1
|
Chen M, Mei L, Wang F, Boyagane Dewayalage IKW, Yang J, Dai L, Yang G, Gao B, Cheng C, Liu Y, Zhang J, Hao G. PlantSPEAD: a web resource towards comparatively analysing stress-responsive expression of splicing-related proteins in plant. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:227-229. [PMID: 33010087 PMCID: PMC7868970 DOI: 10.1111/pbi.13486] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/21/2020] [Indexed: 05/03/2023]
Affiliation(s)
- Mo‐Xian Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural BioengineeringKey Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of Education, Research and Development Center for Fine ChemicalsGuizhou UniversityGuiyangChina
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Long‐Can Mei
- Key Laboratory of Pesticide & Chemical BiologyMinistry of EducationCollege of ChemistryCentral China Normal UniversityWuhanChina
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical BiologyMinistry of EducationCollege of ChemistryCentral China Normal UniversityWuhanChina
| | | | - Jing‐Fang Yang
- Key Laboratory of Pesticide & Chemical BiologyMinistry of EducationCollege of ChemistryCentral China Normal UniversityWuhanChina
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering BiologyShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Guang‐Fu Yang
- Key Laboratory of Pesticide & Chemical BiologyMinistry of EducationCollege of ChemistryCentral China Normal UniversityWuhanChina
| | - Bei Gao
- Department of BiologyHong Kong Baptist University and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinChina
| | - Chao‐Lin Cheng
- Department of BiologyHong Kong Baptist University and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinChina
| | - Ying‐Gao Liu
- State Key Laboratory of Crop BiologyCollege of Life ScienceShandong Agricultural UniversityTaianChina
| | - Jianhua Zhang
- Department of BiologyHong Kong Baptist University and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinChina
| | - Ge‐Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural BioengineeringKey Laboratory of Green Pesticide and Agricultural BioengineeringMinistry of Education, Research and Development Center for Fine ChemicalsGuizhou UniversityGuiyangChina
| |
Collapse
|
2
|
Xing Y, Zhao X, Yu T, Liang D, Li J, Wei G, Liu G, Cui X, Zhao H, Cai L. MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs. PLoS One 2016; 11:e0155443. [PMID: 27167218 PMCID: PMC4864242 DOI: 10.1371/journal.pone.0155443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 04/28/2016] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones for 173 human AS events. Every entry includes the interaction partners, interaction type, experimental methods, AS type, tissue specificity or disease-relevant information, a simple description of the functionally tested interaction in the AS event and references. The database can be queried easily using a web server (http://47.88.84.236/Miasdb). We display some interaction figures for several genes. With this database, users can view the regulation network describing AS events for 12 given genes.
Collapse
Affiliation(s)
- Yongqiang Xing
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiujuan Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Tao Yu
- School of Science, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Dong Liang
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Jun Li
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Guanyun Wei
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Guoqing Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Xiangjun Cui
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Hongyu Zhao
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
| | - Lu Cai
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China
- * E-mail:
| |
Collapse
|
3
|
Roy B, Haupt LM, Griffiths LR. Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity. Curr Genomics 2013; 14:182-94. [PMID: 24179441 PMCID: PMC3664468 DOI: 10.2174/1389202911314030004] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 12/22/2022] Open
Abstract
Prior to the completion of the human genome project, the human genome was thought to have a greater number of genes as it seemed structurally and functionally more complex than other simpler organisms. This along with the belief of “one gene, one protein”, were demonstrated to be incorrect. The inequality in the ratio of gene to protein formation gave rise to the theory of alternative splicing (AS). AS is a mechanism by which one gene gives rise to multiple protein products. Numerous databases and online bioinformatic tools are available for the detection and analysis of AS. Bioinformatics provides an important approach to study mRNA and protein diversity by various tools such as expressed sequence tag (EST) sequences obtained from completely processed mRNA. Microarrays and deep sequencing approaches also aid in the detection of splicing events. Initially it was postulated that AS occurred only in about 5% of all genes but was later found to be more abundant. Using bioinformatic approaches, the level of AS in human genes was found to be fairly high with 35-59% of genes having at least one AS form. Our ability to determine and predict AS is important as disorders in splicing patterns may lead to abnormal splice variants resulting in genetic diseases. In addition, the diversity of proteins produced by AS poses a challenge for successful drug discovery and therefore a greater understanding of AS would be beneficial.
