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Panaro MA, Calvello R, Miniero DV, Mitolo V, Cianciulli A. Imaging Intron Evolution. Methods Protoc 2022; 5:mps5040053. [PMID: 35893579 PMCID: PMC9326662 DOI: 10.3390/mps5040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Intron evolution may be readily imaged through the combined use of the “dot plot” function of the NCBI BLAST, aligning two sequences at a time, and the Vertebrate “Multiz” alignment and conservation tool of the UCSC Genome Browser. With the NCBI BLAST, an ideal alignment of two highly conserved sequences generates a diagonal straight line in the plot from the lower left corner to the upper right corner. Gaps in this line correspond to non-conserved sections. In addition, the dot plot of the alignment of a sequence with the same sequence after the removal of the Transposable Elements (TEs) can be observed along the diagonal gaps that correspond to the sites of TE insertion. The UCSC Genome Browser can graph, along the entire sequence of a single gene, the level of overall conservation in vertebrates. This level can be compared with the conservation level of the gene in one or more selected vertebrate species. As an example, we show the graphic analysis of the intron conservation in two genes: the mitochondrial solute carrier 21 (SLC25A21) and the growth hormone receptor (GHR), whose coding sequences are conserved through vertebrates, while their introns show dramatic changes in nucleotide composition and even length. In the SLC25A21, a few short but significant nucleotide sequences are conserved in zebrafish, Xenopus and humans, and the rate of conservation steadily increases from chicken/human to mouse/human alignments. In the GHR, a less conserved gene, the earlier indication of intron conservation is a small signal in chicken/human alignment. The UCSC tool may simultaneously display the conservation level of a gene in different vertebrates, with reference to the level of overall conservation in Vertebrates. It is shown that, at least in SLC25A21, the sites of higher conservation are not always coincident in chicken and zebrafish nor are the sites of higher vertebrate conservation.
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2
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Han F, Yang B, Zhou M, Huang Q, Mai M, Huang Z, Lai M, Xu E, Zhang H. OUP accepted manuscript. J Mol Cell Biol 2022; 14:6537407. [PMID: 35218185 PMCID: PMC9188103 DOI: 10.1093/jmcb/mjac009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 11/12/2022] Open
Abstract
Alternative splicing (AS) and transcription elongation are vital biological processes, and their dysregulation causes multiple diseases, including tumors. However, the coregulatory mechanism of AS and transcription elongation in tumors remains unclear. This study demonstrates a novel AS pattern of tight junction protein 1 (ZO1) regulated by the RNA polymerase II elongation rate in colorectal cancer (CRC). Glioma tumor suppressor candidate region gene 1 (GLTSCR1) decreases the transcription elongation rate of ZO1 to provide a time window for binding of the splicing factor HuR to the specific motif in intron 22 of ZO1 and spliceosome recognition of the weak 3′ and 5′ splice sites in exon 23 to promote exon 23 inclusion. Since exon 23 inclusion in ZO1 suppresses migration and invasion of CRC cells, our findings suggest a novel potential therapeutic target for CRC.
