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Han Y, Tu W, Zhang Y, Huang J, Meng X, Wu Q, Li S, Liu B, Michal JJ, Jiang Z, Tan Y, Zhou X, Wang H. Comprehensive analysis of single-nucleotide variants and alternative polyadenylation between inbred and outbred pigs. Int J Biol Macromol 2024:134416. [PMID: 39098700 DOI: 10.1016/j.ijbiomac.2024.134416] [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: 03/18/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Inbreeding can lead to the accumulation of homozygous single nucleotide polymorphisms (SNPs) in the genome, which can significantly affect gene expression and phenotype. In this study, we examined the impact of homozygous SNPs resulting from inbreeding on alternative polyadenylation (APA) site selection and the underlying genetic mechanisms using inbred Luchuan pigs. Genome resequencing revealed that inbreeding results in a high accumulation of homozygous SNPs within the pig genome. 3' mRNA-seq on leg muscle, submandibular lymph node, and liver tissues was performed to identify differences in APA events between inbred and outbred Luchuan pigs. We revealed different tissue-specific APA usage caused by inbreeding, which were associated with differentially biological process. Furthermore, we explored the role of polyadenylation signal (PAS) SNPs in APA regulation under inbreeding and identified key genes such as PUM1, SCARF1, RIPOR2, C1D, and LRRK2 that are involved in biological processes regulation. This study provides resources and sheds light on the impact of genomic homozygosity on APA regulation, offering insights into genetic characteristics and biological processes associated with inbreeding.
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Affiliation(s)
- Yu Han
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Weilong Tu
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Yingying Zhang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Ji Huang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Xiangge Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qingqing Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Songyu Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jennifer J Michal
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Yongsong Tan
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Hongyang Wang
- Key Laboratory of Livestock and Poultry Resources (Pig) Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China; Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China.
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2
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Gallicchio L, Matias NR, Morales-Polanco F, Nava I, Stern S, Zeng Y, Fuller MT. A Developmental Mechanism to Regulate Alternative Polyadenylation in an Adult Stem Cell Lineage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585561. [PMID: 38562704 PMCID: PMC10983978 DOI: 10.1101/2024.03.18.585561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Alternative Cleavage and Polyadenylation (APA) often results in production of mRNA isoforms with either longer or shorter 3'UTRs from the same genetic locus, potentially impacting mRNA translation, localization and stability. Developmentally regulated APA can thus make major contributions to cell-type-specific gene expression programs as cells differentiate. During Drosophila spermatogenesis, approximately 500 genes undergo APA when proliferating spermatogonia differentiate into spermatocytes, producing transcripts with shortened 3' UTRs, leading to profound stage-specific changes in the proteins expressed. The molecular mechanisms that specify usage of upstream polyadenylation sites in spermatocytes are thus key to understanding the changes in cell state. Here, we show that upregulation of PCF11 and Cbc, the two components of Cleavage Factor II (CFII), orchestrates APA during Drosophila spermatogenesis. Knock down of PCF11 or cbc in spermatocytes caused dysregulation of APA, with many transcripts normally cleaved at a proximal site in spermatocytes now cleaved at their distal site, as in spermatogonia. Forced overexpression of CFII components in spermatogonia switched cleavage of some transcripts to the proximal site normally used in spermatocytes. Our findings reveal a developmental mechanism where changes in expression of specific cleavage factors can direct cell-type-specific APA at selected genes.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford USA
| | - Neuza R. Matias
- Department of Developmental Biology, Stanford University School of Medicine, Stanford USA
| | - Fabian Morales-Polanco
- Department of Biology, Stanford University School of Humanities and Sciences, Stanford USA
- Department of Genetics, Stanford University School of Medicine, USA
| | - Iliana Nava
- Department of Developmental Biology, Stanford University School of Medicine, Stanford USA
| | - Sarah Stern
- Department of Developmental Biology, Stanford University School of Medicine, Stanford USA
| | - Yi Zeng
- Department of Genetics, Stanford University School of Medicine, USA
| | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford USA
- Department of Genetics, Stanford University School of Medicine, USA
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3
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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4
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Xudong X, Heng L, Benchao C, Wenjie C, Bao L, Gaofeng L. Integrated RNA expression and alternative polyadenylation analysis identified CPSF1-CCDC137 oncogenic axis in lung adenocarcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2405-2416. [PMID: 38174951 DOI: 10.1002/tox.24105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024]
Abstract
This study aims to analyze the RNA expression and alternative polyadenylation (APA) events and identify APA tuned genes with prognostic significance in lung adenocarcinoma (LUAD). Genome-wide RNA expression profile and APA events were acquired in LUAD cancer and normal samples in GSE197346. Comparative analysis screened common deregulated genes and transcripts. All 11 and 19 transcripts were up and down expressed and polyadenylated in cancer samples, respectively. Clinical analysis found eight genes with prognostic significance, such as coiled-coil domain containing 137 (CCDC137). Role of CCDC137 in LUAD was first reported in this study. The cellular and animal experiments indicated that downregulated CCDC137 suppressed the malignant tumor phenotype and tumor growth in LUAD. Then, to identify APA regulators for elevated CCDC137, we analyzed the expression of 26 APA regulators in GSE197346 and The Cancer Genome Atlas (TCGA), and found 4 differential regulators: CPSF1, CELF2, NUDT21, and ELAVL1. At last, the correlation of eight genes with four differential APA regulators was analyzed, and CPSF1 showed a strong positive correlation with CCDC137. Based on the above results, we propose an oncogenic axis of CPSF1-CCDC137 in LUAD. This study first constructed a polyadenylation tuned RNA expression map in LUAD, and the proposed oncogenic axis of CPSF1-CCDC137 would shed light on the pathogenesis of LUAD.
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Affiliation(s)
- Xiang Xudong
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Heng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Benchao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chen Wenjie
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lei Bao
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Gaofeng
- No.2 Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
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5
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Zhang P, Xue B, Yang H, Zhang L. Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing. Genes (Basel) 2024; 15:317. [PMID: 38540376 PMCID: PMC10970011 DOI: 10.3390/genes15030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 06/14/2024] Open
Abstract
The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel the transcriptome responses to different salinity conditions in L. marina. Through ONT sequencing under 3‱, 30‱ and 60‱ salinity environments, we obtained 131.78 G clean data and 26,647 non-redundant long-read transcripts, including 6464 novel transcripts. The DEGs obtained from the current ONT lrRNA-seq were highly correlated with those identified in our previously reported Illumina short-read RNA sequencing data. When we compared the 30‱ to the 3‱ salinity condition, we found that GO terms such as oxidoreductase activity, cation transmembrane transport and ion transmembrane transport were shared between the ONT lrRNA-seq and Illumina data. Similarly, GO terms including extracellular space, structural constituents of cuticle, substrate-specific channel activity, ion transport and substrate-specific transmembrane transporter activity were shared between the ONT and Illumina data under 60‱ compared to 30‱ salinity. In addition, we found that 79 genes significantly increased, while 119 genes significantly decreased, as the salinity increased. Furthermore, through the GO enrichment analysis of 214 genes containing DAS, in 30‱ compared to 3‱ salinity, we found that GO terms such as cellular component assembly and coenzyme biosynthetic process were enriched. Additionally, we observed that GO terms such as cellular component assembly and coenzyme biosynthetic process were also enriched in 60‱ compared to 30‱ salinity. Moreover, we found that 86, 125, and 81 genes that contained DAS were also DEGs, in comparisons between 30‱ and 3‱, 60‱ and 30‱, and 60‱ and 3‱ salinity, respectively. In addition, we demonstrated the landscape of alternative polyadenylation in marine nematode under different salinity conditions This report provides several novel insights for the further study of the mechanisms by which euryhalinity formed and evolved, and it might also contribute to the investigation of salinity dynamics induced by global climate change.
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Affiliation(s)
- Pengchi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beining Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanwen Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Liusuo Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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6
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Meng X, Li C, Hei Y, Zhou X, Zhou G. Comparative alternative polyadenylation profiles in differentiated adipocytes of subcutaneous and intramuscular fat tissue in cattle. Gene 2024; 894:147949. [PMID: 37918547 DOI: 10.1016/j.gene.2023.147949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
Alternative polyadenylation (APA) is a key molecular mechanism involved in the post-transcriptional regulation of gene expression, which has been proven to play a critical role in cell differentiation. In the present study, we performed IVT-SAPAS sequencing to profile the dynamic changes of APA sites in bovine subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis. A total of 52621 high quality APA sites were identified in preadipocytes and adipocytes. Compared with preadipocytes, the increased usage of canonical AATAAA was observed in the cell-biased APA sites of adipocytes. Furthermore, 1933 and 2140 differentially expressed APA (DE-APA) sites, as well as 341 and 337 untranslated region-APA (UTR-APA) switching genes were identified in subcutaneous preadipocytes and intramuscular preadipocytes during adipogenesis, respectively. The UTR-APA switching genes showed divergent trends in preadipocytes, among which UTR-APA switching genes in intramuscular preadipocytes tended to use shorter 3'UTR for differentiation into mature adipocytes. APA events mediated by UTR-APA switching in intramuscular adipocytes were enriched in lipid synthesis and adipocyte differentiation. TRIB3, WWTR1, and INSIG1 played important roles in the differentiation of intramuscular preadipocytes. Briefly, our results provided new insights into understanding the mechanisms of bovine adipocyte differentiation.
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Affiliation(s)
- Xiangge Meng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengping Li
- College of Life Science, Liaocheng University, Liaocheng, China
| | - Yu Hei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Guoli Zhou
- College of Life Science, Liaocheng University, Liaocheng, China.