Collapse
Affiliation(s)
- Bishakha Roy
- Genomics Research Centre, Griffith Health Institute, Griffith University Gold Coast, Queensland 4222, Australia
| | | | | |
Collapse
|
4
|
Kelemen O, Convertini P, Zhang Z, Wen Y, Shen M, Falaleeva M, Stamm S. Function of alternative splicing. Gene 2013; 514:1-30. [PMID: 22909801 PMCID: PMC5632952 DOI: 10.1016/j.gene.2012.07.083] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 07/21/2012] [Accepted: 07/30/2012] [Indexed: 12/15/2022]
Abstract
Almost all polymerase II transcripts undergo alternative pre-mRNA splicing. Here, we review the functions of alternative splicing events that have been experimentally determined. The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome. Alternative splicing changes proteins encoded by mRNAs, which has profound functional effects. Experimental analysis of these protein isoforms showed that alternative splicing regulates binding between proteins, between proteins and nucleic acids as well as between proteins and membranes. Alternative splicing regulates the localization of proteins, their enzymatic properties and their interaction with ligands. In most cases, changes caused by individual splicing isoforms are small. However, cells typically coordinate numerous changes in 'splicing programs', which can have strong effects on cell proliferation, cell survival and properties of the nervous system. Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.
Collapse
Affiliation(s)
- Olga Kelemen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Paolo Convertini
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Yuan Wen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Manli Shen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Marina Falaleeva
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| |
Collapse
|
5
|
Shi BJ, Xue M, Zhong GS, Jiang Y, Chen DY, Feng J, Hao J, Diao QC. The ATP2A2 gene in patients with Darier's disease: one novel splicing mutation. Int J Dermatol 2012; 51:1074-7. [PMID: 22909361 DOI: 10.1111/j.1365-4632.2012.05514.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Darier's disease (DD) is a rare, inherited skin disorder characterized by warty papules and plaques over the seborrheic area, such as central trunk, flexures, scalp, and forehead. Mutations in ATP2A2 gene encoding the enzyme sarco/endoplasmic reticulum Ca(2+) ATPase type 2 are responsible for the disease. Here we report two Chinese families affected by DD with two ATP2A2 mutations. MATERIALS AND METHODS DNA was extracted from the peripheral blood samples and then subjected to polymerase chain reaction amplification and direct automated DNA sequencing. RESULTS A heterozygous G to T transition in the first nucleotide of intron 7 (c.630 + 1G>T) and G to A transversion at nucleotide 2898 in exon 20 of the ATP2A2 gene were identified in two pedigrees, respectively. The former mutation in the splice site is a novel mutation and is thought to lead to aberrant splicing and premature protein truncation. The latter has already been described, which leads to premature termination codons (PTC) (W966X). CONCLUSION The results will contribute to the expanding database of ATP2A2 mutations in patients with DD and be useful for inherited counseling and prenatal examination for affected families.
Collapse
Affiliation(s)
- Bing-Jun Shi
- Department of Dermatology, the First People's Hospital of Chongqing City, Chongqing, China
| | | | | | | | | | | | | | | |
Collapse
|
6
|
Chen L. Statistical and Computational Methods for High-Throughput Sequencing Data Analysis of Alternative Splicing. STATISTICS IN BIOSCIENCES 2012; 5:138-155. [PMID: 24058384 DOI: 10.1007/s12561-012-9064-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The burgeoning field of high-throughput sequencing significantly improves our ability to understand the complexity of transcriptomes. Alternative splicing, as one of the most important driving forces for transcriptome diversity, can now be studied at an unprecedent resolution. Efficient and powerful computational and statistical methods are in urgent need to facilitate the characterization and quantification of alternative splicing events. Here we discuss methods in splice junction read mapping, and methods in exon-centric or isoform-centric quantification of alternative splicing. In addition, we discuss HITS-CLIP and splicing QTL analyses which are novel high-throughput sequencing based approaches in the dissection of splicing regulation.
