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Zhang X, Zhang Y, Wang T, Li Z, Cheng J, Ge H, Tang Q, Chen K, Liu L, Lu C, Guo J, Zheng B, Zheng Y. A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants. THE PLANT CELL 2019; 31:956-973. [PMID: 30894459 PMCID: PMC6533014 DOI: 10.1105/tpc.18.00711] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/29/2019] [Accepted: 03/14/2019] [Indexed: 05/20/2023]
Abstract
Lariats are formed by excised introns, when the 5' splice site joins with the branchpoint (BP) during splicing. Although lariat RNAs are usually degraded by RNA debranching enzyme 1, recent findings in animals detected many lariat RNAs under physiological conditions. By contrast, the features of BPs and to what extent lariat RNAs accumulate naturally are largely unexplored in plants. Here, we analyzed 948 RNA sequencing data sets to document plant BPs and lariat RNAs on a genome-wide scale. In total, we identified 13,872, 5199, 29,582, and 13,478 BPs in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), and maize (Zea mays), respectively. Features of plant BPs are highly similar to those in yeast and human, in that BPs are adenine-preferred and flanked by uracil-enriched sequences. Intriguingly, ∼20% of introns harbor multiple BPs, and BP usage is tissue-specific. Furthermore, 10,580 lariat RNAs accumulate in wild-type Arabidopsis plants, and most of these lariat RNAs originate from longer or retroelement-depleted introns. Moreover, the expression of these lariat RNAs is accompanied by the incidence of back-splicing of parent exons. Collectively, our results provide a comprehensive map of intron BPs and lariat RNAs in four plant species and uncover a link between lariat turnover and splicing.
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Affiliation(s)
- Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yong Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Taiyun Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ziwei Li
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jinping Cheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Haoran Ge
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kun Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Li Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyu Lu
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Junqiang Guo
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yun Zheng
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
- Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
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Zhang Q, Fan X, Wang Y, Sun MA, Shao J, Guo D. BPP: a sequence-based algorithm for branch point prediction. Bioinformatics 2018. [PMID: 28633445 DOI: 10.1093/bioinformatics/btx401] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Motivation Although high-throughput sequencing methods have been proposed to identify splicing branch points in the human genome, these methods can only detect a small fraction of the branch points subject to the sequencing depth, experimental cost and the expression level of the mRNA. An accurate computational model for branch point prediction is therefore an ongoing objective in human genome research. Results We here propose a novel branch point prediction algorithm that utilizes information on the branch point sequence and the polypyrimidine tract. Using experimentally validated data, we demonstrate that our proposed method outperforms existing methods. Availability and implementation: https://github.com/zhqingit/BPP. Contact djguo@cuhk.edu.hk. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qing Zhang
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Yejun Wang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Ming-An Sun
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
| | - Jianlin Shao
- First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Dianjing Guo
- School of Life Sciences and the State Key Laboratory of Agrobiotechnology
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Wen J, Wang J, Zhang Q, Guo D. A heuristic model for computational prediction of human branch point sequence. BMC Bioinformatics 2017; 18:459. [PMID: 29065858 PMCID: PMC5655975 DOI: 10.1186/s12859-017-1864-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 10/09/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Pre-mRNA splicing is the removal of introns from precursor mRNAs (pre-mRNAs) and the concurrent ligation of the flanking exons to generate mature mRNA. This process is catalyzed by the spliceosome, where the splicing factor 1 (SF1) specifically recognizes the seven-nucleotide branch point sequence (BPS) and the U2 snRNP later displaces the SF1 and binds to the BPS. In mammals, the degeneracy of BPS motifs together with the lack of a large set of experimentally verified BPSs complicates the task of BPS prediction in silico. RESULTS In this paper, we develop a simple and yet efficient heuristic model for human BPS prediction based on a novel scoring scheme, which quantifies the splicing strength of putative BPSs. The candidate BPS is restricted exclusively within a defined BPS search region to avoid the influences of other elements in the intron and therefore the prediction accuracy is improved. Moreover, using two types of relative frequencies for human BPS prediction, we demonstrate our model outperformed other current implementations on experimentally verified human introns. CONCLUSION We propose that the binding energy contributes to the molecular recognition involved in human pre-mRNA splicing. In addition, a genome-wide human BPS prediction is carried out. The characteristics of predicted BPSs are in accordance with experimentally verified human BPSs, and branch site positions relative to the 3'ss and the 5'end of the shortened AGEZ are consistent with the results of published papers. Meanwhile, a webserver for BPS predictor is freely available at http://biocomputer.bio.cuhk.edu.hk/BPS .