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7
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Ge Y, Huang J, Chen R, Fu Y, Ling T, Ou X, Rong X, Cheng Y, Lin Y, Zhou F, Lu C, Yuan S, Xu A. Downregulation of CPSF6 leads to global mRNA 3' UTR shortening and enhanced antiviral immune responses. PLoS Pathog 2024; 20:e1012061. [PMID: 38416782 PMCID: PMC10927093 DOI: 10.1371/journal.ppat.1012061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/11/2024] [Accepted: 02/19/2024] [Indexed: 03/01/2024] Open
Abstract
Alternative polyadenylation (APA) is a widespread mechanism of gene regulation that generates mRNA isoforms with alternative 3' untranslated regions (3' UTRs). Our previous study has revealed the global 3' UTR shortening of host mRNAs through APA upon viral infection. However, how the dynamic changes in the APA landscape occur upon viral infection remains largely unknown. Here we further found that, the reduced protein abundance of CPSF6, one of the core 3' processing factors, promotes the usage of proximal poly(A) sites (pPASs) of many immune related genes in macrophages and fibroblasts upon viral infection. Shortening of the 3' UTR of these transcripts may improve their mRNA stability and translation efficiency, leading to the promotion of type I IFN (IFN-I) signalling-based antiviral immune responses. In addition, dysregulated expression of CPSF6 is also observed in many immune related physiological and pathological conditions, especially in various infections and cancers. Thus, the global APA dynamics of immune genes regulated by CPSF6, can fine-tune the antiviral response as well as the responses to other cellular stresses to maintain the tissue homeostasis, which may represent a novel regulatory mechanism for antiviral immunity.
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Affiliation(s)
- Yong Ge
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Jingrong Huang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Rong Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yonggui Fu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ling
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Xin Ou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Xiaohui Rong
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Youxiang Cheng
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yi Lin
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Fengyi Zhou
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Chuanjian Lu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Shaochun Yuan
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Anlong Xu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
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8
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Kaye EG, Basavaraju K, Nelson GM, Zomer HD, Roy D, Joseph II, Rajabi-Toustani R, Qiao H, Adelman K, Reddi PP. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. Nat Commun 2024; 15:848. [PMID: 38287033 PMCID: PMC10824759 DOI: 10.1038/s41467-024-45177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double-strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.
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Affiliation(s)
- Emily G Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kavyashree Basavaraju
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Helena D Zomer
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Debarun Roy
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Irene Infancy Joseph
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Reza Rajabi-Toustani
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Huanyu Qiao
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Prabhakara P Reddi
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA.
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9
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Moon Y, Burri D, Zavolan M. Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR Genom Bioinform 2023; 5:lqad079. [PMID: 37705828 PMCID: PMC10495540 DOI: 10.1093/nargab/lqad079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/15/2023] [Accepted: 08/23/2023] [Indexed: 09/15/2023] Open
Abstract
Alternative polyadenylation is a main driver of transcriptome diversity in mammals, generating transcript isoforms with different 3' ends via cleavage and polyadenylation at distinct polyadenylation (poly(A)) sites. The regulation of cell type-specific poly(A) site choice is not completely resolved, and requires quantitative poly(A) site usage data across cell types. 3' end-based single-cell RNA-seq can now be broadly used to obtain such data, enabling the identification and quantification of poly(A) sites with direct experimental support. We propose SCINPAS, a computational method to identify poly(A) sites from scRNA-seq datasets. SCINPAS modifies the read deduplication step to favor the selection of distal reads and extract those with non-templated poly(A) tails. This approach improves the resolution of poly(A) site recovery relative to standard software. SCINPAS identifies poly(A) sites in genic and non-genic regions, providing complementary information relative to other tools. The workflow is modular, and the key read deduplication step is general, enabling the use of SCINPAS in other typical analyses of single cell gene expression. Taken together, we show that SCINPAS is able to identify experimentally-supported, known and novel poly(A) sites from 3' end-based single-cell RNA sequencing data.
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Affiliation(s)
- Youngbin Moon
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dominik Burri
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mihaela Zavolan
- Computational and Systems Biology, Biozentrum University of Basel, Spitalstrasse 41, CH-4056 Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
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10
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LaForce GR, Philippidou P, Schaffer AE. mRNA isoform balance in neuronal development and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1762. [PMID: 36123820 PMCID: PMC10024649 DOI: 10.1002/wrna.1762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/11/2022] [Accepted: 08/15/2022] [Indexed: 11/07/2022]
Abstract
Balanced mRNA isoform diversity and abundance are spatially and temporally regulated throughout cellular differentiation. The proportion of expressed isoforms contributes to cell type specification and determines key properties of the differentiated cells. Neurons are unique cell types with intricate developmental programs, characteristic cellular morphologies, and electrophysiological potential. Neuron-specific gene expression programs establish these distinctive cellular characteristics and drive diversity among neuronal subtypes. Genes with neuron-specific alternative processing are enriched in key neuronal functions, including synaptic proteins, adhesion molecules, and scaffold proteins. Despite the similarity of neuronal gene expression programs, each neuronal subclass can be distinguished by unique alternative mRNA processing events. Alternative processing of developmentally important transcripts alters coding and regulatory information, including interaction domains, transcript stability, subcellular localization, and targeting by RNA binding proteins. Fine-tuning of mRNA processing is essential for neuronal activity and maintenance. Thus, the focus of neuronal RNA biology research is to dissect the transcriptomic mechanisms that underlie neuronal homeostasis, and consequently, predispose neuronal subtypes to disease. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Polyxeni Philippidou
- Department of Neurosciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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11
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Mukherjee S, Graber JH, Moore CL. Macrophage differentiation is marked by increased abundance of the mRNA 3' end processing machinery, altered poly(A) site usage, and sensitivity to the level of CstF64. Front Immunol 2023; 14:1091403. [PMID: 36761770 PMCID: PMC9905730 DOI: 10.3389/fimmu.2023.1091403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Regulation of mRNA polyadenylation is important for response to external signals and differentiation in several cell types, and results in mRNA isoforms that vary in the amount of coding sequence or 3' UTR regulatory elements. However, its role in differentiation of monocytes to macrophages has not been investigated. Macrophages are key effectors of the innate immune system that help control infection and promote tissue-repair. However, overactivity of macrophages contributes to pathogenesis of many diseases. In this study, we show that macrophage differentiation is characterized by shortening and lengthening of mRNAs in relevant cellular pathways. The cleavage/polyadenylation (C/P) proteins increase during differentiation, suggesting a possible mechanism for the observed changes in poly(A) site usage. This was surprising since higher C/P protein levels correlate with higher proliferation rates in other systems, but monocytes stop dividing after induction of differentiation. Depletion of CstF64, a C/P protein and known regulator of polyadenylation efficiency, delayed macrophage marker expression, cell cycle exit, attachment, and acquisition of structural complexity, and impeded shortening of mRNAs with functions relevant to macrophage biology. Conversely, CstF64 overexpression increased use of promoter-proximal poly(A) sites and caused the appearance of differentiated phenotypes in the absence of induction. Our findings indicate that regulation of polyadenylation plays an important role in macrophage differentiation.
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Affiliation(s)
- Srimoyee Mukherjee
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
| | - Joel H. Graber
- Computational Biology and Bioinformatics Core, Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA, United States
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12
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Paukszto Ł, Wiśniewska J, Liszewska E, Majewska M, Jastrzębski J, Jankowski J, Ciereszko A, Słowińska M. Specific expression of alternatively spliced genes in the turkey (Meleagris gallopavo) reproductive tract revealed their function in spermatogenesis and post-testicular sperm maturation. Poult Sci 2023; 102:102484. [PMID: 36709584 PMCID: PMC9922982 DOI: 10.1016/j.psj.2023.102484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
The tissue-specific profile of alternatively spliced genes (ASGs) and their involvement in reproduction processes characteristic of turkey testis, epididymis, and ductus deferens were investigated for the first time in birds. Deep sequencing of male turkey reproductive tissue RNA samples (n = 6) was performed using Illumina RNA-Seq with 2 independent methods, rMATs and SUPPA2, for differential alternative splicing (DAS) event prediction. The expression of selected ASGs was validated using quantitative real-time reverse transcriptase-polymerase chain reaction. The testis was found to be the site of the highest number of posttranscriptional splicing events within the reproductive tract, and skipping exons were the most frequently occurring class of alternative splicing (AS) among the reproductive tract. Statistical analysis revealed 86, 229, and 6 DAS events in the testis/epididymis, testis/ductus deferens, and epididymis/ductus deferens comparison, respectively. Alternative splicing was found to be a mechanism of gene expression regulation within the turkey reproduction tract. In testis, modification was observed for spermatogenesis specific genes; the changes in 5' UTR could act as regulator of MEIG1 expression (a player during spermatocytes meiosis), and modification of 3' UTR led to diversification of CREM mRNA (modulator of gene expression related to the structuring of mature spermatozoa). Sperm tail formation can be regulated by changes in the 5' UTR of testicular SLC9A3R1 and gene silencing by producing dysfunctional variants of ODF2 in the testis and ATP1B3 in the epididymis. Predicted differentially ASGs in the turkey reproductive tract seem to be involved in the regulation of spermatogenesis, including acrosome formation and sperm tail formation and binding of sperm to the zona pellucida. Several ASGs were classified as cilia by actin and microtubule cytoskeleton organization. Such genes may play a role in the organization of sperm flagellum and post-testicular motility development. To our knowledge, this is the first functional investigation of alternatively spliced genes associated with tissue-specific processes in the turkey reproductive tract.