Collapse
Affiliation(s)
- Liang Chen
- Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
7
|
Hsu JBK, Chiu CM, Hsu SD, Huang WY, Chien CH, Lee TY, Huang HD. miRTar: an integrated system for identifying miRNA-target interactions in human. BMC Bioinformatics 2011; 12:300. [PMID: 21791068 PMCID: PMC3162936 DOI: 10.1186/1471-2105-12-300] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Accepted: 07/26/2011] [Indexed: 01/28/2023] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNA molecules that are ~22-nt-long sequences capable of suppressing protein synthesis. Previous research has suggested that miRNAs regulate 30% or more of the human protein-coding genes. The aim of this work is to consider various analyzing scenarios in the identification of miRNA-target interactions, as well as to provide an integrated system that will aid in facilitating investigation on the influence of miRNA targets by alternative splicing and the biological function of miRNAs in biological pathways. Results This work presents an integrated system, miRTar, which adopts various analyzing scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in biological pathways. The system has three major features. First, the prediction system is able to consider various analyzing scenarios (1 miRNA:1 gene, 1:N, N:1, N:M, all miRNAs:N genes, and N miRNAs: genes involved in a pathway) to easily identify the regulatory relationships between interesting miRNAs and their targets, in 3'UTR, 5'UTR and coding regions. Second, miRTar can analyze and highlight a group of miRNA-regulated genes that participate in particular KEGG pathways to elucidate the biological roles of miRNAs in biological pathways. Third, miRTar can provide further information for elucidating the miRNA regulation, i.e., miRNA-target interactions, affected by alternative splicing. Conclusions In this work, we developed an integrated resource, miRTar, to enable biologists to easily identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. miRTar is now available at http://miRTar.mbc.nctu.edu.tw/.
Collapse
Affiliation(s)
- Justin Bo-Kai Hsu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan
| | | | | | | | | | | | | |
Collapse
|
8
|
Zhang Z, Stamm S. Analysis of mutations that influence pre-mRNA splicing. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2010; 703:137-60. [PMID: 21125488 DOI: 10.1007/978-1-59745-248-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A rapidly increasing number of human diseases are now recognized as being caused by the selection of wrong splice sites. In most cases, these changes in alternative splice site selection are due to single nucleotide exchanges in splicing regulatory elements. This chapter describes the use of bioinformatics tools to predict the influence of a mutation on alternative pre-mRNA splicing and the experimental testing of these predictions. The bioinformatic analysis determines the influence of a mutation on splicing enhancers and silencers, splice sites and RNA secondary structures. This approach generates hypotheses that are tested using splicing reporter constructs, which are then analyzed in transfection assays. We describe a recombination-based system that allows for the generation of splicing reporter constructs in the first week and their subsequent analysis in the second week.
Collapse
Affiliation(s)
- Zhaiyi Zhang
- Department of Molecular and Cellular Biochemistry, Biomedical Biological Sciences Research Building, College of Medicine, University of Kentucky, Lexington, KY, USA.
| | | |
Collapse
|
9
|
Ren H, Li Y, Tang Z, Yang S, Mu Y, Cui W, Ao H, Du L, Wang L, Li K. Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE libraries. Anim Genet 2009; 40:499-508. [DOI: 10.1111/j.1365-2052.2009.01868.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
10
|
Bingham JL, Carrigan PE, Miller LJ, Srinivasan S. Extent and diversity of human alternative splicing established by complementary database annotation and microarray analysis. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2008; 12:83-92. [PMID: 18266558 DOI: 10.1089/omi.2007.0041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative splicing generates functional diversity in higher organisms through alternative first and last exons, skipped and included exons, intron retentions and alternative donor, and acceptor sites. In large-scale microarray studies in humans and the mouse, emphasis so far has been placed on exon-skip events, leaving the prevalence and importance of other splice types largely unexplored. Using a new human splice variant database and a genome-wide microarray to probes thousands of splice events of each type, we measured differential expression of splice types across six pair of diverse cell lines and validated the database annotation process. Results suggest that splicing in humans is more complex than simple exon-skip events, which account for a minority of splicing differences. The relative frequency of differential expression of the splice types correlates with what is found by our annotation efforts. In conclusion, alternative splicing in human cells is considerably more complex than the canonical example of the exon skip. The complementary approaches of genome-wide annotation of alternative splicing in human and design of genome-wide splicing microarrays to measure differential splicing in biological samples provide a powerful high-throughput tool to study the role of alternative splicing in human biology.