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Affiliation(s)
| | | | | | - Qiong Huang
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou 310058, China
- Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Minglang Mai
- Department of Pathology and Women's Hospital, Zhejiang University School of Medicine, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences (2019RU042), Hangzhou 310058, China
| | - Zhaohui Huang
- Cancer Epigenetics Program, Wuxi School of Medicine, Jiangnan University, Wuxi 214122, China
| | - Maode Lai
- Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China
| | - Enping Xu
- Correspondence to: Enping Xu, E-mail:
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3
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Aebischer-Gumy C, Moretti P, Ollier R, Ries Fecourt C, Rousseau F, Bertschinger M. SPLICELECT™: an adaptable cell surface display technology based on alternative splicing allowing the qualitative and quantitative prediction of secreted product at a single-cell level. MAbs 2021; 12:1709333. [PMID: 31955651 PMCID: PMC6973322 DOI: 10.1080/19420862.2019.1709333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We describe a mammalian expression construct (SPLICELECT™) that allows the redirection of a proportion of a secreted protein onto the cell surface using alternative splicing: whereas the majority of the RNA is spliced into a transcript encoding a secreted protein, a weak splice donor site yields a secondary transcript encoding, in addition, a C-terminal transmembrane domain. The different sequence elements can be modified in order to modulate the level of cell surface display and of secretion in an independent manner. In this work, we demonstrated that the cell surface display of stable cell lines is correlated with the level of the secreted protein of interest, but also with the level of heterodimerization in the case of a bispecific antibody. It was also shown that this construct may be useful for rapid screening of multiple antibody candidates in binding assays following transient transfection. Thus, the correlation of product quantity and quality of the secreted and of membrane-displayed product in combination with the flexibility of the construct with regards to cell surface display/secretion levels make SPLICELECT™ a valuable tool with many potential applications, not limited to industrial cell line development or antibody engineering.
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Affiliation(s)
- Christel Aebischer-Gumy
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Pierre Moretti
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Romain Ollier
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Christelle Ries Fecourt
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - François Rousseau
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Martin Bertschinger
- Cell Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
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4
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Rondelet A, Pozniakovsky A, Namboodiri D, Cardoso da Silva R, Singh D, Leuschner M, Poser I, Ssykor A, Berlitz J, Schmidt N, Röhder L, Vader G, Hyman AA, Bird AW. ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes. Life Sci Alliance 2020; 4:4/2/e202000836. [PMID: 33293335 PMCID: PMC7756954 DOI: 10.26508/lsa.202000836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 01/23/2023] Open
Abstract
A simple and efficient recombineering-based method for introducing point mutations into bacterial artificial chromosomes using an artificial intron cassette. Bacterial artificial chromosome (BAC)–based transgenes have emerged as a powerful tool for controlled and conditional interrogation of protein function in higher eukaryotes. Although homologous recombination-based recombineering methods have streamlined the efficient integration of protein tags onto BAC transgenes, generating precise point mutations has remained less efficient and time-consuming. Here, we present a simplified method for inserting point mutations into BAC transgenes requiring a single recombineering step followed by antibiotic selection. This technique, which we call exogenous/synthetic intronization (ESI) mutagenesis, relies on co-integration of a mutation of interest along with a selectable marker gene, the latter of which is harboured in an artificial intron adjacent to the mutation site. Cell lines generated from ESI-mutated BACs express the transgenes equivalently to the endogenous gene, and all cells efficiently splice out the synthetic intron. Thus, ESI mutagenesis provides a robust and effective single-step method with high precision and high efficiency for mutating BAC transgenes.
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Affiliation(s)
- Arnaud Rondelet
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Divya Singh
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marit Leuschner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrea Ssykor
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julian Berlitz
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Nadine Schmidt
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lea Röhder
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerben Vader
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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5
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Saha K, England W, Fernandez MM, Biswas T, Spitale RC, Ghosh G. Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing. Nucleic Acids Res 2020; 48:6294-6309. [PMID: 32402057 PMCID: PMC7293017 DOI: 10.1093/nar/gkaa358] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/31/2022] Open
Abstract
Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem-loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.
