1
|
Taylor R, Nikolaou N. RNA in axons, dendrites, synapses and beyond. Front Mol Neurosci 2024; 17:1397378. [PMID: 39359690 PMCID: PMC11446172 DOI: 10.3389/fnmol.2024.1397378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 08/01/2024] [Indexed: 10/04/2024] Open
Abstract
In neurons, a diverse range of coding and non-coding RNAs localize to axons, dendrites, and synapses, where they facilitate rapid responses to local needs, such as axon and dendrite extension and branching, synapse formation, and synaptic plasticity. Here, we review the extent of our current understanding of RNA subclass diversity in these functionally demanding subcellular compartments. We discuss the similarities and differences identified between axonal, dendritic and synaptic local transcriptomes, and discuss the reported and hypothesized fates and functions of localized RNAs. Furthermore, we outline the RNA composition of exosomes that bud off from neurites, and their implications for the biology of neighboring cells. Finally, we highlight recent advances in third-generation sequencing technologies that will likely provide transformative insights into splice isoform and RNA modification diversity in local transcriptomes.
Collapse
Affiliation(s)
- Richard Taylor
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Nikolas Nikolaou
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| |
Collapse
|
2
|
Zhou H, Yuan L, Ju Y, Hu Y, Wang S, Cao R, Wang Z, Zhang G. IDeAS: an interactive database for dysregulated alternative splicing in cancers across Chinese and western patients. J Mol Cell Biol 2024; 15:mjad074. [PMID: 38012117 PMCID: PMC11004917 DOI: 10.1093/jmcb/mjad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/01/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023] Open
Affiliation(s)
- Hanwen Zhou
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 101408, China
| | - Liyun Yuan
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuanhu Ju
- Shanghai Southgene Technology Co., Ltd, Shanghai 201210, China
| | - Yue Hu
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 101408, China
| | - Siqi Wang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 101408, China
| | - Ruifang Cao
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 101408, China
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Guoqing Zhang
- National Genomics Data Center & Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 101408, China
| |
Collapse
|
3
|
Sheng M, Zhang Y, Wang Y, Liu W, Wang X, Ke T, Liu P, Wang S, Shao W. Decoding the role of aberrant RNA alternative splicing in hepatocellular carcinoma: a comprehensive review. J Cancer Res Clin Oncol 2023; 149:17691-17708. [PMID: 37898981 DOI: 10.1007/s00432-023-05474-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 10/10/2023] [Indexed: 10/31/2023]
Abstract
During eukaryotic gene expression, alternative splicing of messenger RNA precursors is critical in increasing protein diversity and regulatory complexity. Multiple transcript isoforms could be produced by alternative splicing from a single gene; they could eventually be translated into protein isoforms with deleted, added, or altered domains or produce transcripts containing premature termination codons that could be targeted by nonsense-mediated mRNA decay. Alternative splicing can generate proteins with similar, different, or even opposite functions. Increasingly strong evidence indicates that abnormal RNA splicing is a prevalent and crucial occurrence in cellular differentiation, tissue advancement, and the development and progression of cancer. Aberrant alternative splicing could affect cancer cell activities such as growth, apoptosis, invasiveness, drug resistance, angiogenesis, and metabolism. This systematic review provides a comprehensive overview of the impact of abnormal RNA alternative splicing on the development and progression of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Mengfei Sheng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yuanyuan Zhang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yaoyun Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Weiyi Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Xingyu Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Tiaoying Ke
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Pingyang Liu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Sihan Wang
- Department of Clinical Medicine, Bengbu Medical College, Bengbu, China
| | - Wei Shao
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
| |
Collapse
|
4
|
Castaldi PJ, Abood A, Farber CR, Sheynkman GM. Bridging the splicing gap in human genetics with long-read RNA sequencing: finding the protein isoform drivers of disease. Hum Mol Genet 2022; 31:R123-R136. [PMID: 35960994 PMCID: PMC9585682 DOI: 10.1093/hmg/ddac196] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Abstract
Aberrant splicing underlies many human diseases, including cancer, cardiovascular diseases and neurological disorders. Genome-wide mapping of splicing quantitative trait loci (sQTLs) has shown that genetic regulation of alternative splicing is widespread. However, identification of the corresponding isoform or protein products associated with disease-associated sQTLs is challenging with short-read RNA-seq, which cannot precisely characterize full-length transcript isoforms. Furthermore, contemporary sQTL interpretation often relies on reference transcript annotations, which are incomplete. Solutions to these issues may be found through integration of newly emerging long-read sequencing technologies. Long-read sequencing offers the capability to sequence full-length mRNA transcripts and, in some cases, to link sQTLs to transcript isoforms containing disease-relevant protein alterations. Here, we provide an overview of sQTL mapping approaches, the use of long-read sequencing to characterize sQTL effects on isoforms, the linkage of RNA isoforms to protein-level functions and comment on future directions in the field. Based on recent progress, long-read RNA sequencing promises to be part of the human disease genetics toolkit to discover and treat protein isoforms causing rare and complex diseases.
Collapse
Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Division of General Medicine and Primary Care, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Abdullah Abood
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Charles R Farber
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Gloria M Sheynkman
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22903, USA
| |
Collapse
|
5
|
Falzarano MS, Grilli A, Zia S, Fang M, Rossi R, Gualandi F, Rimessi P, El Dani R, Fabris M, Lu Z, Li W, Mongini T, Ricci F, Pegoraro E, Bello L, Barp A, Sansone VA, Hegde M, Roda B, Reschiglian P, Bicciato S, Selvatici R, Ferlini A. RNA-seq in DMD urinary stem cells recognized muscle-related transcription signatures and addressed the identification of atypical mutations by whole-genome sequencing. HGG ADVANCES 2022; 3:100054. [PMID: 35047845 PMCID: PMC8756543 DOI: 10.1016/j.xhgg.2021.100054] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Urinary stem cells (USCs) are a non-invasive, simple, and affordable cell source to study human diseases. Here we show that USCs are a versatile tool for studying Duchenne muscular dystrophy (DMD), since they are able to address RNA signatures and atypical mutation identification. Gene expression profiling of DMD individuals' USCs revealed a profound deregulation of inflammation, muscle development, and metabolic pathways that mirrors the known transcriptional landscape of DMD muscle and worsens following USCs' myogenic transformation. This pathogenic transcription signature was reverted by an exon-skipping corrective approach, suggesting the utility of USCs in monitoring DMD antisense therapy. The full DMD transcript profile performed in USCs from three undiagnosed DMD individuals addressed three splicing abnormalities, which were decrypted and confirmed as pathogenic variations by whole-genome sequencing (WGS). This combined genomic approach allowed the identification of three atypical and complex DMD mutations due to a deep intronic variation and two large inversions, respectively. All three mutations affect DMD gene splicing and cause a lack of dystrophin protein production, and one of these also generates unique fusion genes and transcripts. Further characterization of USCs using a novel cell-sorting technology (Celector) highlighted cell-type variability and the representation of cell-specific DMD isoforms. Our comprehensive approach to USCs unraveled RNA, DNA, and cell-specific features and demonstrated that USCs are a robust tool for studying and diagnosing DMD.