Collapse
|
11
|
Abstract
The sequencing of the human genome and ensuing wave of data generation have brought new light upon the extent and importance of alternative splicing as an RNA regulatory mechanism. Alternative splicing could potentially explain the complexity of protein repertoire during evolution, and defects in the splicing mechanism are responsible for diseases as complex as cancer. Among the challenges that rise in light of these discoveries are cataloguing splice variation in the human and other eukaryotic genomes, and identifying and characterizing the splicing regulatory elements that control their expression. Bioinformatics efforts tackling these two questions are just at the beginning. This article is a survey of these methods.
Collapse
Affiliation(s)
- Liliana Florea
- Department of Computer Science, George Washington University, Academic Center-Rm 714, Washington DC 20052, USA.
| |
Collapse
|
12
|
Lee YW, Lee DH, Vockley J, Kim ND, Lee YK, Ki CS. Different spectrum of mutations of isovaleryl-CoA dehydrogenase (IVD) gene in Korean patients with isovaleric acidemia. Mol Genet Metab 2007; 92:71-7. [PMID: 17576084 PMCID: PMC4136440 DOI: 10.1016/j.ymgme.2007.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Revised: 05/08/2007] [Accepted: 05/08/2007] [Indexed: 12/15/2022]
Abstract
Isovaleric acidemia (IVA) is an autosomal recessive inborn error of the leucine metabolism that is caused by a deficiency of isovaleryl-CoA dehydrogenase (IVD). Recent application of tandem mass spectrometry to newborn screening has allowed a significant expansion of the recognition of individuals with IVD deficiency. Although many patients have been reported worldwide, there are no genetically confirmed patients in Korea. This study characterizes IVD mutations in seven Korean IVA patients from six unrelated families. Bi-directional sequencing analysis identified two novel variations affecting consensus splice sites (c.144+1G>T in intron 1 and c.457-3_2CA>GG in intron 4) and three novel variations altering coding sequences (c.149G>T; Arg21Leu, c.832A>G; Ser249Gly, and c.1135T>G; Phe350Val). Five patients from four families were found to be compound heterozygotes while two unrelated patients were homozygous for the c.457-3_2CA>GG variation. Reverse-transcription polymerase chain reaction confirmed that both intron variations cause aberrant splicing. Furthermore, analysis of cultured lymphocyte extracts of the seven patients showed no detectable enzyme activity and reduced levels of IVD protein (<10.0% of control) in all samples. These results confirm IVD mutations in Korean patients with IVA and reveal that the mutation spectrum is different from previously reported patients.
Collapse
Affiliation(s)
- Yong-Wha Lee
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea
| | - Dong Hwan Lee
- Department of Pediatrics, Soonchunhyang University College of Medicine, Seoul, Republic of Korea
| | - Jerry Vockley
- Department of Pediatrics, University of Pittsburgh School of Medicine, The Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Nam-Doo Kim
- R&D Center, Equispharm Co., Ltd., Ansan, Republic of Korea
| | - You Kyoung Lee
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Republic of Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, 50 Irwon-dong, Gangnam-gu, Seoul, Republic of Korea
- Corresponding author. Fax: +82 2 3410 2719. (C.-S. Ki)
| |
Collapse
|
13
|
Müller T, Philippi N, Dandekar T, Schultz J, Wolf M. Distinguishing species. RNA (NEW YORK, N.Y.) 2007; 13:1469-72. [PMID: 17652131 PMCID: PMC1950759 DOI: 10.1261/rna.617107] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious for closely related ones. A molecular marker giving a clear distinction would therefore be of immense benefit. The internal transcribed spacer 2 (ITS2) has been widely used for low-level phylogenetic analyses. Case studies revealed that a compensatory base change (CBC) in the helix II or helix III ITS2 secondary structure between two organisms correlated with sexual incompatibility. We analyzed more than 1300 closely related species to test whether this correlation is generally applicable. In 93%, where a CBC was found between organisms classified within the same genus, they belong to different species. Thus, a CBC in an ITS2 sequence-structure alignment is a sufficient condition to distinguish even closely related species.