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Affiliation(s)
- Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology; University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Joanna Wiśniewska
- Department of Biological Function of Food, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Ewa Liszewska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Marta Majewska
- Department of Human Physiology and Pathophysiology, School of Medicine, Collegium Medicum; University of Warmia and Mazury in Olsztyn, 10-561 Olsztyn, Poland
| | - Jan Jastrzębski
- Department of Plant Physiology, Genetics, and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Jan Jankowski
- Department of Poultry Science, University of Warmia and Mazury in Olsztyn, 10-719, Olsztyn, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences in Olsztyn, 10-748, Olsztyn, Poland.
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13
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Gallicchio L, Olivares GH, Berry CW, Fuller MT. Regulation and function of alternative polyadenylation in development and differentiation. RNA Biol 2023; 20:908-925. [PMID: 37906624 PMCID: PMC10730144 DOI: 10.1080/15476286.2023.2275109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/02/2023] Open
Abstract
Alternative processing of nascent mRNAs is widespread in eukaryotic organisms and greatly impacts the output of gene expression. Specifically, alternative cleavage and polyadenylation (APA) is a co-transcriptional molecular process that switches the polyadenylation site (PAS) at which a nascent mRNA is cleaved, resulting in mRNA isoforms with different 3'UTR length and content. APA can potentially affect mRNA translation efficiency, localization, stability, and mRNA seeded protein-protein interactions. APA naturally occurs during development and cellular differentiation, with around 70% of human genes displaying APA in particular tissues and cell types. For example, neurons tend to express mRNAs with long 3'UTRs due to preferential processing at PASs more distal than other PASs used in other cell types. In addition, changes in APA mark a variety of pathological states, including many types of cancer, in which mRNAs are preferentially cleaved at more proximal PASs, causing expression of mRNA isoforms with short 3'UTRs. Although APA has been widely reported, both the function of APA in development and the mechanisms that regulate the choice of 3'end cut sites in normal and pathogenic conditions are still poorly understood. In this review, we summarize current understanding of how APA is regulated during development and cellular differentiation and how the resulting change in 3'UTR content affects multiple aspects of gene expression. With APA being a widespread phenomenon, the advent of cutting-edge scientific techniques and the pressing need for in-vivo studies, there has never been a better time to delve into the intricate mechanisms of alternative cleavage and polyadenylation.
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Affiliation(s)
- Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
| | - Gonzalo H. Olivares
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Center for Integrative Biology (CIB), Universidad Mayor, Chile and Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | | | - Margaret T. Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
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14
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Li N, Cai Y, Zou M, Zhou J, Zhang L, Zhou L, Xiang W, Cui Y, Li H. CFIm-mediated alternative polyadenylation safeguards the development of mammalian pre-implantation embryos. Stem Cell Reports 2022; 18:81-96. [PMID: 36563685 PMCID: PMC9860127 DOI: 10.1016/j.stemcr.2022.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 12/24/2022] Open
Abstract
Alternative polyadenylation (APA) gives rise to transcripts with distinct 3' untranslated regions (3' UTRs), thereby affecting the fate of mRNAs. APA is strongly associated with cell proliferation and differentiation status, and thus likely plays a critical role in the embryo development. However, the pattern of APA in mammalian early embryos is still unknown. Here, we analyzed the 3' UTR lengths in human and mouse pre-implantation embryos using available single cell RNA-seq datasets and explored the underlying mechanism driving the changes. Although human and mouse early embryos displayed distinct patterns of 3' UTR changing, RNA metabolism pathways were involved in both species. The 3' UTR lengths are likely determined by the abundance of the cleavage factor I complex (CFIm) components NUDT21 and CPSF6 in the nucleus. Importantly, depletion of either component resulted in early embryo development arrest and 3' UTR shortening. Collectively, these data highlight an essential role for APA in the development of mammalian early embryos.
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Affiliation(s)
- Na Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ying Cai
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Min Zou
- Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430013, China
| | - Jian Zhou
- Wuhan Jianwen Biological Technology Co. LTD, Wuhan 430205, China
| | - Ling Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liquan Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wenpei Xiang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Yan Cui
- International Center for Aging and Cancer, Hainan Medical University, Haikou 571199, China.
| | - Huaibiao Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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15
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Pieraccioli M, Caggiano C, Mignini L, Zhong C, Babini G, Lattanzio R, Di Stasi S, Tian B, Sette C, Bielli P. The transcriptional terminator XRN2 and the RNA-binding protein Sam68 link alternative polyadenylation to cell cycle progression in prostate cancer. Nat Struct Mol Biol 2022; 29:1101-1112. [PMID: 36344846 PMCID: PMC9872553 DOI: 10.1038/s41594-022-00853-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Alternative polyadenylation (APA) yields transcripts differing in their 3'-end, and its regulation is altered in cancer, including prostate cancer. Here we have uncovered a mechanism of APA regulation impinging on the interaction between the exonuclease XRN2 and the RNA-binding protein Sam68, whose increased expression in prostate cancer is promoted by the transcription factor MYC. Genome-wide transcriptome profiling revealed a widespread impact of the Sam68/XRN2 complex on APA. XRN2 promotes recruitment of Sam68 to its target transcripts, where it competes with the cleavage and polyadenylation specificity factor for binding to strong polyadenylation signals at distal ends of genes, thus promoting usage of suboptimal proximal polyadenylation signals. This mechanism leads to 3' untranslated region shortening and translation of transcripts encoding proteins involved in G1/S progression and proliferation. Thus, our findings indicate that the APA program driven by Sam68/XRN2 promotes cell cycle progression and may represent an actionable target for therapeutic intervention.
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Affiliation(s)
- Marco Pieraccioli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Cinzia Caggiano
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy.,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Luca Mignini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Chuwei Zhong
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Gabriele Babini
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy
| | - Rossano Lattanzio
- Department of Innovative Technologies in Medicine & Dentistry, G. d’Annunzio University, Chieti, Italy.,Center for Advanced Studies and Technology (CAST), G. d’Annunzio University, Chieti, Italy
| | - Savino Di Stasi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Bin Tian
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Hearth, Rome, Italy. .,GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, Rome, Italy.
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy. .,Laboratory of Neuroembryology, IRCCS Fondazione Santa Lucia, Rome, Italy.
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16
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Meyer E, Chaung K, Dehghannasiri R, Salzman J. ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq. Genome Biol 2022; 23:226. [PMID: 36284317 PMCID: PMC9594907 DOI: 10.1186/s13059-022-02795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak calling heuristics, and collapsing measurements by cell type. We introduce ReadZS, an annotation-free statistical approach to identify regulated RNA processing in single cells. ReadZS discovers cell type-specific RNA processing in human lung and conserved, developmentally regulated RNA processing in mammalian spermatogenesis-including global 3' UTR shortening in human spermatogenesis. ReadZS also discovers global 3' UTR lengthening in Arabidopsis development, highlighting the usefulness of this method in under-annotated transcriptomes.
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Affiliation(s)
- Elisabeth Meyer
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Kaitlin Chaung
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
- Department of Statistics (by courtesy), Stanford University, Stanford, CA, 94305, USA.
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17
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Lee S, Chen YC, Gillen AE, Taliaferro JM, Deplancke B, Li H, Lai EC. Diverse cell-specific patterns of alternative polyadenylation in Drosophila. Nat Commun 2022; 13:5372. [PMID: 36100597 PMCID: PMC9470587 DOI: 10.1038/s41467-022-32305-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids. We trace dynamic 3' UTR patterns across cell lineages, including in the male germline, and discover new APA patterns in the intestinal stem cell lineage. Finally, we correlate expression of RNA binding proteins (RBPs), miRNAs and global levels of cleavage and polyadenylation (CPA) factors in several cell types that exhibit characteristic APA landscapes, yielding candidate regulators of transcriptome complexity. These analyses provide a comprehensive foundation for future investigations of mechanisms and biological impacts of alternative 3' isoforms across the major cell types of this widely-studied model organism.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY, 10065, USA
| | - Yen-Chung Chen
- Department of Biology, New York University, New York, NY, 10013, USA
| | | | - Austin E Gillen
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Matthew Taliaferro
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering & Global Health Institute, School of Life Sciences, EPFL, CH-1015, Lausanne, Switzerland
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY, 10065, USA.
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18
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Berry CW, Olivares GH, Gallicchio L, Ramaswami G, Glavic A, Olguín P, Li JB, Fuller MT. Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage. Genes Dev 2022; 36:916-935. [PMID: 36175033 PMCID: PMC9575692 DOI: 10.1101/gad.349689.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/12/2022] [Indexed: 02/03/2023]
Abstract
Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3' cleavage site, resulting in the production of mRNA isoforms with different length 3' UTRs. Although widespread, the role of APA in the biology of cells, tissues, and organisms has been controversial. We identified >500 Drosophila genes that express mRNA isoforms with a long 3' UTR in proliferating spermatogonia but a short 3' UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3' end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3' UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed >250 genes where the long 3' UTR versus short 3' UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3' end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.
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Affiliation(s)
- Cameron W Berry
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gonzalo H Olivares
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Huechuraba 8580745, Chile
- Center of Integrative Biology (CIB), Universidad Mayor, Huechuraba 8580745, Chile
| | - Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alvaro Glavic
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
| | - Patricio Olguín
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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19
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scAPAmod: Profiling Alternative Polyadenylation Modalities in Single Cells from Single-Cell RNA-Seq Data. Int J Mol Sci 2022; 23:ijms23158123. [PMID: 35897701 PMCID: PMC9329739 DOI: 10.3390/ijms23158123] [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: 03/29/2022] [Revised: 07/01/2022] [Accepted: 07/21/2022] [Indexed: 11/17/2022] Open
Abstract
Alternative polyadenylation (APA) is a key layer of gene expression regulation, and APA choice is finely modulated in cells. Advances in single-cell RNA-seq (scRNA-seq) have provided unprecedented opportunities to study APA in cell populations. However, existing studies that investigated APA in single cells were either confined to a few cells or focused on profiling APA dynamics between cell types or identifying APA sites. The diversity and pattern of APA usages on a genomic scale in single cells remains unappreciated. Here, we proposed an analysis framework based on a Gaussian mixture model, scAPAmod, to identify patterns of APA usage from homogeneous or heterogeneous cell populations at the single-cell level. We systematically evaluated the performance of scAPAmod using simulated data and scRNA-seq data. The results show that scAPAmod can accurately identify different patterns of APA usages at the single-cell level. We analyzed the dynamic changes in the pattern of APA usage using scAPAmod in different cell differentiation and developmental stages during mouse spermatogenesis and found that even the same gene has different patterns of APA usages in different differentiation stages. The preference of patterns of usages of APA sites in different genomic regions was also analyzed. We found that patterns of APA usages of the same gene in 3′ UTRs (3′ untranslated region) and non-3′ UTRs are different. Moreover, we analyzed cell-type-specific APA usage patterns and changes in patterns of APA usages across cell types. Different from the conventional analysis of single-cell heterogeneity based on gene expression profiling, this study profiled the heterogeneous pattern of APA isoforms, which contributes to revealing the heterogeneity of single-cell gene expression with higher resolution.
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20
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Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD. A joint NCBI and EMBL-EBI transcript set for clinical genomics and research. Nature 2022; 604:310-315. [PMID: 35388217 PMCID: PMC9007741 DOI: 10.1038/s41586-022-04558-8] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/07/2022] [Indexed: 12/25/2022]
Abstract
Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.
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Affiliation(s)
- Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Alex Astashyn
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Andrew Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Olga Ermolaeva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Reham Fatima
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jose M Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Hardy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - John Jackson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Vinita S Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Michael Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Aoife McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael R Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lillian D Riddick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Glen Threadgold
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Anjana R Vatsan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Webb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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21
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Li Y, Mi P, Chen X, Wu J, Liu X, Tang Y, Cheng J, Huang Y, Qin W, Cheng CY, Sun F. Tex13a Optimizes Sperm Motility via Its Potential Roles in mRNA Turnover. Front Cell Dev Biol 2021; 9:761627. [PMID: 34733855 PMCID: PMC8558480 DOI: 10.3389/fcell.2021.761627] [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: 08/20/2021] [Accepted: 09/22/2021] [Indexed: 11/24/2022] Open
Abstract
mRNAs have been found to undergo substantial selective degradation during the late stages of spermiogenesis. However, the mechanisms regulating this biological process are unknown. In this report, we have identified Tex13a, a spermatid-specific gene that interacts with the CCR4–NOT complex and is implicated in the targeted degradation of mRNAs encoding particular structural components of sperm. Deletion of Tex13a led to a delayed decay of these mRNAs, lowered the levels of house-keeping genes, and ultimately lowered several key parameters associated with the control of sperm motility, such as the path velocity (VAP, average path velocity), track speed (VCL, velocity curvilinear), and rapid progression.
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Affiliation(s)
- Yinchuan Li
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Panpan Mi
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Xue Chen
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Jiabao Wu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Xiaohua Liu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Yunge Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Jinmei Cheng
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Yingying Huang
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - C Yan Cheng
- The Mary M. Wohlford Laboratory for Male Contraceptive Research, Center for Biomedical Research, Population Council, New York, NY, United States
| | - Fei Sun
- Institute of Reproductive Medicine, Medical School of Nantong University, Nantong, China
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22
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Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs. Nat Commun 2021; 12:5970. [PMID: 34645830 PMCID: PMC8514520 DOI: 10.1038/s41467-021-26233-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. piRNAs originate from transposable element (TE) RNAs, long non-coding RNAs, or 3´ untranslated regions (3´UTRs) of protein-coding messenger genes, with the last being the least characterized of the three piRNA classes. Here, we demonstrate that the precursors of 3´UTR piRNAs are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3´UTRs in mice and chickens. At the pachytene stage, when other co-translational RNA surveillance pathways are sequestered, piRNA biogenesis degrades mRNAs right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Although 3´UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded TEs and produce piRNAs that cleave TEs. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes.
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23
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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24
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Non-Coding RNAs and Splicing Activity in Testicular Germ Cell Tumors. Life (Basel) 2021; 11:life11080736. [PMID: 34440480 PMCID: PMC8399856 DOI: 10.3390/life11080736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023] Open
Abstract
Testicular germ cell tumors (TGCTs) are the most common tumors in adolescent and young men. Recently, genome-wide studies have made it possible to progress in understanding the molecular mechanisms underlying the development of tumors. It is becoming increasingly clear that aberrant regulation of RNA metabolism can drive tumorigenesis and influence chemotherapeutic response. Notably, the expression of non-coding RNAs as well as specific splice variants is deeply deregulated in human cancers. Since these cancer-related RNA species are considered promising diagnostic, prognostic and therapeutic targets, understanding their function in cancer development is becoming a major challenge. Here, we summarize how the different expression of RNA species repertoire, including non-coding RNAs and protein-coding splicing variants, impacts on TGCTs’ onset and progression and sustains therapeutic resistance. Finally, the role of transcription-associated R-loop misregulation in the maintenance of genomic stability in TGCTs is also discussed.
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25
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Ye C, Zhao D, Ye W, Wu X, Ji G, Li QQ, Lin J. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. Brief Bioinform 2021; 22:6319934. [PMID: 34255024 DOI: 10.1093/bib/bbab268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023] Open
Abstract
The dynamic choice of different polyadenylation sites in a gene is referred to as alternative polyadenylation, which functions in many important biological processes. Large-scale messenger RNA 3' end sequencing has revealed that cleavage sites for polyadenylation are presented with microheterogeneity. To date, the conventional determination of polyadenylation site clusters is subjective and arbitrary, leading to inaccurate annotations. Here, we present a weighted density peak clustering method, QuantifyPoly(A), to accurately quantify genome-wide polyadenylation choices. Applying QuantifyPoly(A) on published 3' end sequencing datasets from both animals and plants, their polyadenylation profiles are reshaped into myriads of novel polyadenylation site clusters. Most of these novel polyadenylation site clusters show significantly dynamic usage across different biological samples or associate with binding sites of trans-acting factors. Upstream sequences of these clusters are enriched with polyadenylation signals UGUA, UAAA and/or AAUAAA in a species-dependent manner. Polyadenylation site clusters also exhibit species specificity, while plants ones generally show higher microheterogeneity than that of animals. QuantifyPoly(A) is broadly applicable to any types of 3' end sequencing data and species for accurate quantification and construction of the complex and dynamic polyadenylation landscape and enables us to decode alternative polyadenylation events invisible to conventional methods at a much higher resolution.
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Affiliation(s)
- Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Danhui Zhao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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26
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Goering R, Engel KL, Gillen AE, Fong N, Bentley DL, Taliaferro JM. LABRAT reveals association of alternative polyadenylation with transcript localization, RNA binding protein expression, transcription speed, and cancer survival. BMC Genomics 2021; 22:476. [PMID: 34174817 PMCID: PMC8234626 DOI: 10.1186/s12864-021-07781-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The sequence content of the 3' UTRs of many mRNA transcripts is regulated through alternative polyadenylation (APA). The study of this process using RNAseq data, though, has been historically challenging. RESULTS To combat this problem, we developed LABRAT, an APA isoform quantification method. LABRAT takes advantage of newly developed transcriptome quantification techniques to accurately determine relative APA site usage and how it varies across conditions. Using LABRAT, we found consistent relationships between gene-distal APA and subcellular RNA localization in multiple cell types. We also observed connections between transcription speed and APA site choice as well as tumor-specific transcriptome-wide shifts in APA isoform abundance in hundreds of patient-derived tumor samples that were associated with patient prognosis. We investigated the effects of APA on transcript expression and found a weak overall relationship, although many individual genes showed strong correlations between relative APA isoform abundance and overall gene expression. We interrogated the roles of 191 RNA-binding proteins in the regulation of APA isoforms, finding that dozens promote broad, directional shifts in relative APA isoform abundance both in vitro and in patient-derived samples. Finally, we find that APA site shifts in the two classes of APA, tandem UTRs and alternative last exons, are strongly correlated across many contexts, suggesting that they are coregulated. CONCLUSIONS We conclude that LABRAT has the ability to accurately quantify APA isoform ratios from RNAseq data across a variety of sample types. Further, LABRAT is able to derive biologically meaningful insights that connect APA isoform regulation to cellular and molecular phenotypes.
