1
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Zhang Y, Cai Q, Luo Y, Zhang Y, Li H. Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity. J Pharm Anal 2023; 13:63-72. [PMID: 36820077 PMCID: PMC9937802 DOI: 10.1016/j.jpha.2022.11.003] [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: 07/26/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Ribosomes are abundant, large RNA-protein complexes that are the sites of all protein synthesis in cells. Defects in ribosomal proteins (RPs), including proteoforms arising from genetic variations, alternative splicing of RNA transcripts, post-translational modifications and alterations of protein expression level, have been linked to a diverse range of diseases, including cancer and aging. Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets. In the present work, using E. coli 70S RPs as an example, we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry (MS) system, and then applied it to the HeLa 80S ribosome. The results were complemented by a bottom-up approach. In total, 50 out of 55 RPs were identified using the top-down approach. Among these, more than 30 RPs were found to have their N-terminal methionine removed. Additional modifications such as methylation, acetylation, and hydroxylation were also observed, and the modification sites were identified by bottom-up MS. In a HeLa 80S ribosomal sample, we identified 98 ribosomal proteoforms, among which multiple truncated 80S ribosomal proteoforms were observed, the type of information which is often overlooked by bottom-up experiments. Although their relevance to diseases is not yet known, the integration of top-down and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.
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Affiliation(s)
- Ying Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Qinghua Cai
- Henan Engineering Laboratory for Mammary Bioreactor, School of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yuxiang Luo
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yu Zhang
- The Shennong Laboratory, Zhengzhou, 450002, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
- Corresponding author. School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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ApiAP2 Gene-Network Regulates Gametocytogenesis in Plasmodium Parasites. Cell Microbiol 2022. [DOI: 10.1155/2022/5796578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Malaria is a mosquito-borne infectious disease, caused by unicellular Apicomplexan protozoa of the genus Plasmodium. The sexual stage of Plasmodium is one of the most fascinating aspects of the Plasmodium life cycle, yet relatively less explored until now. The production of sexually fit gametocytes through gametocytogenesis is essential to the transmission of the Plasmodium parasite into an anopheline mosquito vector. Understanding how gametocytogenesis is regulated promotes the identification of novel drug targets and also the development of transmission-blocking vaccines that would help reduce the disease burden in endemic areas. Transcriptional regulation in Plasmodium parasites is primarily controlled by a family of twenty-seven Apicomplexan Apetela 2 (ApiAP2) genes which act in a cascade to enable the parasite to progress through its asexual replication as well as gametocytogenesis. Here, we review the latest progress made on members of the ApiAP2 family characterized as key players of the transcriptional machinery of gametocytes. Further, we will highlight the transcriptional regulation network of ApiAP2 genes at each stage of gametocytogenesis.
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3
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Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet 2022; 23:697-710. [PMID: 35821097 DOI: 10.1038/s41576-022-00514-4] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/27/2022]
Abstract
A major goal of evolutionary genetics is to understand the genetic processes that give rise to phenotypic diversity in multicellular organisms. Alternative splicing generates multiple transcripts from a single gene, enriching the diversity of proteins and phenotypic traits. It is well established that alternative splicing contributes to key innovations over long evolutionary timescales, such as brain development in bilaterians. However, recent developments in long-read sequencing and the generation of high-quality genome assemblies for diverse organisms has facilitated comparisons of splicing profiles between closely related species, providing insights into how alternative splicing evolves over shorter timescales. Although most splicing variants are probably non-functional, alternative splicing is nonetheless emerging as a dynamic, evolutionarily labile process that can facilitate adaptation and contribute to species divergence.
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Affiliation(s)
- Charlotte J Wright
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK. .,Department of Zoology, University of Cambridge, Cambridge, UK.
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK.
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4
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Gao P, Quilichini TD, Zhai C, Qin L, Nilsen KT, Li Q, Sharpe AG, Kochian LV, Zou J, Reddy AS, Wei Y, Pozniak C, Patterson N, Gillmor CS, Datla R, Xiang D. Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1624-1643. [PMID: 33706417 PMCID: PMC8384600 DOI: 10.1111/pbi.13579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat crops are poorly understood. To address this knowledge gap, we developed a pipeline for the analysis of alternatively spliced transcript isoforms, which takes the high sequence similarity among polyploid wheat subgenomes into account. Through analysis of synteny and detection of collinearity of homoeologous subgenomes, conserved and specific AS events across five wheat and grass species were identified. A global analysis of the regulation of AS in diploid grass and polyploid wheat grains revealed diversity in AS events not only between the endosperm, pericarp and embryo overdevelopment, but also between subgenomes. Analysis of AS in homoeologous triads of polyploid wheats revealed evolutionary divergence between gene-level and transcript-level regulation of embryogenesis. Evolutionary age analysis indicated that the generation of novel transcript isoforms has occurred in young genes at a more rapid rate than in ancient genes. These findings, together with the development of comprehensive AS resources for wheat and grass species, advance understanding of the evolution of regulatory features of AS during embryogenesis and grain development in wheat.
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Affiliation(s)
- Peng Gao
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Teagen D. Quilichini
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Chun Zhai
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Li Qin
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Kirby T. Nilsen
- Agriculture and Agri‐Food CanadaBrandon Research and Development CentreBrandonMBCanada
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Andrew G. Sharpe
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Leon V. Kochian
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Jitao Zou
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Anireddy S.N. Reddy
- Department of Biology and Program in Cell and Molecular BiologyColorado State UniversityFort CollinsCOUSA
| | - Yangdou Wei
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSKCanada
| | - Nii Patterson
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)Unidad de Genómica AvanzadaCentro de Investigación y Estudios Avanzados del IPN (CINVESTAV‐IPN)IrapuatoGuanajuatoMexico
| | - Raju Datla
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
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Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. mSystems 2021; 6:6/2/e01081-20. [PMID: 33688018 PMCID: PMC8561664 DOI: 10.1128/msystems.01081-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterized in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic features, such as the high AU content of Plasmodium RNA, but also the limitations of short-read sequencing in deciphering complex splicing events. In this study, we utilized the long read direct RNA sequencing platform developed by Oxford Nanopore Technologies to survey the alternative splicing landscape of Toxoplasma gondii and Plasmodium falciparum. We find that while native RNA sequencing has a reduced throughput, it allows us to obtain full-length or nearly full-length transcripts with comparable quantification to Illumina sequencing. By comparing these data with available gene models, we find widespread alternative splicing, particularly intron retention, in these parasites. Most of these transcripts contain premature stop codons, suggesting that in these parasites, alternative splicing represents a pathway to transcriptomic diversity, rather than expanding proteomic diversity. Moreover, alternative splicing rates are comparable between parasites, suggesting a shared splicing machinery, despite notable transcriptomic differences between the parasites. This study highlights a strategy in using long-read sequencing to understand splicing events at the whole-transcript level and has implications in the future interpretation of transcriptome sequencing studies. IMPORTANCE We have used a novel nanopore sequencing technology to directly analyze parasite transcriptomes. The very long reads of this technology reveal the full-length genes of the parasites that cause malaria and toxoplasmosis. Gene transcripts must be processed in a process called splicing before they can be translated to protein. Our analysis reveals that these parasites very frequently only partially process their gene products, in a manner that departs dramatically from their human hosts.