Collapse
Affiliation(s)
- Maria S Falzarano
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Andrea Grilli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | | | | | - Rachele Rossi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Francesca Gualandi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Paola Rimessi
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Reem El Dani
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Marina Fabris
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | | | - Wenyan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Elena Pegoraro
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Luca Bello
- ERN Neuromuscular Center, Department of Neurosciences, Unit of Neurology, University of Padua, Padua 35122, Italy
| | - Andrea Barp
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Valeria A Sansone
- The NEMO Clinical Center, Neurorehabilitation Unit, University of Milan, Milan 20162, Italy
| | - Madhuri Hegde
- PerkinElmer Genomics, 3950 Shackleford Rd., Ste. 195, Duluth, GA 30096, USA
| | - Barbara Roda
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Pierluigi Reschiglian
- Stem Sel s.r.l., Bologna 40127, Italy
- Department of Chemistry "G. Ciamician," University of Bologna, Bologna 40126, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41121, Italy
| | - Rita Selvatici
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| | - Alessandra Ferlini
- Department of Medical Sciences, Unit of Medical Genetics, University of Ferrara, Ferrara 44121, Italy
| |
Collapse
|
6
|
Didonna A, Damotte V, Shams H, Matsunaga A, Caillier SJ, Dandekar R, Misra MK, Mofrad MRK, Oksenberg JR, Hollenbach JA. A splice acceptor variant in HLA-DRA affects the conformation and cellular localization of the class II DR alpha-chain. Immunology 2020; 162:194-207. [PMID: 32986852 DOI: 10.1111/imm.13273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/12/2020] [Accepted: 09/14/2020] [Indexed: 01/21/2023] Open
Abstract
Class II human leucocyte antigen (HLA) proteins are involved in the immune response by presenting pathogen-derived peptides to CD4+ T lymphocytes. At the molecular level, they are constituted by α/β-heterodimers on the surface of professional antigen-presenting cells. Here, we report that the acceptor variant (rs8084) in the HLA-DRA gene mediates the transcription of an alternative version of the α-chain lacking 25 amino acids in its extracellular domain. Molecular dynamics simulations suggest this isoform undergoes structural refolding which in turn affects its stability and cellular trafficking. The short HLA-DRA isoform cannot reach the cell surface, although it is still able to bind the corresponding β-chain. Conversely, it remains entrapped within the endoplasmic reticulum where it is targeted for degradation. Furthermore, we demonstrate that the short isoform can be transported to the cell membrane via interactions with the peptide-binding site of canonical HLA heterodimers. Altogether, our findings indicate that short HLA-DRA functions as a novel intact antigen for class II HLA molecules.
Collapse
Affiliation(s)
- Alessandro Didonna
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Vincent Damotte
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Hengameh Shams
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Atsuko Matsunaga
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Stacy J Caillier
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Ravi Dandekar
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Maneesh K Misra
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.,Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jill A Hollenbach
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
7
|
Sinopoli VM, Erdman L, Burton CL, Easter P, Rajendram R, Baldwin G, Peterman K, Coste J, Shaheen SM, Hanna GL, Rosenberg DR, Arnold PD. Serotonin system gene variants and regional brain volume differences in pediatric OCD. Brain Imaging Behav 2020; 14:1612-1625. [PMID: 31187473 PMCID: PMC10521965 DOI: 10.1007/s11682-019-00092-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Obsessive-compulsive disorder (OCD) is phenotypically heterogeneous and genetically complex. This study aimed to reduce heterogeneity using structural brain imaging to study putative intermediate phenotypes for OCD. We hypothesized that select serotonin gene variants would differ in their relationship with brain volume in specific regions of the cortico-striato-thalamo-cortical (CSTC) circuits between OCD patients and controls. In a total of 200 pediatric subjects, we genotyped candidate serotonin genes (SLC6A4, HTR2A, HTR1B, and HTR2C) and conducted structural magnetic resonance imaging (sMRI) to measure regional brain volumes within CSTC circuits. In males and females separately, we first tested the association between serotonin gene variants and OCD and the effect of serotonin gene variants on brain volume irrespective of diagnosis. We then carried out a series of analyses to assess the effect of genotype-diagnosis interaction on brain volume. In females, but not in males, we identified a statistically significant genotype-diagnosis interaction for two single nucleotide polymorphisms (SNPs) in HTR2C, rs12860460 (interaction term estimate of 5.45 cc and interaction P value of 9.70e-8) and rs12854485 (interaction term estimate of 4.28 cc and interaction P value of 2.07e-6). The tested allele in each SNP was associated with decreased anterior cingulate cortex (ACC) volume in controls and with increased ACC volume in OCD patients. Our findings suggest that, in females, sequence variation in HTR2C influences ACC volume in pediatric OCD. The variants may contribute to differences in ACC volume and to OCD in a sex-specific manner when acting together with other genetic, biological, and/or environmental factors.
Collapse
Affiliation(s)
- Vanessa M Sinopoli
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauren Erdman
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Christie L Burton
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - Phillip Easter
- Department of Psychiatry, Wayne State University School of Medicine, Detroit, MI, USA
| | | | - Gregory Baldwin
- Department of Psychiatry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Kelli Peterman
- Department of Psychiatry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Julie Coste
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - S-M Shaheen
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, University of Calgary, 4th floor, Teaching, Research and Wellness (TRW) Building, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, ON, Canada
| | - Gregory L Hanna
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - David R Rosenberg
- Department of Psychiatry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Paul D Arnold
- Program in Genetics & Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
- Mathison Centre for Mental Health Research & Education, Hotchkiss Brain Institute, University of Calgary, 4th floor, Teaching, Research and Wellness (TRW) Building, 3280 Hospital Dr NW, Calgary, AB, T2N 4Z6, ON, Canada.
- Departments of Psychiatry and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, ON, Canada.
| |
Collapse
|
8
|
Demirdjian L, Xu Y, Bahrami-Samani E, Pan Y, Stein S, Xie Z, Park E, Wu YN, Xing Y. Detecting Allele-Specific Alternative Splicing from Population-Scale RNA-Seq Data. Am J Hum Genet 2020; 107:461-472. [PMID: 32781045 PMCID: PMC7477012 DOI: 10.1016/j.ajhg.2020.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 07/10/2020] [Indexed: 12/20/2022] Open
Abstract
RNA sequencing (RNA-seq) is a powerful technology for studying human transcriptome variation. We introduce PAIRADISE (Paired Replicate Analysis of Allelic Differential Splicing Events), a method for detecting allele-specific alternative splicing (ASAS) from RNA-seq data. Unlike conventional approaches that detect ASAS events one sample at a time, PAIRADISE aggregates ASAS signals across multiple individuals in a population. By treating the two alleles of an individual as paired, and multiple individuals sharing a heterozygous SNP as replicates, we formulate ASAS detection using PAIRADISE as a statistical problem for identifying differential alternative splicing from RNA-seq data with paired replicates. PAIRADISE outperforms alternative statistical models in simulation studies. Applying PAIRADISE to replicate RNA-seq data of a single individual and to population-scale RNA-seq data across many individuals, we detect ASAS events associated with genome-wide association study (GWAS) signals of complex traits or diseases. Additionally, PAIRADISE ASAS analysis detects the effects of rare variants on alternative splicing. PAIRADISE provides a useful computational tool for elucidating the genetic variation and phenotypic association of alternative splicing in populations.