Collapse
Affiliation(s)
- Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Germany.
| | | | | | | | | |
Collapse
|
14
|
Skotheim RI, Nees M. Alternative splicing in cancer: Noise, functional, or systematic? Int J Biochem Cell Biol 2007; 39:1432-49. [PMID: 17416541 DOI: 10.1016/j.biocel.2007.02.016] [Citation(s) in RCA: 157] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 02/13/2007] [Accepted: 02/22/2007] [Indexed: 12/22/2022]
Abstract
Pre-messenger RNA splicing is a fine-tuned process that generates multiple functional variants from individual genes. Various cell types and developmental stages regulate alternative splicing patterns differently in their generation of specific gene functions. In cancers, splicing is significantly altered, and understanding the underlying mechanisms and patterns in cancer will shed new light onto cancer biology. Cancer-specific transcript variants are promising biomarkers and targets for diagnostic, prognostic, and treatment purposes. In this review, we explore how alternative splicing cannot simply be considered as noise or an innocent bystander, but is actively regulated or deregulated in cancers. A special focus will be on aspects of cell biology and biochemistry of alternative splicing in cancer cells, addressing differences in splicing mechanisms between normal and malignant cells. The systems biology of splicing is only now applied to the field of cancer research. We explore functional annotations for some of the most intensely spliced gene classes, and provide a literature mining and clustering that reflects the most intensely investigated genes. A few well-established cancer-specific splice events, such as the CD44 antigen, are used to illustrate the potential behind the exploration of the mechanisms of their regulation. Accordingly, we describe the functional connection between the regulatory machinery (i.e., the spliceosome and its accessory proteins) and their global impact on qualitative transcript variation that are only now emerging from the use of genomic technologies such as microarrays. These studies are expected to open an entirely new level of genetic information that is currently still poorly understood.
Collapse
Affiliation(s)
- Rolf I Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Oslo, Norway
| | | |
Collapse
|
15
|
Bhasi A, Pandey RV, Utharasamy SP, Senapathy P. EuSplice: a unified resource for the analysis of splice signals and alternative splicing in eukaryotic genes. Bioinformatics 2007; 23:1815-23. [PMID: 17344236 DOI: 10.1093/bioinformatics/btm084] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Despite increased availability of genome annotation data, a comprehensive resource for in-depth analysis of splice signal distributions and alternative splicing (AS) patterns in eukaryote genomes is still lacking. To meet this need, we have developed EuSplice--a unique splice-centric database which provides reliable splice signal and AS information for 23 eukaryotes. RESULTS The EuSplice database contains 95,822 AS events and 2.1 million splice signals associated with over 270,000 protein-coding genes. The intuitive, user-friendly EuSplice web interface has powerful data mining and graphics capabilities for inter-genomic comparative analysis of splice signals, putative cryptic splice sites and AS events. Moreover, the seamless integration of splicing data to extensive gene-specific annotations, such as homolog annotations, functional information, mutations and sequence details makes EuSplice a powerful one-stop information resource for investigating the molecular mechanisms of complex splicing events, disease associations and the evolution of splicing in eukaryotes. AVAILABILITY http://66.170.16.154/EuSplice. SUPPLEMENTARY INFORMATION Supplementary tables and figures at Bioinfo online.