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Lou S, Zhang J, Zhai Z, Yin X, Wang Y, Fang T, Xue Y. Development and validation of an individual alternative splicing prognostic signature in gastric cancer. Aging (Albany NY) 2021; 13:5824-5844. [PMID: 33612482 PMCID: PMC7950272 DOI: 10.18632/aging.202507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is a heterogeneous disease with different clinical manifestations and prognoses. Alternative splicing (AS) is a determinant of gene expression and contributes to protein diversity from a rather limited gene transcript in metazoans. AS events are associated with different aspects of cancer biology, including cell proliferation, apoptosis, invasion, etc. Here, we present a comprehensive analysis of the prognostic AS profile in GC. GC-specific AS (GCAS) events were analyzed, and overall survival-associated GCAS (OS-GCAS) events were verified among the genome-wide AS events identified in The Cancer Genome Atlas (TCGA) database. In total, 1,287 GCAS events of 837 genes and 173 OS-GCAS events of 130 genes were identified. The parental genes of OS-GCAS events were significantly enriched in the development of GC. Protein-protein interaction (PPI) and OS-GCAS-associated splicing factor (SF) interaction networks were constructed. Multivariate Cox regression analysis with least absolute shrinkage and selection operator (LASSO) penalty was performed to establish a prognostic risk formula, representing 23 OS-GCAS events. The low-risk group had better OS than the high-risk group and lower immune and stromal scores. Cox proportional hazard regression was applied to generate an AS-clinical integrated prognostic model with a considerable area under the curve (AUC) value in both the training and validation datasets. Our study provides a profile of OS-GCAS events and an AS-clinical nomogram to predict the prognosis of GC.
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Affiliation(s)
- Shenghan Lou
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Jian Zhang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Zhao Zhai
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Xin Yin
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Yimin Wang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Tianyi Fang
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
| | - Yingwei Xue
- Department of Gastroenterological Surgery, Harbin Medical University Cancer Hospital, Harbin 150081, Heilongjiang Province, China
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7
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Yu G, Wang K, Domeniconi C, Guo M, Wang J. Isoform function prediction based on bi-random walks on a heterogeneous network. Bioinformatics 2020; 36:303-310. [PMID: 31250882 DOI: 10.1093/bioinformatics/btz535] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 01/29/2023] Open
Abstract
MOTIVATION Alternative splicing contributes to the functional diversity of protein species and the proteoforms translated from alternatively spliced isoforms of a gene actually execute the biological functions. Computationally predicting the functions of genes has been studied for decades. However, how to distinguish the functional annotations of isoforms, whose annotations are essential for understanding developmental abnormalities and cancers, is rarely explored. The main bottleneck is that functional annotations of isoforms are generally unavailable and functional genomic databases universally store the functional annotations at the gene level. RESULTS We propose IsoFun to accomplish Isoform Function prediction based on bi-random walks on a heterogeneous network. IsoFun firstly constructs an isoform functional association network based on the expression profiles of isoforms derived from multiple RNA-seq datasets. Next, IsoFun uses the available Gene Ontology annotations of genes, gene-gene interactions and the relations between genes and isoforms to construct a heterogeneous network. After this, IsoFun performs a tailored bi-random walk on the heterogeneous network to predict the association between GO terms and isoforms, thus accomplishing the prediction of GO annotations of isoforms. Experimental results show that IsoFun significantly outperforms the state-of-the-art algorithms and improves the area under the receiver-operating curve (AUROC) and the area under the precision-recall curve (AUPRC) by 17% and 44% at the gene-level, respectively. We further validated the performance of IsoFun on the genes ADAM15 and BCL2L1. IsoFun accurately differentiates the functions of respective isoforms of these two genes. AVAILABILITY AND IMPLEMENTATION The code of IsoFun is available at http://mlda.swu.edu.cn/codes.php? name=IsoFun. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guoxian Yu
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Keyao Wang
- College of Computer and Information Science, Southwest University, Chongqing, China
| | - Carlotta Domeniconi
- Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
| | - Maozu Guo
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China.,Beijing Key Laboratory of Intelligent Processing for Building Big Data, Beijing, China
| | - Jun Wang
- College of Computer and Information Science, Southwest University, Chongqing, China
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8
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Liu C, Hu C, Li Z, Feng J, Huang J, Yang B, Wen T. Systematic profiling of alternative splicing in Helicobacter pylori-negative gastric cancer and their clinical significance. Cancer Cell Int 2020; 20:279. [PMID: 32617077 PMCID: PMC7325377 DOI: 10.1186/s12935-020-01368-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
Background Alternative splicing (AS) may cause structural and functional variations in the protein to promote the proliferation of tumor cells. However, there is no comprehensive analysis of the clinical significance of AS in Helicobacter pylori-negative gastric cancer (HP− GC). Methods The clinical, gene expression profile data and AS events of 138 HP− GC patients were obtained from the database named the cancer genome atlas. Differently expressed AS (DEAS) events were determined by a comparison of the PSI values between HP− GC samples and adjacent normal samples. Unsupervised clustering analysis, proportional regression and Kaplan–Meier analysis were used to explore the association between clinical data and immune features and to establish two nomograms about the prognosis of HP− GC. Finally, splicing networks were constructed using Cytoscape. Results A total of 48141 AS events and 1041 DEAS events were found in HP− GC. Various functions and pathways of DEAS events parent genes were enriched, such as cell-substrate junction, cell leading edge, focal adhension, and AMPK signaling. Seven overall survival (OS)-related and seven disease-free survival (DFS)-related AS events were used to construct the prognostic signatures. Based on the independent prognostic factors, two nomograms were established and showed excellent performance. Then, splicing regulatory networks among the correlations suggested that splicing factors were significantly associated with prognostic DEASs. Finally, the unsupervised clustering analysis revealed that DEAS-based clusters were associated with clinical characteristics, tumor microenvironment, tumor mutation burden, and immune features. Conclusion Seven OS-related and seven DFS-related AS events have been found to be correlated with the prognosis of HP− GC and can be used as prognostic factors to establish an effective nomogram.