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Affiliation(s)
- Kaushik Saha
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA 92697, USA
| | - Mike Minh Fernandez
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, 147 Bison Modular, Building 515, Irvine, CA 92697, USA
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0375, USA
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6
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Tubeuf H, Charbonnier C, Soukarieh O, Blavier A, Lefebvre A, Dauchel H, Frebourg T, Gaildrat P, Martins A. Large-scale comparative evaluation of user-friendly tools for predicting variant-induced alterations of splicing regulatory elements. Hum Mutat 2020; 41:1811-1829. [PMID: 32741062 DOI: 10.1002/humu.24091] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 07/11/2020] [Accepted: 07/26/2020] [Indexed: 12/20/2022]
Abstract
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits remains a major challenge in human genetics. In theory, any intragenic variant can potentially affect RNA splicing by altering splicing regulatory elements (SREs). However, these alterations are often ignored mainly because pioneer SRE predictors have proved inefficient. Here, we report the first large-scale comparative evaluation of four user-friendly SRE-dedicated algorithms (QUEPASA, HEXplorer, SPANR, and HAL) tested both as standalone tools and in multiple combined ways based on two independent benchmark datasets adding up to >1,300 exonic variants studied at the messenger RNA level and mapping to 89 different disease-causing genes. These methods display good predictive power, based on decision thresholds derived from the receiver operating characteristics curve analyses, with QUEPASA and HAL having the best accuracies either as standalone or in combination. Still, overall there was a tight race between the four predictors, suggesting that all methods may be of use. Additionally, QUEPASA and HEXplorer may be beneficial as well for predicting variant-induced creation of pseudoexons deep within introns. Our study highlights the potential of SRE predictors as filtering tools for identifying disease-causing candidates among the plethora of variants detected by high-throughput DNA sequencing and provides guidance for their use in genomic medicine settings.
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Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Camille Charbonnier
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Arnaud Lefebvre
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Hélène Dauchel
- Computer Science, Information Processing and Systems Laboratory, UNIROUEN, Normandie University, Mont-Saint-Aignan, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
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7
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Haruna IL, Hadebe SA, Oladosu OJ, Mahmoud G, Zhou H, Hickford JGH. Identification of novel nucleotide sequence variations in an extended region of the bovine leptin gene ( LEP) across a variety of cattle breeds from New Zealand and Nigeria. Arch Anim Breed 2020; 63:241-248. [PMID: 32775609 PMCID: PMC7405650 DOI: 10.5194/aab-63-241-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/13/2023] Open
Abstract
Leptin is mainly secreted by white adipose tissue in animals. Leptin acts by stimulating or inhibiting the release of a neurotransmitter, which eventually results in a decrease in food/feed intake and an increase in energy expenditure. In this investigation, the polymerase chain reaction (PCR) coupled with single-strand conformation polymorphism (SSCP) analysis was used to reveal nucleotide sequence variations in bovine leptin gene (LEP) in 338 cattle of a variety of breeds farmed in New Zealand (NZ) and Nigeria. These included NZ Hereford, Angus, Shorthorn, and crossbred Holstein-Friesian × Jersey cattle and the Nigerian Sokoto Gudali, Red Bororo, White Fulani, and crossbred Holstein-Friesian × White Fulani cattle. Sequence analysis of three regions of bovine LEP that encompassed selected coding and non-coding regions, revealed a total of 12 nucleotide sequence variations (six in exons and six in introns). Of these, three are reported here for the first time, whereas nine have been previously described. Some of the variations identified were common in both the NZ and Nigerian cattle breeds, while others were peculiar to particular breeds from a specific region. The sharing of common variants across different breeds irrespective of geography may indicate an evolutionary relationship, just as the differences within a breed might be attributable to either selective pressure for specific traits or random genetic drift. The detection of both new and previously documented variations in bovine LEP suggests that the gene is highly variable.