Collapse
Affiliation(s)
- Ashwini Bhasi
- Department of Human Genetics, Genome Technologies, Inc., 8000 Excelsior Drive, Madison, WI 53717, USA
| | | | | | | |
Collapse
|
16
|
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. BMC Bioinformatics 2007; 8:75. [PMID: 17338820 PMCID: PMC1839109 DOI: 10.1186/1471-2105-8-75] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Accepted: 03/05/2007] [Indexed: 12/12/2022] Open
Abstract
Background There are many fewer genes in the human genome than there are expressed transcripts. Alternative splicing is the reason. Alternatively spliced transcripts are often specific to tissue type, developmental stage, environmental condition, or disease state. Accurate analysis of microarray expression data and design of new arrays for alternative splicing require assessment of probes at the sequence and exon levels. Description SpliceMiner is a web interface for querying Evidence Viewer Database (EVDB). EVDB is a comprehensive, non-redundant compendium of splice variant data for human genes. We constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV). EVDB is based on data obtained from NCBI Entrez Gene and EV. The automated EVDB build process uses only complete coding sequences, which may or may not include partial or complete 5' and 3' UTRs, and filters redundant splice variants. Unlike EV, which supports only one-at-a-time queries, SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format. SpliceMiner maps probes to splice variants, effectively delineating the variants identified by a probe. Conclusion EVDB can be queried by gene symbol, genomic coordinates, or probe sequence via a user-friendly web-based tool we call SpliceMiner (). The EVDB/SpliceMiner combination provides an interface with human splice variant information and, going beyond the very valuable NCBI Evidence Viewer, supports fluent, high-throughput analysis. Integration of EVDB information into microarray analysis and design pipelines has the potential to improve the analysis and bioinformatic interpretation of gene expression data, for both batch and interactive processing. For example, whenever a gene expression value is recognized as important or appears anomalous in a microarray experiment, the interactive mode of SpliceMiner can be used quickly and easily to check for possible splice variant issues.
Collapse
|
17
|
Le Texier V, Riethoven JJ, Kumanduri V, Gopalakrishnan C, Lopez F, Gautheret D, Thanaraj TA. AltTrans: transcript pattern variants annotated for both alternative splicing and alternative polyadenylation. BMC Bioinformatics 2006; 7:169. [PMID: 16556303 PMCID: PMC1435940 DOI: 10.1186/1471-2105-7-169] [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: 12/14/2005] [Accepted: 03/23/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three major mechanisms that regulate transcript formation involve the selection of alternative sites for transcription start (TS), splicing, and polyadenylation. Currently there are efforts that collect data & annotation individually for each of these variants. It is important to take an integrated view of these data sets and to derive a data set of alternate transcripts along with consolidated annotation. We have been developing in the past computational pipelines that generate value-added data at genome-scale on individual variant types; these include AltSplice on splicing and AltPAS on polyadenylation. We now extend these pipelines and integrate the resultant data sets to facilitate an integrated view of the contributions from splicing and polyadenylation in the formation of transcript variants. DESCRIPTION The AltSplice pipeline examines gene-transcript alignments and delineates alternative splice events and splice patterns; this pipeline is extended as AltTrans to delineate isoform transcript patterns for each of which both introns/exons and 'terminating' polyA site are delineated; EST/mRNA sequences that qualify the transcript pattern confirm both the underlying splicing and polyadenylation. The AltPAS pipeline examines gene-transcript alignments and delineates all potential polyA sites irrespective of underlying splicing patterns. Resultant polyA sites from both AltTrans and AltPAS are merged. The generated database reports data on alternative splicing, alternative polyadenylation and the resultant alternate transcript patterns; the basal data is annotated for various biological features. The data (named as integrated AltTrans data) generated for both the organisms of human and mouse is made available through the Alternate Transcript Diversity web site at http://www.ebi.ac.uk/atd/. CONCLUSION The reported data set presents alternate transcript patterns that are annotated for both alternative splicing and alternative polyadenylation. Results based on current transcriptome data indicate that the contribution of alternative splicing is larger than that of alternative polyadenylation.