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Affiliation(s)
- Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Austin E Gillen
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Division of Hematology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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27
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Bianchi E, Stermer A, Nolan T, Li H, Hall S, Boekelheide K, Sigman M, Hwang K. Highly conserved sperm function-related transcripts across three species: human, rat and mouse. Reprod Toxicol 2021; 104:44-51. [PMID: 34174366 DOI: 10.1016/j.reprotox.2021.06.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 01/24/2023]
Abstract
Assessing male reproductive toxicity of environmental and therapeutic agents relies on the histopathology of the testis and epididymis in a pre-clinical setting. Animal histopathology poorly correlates with human sperm parameters, and none of these current methods are strong indicators of sperm health or reproductive potential. Therefore, there is an urgent need to identify a translatable, non-invasive and reliable approach to monitor environmental and therapeutic agents' effects on male reproductive health. mRNA sequences were analyzed in mouse, rat and human sperm samples to identify sperm transcriptomic similarities across species that could be used as biomarkers to predict male reproductive toxicity in animal models. Semen specimens were collected from men aged 18 to 55 years with proven fertility. Rat and mouse semen specimens were collected via needle punctures of the cauda epididymides. Sperm RNAs were extracted using an optimized sperm RNA isolation protocol and subjected to polyA-purified mRNA-sequencing. Bioinformatics analyses, including differential abundance and gene set enrichment analysis, were used to investigate the biological and molecular functions of all shared and differentially abundant transcripts across species. Transcriptome profiling identified 6,684 similarly expressed transcripts within the three species of which 1,579 transcripts were found to be involved in spermatogenic functions. Our findings have shown that sperm transcriptome is highly species dependent, however, there are some key similarities among transcripts that are required for fertility. Based on these similarities, sperm mRNA biomarker may be developed to monitor male reproductive toxicity where rodent models would make suitable laboratory substitutes for human.
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Affiliation(s)
- Enrica Bianchi
- Division of Urology, Rhode Island Hospital, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Angela Stermer
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Timothy Nolan
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Hui Li
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Susan Hall
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Mark Sigman
- Division of Urology, Rhode Island Hospital, Providence, RI, USA; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Kathleen Hwang
- Department of Urology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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28
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Ogorodnikov A, Danckwardt S. TRENDseq-A highly multiplexed high throughput RNA 3' end sequencing for mapping alternative polyadenylation. Methods Enzymol 2021; 655:37-72. [PMID: 34183130 DOI: 10.1016/bs.mie.2021.03.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alternative polyadenylation (APA) is a widespread and highly dynamic mechanism of gene regulation. It affects more than 70% of all genes, resulting in transcript isoforms with distinct 3' end termini. APA thereby considerably expands the diversity of the transcriptome 3' end (TREND). This leads to mRNA isoforms with profoundly different physiological effects, by affecting protein output, production of distinct protein isoforms, or modulating protein localization. APA is globally regulated in various conditions, including developmental and adaptive programs. Since perturbations of APA can disrupt biological processes, ultimately resulting in most devastating disorders, querying the APA landscape is crucial to decipher underlying mechanisms, resulting consequences and potential diagnostic and therapeutic implications. Here we provide a detailed step-by-step protocol for TRENDseq, a method for transcriptome-wide high-throughput sequencing of polyadenylated RNA 3' ends in a highly multiplexed fashion. TRENDseq exploits linear amplification of the starting material to improve sensitivity while significantly reducing the amount of input material. It thereby represents a powerful tool to study APA in numerous experimental set-ups and/or limited human samples in a highly multiplexed and reproducible manner.
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Affiliation(s)
- Anton Ogorodnikov
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany; Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany; Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany
| | - Sven Danckwardt
- Posttranscriptional Gene Regulation, University Medical Centre Mainz, Mainz, Germany; Institute for Clinical Chemistry and Laboratory Medicine, University Medical Centre Mainz, Mainz, Germany; Centre for Thrombosis and Hemostasis (CTH), University Medical Centre Mainz, Mainz, Germany; German Centre for Cardiovascular Research (DZHK), Berlin, Germany.
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29
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Sommerkamp P, Cabezas-Wallscheid N, Trumpp A. Alternative Polyadenylation in Stem Cell Self-Renewal and Differentiation. Trends Mol Med 2021; 27:660-672. [PMID: 33985920 DOI: 10.1016/j.molmed.2021.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/13/2022]
Abstract
Cellular function is shaped by transcriptional and post-transcriptional mechanisms, including alternative polyadenylation (APA). By directly controlling 3'- untranslated region (UTR) length and the selection of the last exon, APA regulates up to 70% of all cellular transcripts influencing RNA stability, output, and protein isoform expression. Cell-state-dependent 3'-UTR shortening has been identified as a hallmark of cellular proliferation. Hence, quiescent/dormant stem cells are characterized by long 3'-UTRs, whereas proliferative stem/progenitor cells exhibit 3'-UTR shortening. Here, the latest studies analyzing the role of APA in regulating stem cell state, self-renewal, differentiation, and metabolism are reviewed. The new role of APA in controlling stem cell fate opens novel potential therapeutic avenues in the field of regenerative medicine.
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Affiliation(s)
- Pia Sommerkamp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
| | | | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.
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30
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Pereira-Castro I, Moreira A. On the function and relevance of alternative 3'-UTRs in gene expression regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1653. [PMID: 33843145 DOI: 10.1002/wrna.1653] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022]
Abstract
Messanger RNA (mRNA) isoforms with alternative 3'-untranslated regions (3'-UTRs) are produced by alternative polyadenylation (APA), which occurs during transcription in most eukaryotic genes. APA fine-tunes gene expression in a cell-type- and cellular state-dependent manner. Selection of an APA site entails the binding of core cleavage and polyadenylation factors to a particular polyadenylation site localized in the pre-mRNA and is controlled by multiple regulatory determinants, including transcription, pre-mRNA cis-regulatory sequences, and protein factors. Alternative 3'-UTRs serve as platforms for specific RNA binding proteins and microRNAs, which regulate gene expression in a coordinated manner by controlling mRNA fate and function in the cell. Genome-wide studies illustrated the full extent of APA prevalence and revealed that specific 3'-UTR profiles are associated with particular cellular states and diseases. Generally, short 3'-UTRs are associated with proliferative and cancer cells, and long 3'-UTRs are mostly found in polarized and differentiated cells. Fundamental new insights on the physiological consequences of this widespread event and the molecular mechanisms involved have been revealed through single-cell studies. Publicly available comprehensive databases that cover all APA mRNA isoforms identified in many cellular states and diseases reveal specific APA signatures. Therapies tackling APA mRNA isoforms or APA regulators may be regarded as innovative and attractive tools for diagnostics or treatment of several pathologies. We highlight the function of APA and alternative 3'-UTRs in gene expression regulation, the control of these mechanisms, their physiological consequences, and their potential use as new biomarkers and therapeutic tools. This article is categorized under: RNA Processing > 3' End Processing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Isabel Pereira-Castro
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Alexandra Moreira
- Gene Regulation, i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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31
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Geisinger A, Rodríguez-Casuriaga R, Benavente R. Transcriptomics of Meiosis in the Male Mouse. Front Cell Dev Biol 2021; 9:626020. [PMID: 33748111 PMCID: PMC7973102 DOI: 10.3389/fcell.2021.626020] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/15/2021] [Indexed: 12/18/2022] Open
Abstract
Molecular studies of meiosis in mammals have been long relegated due to some intrinsic obstacles, namely the impossibility to reproduce the process in vitro, and the difficulty to obtain highly pure isolated cells of the different meiotic stages. In the recent years, some technical advances, from the improvement of flow cytometry sorting protocols to single-cell RNAseq, are enabling to profile the transcriptome and its fluctuations along the meiotic process. In this mini-review we will outline the diverse methodological approaches that have been employed, and some of the main findings that have started to arise from these studies. As for practical reasons most studies have been carried out in males, and mostly using mouse as a model, our focus will be on murine male meiosis, although also including specific comments about humans. Particularly, we will center on the controversy about gene expression during early meiotic prophase; the widespread existing gap between transcription and translation in meiotic cells; the expression patterns and potential roles of meiotic long non-coding RNAs; and the visualization of meiotic sex chromosome inactivation from the RNAseq perspective.
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Affiliation(s)
- Adriana Geisinger
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República (UdelaR), Montevideo, Uruguay
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Rosana Rodríguez-Casuriaga
- Department of Molecular Biology, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Montevideo, Uruguay
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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32
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Marini F, Scherzinger D, Danckwardt S. TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. Nucleic Acids Res 2021; 49:D243-D253. [PMID: 32976578 PMCID: PMC7778938 DOI: 10.1093/nar/gkaa722] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative polyadenylation (APA) profoundly expands the transcriptome complexity. Perturbations of APA can disrupt biological processes, ultimately resulting in devastating disorders. A major challenge in identifying mechanisms and consequences of APA (and its perturbations) lies in the complexity of RNA 3′ end processing, involving poorly conserved RNA motifs and multi-component complexes consisting of far more than 50 proteins. This is further complicated in that RNA 3′ end maturation is closely linked to transcription, RNA processing and even epigenetic (histone/DNA/RNA) modifications. Here, we present TREND-DB (http://shiny.imbei.uni-mainz.de:3838/trend-db), a resource cataloging the dynamic landscape of APA after depletion of >170 proteins involved in various facets of transcriptional, co- and post-transcriptional gene regulation, epigenetic modifications and further processes. TREND-DB visualizes the dynamics of transcriptome 3′ end diversification (TREND) in a highly interactive manner; it provides a global APA network map and allows interrogating genes affected by specific APA-regulators and vice versa. It also permits condition-specific functional enrichment analyses of APA-affected genes, which suggest wide biological and clinical relevance across all RNAi conditions. The implementation of the UCSC Genome Browser provides additional customizable layers of gene regulation accounting for individual transcript isoforms (e.g. epigenetics, miRNA-binding sites and RNA-binding proteins). TREND-DB thereby fosters disentangling the role of APA for various biological programs, including potential disease mechanisms, and helps identify their diagnostic and therapeutic potential.