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Affiliation(s)
- Ishaku L. Haruna
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
| | - Sibusiso A. Hadebe
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
| | - Oyekunle J. Oladosu
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
| | - Ghassan Mahmoud
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
| | - Huitong Zhou
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
| | - Jon G. H. Hickford
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647,
New Zealand
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8
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5' and 3' splicing signals evolution in vertebrates: Analysis in a conserved gene family. Comput Biol Chem 2020; 86:107251. [PMID: 32224443 DOI: 10.1016/j.compbiolchem.2020.107251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/08/2020] [Accepted: 03/13/2020] [Indexed: 01/09/2023]
Abstract
The mitochondrial solute carrier genes (SLC25) are highly conserved during vertebrate evolution. In most SLC25 genes of zebrafish, chicken, mouse, and human, the introns are located at exactly superimposable positions. In these topographically corresponding introns we studied the composition of the initial and terminal hexanucleotides (5'ss and 3'ss) which are instrumental in splicing signaling, focusing on the evolutionary conservation/mutation dynamics of these genetically related sequences. At each position, the per cent conservation of zebrafish individual nucleotides in chicken, mouse and human is proportional to their percent frequency in zebrafish; furthermore, nucleotide mutations are biased in favor of the more represented nucleotides, thus compensating for those highly represented zebrafish nucleotides which have not been conserved. As a result of these evolutionary dynamics, the general nucleotide composition at each position has remained relatively conserved throughout vertebrates. At 5'ss, following the canonical GT, A and G are largely prevailing at position +3, A at +4 and G at +5 (GT[A/G]AGx). At 3'ss, T and C are largely prevailing at positions -6, -5 and -3, preceding the canonical intron terminal AG ([C/T] [C/T]x[C/T]AG). However, the actual composition of the tetranucleotides at 5' and 3' often does not conform to the above scheme. At 5'ss the more canonical sequence is completely expressed in 63% of cases and partially (2 or 1 matches) in 37 % of cases. At 3'ss the more canonical sequence is completely expressed in 71 % of cases and partially (2 or 1 matches) in 29 % of cases. The nucleotide conservation loss (nucleotide mutation) is higher in the evolution from fish to the last common ancestor of birds and mammals (58 %), then diminishes in the successive evolution steps up to the mammalian common ancestor (10 %), and becomes still lower at the divergence of rodents and primates (5 %).
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9
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Haruna IL, Ekegbu UJ, Ullah F, Amirpour-Najafabadi H, Zhou H, Hickford JGH. Genetic variations and haplotypic diversity in the Myostatin gene of New Zealand cattle breeds. Gene 2020; 740:144400. [PMID: 31987910 DOI: 10.1016/j.gene.2020.144400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/17/2020] [Accepted: 01/23/2020] [Indexed: 01/02/2023]
Abstract
Myostatin (MSTN) is a circulating factor that is secreted by muscle cells, and that acts upon those cells to inhibit the proliferation of muscle fibres during pre-natal muscle growth. The Polymerase Chain Reaction (PCR) coupled with Single Strand Conformational Polymorphism (SSCP) analysis, was used to reveal variation in the bovine MSTN gene (MSTN) in 722 cattle from a variety of breeds farmed in New Zealand (NZ). These included Hereford, Angus, Charolais, Simmental, Red Poll, South Devon, Shorthorn, Murray Grey, cross-bred Holstein-Friesian × Jersey cattle, and other composite breeds of cattle. Sequence analysis of five regions of MSTN that encompassed coding and non-coding regions of the gene, revealed a total of twelve single-nucleotide substitutions (7 in intron 1 and 5 in a region spanning the intron 2 - exon 3 boundary), and a single nucleotide deletion. Of these 12 substitutions, five are reported here for the first time, whereas seven have been previously described. The deletion c.748-78del, was located in the intron 2 - exon 3 boundary region, and has been reported previously. No nucleotide variation was identified in exons 1, 2 and 3. A total of 18 extended haplotypes were resolved spanning two variable regions (intron 1 and the intron 2 - exon 3 boundary), some of which were common across the breeds, while others were peculiar to particular breeds. The genetic variations identified provide insight into the conserved and polymorphic nature of the coding and non-coding sequences of bovine MSTN respectively, and thus provides a baseline for further study into how variation in the gene might affect growth and carcass traits in NZ cattle.
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Affiliation(s)
- Ishaku L Haruna
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
| | - Ugonna J Ekegbu
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Farman Ullah
- Department of Biotechnology, University of Malakand, Dir lower 18800, Chakdara, Pakistan
| | | | - Huitong Zhou
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Jon G H Hickford
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand.