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Affiliation(s)
- Chuan Liu
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
| | - Chuan Hu
- Qingdao University Medical College, Qingdao, 266071 Shandong China
| | - Zhi Li
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
| | - Jing Feng
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
| | - Jiale Huang
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
| | - Bowen Yang
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
| | - Ti Wen
- Department of Medical Oncology, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001 Liaoning China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001 Liaoning China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001 Liaoning China
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9
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Chaudhary S, Khokhar W, Jabre I, Reddy ASN, Byrne LJ, Wilson CM, Syed NH. Alternative Splicing and Protein Diversity: Plants Versus Animals. FRONTIERS IN PLANT SCIENCE 2019; 10:708. [PMID: 31244866 PMCID: PMC6581706 DOI: 10.3389/fpls.2019.00708] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/13/2019] [Indexed: 05/11/2023]
Abstract
Plants, unlike animals, exhibit a very high degree of plasticity in their growth and development and employ diverse strategies to cope with the variations during diurnal cycles and stressful conditions. Plants and animals, despite their remarkable morphological and physiological differences, share many basic cellular processes and regulatory mechanisms. Alternative splicing (AS) is one such gene regulatory mechanism that modulates gene expression in multiple ways. It is now well established that AS is prevalent in all multicellular eukaryotes including plants and humans. Emerging evidence indicates that in plants, as in animals, transcription and splicing are coupled. Here, we reviewed recent evidence in support of co-transcriptional splicing in plants and highlighted similarities and differences between plants and humans. An unsettled question in the field of AS is the extent to which splice isoforms contribute to protein diversity. To take a critical look at this question, we presented a comprehensive summary of the current status of research in this area in both plants and humans, discussed limitations with the currently used approaches and suggested improvements to current methods and alternative approaches. We end with a discussion on the potential role of epigenetic modifications and chromatin state in splicing memory in plants primed with stresses.
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Affiliation(s)
- Saurabh Chaudhary
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Waqas Khokhar
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Ibtissam Jabre
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Lee J. Byrne
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Cornelia M. Wilson
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
| | - Naeem H. Syed
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, United Kingdom
- *Correspondence: Naeem H. Syed,
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10
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Bush SJ, Chen L, Tovar-Corona JM, Urrutia AO. Alternative splicing and the evolution of phenotypic novelty. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0474. [PMID: 27994117 DOI: 10.1098/rstb.2015.0474] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing, a mechanism of post-transcriptional RNA processing whereby a single gene can encode multiple distinct transcripts, has been proposed to underlie morphological innovations in multicellular organisms. Genes with developmental functions are enriched for alternative splicing events, suggestive of a contribution of alternative splicing to developmental programmes. The role of alternative splicing as a source of transcript diversification has previously been compared to that of gene duplication, with the relationship between the two extensively explored. Alternative splicing is reduced following gene duplication with the retention of duplicate copies higher for genes which were alternatively spliced prior to duplication. Furthermore, and unlike the case for overall gene number, the proportion of alternatively spliced genes has also increased in line with the evolutionary diversification of cell types, suggesting alternative splicing may contribute to the complexity of developmental programmes. Together these observations suggest a prominent role for alternative splicing as a source of functional innovation. However, it is unknown whether the proliferation of alternative splicing events indeed reflects a functional expansion of the transcriptome or instead results from weaker selection acting on larger species, which tend to have a higher number of cell types and lower population sizes.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Lu Chen
- West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, People's Republic of China
| | | | - Araxi O Urrutia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK .,Milner Centre for Evolution, University of Bath, Bath BA2 7AY, UK
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11
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Li HD, Omenn GS, Guan Y. A proteogenomic approach to understand splice isoform functions through sequence and expression-based computational modeling. Brief Bioinform 2016; 17:1024-1031. [PMID: 26740460 DOI: 10.1093/bib/bbv109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 11/03/2015] [Indexed: 01/23/2023] Open
Abstract
The products of multi-exon genes are a mixture of alternatively spliced isoforms, from which the translated proteins can have similar, different or even opposing functions. It is therefore essential to differentiate and annotate functions for individual isoforms. Computational approaches provide an efficient complement to expensive and time-consuming experimental studies. The input data of these methods range from DNA sequence, to RNA selection pressure, to expressed sequence tags, to full-length complementary DNA, to exon array, to RNA-seq expression, to proteomic data. Notably, RNA-seq technology generates quantitative profiling of transcript expression at the genome scale, with an unprecedented amount of expression data available for developing isoform function prediction methods. Integrative analysis of these data at different molecular levels enables a proteogenomic approach to systematically interrogate isoform functions. Here, we briefly review the state-of-the-art methods according to their input data sources, discuss their advantages and limitations and point out potential ways to improve prediction accuracies.
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12
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Pan K, Lee JTH, Huang Z, Wong CM. Coupling and coordination in gene expression processes with pre-mRNA splicing. Int J Mol Sci 2015; 16:5682-96. [PMID: 25768347 PMCID: PMC4394499 DOI: 10.3390/ijms16035682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/28/2015] [Accepted: 03/04/2015] [Indexed: 12/13/2022] Open
Abstract
RNA processing is a tightly regulated and highly complex pathway which includes transcription, splicing, editing, transportation, translation and degradation. It has been well-documented that splicing of RNA polymerase II medicated nascent transcripts occurs co-transcriptionally and is functionally coupled to other RNA processing. Recently, increasing experimental evidence indicated that pre-mRNA splicing influences RNA degradation and vice versa. In this review, we summarized the recent findings demonstrating the coupling of these two processes. In addition, we highlighted the importance of splicing in the production of intronic miRNA and circular RNAs, and hence the discovery of the novel mechanisms in the regulation of gene expression.