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Affiliation(s)
- Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany.,Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz, Germany
| | - Denise Scherzinger
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center Mainz, 55131 Mainz, Germany
| | - Sven Danckwardt
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz, Germany.,Posttranscriptional Gene Regulation, Cancer Research and Experimental Hemostasis, University Medical Center Mainz, 55131 Mainz, Germany.,Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Mainz, 55131 Mainz, Germany.,German Center for Cardiovascular Research (DZHK), Rhine-Main, 55131 Mainz, Germany
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33
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Epidermal progenitors suppress GRHL3-mediated differentiation through intronic polyadenylation promoted by CPSF-HNRNPA3 collaboration. Nat Commun 2021; 12:448. [PMID: 33469008 PMCID: PMC7815847 DOI: 10.1038/s41467-020-20674-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 12/11/2020] [Indexed: 01/29/2023] Open
Abstract
In self-renewing somatic tissue such as skin epidermis, terminal differentiation genes must be suppressed in progenitors to sustain regenerative capacity. Here we show that hundreds of intronic polyadenylation (IpA) sites are differentially used during keratinocyte differentiation, which is accompanied by downregulation of the Cleavage and Polyadenylation Specificity Factor (CPSF) complex. Sustained CPSF expression in undifferentiated keratinocytes requires the contribution from the transcription factor MYC. In keratinocytes cultured in undifferentiation condition, CSPF knockdown induces premature differentiation and partially affects dynamically used IpA sites. These sites include an IpA site located in the first intron of the differentiation activator GRHL3. CRISPR knockout of GRHL3 IpA increased full-length GRHL3 mRNA expression. Using a targeted genetic screen, we identify that HNRNPA3 interacts with CPSF and enhances GRHL3 IpA. Our data suggest a model where the interaction between CPSF and RNA-binding proteins, such as HNRNPA3, promotes site-specific IpA and suppresses premature differentiation in progenitors.
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34
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Florke Gee RR, Chen H, Lee AK, Daly CA, Wilander BA, Fon Tacer K, Potts PR. Emerging roles of the MAGE protein family in stress response pathways. J Biol Chem 2020; 295:16121-16155. [PMID: 32921631 PMCID: PMC7681028 DOI: 10.1074/jbc.rev120.008029] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 09/08/2020] [Indexed: 12/21/2022] Open
Abstract
The melanoma antigen (MAGE) proteins all contain a MAGE homology domain. MAGE genes are conserved in all eukaryotes and have expanded from a single gene in lower eukaryotes to ∼40 genes in humans and mice. Whereas some MAGEs are ubiquitously expressed in tissues, others are expressed in only germ cells with aberrant reactivation in multiple cancers. Much of the initial research on MAGEs focused on exploiting their antigenicity and restricted expression pattern to target them with cancer immunotherapy. Beyond their potential clinical application and role in tumorigenesis, recent studies have shown that MAGE proteins regulate diverse cellular and developmental pathways, implicating them in many diseases besides cancer, including lung, renal, and neurodevelopmental disorders. At the molecular level, many MAGEs bind to E3 RING ubiquitin ligases and, thus, regulate their substrate specificity, ligase activity, and subcellular localization. On a broader scale, the MAGE genes likely expanded in eutherian mammals to protect the germline from environmental stress and aid in stress adaptation, and this stress tolerance may explain why many cancers aberrantly express MAGEs Here, we present an updated, comprehensive review on the MAGE family that highlights general characteristics, emphasizes recent comparative studies in mice, and describes the diverse functions exerted by individual MAGEs.
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Affiliation(s)
- Rebecca R Florke Gee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Helen Chen
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Anna K Lee
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Christina A Daly
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Benjamin A Wilander
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Klementina Fon Tacer
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; School of Veterinary Medicine, Texas Tech University, Amarillo, Texas, USA.
| | - Patrick Ryan Potts
- Cell and Molecular Biology Department, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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35
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Grozdanov PN, Masoumzadeh E, Kalscheuer VM, Bienvenu T, Billuart P, Delrue MA, Latham MP, MacDonald CC. A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3' end processing is associated with intellectual disability in humans. Nucleic Acids Res 2020; 48:9804-9821. [PMID: 32816001 PMCID: PMC7515730 DOI: 10.1093/nar/gkaa689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 08/03/2020] [Accepted: 08/18/2020] [Indexed: 11/25/2022] Open
Abstract
CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1300 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the significance of 3′ end mRNA processing in expression of genes important for brain plasticity and neuronal development.
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Affiliation(s)
- Petar N Grozdanov
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Elahe Masoumzadeh
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Vera M Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease, Ihnestr. 63-73, D-14195 Berlin, Germany
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Pierre Billuart
- Institut de Psychiatrie et de Neurosciences de Paris, Inserm U1266, 102 rue de la Santé, 75014 Paris, France
| | - Marie-Ange Delrue
- Département de Génétique Médicale, CHU Sainte Justine, Montréal, Canada
| | - Michael P Latham
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA
| | - Clinton C MacDonald
- Department of Cell Biology & Biochemistry, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
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36
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Wu X, Liu T, Ye C, Ye W, Ji G. scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data. Brief Bioinform 2020; 22:5952304. [PMID: 33142319 DOI: 10.1093/bib/bbaa273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023] Open
Abstract
Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to transcriptome diversity and gene expression regulation by affecting mRNA stability, translation and localization in cells. The rapid development of 3' tag-based single-cell RNA-sequencing (scRNA-seq) technologies, such as CEL-seq and 10x Genomics, has led to the emergence of computational methods for identifying APA sites and profiling APA dynamics at single-cell resolution. However, existing methods fail to detect the precise location of poly(A) sites or sites with low read coverage. Moreover, they rely on priori genome annotation and can only detect poly(A) sites located within or near annotated genes. Here we proposed a tool called scAPAtrap for detecting poly(A) sites at the whole genome level in individual cells from 3' tag-based scRNA-seq data. scAPAtrap incorporates peak identification and poly(A) read anchoring, enabling the identification of the precise location of poly(A) sites, even for sites with low read coverage. Moreover, scAPAtrap can identify poly(A) sites without using priori genome annotation, which helps locate novel poly(A) sites in previously overlooked regions and improve genome annotation. We compared scAPAtrap with two latest methods, scAPA and Sierra, using scRNA-seq data from different experimental technologies and species. Results show that scAPAtrap identified poly(A) sites with higher accuracy and sensitivity than competing methods and could be used to explore APA dynamics among cell types or the heterogeneous APA isoform expression in individual cells. scAPAtrap is available at https://github.com/BMILAB/scAPAtrap.
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Affiliation(s)
- Xiaohui Wu
- Department of Automation in Xiamen University
| | - Tao Liu
- Department of Automation in Xiamen University
| | - Congting Ye
- College of the Environment and Ecology in Xiamen University
| | - Wenbin Ye
- Department of Automation in Xiamen University
| | - Guoli Ji
- Department of Automation in Xiamen University
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37
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Shulman ED, Elkon R. Systematic identification of functional SNPs interrupting 3'UTR polyadenylation signals. PLoS Genet 2020; 16:e1008977. [PMID: 32804959 PMCID: PMC7451987 DOI: 10.1371/journal.pgen.1008977] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 08/27/2020] [Accepted: 07/01/2020] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as a widespread regulatory layer since the majority of human protein-coding genes contain several polyadenylation (p(A)) sites in their 3’UTRs. By generating isoforms with different 3’UTR length, APA potentially affects mRNA stability, translation efficiency, nuclear export, and cellular localization. Polyadenylation sites are regulated by adjacent RNA cis-regulatory elements, the principals among them are the polyadenylation signal (PAS) AAUAAA and its main variant AUUAAA, typically located ~20-nt upstream of the p(A) site. Mutations in PAS and other auxiliary poly(A) cis-elements in the 3’UTR of several genes have been shown to cause human Mendelian diseases, and to date, only a few common SNPs that regulate APA were associated with complex diseases. Here, we systematically searched for SNPs that affect gene expression and human traits by modulation of 3’UTR APA. First, focusing on the variants most likely to exert the strongest effect, we identified 2,305 SNPs that interrupt the canonical PAS or its main variant. Implementing pA-QTL tests using GTEx RNA-seq data, we identified 330 PAS SNPs (called PAS pA-QTLs) that were significantly associated with the usage of their p(A) site. As expected, PAS-interrupting alleles were mostly linked with decreased cleavage at their p(A) site and the consequential 3’UTR lengthening. However, interestingly, in ~10% of the cases, the PAS-interrupting allele was associated with increased usage of an upstream p(A) site and 3’UTR shortening. As an indication of the functional effects of these PAS pA-QTLs on gene expression and complex human traits, we observed for few dozens of them marked colocalization with eQTL and/or GWAS signals. The PAS-interrupting alleles linked with 3’UTR lengthening were also strongly associated with decreased gene expression, indicating that shorter isoforms generated by APA are generally more stable than longer ones. Last, we carried out an extended, genome-wide analysis of 3’UTR variants and detected thousands of additional pA-QTLs having weaker effects compared to the PAS pA-QTLs. mRNA molecules that encode for proteins end with a long stretch of adenosines, called poly(A) tail. The poly(A) tail contributes to the stability of the mRNA molecules, their translation to proteins and their import from the nucleus to the cytoplasm. The process of adding this tail to the mRNAs is called polyadenylation, and the termination site on the mRNAs at which the poly(A) tail is added is called the poly(A) site. In recent years it became evident that the vast majority of mRNAs of human genes contain several alternative poly(A) sites and their usage generates different mRNA isoforms that differ in their stability and translation efficiency. Therefore, alternative polyadenylation (APA) is emerging as a novel and important, yet underexplored, mechanism that regulate gene expression. The choice between alternative p(A) sites in an mRNA molecule is regulated by regulatory sequences located within a region in the mRNA called the 3’ untranslated region (3’UTR). A major challenge in present human genetics research is to understand how common genetic variants affect individuals’ health. In our study, we systematically identified dozens of genetic variants that affect the choice between alternative p(A) sites and demonstrated that by that, these variants influence the expression level of the target genes. Our results help to illuminate a novel mechanism by which genetic variants that are common in the population affect different traits including our risk for developing diseases.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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38
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Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020; 10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
A crucial feature of gene expression involves RNA processing to produce 3′ ends through a process termed 3′ end cleavage and polyadenylation (CPA). This ensures the nascent RNA molecule can exit the nucleus and be translated to ultimately give rise to a protein which can execute a function. Further, alternative polyadenylation (APA) can produce distinct transcript isoforms, profoundly expanding the complexity of the transcriptome. CPA is carried out by multi-component protein complexes interacting with multiple RNA motifs and is tightly coupled to transcription, other steps of RNA processing, and even epigenetic modifications. CPA and APA contribute to the maintenance of a multitude of diverse physiological processes. It is therefore not surprising that disruptions of CPA and APA can lead to devastating disorders. Here, we review potential CPA and APA mechanisms involving both loss and gain of function that can have tremendous impacts on health and disease. Ultimately we highlight the emerging diagnostic and therapeutic potential CPA and APA offer.
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Affiliation(s)
- Jamie Nourse
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefano Spada
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, Germany
- Correspondence:
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39
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Naro C, Pellegrini L, Jolly A, Farini D, Cesari E, Bielli P, de la Grange P, Sette C. Functional Interaction between U1snRNP and Sam68 Insures Proper 3' End Pre-mRNA Processing during Germ Cell Differentiation. Cell Rep 2020; 26:2929-2941.e5. [PMID: 30865884 DOI: 10.1016/j.celrep.2019.02.058] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 01/15/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Male germ cells express the widest repertoire of transcript variants in mammalian tissues. Nevertheless, factors and mechanisms underlying such pronounced diversity are largely unknown. The splicing regulator Sam68 is highly expressed in meiotic cells, and its ablation results in defective spermatogenesis. Herein, we uncover an extensive splicing program operated by Sam68 across meiosis, primarily characterized by alternative last exon (ALE) regulation in genes of functional relevance for spermatogenesis. Lack of Sam68 preferentially causes premature transcript termination at internal polyadenylation sites, a feature observed also upon depletion of the spliceosomal U1snRNP in somatic cells. Notably, Sam68-regulated ALEs are characterized by proximity between U1snRNP and Sam68 binding motifs. We demonstrate a physical association between Sam68 and U1snRNP and show that U1snRNP recruitment to Sam68-regulated ALEs is impaired in Sam68-/- germ cells. Thus, our study reveals an unexpected cooperation between Sam68 and U1snRNP that insures proper processing of transcripts essential for male fertility.
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Affiliation(s)
- Chiara Naro
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Livia Pellegrini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ariane Jolly
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Donatella Farini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Eleonora Cesari
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata," 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Pierre de la Grange
- GenoSplice Technology, iPEPS-ICM, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Claudio Sette
- Institute of Human Anatomy and Cell Biology, Catholic University of the Sacred Hearth, 00168 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.
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40
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Tang C, Xie Y, Yu T, Liu N, Wang Z, Woolsey RJ, Tang Y, Zhang X, Qin W, Zhang Y, Song G, Zheng W, Wang J, Chen W, Wei X, Xie Z, Klukovich R, Zheng H, Quilici DR, Yan W. m 6A-dependent biogenesis of circular RNAs in male germ cells. Cell Res 2020; 30:211-228. [PMID: 32047269 PMCID: PMC7054367 DOI: 10.1038/s41422-020-0279-8] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
The majority of circular RNAs (circRNAs) spliced from coding genes contain open reading frames (ORFs) and thus, have protein coding potential. However, it remains unknown what regulates the biogenesis of these ORF-containing circRNAs, whether they are actually translated into proteins and what functions they play in specific physiological contexts. Here, we report that a large number of circRNAs are synthesized with increasing abundance when late pachytene spermatocytes develop into round and then elongating spermatids during murine spermatogenesis. For a subset of circRNAs, the back splicing appears to occur mostly at m6A-enriched sites, which are usually located around the start and stop codons in linear mRNAs. Consequently, approximately a half of these male germ cell circRNAs contain large ORFs with m6A-modified start codons in their junctions, features that have been recently shown to be associated with protein-coding potential. Hundreds of peptides encoded by the junction sequences of these circRNAs were detected using liquid chromatography coupled with mass spectrometry, suggesting that these circRNAs can indeed be translated into proteins in both developing (spermatocytes and spermatids) and mature (spermatozoa) male germ cells. The present study discovered not only a novel role of m6A in the biogenesis of coding circRNAs, but also a potential mechanism to ensure stable and long-lasting protein production in the absence of linear mRNAs, i.e., through production of circRNAs containing large ORFs and m6A-modified start codons in junction sequences.
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Affiliation(s)
- Chong Tang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA.
- BGI Co. Ltd., Shenzhen, 518083, China.
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Tian Yu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Na Liu
- BGI Co. Ltd., Shenzhen, 518083, China
| | - Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Rebekah J Woolsey
- Nevada Proteomics Center, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Yunge Tang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Xinzong Zhang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Weibing Qin
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Ying Zhang
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Ge Song
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Weiwei Zheng
- Key Laboratory of Male Reproduction and Genetics, National Health and Family Planning Commission, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
- Family Planning Research Institute of Guangdong Province, No. 17 Meidong Road, Yuexiu District, Guangzhou, 510600, China
| | - Juan Wang
- BGI Co. Ltd., Shenzhen, 518083, China
| | | | | | - Zhe Xie
- BGI Co. Ltd., Shenzhen, 518083, China
- Department of Cell Biology and Physiology, University of Copenhagen 13, 2100, Copenhagen, Denmark
| | - Rachel Klukovich
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - David R Quilici
- Nevada Proteomics Center, University of Nevada, Reno, Reno, NV, 89557, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA.
- Department of Obstetrics and Gynecology, University of Nevada, Reno, School of Medicine, Reno, NV, 89557, USA.
- Department of Biology, University of Nevada, Reno, Reno, NV, 89557, USA.
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41
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Yang SW, Li L, Connelly JP, Porter SN, Kodali K, Gan H, Park JM, Tacer KF, Tillman H, Peng J, Pruett-Miller SM, Li W, Potts PR. A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3' End Processing Complex. Mol Cell 2020; 77:1206-1221.e7. [PMID: 31980388 DOI: 10.1016/j.molcel.2019.12.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Abstract
Alternative polyadenylation (APA) contributes to transcriptome complexity by generating mRNA isoforms with varying 3' UTR lengths. APA leading to 3' UTR shortening (3' US) is a common feature of most cancer cells; however, the molecular mechanisms are not understood. Here, we describe a widespread mechanism promoting 3' US in cancer through ubiquitination of the mRNA 3' end processing complex protein, PCF11, by the cancer-specific MAGE-A11-HUWE1 ubiquitin ligase. MAGE-A11 is normally expressed only in the male germline but is frequently re-activated in cancers. MAGE-A11 is necessary for cancer cell viability and is sufficient to drive tumorigenesis. Screening for targets of MAGE-A11 revealed that it ubiquitinates PCF11, resulting in loss of CFIm25 from the mRNA 3' end processing complex. This leads to APA of many transcripts affecting core oncogenic and tumor suppressors, including cyclin D2 and PTEN. These findings provide insights into the molecular mechanisms driving APA in cancer and suggest therapeutic strategies.
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Affiliation(s)
- Seung Wook Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Lei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jon P Connelly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kiran Kodali
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Haiyun Gan
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jung Mi Park
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Klementina Fon Tacer
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Heather Tillman
- Veterinary Pathology Core, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA; Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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42
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Zagore LL, Sweet TJ, Hannigan MM, Weyn-Vanhentenryck SM, Jobava R, Hatzoglou M, Zhang C, Licatalosi DD. DAZL Regulates Germ Cell Survival through a Network of PolyA-Proximal mRNA Interactions. Cell Rep 2019; 25:1225-1240.e6. [PMID: 30380414 PMCID: PMC6878787 DOI: 10.1016/j.celrep.2018.10.012] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/26/2018] [Accepted: 10/01/2018] [Indexed: 01/25/2023] Open
Abstract
The RNA binding protein DAZL is essential for gametogenesis, but its direct in vivo functions, RNA targets, and the molecular basis for germ cell loss in Dazl-null mice are unknown. Here, we mapped transcriptome-wide DAZL-RNA interactions in vivo, revealing DAZL binding to thousands of mRNAs via polyA-proximal 3′ UTR interactions. In parallel, fluorescence-activated cell sorting and RNA-seq identified mRNAs sensitive to DAZL deletion in male germ cells. Despite binding a broad set of mRNAs, integrative analyses indicate that DAZL post-transcriptionally controls only a subset of its mRNA targets, namely those corresponding to a network of genes that are critical for germ cell proliferation and survival. In addition, we provide evidence that polyA sequences have key roles in specifying DAZL-RNA interactions across the transcriptome. Our results reveal a mechanism for DAZL-RNA binding and illustrate that DAZL functions as a master regulator of a post-transcriptional mRNA program essential for germ cell survival. Combining transgenic mice, FACS, and multiple RNA-profiling methods, Zagore et al. show that DAZL binds thousands of mRNAs via GUU sites upstream of polyA tails. Loss of DAZL results in decreased mRNA levels for a network of genes that are essential for germ cell proliferation and differentiation.