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10
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Izadpanah P, Khabbzi E, Erfanian S, Jafaripour S, Shojaie M. Case-control study on the association between the GATA2 gene and premature myocardial infarction in the Iranian population. Herz 2019; 46:71-75. [PMID: 31468074 DOI: 10.1007/s00059-019-04841-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/05/2019] [Accepted: 07/13/2019] [Indexed: 10/26/2022]
Abstract
In recent decades, due to the high prevalence of coronary artery disease (CAD) and myocardial infarction (MI), numerous studies have attempted to elucidate genetic contributing factors in these complex disorders. A very interesting gene in this regard is GATA-binding protein 2 (GATA2), an important regulator of various gene expressions in vascular endothelial cells. Accordingly, the association of different GATA2 polymorphisms with CAD and MI has already been evaluated. Rs2713604 is a genetic marker whose association with CAD has not been reproduced in previous studies. Considering the importance of replicating the initial association, the present case-control study aimed to examine the association of this intronic variant with premature MI in a sample of the Iranian population. In this study, 193 participants from Jahrom Hospital (Jahrom, Iran) were consecutively recruited during a 1.5-year period, and, following blood sampling, genomic DNA was extracted. We then proceeded to genotype rs2713604 using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and statistically analyzed the data. After adjustment for hyperlipidemia, hypertension, and type 2 diabetes mellitus, the results of the multivariate regression analysis showed no significant association between rs2713604 and premature MI. Interestingly, the risk allele (A-allele) of rs2713604 displayed a slightly higher frequency among controls compared to cases.
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Affiliation(s)
- Peyman Izadpanah
- Cardiology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Khabbzi
- School of Medicine, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Saiedeh Erfanian
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran. .,Department of Advanced Medical Sciences and Technologies, School of Medicine, Jahrom University of Medical Sciences, Motahhari Street, 74148-46199, Jahrom, Iran.
| | - Simin Jafaripour
- Department of Medical Genetics, School of Medicine, Mashhad University of Medical Sciences, Vakil abad Blv., 99191-91778, Mashhad, Iran.
| | - Mohammad Shojaie
- Research Center for Non-Communicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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12
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Chiara M, Primon I, Tarantini L, Agnelli L, Brancaleoni V, Granata F, Bollati V, Di Pierro E. Targeted resequencing of FECH locus reveals that a novel deep intronic pathogenic variant and eQTLs may cause erythropoietic protoporphyria (EPP) through a methylation-dependent mechanism. Genet Med 2019; 22:35-43. [DOI: 10.1038/s41436-019-0584-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 06/05/2019] [Indexed: 12/29/2022] Open
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13
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Morton M, AlTamimi N, Butt H, Reddy ASN, Mahfouz M. Serine/Arginine-rich protein family of splicing regulators: New approaches to study splice isoform functions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:127-134. [PMID: 31128682 DOI: 10.1016/j.plantsci.2019.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 05/06/2023]
Abstract
Serine/arginine-rich (SR) proteins are conserved RNA-binding proteins that play major roles in RNA metabolism. They function as molecular adaptors, facilitate spliceosome assembly and modulate constitutive and alternative splicing of pre-mRNAs. Pre-mRNAs encoding SR proteins and many other proteins involved in stress responses are extensively alternatively spliced in response to diverse stresses. Hence, it is proposed that stress-induced changes in splice isoforms contribute to the adaptation of plants to stress responses. However, functions of most SR genes and their splice isoforms in stress responses are not known. Lack of easy and robust tools hindered the progress in this area. Emerging technologies such as CRISPR/Cas9 will facilitate studies of SR function by enabling the generation of single and multiple knock-out mutants of SR subfamily members. Moreover, CRISPR/Cas13 allows targeted manipulation of splice isoforms from SR and other genes in a constitutive or tissue-specific manner to evaluate functions of individual splice variants. Identification of the in vivo targets of SR proteins and their splice variants using the recently developed TRIBE (Targets of RNA-binding proteins Identified By Editing) and other methods will help unravel their mode of action and splicing regulatory elements under various conditions. These new approaches are expected to provide significant new insights into the roles of SRs and splice isoforms in plants adaptation to diverse stresses.