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13
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Deng N, Sanchez CG, Lasky JA, Zhu D. Detecting splicing variants in idiopathic pulmonary fibrosis from non-differentially expressed genes. PLoS One 2013; 8:e68352. [PMID: 23844188 PMCID: PMC3699530 DOI: 10.1371/journal.pone.0068352] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/01/2013] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease of unknown cause that lacks a proven therapy for altering its high mortality rate. Microarrays have been employed to investigate the pathogenesis of IPF, but are presented mostly at the gene-expression level due to technologic limitations. In as much as, alternative RNA splicing isoforms are increasingly identified as potential regulators of human diseases, including IPF, we propose a new approach with the capacity to detect splicing variants using RNA-seq data. We conducted a joint analysis of differential expression and differential splicing on annotated human genes and isoforms, and identified 122 non-differentially expressed genes with a high degree of "switch" between major and minor isoforms. Three cases with variant mechanisms for alternative splicing were validated using qRT-PCR, among the group of genes in which expression was not significantly changed at the gene level. We also identified 35 novel transcripts that were unique to the fibrotic lungs using exon-exon junction evidence, and selected a representative for qRT-PCR validation. The results of our study are likely to provide new insight into the pathogenesis of pulmonary fibrosis and may eventuate in new treatment targets.
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Affiliation(s)
- Nan Deng
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
| | - Cecilia G. Sanchez
- Tulane Cancer Center, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Joseph A. Lasky
- Tulane Cancer Center, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail: (DZ); (JAL)
| | - Dongxiao Zhu
- Department of Computer Science, Wayne State University, Detroit, Michigan, United States of America
- * E-mail: (DZ); (JAL)
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Deng C, Hsueh AJW. Evolution of a potential hormone antagonist following gene splicing during primate evolution. PLoS One 2013; 8:e64610. [PMID: 23724068 PMCID: PMC3665846 DOI: 10.1371/journal.pone.0064610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/15/2013] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing of genes generates novel mRNAs, leading to the evolution of new functional proteins. Cholecystokinin (CCK) induces the release of pancreatic enzymes and the contraction of the gallbladder to promote the digestion of fat and proteins. CCK activates two G-protein-coupled receptors, CCKA and CCKB. Here, we showed that a CCKsv (splicing variant), originated de novo during Catarrhini evolution by including a portion of intronic sequence of the CCK gene, encodes novel C-terminal peptide sequence followed by a new poly-adenylation signal. CCKsv is expressed in many human tissues and likely a secreted peptide retaining the original signal peptide and the N-terminal proteolytic processing signal, together with novel C-terminal sequences. Although CCKsv cannot activate CCK receptors, it partially inhibits the CRE- or SRF-driven reporter activities stimulated by wide type CCK-8 mediated by both CCK receptors. Co-treatment with CCKsv also partially antagonizes Ewing tumor cell growth stimulated by CCK-8. Our study provides an example of new peptide hormone antagonist evolution in primates.
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Affiliation(s)
- Cheng Deng
- Program of Reproductive and Stem Cell Biology, Department of Obstetrics/Gynecology, Stanford University School of Medicine, Stanford, California, United States of America.
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15
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Su Z, Li R, Song X, Liu G, Li Y, Chang X, Li C, Huang D. Identification of a novel isoform of DHRS4 protein with a nuclear localization signal. Gene 2012; 494:161-7. [PMID: 22227495 DOI: 10.1016/j.gene.2011.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 11/30/2011] [Accepted: 12/16/2011] [Indexed: 02/05/2023]
Abstract
The DHRS4 gene encodes an NADP(H)-dependent retinol dehydrogenase/reductase (NRDR) and plays an important role in regulating the synthesis of retinoic acid. In the present study, we identified a novel splice RNA variant, designated NRDRA2, of the human DHRS4 gene by RT-PCR, 3' RACE, and 5' RACE. NRDRA2 mRNA lacked exons 4 and 6, and had a shift in the reading frame when compared to DHRS4 mRNA, resulting in loss of the peroxisomal targeting signal of NRDR and gain of a nuclear localization signal in the predicted NRDRA2 protein. Endogenous NRDRA2 protein was identified in the human cervical carcinoma cell line HeLa by immunoprecipitation and mass spectrometric assay. A green fluorescent protein reporter assay showed that NRDRA2 protein mainly localized to the nuclei, confirming the sequence at its C-terminus as a legitimate nuclear localization signal sequence. This study identifies the alternative transcript variant NRDRA2 encoding a subcellular nuclear localized NRDRA2 protein.
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Affiliation(s)
- Zhongjing Su
- Department of Cell Biology, Shantou University Medical College, Shantou Guangdong, China
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16
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Korzinov OM, Astakhova TV, Vlasov PK, Roytberg MA. Statistical analysis of DNA sequences in the neighborhood of splice sites. Mol Biol 2011. [DOI: 10.1134/s0026893308010202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Kanapin AA, Mulder N, Kuznetsov VA. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity. BMC Genomics 2010; 11 Suppl 1:S4. [PMID: 20158875 PMCID: PMC2822532 DOI: 10.1186/1471-2164-11-s1-s4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We consider the problem of biological complexity via a projection of protein-coding genes of complex organisms onto the functional space of the proteome. The latter can be defined as a set of all functions committed by proteins of an organism. Alternative splicing (AS) allows an organism to generate diverse mature RNA transcripts from a single mRNA strand and thus it could be one of the key mechanisms of increasing of functional complexity of the organism's proteome and a driving force of biological evolution. Thus, the projection of transcription units (TU) and alternative splice-variant (SV) forms onto proteome functional space could generate new types of relational networks (e.g. SV-protein function networks, SFN) and lead to discoveries of novel evolutionarily conservative functional modules. Such types of networks might provide new reliable characteristics of organism complexity and a better understanding of the evolutionary integration and plasticity of interconnection of genome-transcriptome-proteome functions.