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Affiliation(s)
- Jia Wen
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jue Wang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Qing Zhang
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Dianjing Guo
- School of Life Science, State Key Laboratory of Agrobiotechnology and ShenZhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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Human DBR1 modulates the recycling of snRNPs to affect alternative RNA splicing and contributes to the suppression of cancer development. Oncogene 2017; 36:5382-5391. [PMID: 28504715 PMCID: PMC5608638 DOI: 10.1038/onc.2017.150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/03/2017] [Accepted: 04/14/2017] [Indexed: 12/16/2022]
Abstract
The contribution of RNA processing to tumorigenesis is understudied. Here, we report that the human RNA debranching enzyme (hDBR1), when inappropriately regulated, induces oncogenesis by causing RNA processing defects, for example, splicing defects. We found that wild-type p53 and hypoxia-inducible factor 1 co-regulate hDBR1 expression, and insufficient hDBR1 leads to a higher rate of exon skipping. Transcriptomic sequencing confirmed the effect of hDBR1 on RNA splicing, and metabolite profiling supported the observation that neoplasm is triggered by a decrease in hDBR1 expression both in vitro and in vivo. Most importantly, when modulating the expression of hDBR1, which was found to be generally low in malignant human tissues, higher expression of hDBR1 only affected exon-skipping activity in malignant cells. Together, our findings demonstrate previously unrecognized regulation and functions of hDBR1, with immediate clinical implications regarding the regulation of hDBR1 as an effective strategy for combating human cancer.
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Quaking promotes monocyte differentiation into pro-atherogenic macrophages by controlling pre-mRNA splicing and gene expression. Nat Commun 2016; 7:10846. [PMID: 27029405 PMCID: PMC4821877 DOI: 10.1038/ncomms10846] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 01/26/2016] [Indexed: 02/06/2023] Open
Abstract
A hallmark of inflammatory diseases is the excessive recruitment and influx of monocytes to sites of tissue damage and their ensuing differentiation into macrophages. Numerous stimuli are known to induce transcriptional changes associated with macrophage phenotype, but posttranscriptional control of human macrophage differentiation is less well understood. Here we show that expression levels of the RNA-binding protein Quaking (QKI) are low in monocytes and early human atherosclerotic lesions, but are abundant in macrophages of advanced plaques. Depletion of QKI protein impairs monocyte adhesion, migration, differentiation into macrophages and foam cell formation in vitro and in vivo. RNA-seq and microarray analysis of human monocyte and macrophage transcriptomes, including those of a unique QKI haploinsufficient patient, reveal striking changes in QKI-dependent messenger RNA levels and splicing of RNA transcripts. The biological importance of these transcripts and requirement for QKI during differentiation illustrates a central role for QKI in posttranscriptionally guiding macrophage identity and function. Post-transcriptional control of RNA is important in health and disease. Here, the authors show that the RNA-binding protein Quaking guides pre-mRNA splicing and transcript abundance during monocyte to macrophage differentiation, and that Quaking depletion impairs pro-atherogenic foam cell formation.