Collapse
Affiliation(s)
- Vincent Le Texier
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jean-Jack Riethoven
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- 18 Crispin Close, Haverhill, Suffolk, CB9 9PT, UK
| | - Vasudev Kumanduri
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Chellappa Gopalakrishnan
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Fabrice Lopez
- INSERM ERM206, Université de la Méditerranée, Luminy case 928 – 13 288 Marseille Cedex 09, France
| | - Daniel Gautheret
- INSERM ERM206, Université de la Méditerranée, Luminy case 928 – 13 288 Marseille Cedex 09, France
| | - Thangavel Alphonse Thanaraj
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
- 4 Copperfields, Saffron Walden, Essex, CB11 4FG, UK
| |
Collapse
|
18
|
Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA. ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 2006; 34:D46-55. [PMID: 16381912 PMCID: PMC1347394 DOI: 10.1093/nar/gkj031] [Citation(s) in RCA: 190] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Revised: 09/22/2005] [Accepted: 09/22/2005] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing is an important regulatory mechanism of mammalian gene expression. The alternative splicing database (ASD) consortium is systematically collecting and annotating data on alternative splicing. We present the continuation and upgrade of the ASD [T. A. Thanaraj, S. Stamm, F. Clark, J. J. Riethoven, V. Le Texier, J. Muilu (2004) Nucleic Acids Res. 32, D64-D69] that consists of computationally and manually generated data. Its largest parts are AltSplice, a value-added database of computationally delineated alternative splicing events. Its data include alternatively spliced introns/exons, events, isoform splicing patterns and isoform peptide sequences. AltSplice data are generated by examining gene-transcript alignments. The data are annotated for various biological features including splicing signals, expression states, (SNP)-mediated splicing and cross-species conservation. AEdb forms the manually curated component of ASD. It is a literature-based data set containing sequence and properties of alternatively spliced exons, functional enumeration of observed splicing events, characterization of observed splicing regulatory elements, and a collection of experimentally clarified minigene constructs. ASD includes a workbench, which is an analysis tool that enables users to carry out splicing related analysis such as characterization of introns for various splicing signals, identification of splicing regulatory elements on a given RNA sequence, prediction of putative exons and prediction of putative translation start codons. The different ASD modules are integrated and can be accessed through user-friendly interfaces and visualization tools. ASD data has been integrated with Ensembl genome annotation project as a Distributed Annotation System (DAS) resource and can be viewed on Ensembl genome browser. The ASD resource is presented at (http://www.ebi.ac.uk/asd).
Collapse
Affiliation(s)
- Stefan Stamm
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
| | - Jean-Jack Riethoven
- European Bioinformatics Institute, Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SD, UK
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon1649-028 Lisbon, Portugal
| | - Vincent Le Texier
- European Bioinformatics Institute, Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SD, UK
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon1649-028 Lisbon, Portugal
| | - Chellappa Gopalakrishnan
- European Bioinformatics Institute, Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SD, UK
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon1649-028 Lisbon, Portugal
| | - Vasudev Kumanduri
- European Bioinformatics Institute, Wellcome Trust Genome CampusHinxton, Cambridge, CB10 1SD, UK
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon1649-028 Lisbon, Portugal
| | - Yesheng Tang
- University of Erlangen, Institute for BiochemistryFahrstrasse 17, 91054 Erlangen, Germany
| | - Nuno L. Barbosa-Morais
- Faculty of Medicine, Institute of Molecular Medicine, University of Lisbon1649-028 Lisbon, Portugal
| | | |
Collapse
|
19
|
Holste D, Huo G, Tung V, Burge CB. HOLLYWOOD: a comparative relational database of alternative splicing. Nucleic Acids Res 2006; 34:D56-62. [PMID: 16381932 PMCID: PMC1347411 DOI: 10.1093/nar/gkj048] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Revised: 09/26/2005] [Accepted: 10/04/2005] [Indexed: 01/05/2023] Open
Abstract
RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at http://hollywood.mit.edu.
Collapse
Affiliation(s)
- Dirk Holste
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02319, USA.
| | | | | | | |
Collapse
|
20
|
de la Grange P, Dutertre M, Martin N, Auboeuf D. FAST DB: a website resource for the study of the expression regulation of human gene products. Nucleic Acids Res 2005; 33:4276-84. [PMID: 16052034 PMCID: PMC1181862 DOI: 10.1093/nar/gki738] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Human genes use various mechanisms to generate different transcripts having different exon content, which in turn generate multiple protein isoforms having differential and even opposite biological activities. To understand the biological consequences of gene transcriptional activity modulation, it is necessary to integrate the capability of genes to generate distinct functional products, particularly because transcriptional stimuli also affect the exon content of their target gene products. For this purpose, we have developed a bioinformatics suite, FAST DB, which defines easily and accurately the exon content of all known transcripts produced by human genes. In addition, several tools have been developed, including a graphical presentation of all gene products, a sequence multi-alignment of all gene transcripts and an in silico PCR computer program. The FAST DB interface also offers extensive links to website resources for promoter analysis and transcription factor binding site prediction, splicing regulatory sequence prediction, as well as 5′- and 3′-untranslated region analysis. FAST DB has been designed to facilitate studies that integrate transcriptional and post-transcriptional events to investigate the expression regulation of human gene products.
Collapse
Affiliation(s)
| | | | | | - Didier Auboeuf
- To whom correspondence should be addressed. Tel: +33 1 53 72 21 30; Fax: +33 1 42 40 95 57;
| |
Collapse
|
21
|
Hiller M, Huse K, Platzer M, Backofen R. Creation and disruption of protein features by alternative splicing -- a novel mechanism to modulate function. Genome Biol 2005; 6:R58. [PMID: 15998447 PMCID: PMC1175989 DOI: 10.1186/gb-2005-6-7-r58] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 04/19/2005] [Accepted: 05/09/2005] [Indexed: 11/23/2022] Open
Abstract
A new mechanism of alternative splicing is proposed which creates a protein feature by putting together two non-consecutive exons and destroys a feature by inserting an exon in its body. Evidence for this rare mechanism is provided by a genome-wide search with four specific protein features. Background Alternative splicing often occurs in the coding sequence and alters protein structure and function. It is mainly carried out in two ways: by skipping exons that encode a certain protein feature and by introducing a frameshift that changes the downstream protein sequence. These mechanisms are widespread and well investigated. Results Here, we propose an additional mechanism of alternative splicing to modulate protein function. This mechanism creates a protein feature by putting together two non-consecutive exons or destroys a feature by inserting an exon in its body. In contrast to other mechanisms, the individual parts of the feature are present in both splice variants but the feature is only functional in the splice form where both parts are merged. We provide evidence for this mechanism by performing a genome-wide search with four protein features: transmembrane helices, phosphorylation and glycosylation sites, and Pfam domains. Conclusion We describe a novel type of event that creates or removes a protein feature by alternative splicing. Current data suggest that these events are rare. Besides the four features investigated here, this mechanism is conceivable for many other protein features, especially for small linear protein motifs. It is important for the characterization of functional differences of two splice forms and should be considered in genome-wide annotation efforts. Furthermore, it offers a novel strategy for ab initio prediction of alternative splice events.
Collapse
Affiliation(s)
- Michael Hiller
- Institute of Computer Science, Friedrich-Schiller-University Jena, Chair for Bioinformatics, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Klaus Huse
- Genome Analysis, Institute of Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Matthias Platzer
- Genome Analysis, Institute of Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena, Germany
| | - Rolf Backofen
- Institute of Computer Science, Friedrich-Schiller-University Jena, Chair for Bioinformatics, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| |
Collapse
|
22
|
Abstract
The Nucleic Acids Research Molecular Biology Database Collection is a public online resource that lists the databases described in this and previous issues of Nucleic Acids Research together with other databases of value to the biologist and available throughout the world. All databases included in this Collection are freely available to the public. The 2005 update includes 719 databases, 171 more than the 2004 one. The databases are organized in a hierarchical classification that simplifies the process of finding the right database for any given task. The growing number of databases related to immunology, plant and organelle research have been accommodated by separating them into three new categories. The database summaries provide brief descriptions of the databases, contact details, appropriate references and acknowledgements. The online summaries also serve as a venue for the maintainers of each database to introduce database updates and other improvements in the scope and tools. These updates are particularly important for those databases that have not been described in print in the recent past. The database list and summaries are available online at the Nucleic Acids Research web site, http://nar.oupjournals.org/.
Collapse
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
| |
Collapse
|