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Evolutionary characteristics of exons expressed at different abundance levels in mammals. Sci Bull (Beijing) 2009. [DOI: 10.1007/s11434-009-0535-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene. The results strongly support the hypothesis that most alternative splicing is a consequence of stochastic noise in the splicing machinery, and has no functional significance. The results are also consistent with error rates tuned to ensure that an adequate level of functional product is produced and to reduce the toxic effect of accumulation of misfolding proteins. Based on simulation of sampling of virtual cDNA libraries, we estimate that error rates range from 1 to 10% depending on the number of introns and the expression level of a gene.
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Affiliation(s)
- Eugene Melamud
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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20
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Floris M, Orsini M, Thanaraj TA. Splice-mediated Variants of Proteins (SpliVaP) - data and characterization of changes in signatures among protein isoforms due to alternative splicing. BMC Genomics 2008; 9:453. [PMID: 18831736 PMCID: PMC2573899 DOI: 10.1186/1471-2164-9-453] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 10/02/2008] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND It is often the case that mammalian genes are alternatively spliced; the resulting alternate transcripts often encode protein isoforms that differ in amino acid sequences. Changes among the protein isoforms can alter the cellular properties of proteins. The effect can range from a subtle modulation to a complete loss of function. RESULTS (i) We examined human splice-mediated protein isoforms (as extracted from a manually curated data set, and from a computationally predicted data set) for differences in the annotation for protein signatures (Pfam domains and PRINTS fingerprints) and we characterized the differences & their effects on protein functionalities. An important question addressed relates to the extent of protein isoforms that may lack any known function in the cell. (ii) We present a database that reports differences in protein signatures among human splice-mediated protein isoform sequences. CONCLUSION (i) Characterization: The work points to distinct sets of alternatively spliced genes with varying degrees of annotation for the splice-mediated protein isoforms. Protein molecular functions seen to be often affected are those that relate to: binding, catalytic, transcription regulation, structural molecule, transporter, motor, and antioxidant; and the processes that are often affected are nucleic acid binding, signal transduction, and protein-protein interactions. Signatures are often included/excluded and truncated in length among protein isoforms; truncation is seen as the predominant type of change. Analysis points to the following novel aspects: (a) Analysis using data from the manually curated Vega indicates that one in 8.9 genes can lead to a protein isoform of no "known" function; and one in 18 expressed protein isoforms can be such an "orphan" isoform; the corresponding numbers as seen with computationally predicted ASD data set are: one in 4.9 genes and one in 9.8 isoforms. (b) When swapping of signatures occurs, it is often between those of same functional classifications. (c) Pfam domains can occur in varying lengths, and PRINTS fingerprints can occur with varying number of constituent motifs among isoforms - since such a variation is seen in large number of genes, it could be a general mechanism to modulate protein function. (ii) DATA The reported resource (at http://www.bioinformatica.crs4.org/tools/dbs/splivap/) provides the community ability to access data on splice-mediated protein isoforms (with value-added annotation such as association with diseases) through changes in protein signatures.
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Affiliation(s)
- Matteo Floris
- CRS4-Bioinformatica, Parco Scientifico e Technologico, POLARIS, Edificio 3, 09010 PULA (CA), Sardinia, Italy.
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21
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Kochetov AV. Alternative translation start sites and hidden coding potential of eukaryotic mRNAs. Bioessays 2008; 30:683-91. [PMID: 18536038 DOI: 10.1002/bies.20771] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is widely suggested that a eukaryotic mRNA typically contains one translation start site and encodes a single functional protein product. However, according to current points of view on translation initiation mechanisms, eukaryotic ribosomes can recognize several alternative translation start sites and the number of experimentally verified examples of alternative translation is growing rapidly. Also, the frequent occurrence of alternative translation events and their functional significance are supported by the results of computational evaluations. The functional role of alternative translation and its contribution to eukaryotic proteome complexity are discussed.
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Ramensky VE, Nurtdinov RN, Neverov AD, Mironov AA, Gelfand MS. Positive selection in alternatively spliced exons of human genes. Am J Hum Genet 2008; 83:94-8. [PMID: 18571144 DOI: 10.1016/j.ajhg.2008.05.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 04/08/2008] [Accepted: 05/30/2008] [Indexed: 10/21/2022] Open
Abstract
Alternative splicing is a well-recognized mechanism of accelerated genome evolution. We have studied single-nucleotide polymorphisms and human-chimpanzee divergence in the exons of 6672 alternatively spliced human genes, with the aim of understanding the forces driving the evolution of alternatively spliced sequences. Here, we show that alternatively spliced exons and exon fragments (alternative exons) from minor isoforms experience lower selective pressure at the amino acid level, accompanied by selection against synonymous sequence variation. The results of the McDonald-Kreitman test suggest that alternatively spliced exons, unlike exons constitutively included in the mRNA, are also subject to positive selection, with up to 27% of amino acids fixed by positive selection.
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23
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Sticking together? Falling apart? Exploring the dynamics of the interactome. Trends Biochem Sci 2008; 33:195-200. [PMID: 18424047 DOI: 10.1016/j.tibs.2008.03.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 03/03/2008] [Accepted: 03/03/2008] [Indexed: 12/25/2022]
Abstract
Advances in techniques for the study of protein-protein interactions have dramatically improved our understanding of the interactome. However, we know little about the dynamics of this complex system. To better understand the dynamics of the interactome, it is important to consider what happens when single proteins are perturbed. Changes in protein abundance and post-translational modification can function as switches in the interactome, affecting protein-complex assembly and function. Changes in protein sequence or a dramatic increase in abundance might cause a promiscuous gain of interactions. These effects are not identical for all proteins and will differ depending on the number and type of interaction partners that a protein has.