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Ajiro M, Jia R, Zhang L, Liu X, Zheng ZM. Intron definition and a branch site adenosine at nt 385 control RNA splicing of HPV16 E6*I and E7 expression. PLoS One 2012; 7:e46412. [PMID: 23056301 PMCID: PMC3464268 DOI: 10.1371/journal.pone.0046412] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/29/2012] [Indexed: 11/19/2022] Open
Abstract
HPV16 E6 and E7, two viral oncogenes, are expressed from a single bicistronic pre-mRNA. In this report, we provide the evidence that the bicistronic pre-mRNA intron 1 contains three 5' splice sites (5' ss) and three 3' splice sites (3' ss) normally used in HPV16(+) cervical cancer and its derived cell lines. The choice of two novel alternative 5' ss (nt 221 5' ss and nt 191 5' ss) produces two novel isoforms of E6E7 mRNAs (E6*V and E6*VI). The nt 226 5' ss and nt 409 3' ss is preferentially selected over the other splice sites crossing over the intron to excise a minimal length of the intron in RNA splicing. We identified AACAAAC as the preferred branch point sequence (BPS) and an adenosine at nt 385 (underlined) in the BPS as a branch site to dictate the selection of the nt 409 3' ss for E6*I splicing and E7 expression. Introduction of point mutations into the mapped BPS led to reduced U2 binding to the BPS and thereby inhibition of the second step of E6E7 splicing at the nt 409 3' ss. Importantly, the E6E7 bicistronic RNA with a mutant BPS and inefficient splicing makes little or no E7 and the resulted E6 with mutations of (91)QYNK(94) to (91)PSFW(94) displays attenuate activity on p53 degradation. Together, our data provide structural basis of the E6E7 intron 1 for better understanding of how viral E6 and E7 expression is regulated by alternative RNA splicing. This study elucidates for the first time a mapped branch point in HPV16 genome involved in viral oncogene expression.
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Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Rong Jia
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Lifang Zhang
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Xuefeng Liu
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV and AIDS Malignancy Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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Cheng Z, Menees TM. RNA splicing and debranching viewed through analysis of RNA lariats. Mol Genet Genomics 2011; 286:395-410. [DOI: 10.1007/s00438-011-0635-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 06/30/2011] [Indexed: 01/24/2023]
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Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA (NEW YORK, N.Y.) 2011; 17:1884-94. [PMID: 21865603 PMCID: PMC3185920 DOI: 10.1261/rna.2696311] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 07/08/2011] [Indexed: 05/22/2023]
Abstract
RNA sequence elements involved in the regulation of pre-mRNA splicing have previously been identified in vertebrate genomes by computational methods. Here, we apply such approaches to predict splicing regulatory elements in Drosophila melanogaster and compare them with elements previously found in the human, mouse, and pufferfish genomes. We identified 99 putative exonic splicing enhancers (ESEs) and 231 putative intronic splicing enhancers (ISEs) enriched near weak 5' and 3' splice sites of constitutively spliced introns, distinguishing between those found near short and long introns. We found that a significant proportion (58%) of fly enhancer sequences were previously reported in at least one of the vertebrates. Furthermore, 20% of putative fly ESEs were previously identified as ESEs in human, mouse, and pufferfish; while only two fly ISEs, CTCTCT and TTATAA, were identified as ISEs in all three vertebrate species. Several putative enhancer sequences are similar to characterized binding-site motifs for Drosophila and mammalian splicing regulators. To provide additional evidence for the function of putative ISEs, we separately identified 298 intronic hexamers significantly enriched within sequences phylogenetically conserved among 15 insect species. We found that 73 putative ISEs were among those enriched in conserved regions of the D. melanogaster genome. The functions of nine enhancer sequences were verified in a heterologous splicing reporter, demonstrating that these sequences are sufficient to enhance splicing in vivo. Taken together, these data identify a set of predicted positive-acting splicing regulatory motifs in the Drosophila genome and reveal regulatory sequences that are present in distant metazoan genomes.
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Affiliation(s)
- Angela N. Brooks
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Julie L. Aspden
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Anna I. Podgornaia
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Donald C. Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Integrative Genomics, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Corresponding author.E-mail .
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