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Affiliation(s)
- Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Thomas J Sweet
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Raul Jobava
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Chaolin Zhang
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.
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43
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Pillman KA, Scheer KG, Hackett-Jones E, Saunders K, Bert AG, Toubia J, Whitfield HJ, Sapkota S, Sourdin L, Pham H, Le TD, Cursons J, Davis MJ, Gregory PA, Goodall GJ, Bracken CP. Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA). Nucleic Acids Res 2019; 47:8606-8619. [PMID: 31372646 PMCID: PMC6895270 DOI: 10.1093/nar/gkz664] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.
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Affiliation(s)
- Katherine A Pillman
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Kaitlin G Scheer
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Emily Hackett-Jones
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Klay Saunders
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - John Toubia
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Holly J Whitfield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Sunil Sapkota
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Laura Sourdin
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia
| | - Hoang Pham
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Thuc D Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia
| | - Joseph Cursons
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Melissa J Davis
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, Australia.,Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA, Australia.,School of Medicine, Discipline of Medicine, University of Adelaide, SA, Australia
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44
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Shulman ED, Elkon R. Cell-type-specific analysis of alternative polyadenylation using single-cell transcriptomics data. Nucleic Acids Res 2019; 47:10027-10039. [PMID: 31501864 PMCID: PMC6821429 DOI: 10.1093/nar/gkz781] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 08/27/2019] [Accepted: 09/01/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as an important layer of gene regulation because the majority of mammalian protein-coding genes contain multiple polyadenylation (pA) sites in their 3' UTR. By alteration of 3' UTR length, APA can considerably affect post-transcriptional gene regulation. Yet, our understanding of APA remains rudimentary. Novel single-cell RNA sequencing (scRNA-seq) techniques allow molecular characterization of different cell types to an unprecedented degree. Notably, the most popular scRNA-seq protocols specifically sequence the 3' end of transcripts. Building on this property, we implemented a method for analysing patterns of APA regulation from such data. Analyzing multiple datasets from diverse tissues, we identified widespread modulation of APA in different cell types resulting in global 3' UTR shortening/lengthening and enhanced cleavage at intronic pA sites. Our results provide a proof-of-concept demonstration that the huge volume of scRNA-seq data that accumulates in the public domain offers a unique resource for the exploration of APA based on a very broad collection of cell types and biological conditions.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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45
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Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nat Commun 2019; 10:4714. [PMID: 31624240 PMCID: PMC6797763 DOI: 10.1038/s41467-019-12575-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022] Open
Abstract
Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
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46
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mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq. Cell Syst 2019; 9:393-400.e6. [PMID: 31542416 DOI: 10.1016/j.cels.2019.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/06/2019] [Accepted: 07/24/2019] [Indexed: 12/28/2022]
Abstract
Alternative transcription start (ATS) and alternative polyadenylation (APA) create alternative RNA isoforms and modulate many aspects of RNA expression and protein production. However, ATS and APA remain difficult to detect in RNA sequencing (RNA-seq). Here, we developed mountainClimber, a de novo cumulative-sum-based approach to identify ATS and APA as change points. Unlike many existing methods, mountainClimber runs on a single sample and identifies multiple ATS or APA sites anywhere in the transcript. We analyzed 2,342 GTEx samples (36 tissues, 215 individuals) and found that tissue type is the predominant driver of transcript end variations. 75% and 65% of genes exhibited differential APA and ATS across tissues, respectively. In particular, testis displayed longer 5' untranslated regions (UTRs) and shorter 3' UTRs, often in genes related to testis-specific biology. Overall, we report the largest study of transcript ends across human tissues to our knowledge. mountainClimber is available at github.com/gxiaolab/mountainClimber.
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47
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MacDonald CC. Tissue-specific mechanisms of alternative polyadenylation: Testis, brain, and beyond (2018 update). WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1526. [PMID: 30816016 PMCID: PMC6617714 DOI: 10.1002/wrna.1526] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/05/2018] [Accepted: 01/14/2019] [Indexed: 12/21/2022]
Abstract
Alternative polyadenylation (APA) is how genes choose different sites for 3′ end formation for mRNAs during transcription. APA often occurs in a tissue‐ or developmental stage‐specific manner that can significantly affect gene activity by changing the protein product generated, the stability of the transcript, its localization within the cell, or its translatability. Despite the important regulatory effects that APA has on tissue‐specific gene expression, only a few examples have been characterized mechanistically. In this 2018 update to our 2010 review, we examine mechanisms for the control of APA and update our understanding of the older mechanisms since 2010. We once postulated the existence of tissue‐specific factors in APA. However, while a few tissue‐specific polyadenylation factors are known, the emerging conclusion is that the majority of APA is accomplished by altering levels of core polyadenylation proteins. Examples of those core proteins include CSTF2, CPSF1, and subunits of mammalian cleavage factor I. But despite support for these mechanisms, no one has yet documented any of these proteins changing in either a tissue‐specific or developmental manner. Given the profound effect that APA can have on gene expression and human health, improved understanding of tissue‐specific APA could lead to numerous advances in gene activity control. This article is categorized under:RNA Processing > 3′ End Processing RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Clinton C MacDonald
- Department of Cell Biology & Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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48
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Ye W, Long Y, Ji G, Su Y, Ye P, Fu H, Wu X. Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis. BMC Genomics 2019; 20:75. [PMID: 30669970 PMCID: PMC6343338 DOI: 10.1186/s12864-019-5433-7] [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: 09/09/2018] [Accepted: 01/03/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alternative polyadenylation (APA) has emerged as a pervasive mechanism that contributes to the transcriptome complexity and dynamics of gene regulation. The current tsunami of whole genome poly(A) site data from various conditions generated by 3' end sequencing provides a valuable data source for the study of APA-related gene expression. Cluster analysis is a powerful technique for investigating the association structure among genes, however, conventional gene clustering methods are not suitable for APA-related data as they fail to consider the information of poly(A) sites (e.g., location, abundance, number, etc.) within each gene or measure the association among poly(A) sites between two genes. RESULTS Here we proposed a computational framework, named PASCCA, for clustering genes from replicated or unreplicated poly(A) site data using canonical correlation analysis (CCA). PASCCA incorporates multiple layers of gene expression data from both the poly(A) site level and gene level and takes into account the number of replicates and the variability within each experimental group. Moreover, PASCCA characterizes poly(A) sites in various ways including the abundance and relative usage, which can exploit the advantages of 3' end deep sequencing in quantifying APA sites. Using both real and synthetic poly(A) site data sets, the cluster analysis demonstrates that PASCCA outperforms other widely-used distance measures under five performance metrics including connectivity, the Dunn index, average distance, average distance between means, and the biological homogeneity index. We also used PASCCA to infer APA-specific gene modules from recently published poly(A) site data of rice and discovered some distinct functional gene modules. We have made PASCCA an easy-to-use R package for APA-related gene expression analyses, including the characterization of poly(A) sites, quantification of association between genes, and clustering of genes. CONCLUSIONS By providing a better treatment of the noise inherent in repeated measurements and taking into account multiple layers of poly(A) site data, PASCCA could be a general tool for clustering and analyzing APA-specific gene expression data. PASCCA could be used to elucidate the dynamic interplay of genes and their APA sites among various biological conditions from emerging 3' end sequencing data to address the complex biological phenomenon.
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Affiliation(s)
- Wenbin Ye
- Department of Automation, Xiamen University, Xiamen, 361005, China.,Innovation Center for Cell Biology, Xiamen University, Xiamen, 361005, China
| | - Yuqi Long
- Department of Automation, Xiamen University, Xiamen, 361005, China.,Software Quality Testing Engineering Research Center, China Electronic Product Reliability and Environmental Testing Research Institute, Guangzhou, 510610, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, 361005, China.,Innovation Center for Cell Biology, Xiamen University, Xiamen, 361005, China
| | - Yaru Su
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou, 350116, China
| | - Pengchao Ye
- Department of Automation, Xiamen University, Xiamen, 361005, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen, 361005, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, 361005, China. .,Innovation Center for Cell Biology, Xiamen University, Xiamen, 361005, China.
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49
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Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018; 28:1427-1441. [PMID: 30143597 PMCID: PMC6169888 DOI: 10.1101/gr.237826.118] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Cleavage and polyadenylation is essential for 3' end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3' UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3' end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian mRNA genes contain at least one conserved PAS, and ∼50% have conserved APA events. PAS conservation generally reduces promiscuous 3' end processing, stabilizing gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with conserved APA events. Whereas tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. In addition, we show enrichment of mRNA destabilizing motifs in alternative 3' UTR sequences, leading to substantial differences in mRNA stability between 3' UTR isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Furthermore, we show that mutations of U-rich motifs around the PAS often accompany APA profile differences between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation through evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic perspective on APA functions.
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Affiliation(s)
- Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Ghassan Yehia
- Genome Editing Core Facility, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
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50
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Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018. [PMID: 30143597 DOI: 10.1101/gr.237826.118.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
Cleavage and polyadenylation is essential for 3' end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3' UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3' end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian mRNA genes contain at least one conserved PAS, and ∼50% have conserved APA events. PAS conservation generally reduces promiscuous 3' end processing, stabilizing gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with conserved APA events. Whereas tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. In addition, we show enrichment of mRNA destabilizing motifs in alternative 3' UTR sequences, leading to substantial differences in mRNA stability between 3' UTR isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Furthermore, we show that mutations of U-rich motifs around the PAS often accompany APA profile differences between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation through evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic perspective on APA functions.
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Affiliation(s)
- Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Ghassan Yehia
- Genome Editing Core Facility, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
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