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Affiliation(s)
- Mitchell Morton
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Nadia AlTamimi
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Anireddy S N Reddy
- Department of Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Magdy Mahfouz
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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14
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Leisegang MS, Gu L, Preussner J, Günther S, Hitzel J, Ratiu C, Weigert A, Chen W, Schwarz EC, Looso M, Fork C, Brandes RP. The histone demethylase
PHF
8 facilitates alternative splicing of the histocompatibility antigen
HLA
‐G. FEBS Lett 2019; 593:487-498. [DOI: 10.1002/1873-3468.13337] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias S. Leisegang
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
| | - Lunda Gu
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
| | - Jens Preussner
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
- ECCPS Bioinformatics and Sequencing Facility Max‐Planck‐Institute for Heart and Lung Research Bad Nauheim Germany
| | - Stefan Günther
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
- ECCPS Bioinformatics and Sequencing Facility Max‐Planck‐Institute for Heart and Lung Research Bad Nauheim Germany
| | - Juliane Hitzel
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
| | - Corina Ratiu
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
- Department of Functional Sciences – Pathophysiology “Victor Babes” University of Medicine and Pharmacy Timisoara Romania
| | - Andreas Weigert
- Faculty of Medicine Institute of Biochemistry I Goethe University Frankfurt Germany
| | - Wei Chen
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
- Laboratory for Novel Sequencing Technology, Functional and Medical Genomics Max‐Delbrück‐Center for Molecular Medicine Berlin Germany
- Department of Biology Southern University of Science and Technology Shenzhen China
| | - Eva C. Schwarz
- Biophysics Center for Integrative Physiology and Molecular Medicine School of Medicine Saarland University Homburg Germany
| | - Mario Looso
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
- ECCPS Bioinformatics and Sequencing Facility Max‐Planck‐Institute for Heart and Lung Research Bad Nauheim Germany
| | - Christian Fork
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology Medical Faculty Goethe University Frankfurt Germany
- German Center for Cardiovascular Research (DZHK), Partner site RheinMain Frankfurt Germany
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15
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Baeza-Centurion P, Miñana B, Schmiedel JM, Valcárcel J, Lehner B. Combinatorial Genetics Reveals a Scaling Law for the Effects of Mutations on Splicing. Cell 2019; 176:549-563.e23. [PMID: 30661752 DOI: 10.1016/j.cell.2018.12.010] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 08/29/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
Despite a wealth of molecular knowledge, quantitative laws for accurate prediction of biological phenomena remain rare. Alternative pre-mRNA splicing is an important regulated step in gene expression frequently perturbed in human disease. To understand the combined effects of mutations during evolution, we quantified the effects of all possible combinations of exonic mutations accumulated during the emergence of an alternatively spliced human exon. This revealed that mutation effects scale non-monotonically with the inclusion level of an exon, with each mutation having maximum effect at a predictable intermediate inclusion level. This scaling is observed genome-wide for cis and trans perturbations of splicing, including for natural and disease-associated variants. Mathematical modeling suggests that competition between alternative splice sites is sufficient to cause this non-linearity in the genotype-phenotype map. Combining the global scaling law with specific pairwise interactions between neighboring mutations allows accurate prediction of the effects of complex genotype changes involving >10 mutations.
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Affiliation(s)
- Pablo Baeza-Centurion
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Belén Miñana
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jörn M Schmiedel
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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16
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Abstract
This chapter is the first one to introduce the detection of viral RNA splicing as a new tool for clinical diagnosis of virus infections. These include various infections caused by influenza viruses, human immunodeficiency viruses (HIV), human T-cell leukemia viruses (HTLV), