/07/2017] [Indexed: 11/23/2022]
Abstract
In this study, we established a general framework to use PacBio full-length transcriptome sequencing for the investigation of mitochondrial RNAs. As a result, we produced the first full-length human mitochondrial transcriptome using public PacBio data and characterized the human mitochondrial genome with more comprehensive and accurate information. Other results included determination of the H-strand primary transcript, identification of the ND5/ND6AS/tRNAGluAS transcript, discovery of palindrome small RNAs (psRNAs) and construction of the "mitochondrial cleavage" model, etc. These results reported for the first time in this study fundamentally changed annotations of human mitochondrial genome and enriched knowledge in the field of animal mitochondrial studies. The most important finding was two novel long non-coding RNAs (lncRNAs) of MDL1 and MDL1AS exist ubiquitously in animal mitochondrial genomes.
Collapse
|