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24
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Ermakova EO, Nurtdinov RN, Gelfand MS. Overlapping alternative donor splice sites in the human genome. J Bioinform Comput Biol 2008; 5:991-1004. [PMID: 17933007 DOI: 10.1142/s0219720007003089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 05/30/2007] [Accepted: 06/01/2007] [Indexed: 11/18/2022]
Abstract
Over 50% of donor splice sites in the human genome have a potential alternative donor site at a distance of three to six nucleotides. Conservation of these potential sites is determined by the consensus requirements and by its exonic or intronic location. Several hundred pairs of overlapping sites are confirmed to be alternatively spliced as both sites in a pair are supported by a protein, by a full-length mRNA, or by expressed sequence tags (ESTs) from at least two independent clone libraries. Overlapping sites may clash with consensus requirements. Pairs with a site shift of four nucleotides are the most abundant, despite the frameshift in the protein-coding region that they introduce. The site usage in pairs is usually uneven, and the major site is more frequently conserved in other mammalian genomes. Overlapping alternative donor sites and acceptor sites may have different functional roles: alternative splicing of overlapping acceptor sites leads mainly to microvariations in protein sequences; whereas alternative donor sites often lead to frameshifts and thus either yield major differences in the protein sequence and structure, or generate nonsense-mediated decay-inducing mRNA isoforms likely involved in regulated unproductive splicing pathways.
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Affiliation(s)
- Ekaterina O Ermakova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetny per. 19, 127994 Moscow, Russia.
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25
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A procedure for identifying homologous alternative splicing events. BMC Bioinformatics 2007; 8:260. [PMID: 17640387 PMCID: PMC1950890 DOI: 10.1186/1471-2105-8-260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 07/19/2007] [Indexed: 01/11/2023] Open
Abstract
Background The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput version) leaves ample room for the development of bioinformatics tools that can provide a useful first picture of the problem. Among the possible approaches, one of the simplest is to follow classical protein function annotation protocols and annotate target alternative splice events with the information available from conserved events in other species. However, the application of this protocol requires a procedure capable of recognising such events. Here we present a simple but accurate method developed for this purpose. Results We have developed a method for identifying homologous, or equivalent, alternative splicing events, based on the combined use of neural networks and sequence searches. The procedure comprises four steps: (i) BLAST search for homologues of the two isoforms defining the target alternative splicing event; (ii) construction of all possible candidate events; (iii) scoring of the latter with a series of neural networks; and (iv) filtering of the results. When tested in a set of 473 manually annotated pairs of homologous events, our method showed a good performance, with an accuracy of 0.99, a precision of 0.98 and a sensitivity of 0.93. When no candidates were available, the specificity of our method varied between 0.81 and 0.91. Conclusion The method described in this article allows the identification of homologous alternative splicing events, with a good success rate, indicating that such method could be used for the development of functional annotation of alternative splice isoforms.
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26
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Talavera D, Vogel C, Orozco M, Teichmann SA, de la Cruz X. The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol 2007; 3:e33. [PMID: 17335345 PMCID: PMC1808492 DOI: 10.1371/journal.pcbi.0030033] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Accepted: 01/04/2007] [Indexed: 11/18/2022] Open
Abstract
Alternative splicing (AS) and gene duplication (GD) both are processes that diversify the protein repertoire. Recent examples have shown that sequence changes introduced by AS may be comparable to those introduced by GD. In addition, the two processes are inversely correlated at the genomic scale: large gene families are depleted in splice variants and vice versa. All together, these data strongly suggest that both phenomena result in interchangeability between their effects. Here, we tested the extent to which this applies with respect to various protein characteristics. The amounts of AS and GD per gene are anticorrelated even when accounting for different gene functions or degrees of sequence divergence. In contrast, the two processes appear to be independent in their influence on variation in mRNA expression. Further, we conducted a detailed comparison of the effect of sequence changes in both alternative splice variants and gene duplicates on protein structure, in particular the size, location, and types of sequence substitutions and insertions/deletions. We find that, in general, alternative splicing affects protein sequence and structure in a more drastic way than gene duplication and subsequent divergence. Our results reveal an interesting paradox between the anticorrelation of AS and GD at the genomic level, and their impact at the protein level, which shows little or no equivalence in terms of effects on protein sequence, structure, and function. We discuss possible explanations that relate to the order of appearance of AS and GD in a gene family, and to the selection pressure imposed by the environment.
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Affiliation(s)
- David Talavera
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
| | - Christine Vogel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
- Institute for Cellular and Molecular Biology, University of Texas Austin, Austin, Texas, United States of America
- * To whom correspondence should be addressed. E-mail: (XdlC); (CV)
| | - Modesto Orozco
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Barcelona, Spain
- Institut per a la Recerca i Estudis Avançats (IRCA), Barcelona, Spain
| | - Sarah A Teichmann
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Xavier de la Cruz
- Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Barcelona, Spain
- Protein Structure and Modelling Node, Instituto Nacional de Bioinfomática, Genoma España, Parc Científic de Barcelona, Barcelona, Spain
- Computational Biology Program, Barcelona Supercomputing Center, Barcelona, Spain
- * To whom correspondence should be addressed. E-mail: (XdlC); (CV)
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Santic R, Schmidhuber SM, Lang R, Rauch I, Voglas E, Eberhard N, Bauer JW, Brain SD, Kofler B. Alarin is a vasoactive peptide. Proc Natl Acad Sci U S A 2007; 104:10217-22. [PMID: 17535903 PMCID: PMC1891251 DOI: 10.1073/pnas.0608585104] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Galanin-like peptide (GALP) is a hypothalamic neuropeptide belonging to the galanin family of peptides. The GALP gene is characterized by extensive differential splicing in a variety of murine tissues. One splice variant excludes exon 3 and results in a frame shift leading to a novel peptide sequence and a stop codon after 49 aa. In this peptide, which we termed alarin, the signal sequence of the GALP precursor peptide and the first 5 aa of the mature GALP are followed by 20 aa without homology to any other murine protein. Alarin mRNA was detected in murine brain, thymus, and skin. In accordance with its vascular localization, the peptide exhibited potent and dose-dependent vasoconstrictor and anti-edema activity in the cutaneous microvasculature, as was also observed with other members of the galanin peptide family. However, in contrast to galanin peptides in general, the physiological effects of alarin do not appear to be mediated via the known galanin receptors. Alarin adds another facet to the surprisingly high-functional redundancy of the galanin family of peptides.
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Affiliation(s)
| | | | - Roland Lang
- Dermatology, University Hospital Salzburg, Paracelsus Medical University, Muellner-Hauptstrasse 48, 5020 Salzburg, Austria; and
| | | | | | | | - Johann W. Bauer
- Dermatology, University Hospital Salzburg, Paracelsus Medical University, Muellner-Hauptstrasse 48, 5020 Salzburg, Austria; and
| | - Susan D. Brain
- Cardiovascular Division, King's College London, Franklin Wilkins Building, Waterloo Campus, London SE1 9NH, United Kingdom
| | - Barbara Kofler
- Departments of *Pediatrics and
- To whom correspondence should be addressed. E-mail:
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Ng DWK, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S, Hall TC. Plant SET domain-containing proteins: structure, function and regulation. ACTA ACUST UNITED AC 2007; 1769:316-29. [PMID: 17512990 PMCID: PMC2794661 DOI: 10.1016/j.bbaexp.2007.04.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2006] [Revised: 04/03/2007] [Accepted: 04/04/2007] [Indexed: 01/01/2023]
Abstract
Modification of the histone proteins that form the core around which chromosomal DNA is looped has profound epigenetic effects on the accessibility of the associated DNA for transcription, replication and repair. The SET domain is now recognized as generally having methyltransferase activity targeted to specific lysine residues of histone H3 or H4. There is considerable sequence conservation within the SET domain and within its flanking regions. Previous reviews have shown that SET proteins from Arabidopsis and maize fall into five classes according to their sequence and domain architectures. These classes generally reflect specificity for a particular substrate. SET proteins from rice were found to fall into similar groupings, strengthening the merit of the approach taken. Two additional classes, VI and VII, were established that include proteins with truncated/interrupted SET domains. Diverse mechanisms are involved in shaping the function and regulation of SET proteins. These include protein-protein interactions through both intra- and inter-molecular associations that are important in plant developmental processes, such as flowering time control and embryogenesis. Alternative splicing that can result in the generation of two to several different transcript isoforms is now known to be widespread. An exciting and tantalizing question is whether, or how, this alternative splicing affects gene function. For example, it is conceivable that one isoform may debilitate methyltransferase function whereas the other may enhance it, providing an opportunity for differential regulation. The review concludes with the speculation that modulation of SET protein function is mediated by antisense or sense-antisense RNA.
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Affiliation(s)
| | | | | | | | | | - Timothy C. Hall
- Corresponding author. Tel: 1-979-845-7728; fax: 1-979-862-4098,
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Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: high-resolution annotation for microarrays. BMC Bioinformatics 2007; 8:108. [PMID: 17394657 PMCID: PMC1853115 DOI: 10.1186/1471-2105-8-108] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Accepted: 03/29/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Extracting biological information from high-density Affymetrix arrays is a multi-step process that begins with the accurate annotation of microarray probes. Shortfalls in the original Affymetrix probe annotation have been described; however, few studies have provided rigorous solutions for routine data analysis. RESULTS Using AceView, a comprehensive human transcript database, we have reannotated the probes by matching them to RNA transcripts instead of genes. Based on this transcript-level annotation, a new probe set definition was created in which every probe in a probe set maps to a common set of AceView gene transcripts. In addition, using artificial data sets we identified that a minimal probe set size of 4 is necessary for reliable statistical summarization. We further demonstrate that applying the new probe set definition can detect specific transcript variants contributing to differential expression and it also improves cross-platform concordance. CONCLUSION We conclude that our transcript-level reannotation and redefinition of probe sets complement the original Affymetrix design. Redefinitions introduce probe sets whose sizes may not support reliable statistical summarization; therefore, we advocate using our transcript-level mapping redefinition in a secondary analysis step rather than as a replacement. Knowing which specific transcripts are differentially expressed is important to properly design probe/primer pairs for validation purposes. For convenience, we have created custom chip-description-files (CDFs) and annotation files for our new probe set definitions that are compatible with Bioconductor, Affymetrix Expression Console or third party software.
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Erkens T, Van Poucke M, Vandesompele J, Goossens K, Van Zeveren A, Peelman LJ. Development of a new set of reference genes for normalization of real-time RT-PCR data of porcine backfat and longissimus dorsi muscle, and evaluation with PPARGC1A. BMC Biotechnol 2006; 6:41. [PMID: 17026777 PMCID: PMC1609116 DOI: 10.1186/1472-6750-6-41] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2006] [Accepted: 10/09/2006] [Indexed: 11/13/2022] Open
Abstract
Background An essential part of using real-time RT-PCR is that expression results have to be normalized before any conclusions can be drawn. This can be done by using one or multiple, validated reference genes, depending on the desired accuracy of the results. In the pig however, very little information is available on the expression stability of reference genes. The aim of this study was therefore to develop a new set of reference genes which can be used for normalization of mRNA expression data of genes expressed in porcine backfat and longissimus dorsi muscle, both representing an economically important part of a pig's carcass. Because of its multiple functions in fat metabolism and muscle fibre type composition, peroxisome proliferative activated receptor γ coactivator 1α (PPARGC1A) is a very interesting candidate gene for meat quality, and was an ideal gene to evaluate our developed set of reference genes for normalization of mRNA expression data of both tissue types. Results The mRNA expression stability of 10 reference genes was determined. The expression of RPL13A and SDHA appeared to be highly unstable. After normalization to the geometric mean of the three most stably expressed reference genes (ACTB, TBP and TOP2B), the results not only showed that the mRNA expression of PPARGC1A was significantly higher in each of the longissimus dorsi muscle samples than in backfat (P < 0.05), but also that the expression was significantly higher in the most cranial of the three muscle samples (P < 0.05). Conclusion This study provides a new set of reference genes (ACTB, TBP and TOP2B) suitable for normalization of real-time RT-PCR data of backfat and longissimus dorsi muscle in the pig. The obtained PPARGC1A expression results, after application of this set of reference genes, are a first step in unravelling the PPARGC1A expression pattern in the pig and provide a basis for possible selection towards improved meat quality while maintaining a lean carcass.
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Affiliation(s)
- Tim Erkens
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Mario Van Poucke
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Jo Vandesompele
- Centre for Medical Genetics, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
| | - Karen Goossens
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Alex Van Zeveren
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Luc J Peelman
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
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Kochetov AV. Alternative translation start sites and their significance for eukaryotic proteomes. Mol Biol 2006. [DOI: 10.1134/s0026893306050049] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nordström KJV, Mirza MAI, Larsson TP, Gloriam DEI, Fredriksson R, Schiöth HB. Comprehensive comparisons of the current human, mouse, and rat RefSeq, Ensembl, EST, and FANTOM3 datasets: Identification of new human genes with specific tissue expression profile. Biochem Biophys Res Commun 2006; 348:1063-74. [PMID: 16904064 DOI: 10.1016/j.bbrc.2006.07.153] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Accepted: 07/25/2006] [Indexed: 10/24/2022]
Abstract
Our understanding of functional genetic elements in the genomes is continuously growing and new entries are entered in various databases on a regular basis. We have here merged the genetic elements in RefSeq, Ensembl, FANTOM3, HINV, and NCBI:s ESTdb using the genome assemblies in order to achieve a comprehensive picture of the current status of the identity and gene number in human, mouse, and rat. The number of human protein coding genes has not increased (25,043) while the increased sequencing of mouse transcripts has provided the considerably higher number of protein coding genes (31,578) in mouse. The results indicate large discrepancies between the datasets, as considerable numbers of unique transcripts can be found in each dataset. Despite the high number of ncRNA (38,129 in mouse) there are also almost 20,000 EST clusters in both mouse and humans with more than one EST that do not overlap any transcript suggesting that several new genetic elements are still to be found. We also demonstrated presence of new genes by identifying new human ones that have specific tissue profiles, using RT-PCR on rat tissues.
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Affiliation(s)
- Karl J V Nordström
- Department of Neuroscience, Uppsala University, BMC Box 593, 751 24 Uppsala, Sweden
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Nurtdinov RN, Neverov AD, Mal’ko DB, Kosmodem’yanskii IA, Ermakova EO, Ramenskii VE, Mironov AA, Gelfand MS. EDAS—A database of alternatively spliced human genes. Biophysics (Nagoya-shi) 2006. [DOI: 10.1134/s0006350906040026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Schmidt T, Frishman D. PROMPT: a protein mapping and comparison tool. BMC Bioinformatics 2006; 7:331. [PMID: 16817977 PMCID: PMC1569443 DOI: 10.1186/1471-2105-7-331] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Accepted: 07/04/2006] [Indexed: 11/12/2022] Open
Abstract
Background Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available. Results PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel. Conclusion PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from .
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Affiliation(s)
- Thorsten Schmidt
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
| | - Dmitrij Frishman
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
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Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C. An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 2006; 34:3150-60. [PMID: 16757580 PMCID: PMC1475746 DOI: 10.1093/nar/gkl396] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 04/13/2006] [Accepted: 05/10/2006] [Indexed: 11/13/2022] Open
Abstract
Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of gene structure and alternative splicing. In this manuscript we introduce a probabilistic formulation of the isoform reconstruction problem, and provide an expectation-maximization (EM) algorithm for its maximum likelihood solution. Using a series of simulated data and expressed sequences from real human genes, we demonstrate that our EM algorithm can correctly handle various situations of fragmentation and coupling in the input data. Our work establishes a general probabilistic framework for splice graph-based reconstructions of full-length isoforms.
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Affiliation(s)
- Yi Xing
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Tianwei Yu
- Department of Statistics, University of CaliforniaLos Angeles, USA
- Dental Research Institute, School of Dentistry, University of CaliforniaLos Angeles, USA
| | - Ying Nian Wu
- Department of Statistics, University of CaliforniaLos Angeles, USA
| | - Meenakshi Roy
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Joseph Kim
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Christopher Lee
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
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Fall AM, Johnsen R, Honeyman K, Iversen P, Fletcher S, Wilton SD. Induction of revertant fibres in the mdx mouse using antisense oligonucleotides. GENETIC VACCINES AND THERAPY 2006; 4:3. [PMID: 16719929 PMCID: PMC1481566 DOI: 10.1186/1479-0556-4-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 05/24/2006] [Indexed: 11/28/2022]
Abstract
Background Duchenne muscular dystrophy is a fatal genetic disorder caused by dystrophin gene mutations that result in premature termination of translation and the absence of functional protein. Despite the primary dystrophin gene lesion, immunostaining studies have shown that at least 50% of DMD patients, mdx mice and a canine model of DMD have rare dystrophin-positive or 'revertant' fibres. Fine epitope mapping has shown that the majority of transcripts responsible for revertant fibres exclude multiple exons, one of which includes the dystrophin mutation. Methods The mdx mouse model of muscular dystrophy has a nonsense mutation in exon 23 of the dystrophin gene. We have shown that antisense oligonucleotides (AOs) can induce the removal of this exon, resulting in an in-frame mRNA transcript encoding a shortened but functional dystrophin protein. To emulate one exonic combination associated with revertant fibres, we target multiple exons for removal by the application of a group of AOs combined as a "cocktail". Results Exons 19–25 were consistently excluded from the dystrophin gene transcript using a cocktail of AOs. This corresponds to an alternatively processed gene transcript that has been sporadically detected in untreated dystrophic mouse muscle, and is presumed to give rise to a revertant dystrophin isoform. The transcript and the resultant correctly localised smaller protein were confirmed by RT-PCR, immunohistochemistry and western blot analysis. Conclusion This work demonstrates the feasibility of AO cocktails to by-pass dystrophin mutation hotspots through multi-exon skipping. Multi-exon skipping could be important in expediting an exon skipping therapy to treat DMD, so that the same AO formulations may be applied to several different mutations within particular domains of the dystrophin gene.
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Affiliation(s)
- Abbie M Fall
- Experimental Molecular Medicine Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Perth, 6009, Western Australia
| | - Russell Johnsen
- Experimental Molecular Medicine Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Perth, 6009, Western Australia
| | - Kaite Honeyman
- Experimental Molecular Medicine Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Perth, 6009, Western Australia
| | | | - Susan Fletcher
- Experimental Molecular Medicine Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Perth, 6009, Western Australia
| | - Stephen D Wilton
- Experimental Molecular Medicine Group, Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Nedlands, Perth, 6009, Western Australia
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