Collapse
|
9
|
Dionnet E, Defour A, Da Silva N, Salvi A, Lévy N, Krahn M, Bartoli M, Puppo F, Gorokhova S. Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay. Hum Mutat 2020; 41:1797-1810. [PMID: 32668095 DOI: 10.1002/humu.24083] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 07/01/2020] [Accepted: 07/09/2020] [Indexed: 01/10/2023]
Abstract
Improving the accuracy of variant interpretation during diagnostic sequencing is a major goal for genomic medicine. To explore an often-overlooked splicing effect of missense variants, we developed the functional assay ("minigene") for the majority of exons of CAPN3, the gene responsible for limb girdle muscular dystrophy. By systematically screening 21 missense variants distributed along the gene, we found that eight clinically relevant missense variants located at a certain distance from the exon-intron borders (deep exonic missense variants) disrupted normal splicing of CAPN3 exons. Several recent machine learning-based computational tools failed to predict splicing impact for the majority of these deep exonic missense variants, highlighting the importance of including variants of this type in the training sets during the future algorithm development. Overall, 24 variants in CAPN3 gene were explored, leading to the change in the American College of Medical Genetics and Genomics classification of seven of them when results of the "minigene" functional assay were considered. Our findings reveal previously unknown splicing impact of several clinically important variants in CAPN3 and draw attention to the existence of deep exonic variants with a disruptive effect on gene splicing that could be overlooked by the current approaches in clinical genetics.
Collapse
Affiliation(s)
- Eugénie Dionnet
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Aurélia Defour
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nathalie Da Silva
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Alexandra Salvi
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Nicolas Lévy
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France.,GIPTIS (Genetics Institute for Patients, Therapies Innovation and Science), Marseille, France
| | - Martin Krahn
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
| | - Marc Bartoli
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Francesca Puppo
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France
| | - Svetlana Gorokhova
- Faculté des Sciences Médicales et Paramédicales, Marseille Medical Genetics, Aix Marseille Université, INSERM, Marseille, France.,Service de génétique Médicale, Hôpital de la Timone, APHM, Marseille, France
| |
Collapse
|
10
|
Tunbridge EM, Narajos M, Harrison CH, Beresford C, Cipriani A, Harrison PJ. Which Dopamine Polymorphisms Are Functional? Systematic Review and Meta-analysis of COMT, DAT, DBH, DDC, DRD1-5, MAOA, MAOB, TH, VMAT1, and VMAT2. Biol Psychiatry 2019; 86:608-620. [PMID: 31303260 DOI: 10.1016/j.biopsych.2019.05.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/11/2019] [Accepted: 05/01/2019] [Indexed: 01/19/2023]
Abstract
BACKGROUND Many polymorphisms in dopamine genes are reported to affect cognitive, imaging, or clinical phenotypes. It is often inferred or assumed that such associations are causal, mediated by a direct effect of the polymorphism on the gene product itself. However, the supporting evidence is not always clear. METHODS We conducted systematic reviews and meta-analyses to assess the empirical evidence for functional polymorphisms in genes encoding dopaminergic enzymes (COMT, DBH, DDC, MAOA, MAOB, and TH), dopamine receptors (DRD1, DRD2, DRD3, DRD4, and DRD5), the dopamine transporter (DAT), and vesicular transporters (VMAT1 and VMAT2). We defined functionality as an effect of the polymorphism on the expression, abundance, activity, or affinity of the gene product. RESULTS We screened 22,728 articles and identified 255 eligible studies. We found robust and medium to large effects for polymorphisms in 4 genes. For catechol-O-methyltransferase (COMT), the Val158Met polymorphism (rs4680) markedly affected enzyme activity, protein abundance, and protein stability. Dopamine β-hydroxylase (DBH) activity was associated with rs1611115, rs2519152, and the DBH-STR polymorphism. Monoamine oxidase A (MAOA) activity was associated with a 5' VNTR polymorphism. Dopamine D2 receptor (DRD2) binding was influenced by the Taq1A (rs1800497) polymorphism, and rs1076560 affected DRD2 splicing. CONCLUSIONS Some widely studied dopaminergic polymorphisms clearly and substantially affect the abundance or activity of the encoded gene product. However, for other polymorphisms, evidence of such an association is negative, inconclusive, or lacking. These findings are relevant when selecting polymorphisms as "markers" of dopamine function, and for interpreting the biological plausibility of associations between these polymorphisms and aspects of brain function or dysfunction.
Collapse
Affiliation(s)
- Elizabeth M Tunbridge
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Marco Narajos
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom
| | | | - Charles Beresford
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrea Cipriani
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom
| | - Paul J Harrison
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, United Kingdom.
| |
Collapse
|
11
|
Full-Length Transcriptome Sequencing and the Discovery of New Transcripts in the Unfertilized Eggs of Zebrafish ( Danio rerio). G3-GENES GENOMES GENETICS 2019; 9:1831-1838. [PMID: 30872328 PMCID: PMC6553537 DOI: 10.1534/g3.119.200997] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Understanding early gene expression in zebrafish embryos is a prerequisite for developmental biology research. In this study, 1,629,447 polymerase reads were obtained from the unfertilized eggs of zebrafish via full-length transcriptome sequencing using the PacBio RS II platform first. Then, 102,920 unique isoforms were obtained by correction, clustering and comparison with the zebrafish genome. 12,782 genes in the genome were captured, accounting for 39.71% of the all annotated genes. Approximately 62.27% of the 12,782 genes have been alternatively spliced. GO and KEGG annotations revealed that the unfertilized eggs primarily stored genes that participate in RNA processing and nuclear protein complex composition. According to this PacBio data that aligned with the genome, 3,970 fusion genes, 819 ncRNAs, and 84 new transcripts were predicted. Illumina RNA-seq and RT-qPCR detection found that the expression of two new transcripts, PB.5289.1 and PB.10209.1, were significantly up-regulated at the 2-cell stage and down-regulated rapidly thereafter, suggesting their involvement in minor ZGA during early embryonic development. This study indicated that the unfertilized eggs of zebrafish may have retained genes directly related to cell division and development to initiate the subsequent development in a limited space and time. On the other hand, NTRs or new transcriptome regions in the genome were discovered, which provided new clues regarding ZGA of MZT during early embryonic development in fish.
Collapse
|
12
|
Li S, Hu Z, Zhao Y, Huang S, He X. Transcriptome-Wide Analysis Reveals the Landscape of Aberrant Alternative Splicing Events in Liver Cancer. Hepatology 2019; 69:359-375. [PMID: 30014619 DOI: 10.1002/hep.30158] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/30/2018] [Indexed: 01/02/2023]
Abstract
Alternative splicing (AS) is assumed to be a pivotal determinant for the generation of diverse transcriptional variants in cancer. However, the comprehensive dysregulation of AS and the prospective biological and clinical relevance in hepatocellular carcinoma (HCC) remain obscure. Here, we identified and depicted the AS landscape in HCC by performing reference-based assembly of sequencing reads from over 600 RNA sequencing (RNA-seq) libraries. We detected various differentially spliced ASEs across patients covering not only protein-coding genes, but also considerable numbers of noncoding genes. Strikingly, alternative transcription initiation was found to frequently occur in HCC. These differential ASEs were highly related to "cancer hallmarks" and involved in metabolism-related pathways in particular. In addition, 243 differential ASEs were identified as risk predictors for HCC patient survival. The isoform switch of metabolism-related gene UGP2 (UDP-glucose pyrophosphorylase 2) might play an essential role in HCC. We further constructed regulatory networks between RNA-binding protein (RBP) genes and the corresponding ASEs. Further analysis demonstrated that the regulated networks were enriched in a variety of metabolism-related pathways. Conclusion: Differential ASEs are prevalent in HCC, where alternative transcription initiation was found to frequently occur. We found that genes having differential ASEs were significantly enriched in metabolism-related pathways. The expression variations, binding relations, and even mutations of RBP genes largely influenced differential ASEs in HCC.
Collapse
Affiliation(s)
- Shengli Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhixiang Hu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yingjun Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Collaborative Innovation Center for Cancer Medicine, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
13
|
Wardak H, Tutakhel OAZ, Van Der Wijst J. Role of the alternative splice variant of NCC in blood pressure control. Channels (Austin) 2018; 12:346-355. [PMID: 30264650 PMCID: PMC6207291 DOI: 10.1080/19336950.2018.1528820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The renal thiazide-sensitive sodium-chloride cotransporter (NCC), located in the distal convoluted tubule (DCT) of the kidney, plays an important role in blood pressure regulation by fine-tuning sodium excretion. The human SLC12A3 gene, encoding NCC, gives rise to three isoforms, of which only the third isoform (NCC3) has been extensively investigated so far. However, recent studies unraveled the importance of the isoforms 1 and 2, collectively referred to as NCC splice variant (NCCSV), in several (patho)physiological conditions. In the human kidney, NCCSV localizes to the apical membrane of the DCT and could constitute a functional route for renal sodium-chloride reabsorption. Analysis of urinary extracellular vesicles (uEVs), a non-invasive method for measuring renal responses, demonstrated that NCCSV abundance changes in response to acute water loading and correlates with patients’ thiazide responsiveness. Furthermore, a novel phosphorylation site at serine 811 (S811), exclusively present in NCCSV, was shown to play an instrumental role in NCCSV as well as NCC3 function. This review aims to summarize these new insights of NCCSV function in humans that broadens the understanding on NCC regulation in blood pressure control.
Collapse
Affiliation(s)
- Hila Wardak
- a Department of Physiology , Radboud Institute for Molecular Life Sciences, Radboud university medical center , Nijmegen , The Netherland
| | - Omar A Z Tutakhel
- a Department of Physiology , Radboud Institute for Molecular Life Sciences, Radboud university medical center , Nijmegen , The Netherland.,b Department of Translational Metabolic Laboratory , Radboud university medical center , Nijmegen , The Netherlands
| | - Jenny Van Der Wijst
- a Department of Physiology , Radboud Institute for Molecular Life Sciences, Radboud university medical center , Nijmegen , The Netherland
| |
Collapse
|
14
|
SpliceVec: Distributed feature representations for splice junction prediction. Comput Biol Chem 2018; 74:434-441. [DOI: 10.1016/j.compbiolchem.2018.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 12/12/2022]
|
15
|
Tutakhel OAZ, Bianchi F, Smits DA, Bindels RJM, Hoenderop JGJ, van der Wijst J. Dominant functional role of the novel phosphorylation site S811 in the human renal NaCl cotransporter. FASEB J 2018; 32:4482-4493. [PMID: 29547703 DOI: 10.1096/fj.201701047r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The NaCl cotransporter (NCC) is essential for electrolyte homeostasis and control of blood pressure. The human SLC12A3 gene, which encodes NCC, gives rise to 3 isoforms, of which only the shortest isoform [NaCl cotransporter isoform 3 (NCC3)] has been studied extensively. All NCC isoforms share key phosphorylation sites at T55 and T60 that are essential mediators of NCC function. Recently, a novel phosphorylation site at S811 was identified in isoforms 1 and 2 [NaCl cotransporter splice variant (NCCSV)], which are only present in humans and higher primates. The aim of the current study, therefore, is to investigate the role of S811 phosphorylation in the regulation of NCC by a combination of biochemical and fluorescent microscopy analyses. We demonstrate that hypotonic low-chloride buffer increases S811 phosphorylation, whereas phosphorylation-deficient S811A mutant hinders phosphorylation at T55 and T60 in NCCSV and NCC3. NCCSV S811A impairs NCC3 activity in a dominant-negative fashion, although it does not affect plasma membrane abundance. This effect may be explained by the heterodimerization of NCCSV with NCC3. Taken together, our study highlights the dominant-negative effect of NCCSV on T55 and T60 phosphorylation and NCC activity. Here, we reveal a new function of NCCSV in humans that broadens the understanding on NCC regulation in blood pressure control.-Tutakhel, O. A. Z., Bianchi, F., Smits, D. A., Bindels, R. J. M., Hoenderop, J. G. J., van der Wijst, J. Dominant functional role of the novel phosphorylation site S811 in the human renal NaCl cotransporter.
Collapse
Affiliation(s)
- Omar A Z Tutakhel
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans Bianchi
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daniël A Smits
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - René J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
16
|
Park E, Pan Z, Zhang Z, Lin L, Xing Y. The Expanding Landscape of Alternative Splicing Variation in Human Populations. Am J Hum Genet 2018; 102:11-26. [PMID: 29304370 PMCID: PMC5777382 DOI: 10.1016/j.ajhg.2017.11.002] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/03/2017] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing is a tightly regulated biological process by which the number of gene products for any given gene can be greatly expanded. Genomic variants in splicing regulatory sequences can disrupt splicing and cause disease. Recent developments in sequencing technologies and computational biology have allowed researchers to investigate alternative splicing at an unprecedented scale and resolution. Population-scale transcriptome studies have revealed many naturally occurring genetic variants that modulate alternative splicing and consequently influence phenotypic variability and disease susceptibility in human populations. Innovations in experimental and computational tools such as massively parallel reporter assays and deep learning have enabled the rapid screening of genomic variants for their causal impacts on splicing. In this review, we describe technological advances that have greatly increased the speed and scale at which discoveries are made about the genetic variation of alternative splicing. We summarize major findings from population transcriptomic studies of alternative splicing and discuss the implications of these findings for human genetics and medicine.
Collapse
Affiliation(s)
- Eddie Park
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhicheng Pan
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zijun Zhang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lan Lin
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
17
|
Li Y, Sahni N, Pancsa R, McGrail DJ, Xu J, Hua X, Coulombe-Huntington J, Ryan M, Tychhon B, Sudhakar D, Hu L, Tyers M, Jiang X, Lin SY, Babu MM, Yi S. Revealing the Determinants of Widespread Alternative Splicing Perturbation in Cancer. Cell Rep 2017; 21:798-812. [PMID: 29045845 PMCID: PMC5689467 DOI: 10.1016/j.celrep.2017.09.071] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 08/10/2017] [Accepted: 09/21/2017] [Indexed: 12/25/2022] Open
Abstract
It is increasingly appreciated that alternative splicing plays a key role in generating functional specificity and diversity in cancer. However, the mechanisms by which cancer mutations perturb splicing remain unknown. Here, we developed a network-based strategy, DrAS-Net, to investigate more than 2.5 million variants across cancer types and link somatic mutations with cancer-specific splicing events. We identified more than 40,000 driver variant candidates and their 80,000 putative splicing targets deregulated in 33 cancer types and inferred their functional impact. Strikingly, tumors with splicing perturbations show reduced expression of immune system-related genes and increased expression of cell proliferation markers. Tumors harboring different mutations in the same gene often exhibit distinct splicing perturbations. Further stratification of 10,000 patients based on their mutation-splicing relationships identifies subtypes with distinct clinical features, including survival rates. Our work reveals how single-nucleotide changes can alter the repertoires of splicing isoforms, providing insights into oncogenic mechanisms for precision medicine.
Collapse
Affiliation(s)
- Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Rita Pancsa
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Xu Hua
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Michael Ryan
- In Silico Solutions, Falls Church, VA 22043, USA
| | - Boranai Tychhon
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dhanistha Sudhakar
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Tyers
- Institute for Research in Immunology and Cancer, Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Xiaoqian Jiang
- Division of Biomedical Informatics, University of California at San Diego, La Jolla, CA 92093, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - M Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Song Yi
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
18
|
Sá ACC, Sadee W, Johnson JA. Whole Transcriptome Profiling: An RNA-Seq Primer and Implications for Pharmacogenomics Research. Clin Transl Sci 2017; 11:153-161. [PMID: 28945944 PMCID: PMC5866981 DOI: 10.1111/cts.12511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/03/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Ana Caroline C Sá
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetic, College of Medicine, Ohio State University, Columbus, Ohio, USA
| | - Julie A Johnson
- Center for Pharmacogenomics & Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA.,Genetics & Genomic Graduate Program, Genetics Institute, University of Florida, Gainesville, Florida, USA.,Division of Cardiovascular Medicine, Colleges of Pharmacy and Medicine, University of Florida, Gainesville, Florida, USA
| |
Collapse
|
19
|
Liu J, Bhadra M, Sinnakannu JR, Yue WL, Tan CW, Rigo F, Ong ST, Roca X. Overcoming imatinib resistance conferred by the BIM deletion polymorphism in chronic myeloid leukemia with splice-switching antisense oligonucleotides. Oncotarget 2017; 8:77567-77585. [PMID: 29100409 PMCID: PMC5652800 DOI: 10.18632/oncotarget.20658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
Many tyrosine kinase-driven cancers, including chronic myeloid leukemia (CML), are characterized by high response rates to specific tyrosine kinase inhibitors (TKIs) like imatinib. In East Asians, primary imatinib resistance is caused by a deletion polymorphism in Intron 2 of the BIM gene, whose product is required for TKI-induced apoptosis. The deletion biases BIM splicing from exon 4 to exon 3, generating splice isoforms lacking the exon 4-encoded pro-apoptotic BH3 domain, which impairs the ability of TKIs to induce apoptosis. We sought to identify splice-switching antisense oligonucleotides (ASOs) that block exon 3 but enhance exon 4 splicing, and thereby resensitize BIM deletion-containing cancers to imatinib. First, we mapped multiple cis-acting splicing elements around BIM exon 3 by minigene mutations, and found an exonic splicing enhancer acting via SRSF1. Second, by a systematic ASO walk, we isolated ASOs that corrected the aberrant BIM splicing. Eight of 67 ASOs increased exon 4 levels in BIM deletion-containing cells, and restored imatinib-induced apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by BIM deletion polymorphism can be resensitized to imatinib via splice-switching BIM ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine adjuvant treatment for BIM-polymorphism-associated TKI-resistant CML and other cancers.
Collapse
Affiliation(s)
- Jun Liu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Malini Bhadra
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Wan Lin Yue
- School of Biological Sciences, Nanyang Technological University, Singapore.,CN Yang Scholars Programme, Nanyang Technological University, Singapore
| | - Cheryl Weiqi Tan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California, USA
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore.,Department of Haematology, Singapore General Hospital, Singapore.,Department of Medical Oncology, National Cancer Centre Singapore, Singapore.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore
| |
Collapse
|
20
|
Transcriptome profile of the human placenta. Funct Integr Genomics 2017; 17:551-563. [PMID: 28251419 PMCID: PMC5561170 DOI: 10.1007/s10142-017-0555-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/09/2017] [Accepted: 02/16/2017] [Indexed: 01/09/2023]
Abstract
The human placenta is a particular organ that inseparably binds the mother and the fetus. The proper development and survival of the conceptus relies on the essential interplay between maternal and fetal factors involved in cooperation within the placenta. In our study, high-throughput sequencing (RNA-seq) was applied to analyze the global transcriptome of the human placenta during uncomplicated pregnancies. The RNA-seq was utilized to identify the global pattern of the gene expression in placentas (N = 4) from women in single and twin pregnancies. During analyses, we obtained 228,044 transcripts. More than 91% of them were multi-exon, and among them 134 were potentially unknown protein coding genes. Expression levels (FPKM) were estimated for 38,948 transcriptional active regions, and more than 3000 of genes were expressed with FPKM >20 in each sample. Additionally, all unannotated transcripts with estimated FPKM values were localized on the human genome. Highly covered splice junctions unannotated in the human genome (6497) were identified, and among them 30 were novel. To gain a better understanding of the biological implications, the assembled transcripts were annotated with gene ontology (GO) terms. Single nucleotide variants were predicted for the transcripts assigned to each analyzed GO category. Our results may be useful for establishing a general pattern of the gene expression in the human placenta. Characterizing placental transcriptome, which is crucial for a pregnancy’s outcome, can serve as a basis for identifying the mechanisms underlying physiological pregnancy, as well as may be useful for an early detection of the genomic defects.
Collapse
|
21
|
Stein S, Bahrami-Samani E, Xing Y. Using RNA-Seq to Discover Genetic Polymorphisms That Produce Hidden Splice Variants. Methods Mol Biol 2017; 1648:129-142. [PMID: 28766294 DOI: 10.1007/978-1-4939-7204-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
RNA-seq is a powerful and popular technology for studying posttranscriptional regulation of gene expression, such as alternative splicing. The first step in analyzing RNA-seq data is to map the sequenced reads back to the genome. However, commonly used RNA-seq aligners use the consensus splice site dinucleotide motifs to map reads across splice junctions. This can be deceiving due to genomic variants that create novel splice site dinucleotides, leaving the personal splice junction reads un-mapped to the reference genome. We developed and evaluated a method called RNA Personal Genome Alignment Analyzer (rPGA) to identify "hidden" splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
Collapse
Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 650 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
| |
Collapse
|
22
|
Ferreira PG, Oti M, Barann M, Wieland T, Ezquina S, Friedländer MR, Rivas MA, Esteve-Codina A, Rosenstiel P, Strom TM, Lappalainen T, Guigó R, Sammeth M. Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing. Sci Rep 2016; 6:32406. [PMID: 27617755 PMCID: PMC5019111 DOI: 10.1038/srep32406] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/03/2016] [Indexed: 12/23/2022] Open
Abstract
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA- and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.
Collapse
Affiliation(s)
- Pedro G. Ferreira
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Instituto de Investigação e Inovação em Saúde, (i3S) Universidade do Porto, 4200-625 Porto, Portugal
- Institute of Molecular Pathology and Immunology (IPATIMUP), University of Porto, 4200-625 Porto, Portugal
| | - Martin Oti
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Suzana Ezquina
- Center for Human Genome and Stem-cell research (HUG-CELL), University of São Paulo (USP), 05508090 São Paulo, Brazil
| | - Marc R. Friedländer
- Science for Life Laboratory, Stockholm University, Box 1031, 17121 Solna, Sweden
| | - Manuel A. Rivas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Anna Esteve-Codina
- Centre Nacional d’Anàlisi Genòmica, 08028 Barcelona, Catalonia, Spain
- Center for Research in Agricultural Genomics (CRAG), Autonome University of Barcelona, 08193 Bellaterra, Catalonia, Spain
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christians-Albrechts-Universität zu Kiel, 24105 Kiel, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Center Munich, 85764 Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany
| | - Tuuli Lappalainen
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, 1211 Geneva, Switzerland
- Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Roderic Guigó
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Pompeu Fabra University (UPF), 08003 Barcelona, Catalonia, Spain
| | - Michael Sammeth
- Bioinformatics and Genomics, Center for Genomic Regulation (CRG), 08003 Barcelona, Catalonia, Spain
- Institute of Biophysics Carlos Chagas Filho (IBCCF), Federal University of Rio de Janeiro (UFRJ), 21941-902 Rio de Janeiro, Brazil
- National Center of Scientific Computing (LNCC), 2233-6000 Petrópolis, Rio de Janeiro, Brazil
| |
Collapse
|
23
|
Katrib A, Hsu W, Bui A, Xing Y. "RADIOTRANSCRIPTOMICS": A synergy of imaging and transcriptomics in clinical assessment. QUANTITATIVE BIOLOGY 2016; 4:1-12. [PMID: 28529815 DOI: 10.1007/s40484-016-0061-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in quantitative imaging and "omics" technology have generated a wealth of mineable biological "big data". With the push towards a P4 "predictive, preventive, personalized, and participatory" approach to medicine, researchers began integrating complementary tools to further tune existing diagnostic and therapeutic models. The field of radiogenomics has long pioneered such multidisciplinary investigations in neuroscience and oncology, correlating genotypic and phenotypic signatures to study structural and functional changes in relation to altered molecular behavior. Given the innate dynamic nature of complex disorders and the role of environmental and epigenetic factors in pathogenesis, the transcriptome can further elucidate serial modifications undetected at the genome level. We therefore propose "radiotranscriptomics" as a new member of the P4 medicine initiative, combining transcriptome information, including gene expression and isoform variation, and quantitative image annotations.
Collapse
Affiliation(s)
- Amal Katrib
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William Hsu
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alex Bui
- Department of Radiological Sciences, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
24
|
Findlay SD, Postovit LM. Brief Report: Common Genetic Variation in Chromosome 10 q22.1 Shows a Strong Sex Bias in Human Embryonic Stem Cell Lines and Directly Controls the Novel Alternative Splicing of Human NODAL which is Associated with XIST Expression in Female Cell Lines. Stem Cells 2015; 34:791-6. [DOI: 10.1002/stem.2258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Scott D. Findlay
- Department of Oncology, University of Alberta; Edmonton Alberta Canada
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, University of Western Ontario; London Ontario Canada
| | | |
Collapse
|
25
|
Stein S, Lu ZX, Bahrami-Samani E, Park JW, Xing Y. Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. Nucleic Acids Res 2015; 43:10612-22. [PMID: 26578562 PMCID: PMC4678817 DOI: 10.1093/nar/gkv1099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/09/2015] [Indexed: 01/27/2023] Open
Abstract
RNA-seq has become a popular technology for studying genetic variation of pre-mRNA alternative splicing. Commonly used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across splice junctions. Consequently, genomic variants that create novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to the reference genome. We developed and evaluated an approach to identify ‘hidden’ splicing variations in personal transcriptomes, by mapping personal RNA-seq data to personal genomes. Computational analysis and experimental validation indicate that this approach identifies personal specific splice junctions at a low false positive rate. Applying this approach to an RNA-seq data set of 75 individuals, we identified 506 personal specific splice junctions, among which 437 were novel splice junctions not documented in current human transcript annotations. 94 splice junctions had splice site SNPs associated with GWAS signals of human traits and diseases. These involve genes whose splicing variations have been implicated in diseases (such as OAS1), as well as novel associations between alternative splicing and diseases (such as ICA1). Collectively, our work demonstrates that the personal genome approach to RNA-seq read alignment enables the discovery of a large but previously unknown catalog of splicing variations in human populations.
Collapse
Affiliation(s)
- Shayna Stein
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhi-Xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
26
|
Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease. PLoS One 2015; 10:e0140885. [PMID: 26480348 PMCID: PMC4610675 DOI: 10.1371/journal.pone.0140885] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/30/2015] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies aim to correlate genotype with phenotype. Many common diseases including Type II diabetes, Alzheimer’s, Parkinson’s and Chronic Obstructive Pulmonary Disease (COPD) are complex genetic traits with hundreds of different loci that are associated with varied disease risk. Identifying common features in the genes associated with each disease remains a challenge. Furthermore, the role of post-transcriptional regulation, and in particular alternative splicing, is still poorly understood in most multigenic diseases. We therefore compiled comprehensive lists of genes associated with Type II diabetes, Alzheimer’s, Parkinson’s and COPD in an attempt to identify common features of their corresponding mRNA transcripts within each gene set. The SERPINA1 gene is a well-recognized genetic risk factor of COPD and it produces 11 transcript variants, which is exceptional for a human gene. This led us to hypothesize that other genes associated with COPD, and complex disorders in general, are highly transcriptionally diverse. We found that COPD-associated genes have a statistically significant enrichment in transcript complexity stemming from a disproportionately high level of alternative splicing, however, Type II Diabetes, Alzheimer’s and Parkinson’s disease genes were not significantly enriched. We also identified a subset of transcriptionally complex COPD-associated genes (~40%) that are differentially expressed between mild, moderate and severe COPD. Although the genes associated with other lung diseases are not extensively documented, we found preliminary data that idiopathic pulmonary disease genes, but not cystic fibrosis modulators, are also more transcriptionally complex. Interestingly, complex COPD transcripts are more often the product of alternative acceptor site usage. To verify the biological importance of these alternative transcripts, we used RNA-sequencing analyses to determine that COPD-associated genes are frequently expressed in lung and liver tissues and are regulated in a tissue-specific manner. Additionally, many complex COPD-associated genes are spliced differently between COPD and non-COPD patients. Our analysis therefore suggests that post-transcriptional regulation, particularly alternative splicing, is an important feature specific to COPD disease etiology that warrants further investigation.
Collapse
|
27
|
Zhou R, Chun RF, Lisse TS, Garcia AJ, Xu J, Adams JS, Hewison M. Vitamin D and alternative splicing of RNA. J Steroid Biochem Mol Biol 2015; 148:310-7. [PMID: 25447737 PMCID: PMC4361308 DOI: 10.1016/j.jsbmb.2014.09.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/23/2014] [Accepted: 09/26/2014] [Indexed: 02/07/2023]
Abstract
The active form of vitamin D (1α,25-dihydroxyvitamin D, 1,25(OH)2D) exerts its genomic effects via binding to a nuclear high-affinity vitamin D receptor (VDR). Recent deep sequencing analysis of VDR binding locations across the complete genome has significantly expanded our understanding of the actions of vitamin D and VDR on gene transcription. However, these studies have also promoted appreciation of the extra-transcriptional impact of vitamin D on gene expression. It is now clear that vitamin D interacts with the epigenome via effects on DNA methylation, histone acetylation, and microRNA generation to maintain normal biological functions. There is also increasing evidence that vitamin D can influence pre-mRNA constitutive splicing and alternative splicing, although the mechanism for this remains unclear. Pre-mRNA splicing has long been thought to be a post-transcription RNA processing event, but current data indicate that this occurs co-transcriptionally. Several steroid hormones have been recognized to coordinately control gene transcription and pre-mRNA splicing through the recruitment of nuclear receptor co-regulators that can both control gene transcription and splicing. The current review will discuss this concept with specific reference to vitamin D, and the potential role of heterogeneous nuclear ribonucleoprotein C (hnRNPC), a nuclear factor with an established function in RNA splicing. hnRNPC, has been shown to be involved in the VDR transcriptional complex as a vitamin D-response element-binding protein (VDRE-BP), and may act as a coupling factor linking VDR-directed gene transcription with RNA splicing. In this way hnRNPC may provide an additional mechanism for the fine-tuning of vitamin D-regulated target gene expression. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.
Collapse
Affiliation(s)
- Rui Zhou
- UCLA Orthopaedic Hospital, Department of Orthopaedic Surgery, Orthopaedic Hospital, University of California at Los Angeles, Los Angeles, CA 90095, USA; Department of Orthopaedics, the Orthopedic Surgery Center of Chinese PLA, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - Rene F Chun
- UCLA Orthopaedic Hospital, Department of Orthopaedic Surgery, Orthopaedic Hospital, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas S Lisse
- Mount Desert Island Biological Laboratory, 159 Old Bar Harbor Road, Salisbury Cove, ME 04672, USA
| | - Alejandro J Garcia
- UCLA Orthopaedic Hospital, Department of Orthopaedic Surgery, Orthopaedic Hospital, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Jianzhong Xu
- Department of Orthopaedics, the Orthopedic Surgery Center of Chinese PLA, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
| | - John S Adams
- UCLA Orthopaedic Hospital, Department of Orthopaedic Surgery, Orthopaedic Hospital, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Martin Hewison
- UCLA Orthopaedic Hospital, Department of Orthopaedic Surgery, Orthopaedic Hospital, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| |
Collapse
|
28
|
Kurmangaliyev YZ, Favorov AV, Osman NM, Lehmann KV, Campo D, Salomon MP, Tower J, Gelfand MS, Nuzhdin SV. Natural variation of gene models in Drosophila melanogaster. BMC Genomics 2015; 16:198. [PMID: 25888292 PMCID: PMC4373058 DOI: 10.1186/s12864-015-1415-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/28/2015] [Indexed: 09/03/2023] Open
Abstract
Background Variation within splicing regulatory sequences often leads to differences in gene models among individuals within a species. Two alleles of the same gene may express transcripts with different exon/intron structures and consequently produce functionally different proteins. Matching genomic and transcriptomic data allows us to identify putative regulatory variants associated with changes in splicing patterns. Results Here we analyzed natural variation of splicing patterns in the transcriptomes of 81 natural strains of Drosophila melanogaster with known genotypes. We identified dozens of genotype-specific splicing patterns associated with putative cis-splicing quantitative trait loci (sQTL). The majority of changes can be explained by mutations in splice sites. Allelic-imbalance in splicing patterns confirmed that the majority are regulated mainly by cis-genetic effects. Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated. The observed alterations are typically outside protein-coding regions or affect only very short protein segments. Conclusions Overall, the sets of gene models appear to be flexible within D. melanogaster populations. The observed variation in splicing patterns are predicted to have limited effects on the encoded protein sequences. To our knowledge, this is the first sQTL mapping study in Drosophila. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1415-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yerbol Z Kurmangaliyev
- University of Southern California, Los Angeles, CA, USA. .,Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia.
| | - Alexander V Favorov
- Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Vavilov Institute of General Genetics, Moscow, Russia. .,Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia.
| | - Noha M Osman
- University of Southern California, Los Angeles, CA, USA. .,National Research Center, Dokki, Giza, Egypt.
| | - Kjong-Van Lehmann
- Memorial Sloan Kettering Cancer Center, Zuckerman Research Center, New York, NY, USA.
| | - Daniel Campo
- University of Southern California, Los Angeles, CA, USA.
| | | | - John Tower
- University of Southern California, Los Angeles, CA, USA.
| | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), Moscow, Russia. .,Lomonosov Moscow State University, Moscow, Russia.
| | - Sergey V Nuzhdin
- University of Southern California, Los Angeles, CA, USA. .,Saint Petersburg Polytechnical University, St Petersburg, Russia.
| |
Collapse
|
29
|
Karambataki M, Malousi A, Kouidou S. Risk-associated coding synonymous SNPs in type 2 diabetes and neurodegenerative diseases: genetic silence and the underrated association with splicing regulation and epigenetics. Mutat Res 2014; 770:85-93. [PMID: 25771874 DOI: 10.1016/j.mrfmmm.2014.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 09/15/2014] [Accepted: 09/16/2014] [Indexed: 06/04/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are tentatively critical with regard to disease predisposition, but coding synonymous SNPs (sSNPs) are generally considered "neutral". Nevertheless, sSNPs in serine/arginine-rich (SR) and splice-site (SS) exonic splicing enhancers (ESEs) or in exonic CpG methylation targets, could be decisive for splicing, particularly in aging-related conditions, where mis-splicing is frequently observed. We presently identified 33 genes T2D-related and 28 related to neurodegenerative diseases, by investigating the impact of the corresponding coding sSNPs on splicing and using gene ontology data and computational tools. Potentially critical (prominent) sSNPs comply with the following criteria: changing the splicing potential of prominent SR-ESEs or of significant SS-ESEs by >1.5 units (Δscore), or formation/deletion of ESEs with maximum splicing score. We also noted the formation/disruption of CpGs (tentative methylation sites of epigenetic sSNPs). All disease association studies involving sSNPs are also reported. Only 21/670 coding SNPs, mostly epigenetic, reported in 33 T2D-related genes, were found to be prominent coding synonymous. No prominent sSNPs have been recorded in three key T2D-related genes (GCGR, PPARGC1A, IGF1). Similarly, 20/366 coding synonymous were identified in ND related genes, mostly epigenetic. Meta-analysis showed that 17 of the above prominent sSNPs were previously investigated in association with various pathological conditions. Three out of four sSNPs (all epigenetic) were associated with T2D and one with NDs (branch site sSNP). Five were associated with other or related pathological conditions. None of the four sSNPs introducing new ESEs was found to be disease-associated. sSNPs introducing smaller Δscore changes (<1.5) in key proteins (INSR, IRS1, DISC1) were also correlated to pathological conditions. This data reveals that genetic variation in splicing-regulatory and particularly CpG sites might be related to disease predisposition and that in-silico analysis is useful for identifying sSNPs, which might be falsely identified as silent or synonymous.
Collapse
Affiliation(s)
- M Karambataki
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Malousi
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - S Kouidou
- Lab of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| |
Collapse
|
30
|
Lee JD, Hsiao KM, Wang TC, Lee TH, Kuo YW, Huang YC, Hsu HL, Lin YH, Wu CY, Huang YC, Lee M, Yang HT, Hsu CY, Pan YT. Mutual Effect of rs688 and rs5925 in Regulating Low-Density Lipoprotein Receptor Splicing. DNA Cell Biol 2014; 33:869-75. [DOI: 10.1089/dna.2014.2577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jiann-Der Lee
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
- Department of Life Science, National Chung Cheng University, Chiayi, Taiwan
| | - Kuang-Ming Hsiao
- Department of Life Science, National Chung Cheng University, Chiayi, Taiwan
| | - Ting-Chung Wang
- Department of Neurosurgery, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Tsong-Hai Lee
- Department of Neurology, Chang Gung Memorial Hospital at Taoyuan, and Chang Gung University, Taoyuan, Taiwan
| | - Ya-Wen Kuo
- Department of Nursing, Asia University, Taichung Taiwan
| | - Yen-Chu Huang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
| | - Huan-Lin Hsu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Ya-Hui Lin
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Chih-Ying Wu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Ying-Chih Huang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Meng Lee
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, and School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Chiayi, Taiwan
| | - Hsin-Ta Yang
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Chia-Yu Hsu
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| | - Yi-Ting Pan
- Department of Neurology, Chang Gung Memorial Hospital at Chiayi, Chiayi, Taiwan
| |
Collapse
|
31
|
Juan WC, Roca X, Ong ST. Identification of cis-acting elements and splicing factors involved in the regulation of BIM Pre-mRNA splicing. PLoS One 2014; 9:e95210. [PMID: 24743263 PMCID: PMC3990581 DOI: 10.1371/journal.pone.0095210] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/25/2014] [Indexed: 11/25/2022] Open
Abstract
Aberrant changes in the expression of the pro-apoptotic protein, BCL-2-like 11 (BIM), can result in either impaired or excessive apoptosis, which can contribute to tumorigenesis and degenerative disorders, respectively. Altering BIM pre-mRNA splicing is an attractive approach to modulate apoptosis because BIM activity is partly determined by the alternative splicing of exons 3 or 4, whereby exon 3-containing transcripts are not apoptotic. Here we identified several cis-acting elements and splicing factors involved in BIM alternative splicing, as a step to better understand the regulation of BIM expression. We analyzed a recently discovered 2,903-bp deletion polymorphism within BIM intron 2 that biased splicing towards exon 3, and which also impaired BIM-dependent apoptosis. We found that this region harbors multiple redundant cis-acting elements that repress exon 3 inclusion. Furthermore, we have isolated a 23-nt intronic splicing silencer at the 3′ end of the deletion that is important for excluding exon 3. We also show that PTBP1 and hnRNP C repress exon 3 inclusion, and that downregulation of PTBP1 inhibited BIM-mediated apoptosis. Collectively, these findings start building our understanding of the cis-acting elements and splicing factors that regulate BIM alternative splicing, and also suggest potential approaches to alter BIM splicing for therapeutic purposes.
Collapse
Affiliation(s)
- Wen Chun Juan
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail: (XR); (STO)
| | - S. Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Graduate Medical School, Singapore, Singapore
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
- Department of Medical Oncology, National Cancer Centre, Singapore, Singapore
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Chapel Hill, North Carolina, United States of America
- * E-mail: (XR); (STO)
| |
Collapse
|
32
|
Zhao K, Lu ZX, Park JW, Zhou Q, Xing Y. GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome Biol 2013; 14:R74. [PMID: 23876401 PMCID: PMC4054007 DOI: 10.1186/gb-2013-14-7-r74] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 06/21/2013] [Accepted: 07/22/2013] [Indexed: 11/10/2022] Open
Abstract
To characterize the genetic variation of alternative splicing, we develop GLiMMPS, a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. GLiMMPS takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data. Analyses of simulated and real RNA-seq datasets demonstrate that GLiMMPS outperforms competing statistical models. Quantitative RT-PCR tests of 26 randomly selected GLiMMPS sQTLs yielded a validation rate of 100%. As population-scale RNA-seq studies become increasingly affordable and popular, GLiMMPS provides a useful tool for elucidating the genetic variation of alternative splicing in humans and model organisms.
Collapse
Affiliation(s)
- Keyan Zhao
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Zhi-xiang Lu
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| | - Qing Zhou
- Department of Statistics, University of California, Los Angeles, 8125 Math
Sciences Building, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of
California, Los Angeles, CHS 33-228, 650 Charles E. Young Drive South, Los
Angeles, CA 90095, USA
- Department of Internal Medicine, University of Iowa, 200 Hawkins Drive, Iowa City,
IA 52242, USA
| |
Collapse
|
33
|
Buljan M, Chalancon G, Dunker AK, Bateman A, Balaji S, Fuxreiter M, Babu MM. Alternative splicing of intrinsically disordered regions and rewiring of protein interactions. Curr Opin Struct Biol 2013; 23:443-50. [DOI: 10.1016/j.sbi.2013.03.006] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Revised: 03/19/2013] [Accepted: 03/25/2013] [Indexed: 12/31/2022]
|
34
|
Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS. Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet 2013; 22:3449-59. [PMID: 23640990 DOI: 10.1093/hmg/ddt200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Proper splicing is often crucial for gene functioning and its disruption may be strongly deleterious. Nevertheless, even the essential for splicing canonical dinucleotides of the splice sites are often polymorphic. Here, we use data from The 1000 Genomes Project to study single-nucleotide polymorphisms (SNPs) in the canonical dinucleotides. Splice sites carrying SNPs are enriched in weakly expressed genes and in rarely used alternative splice sites. Genes with disrupted splice sites tend to have low selective constraint, and the splice sites disrupted by SNPs are less likely to be conserved in mouse. Furthermore, SNPs are enriched in splice sites whose effects on gene function are minor: splice sites located outside of protein-coding regions, in shorter exons, closer to the 3'-ends of proteins, and outside of functional protein domains. Most of these effects are more pronounced for high-frequency SNPs. Despite these trends, many of the polymorphic sites may still substantially affect the function of the corresponding genes. A number of the observed splice site-disrupting SNPs, including several high-frequency ones, were found among mutations described in OMIM.
Collapse
Affiliation(s)
- Yerbol Z Kurmangaliyev
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow 127994, Russia
| | | | | | | | | |
Collapse
|
35
|
Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
Collapse
Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
| | | | | |
Collapse
|
36
|
The Identification of a Novel Transcript Variant of Chicken Lmbr1 and the Sequence Variation Analysis. J Poult Sci 2013. [DOI: 10.2141/jpsa.0120133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|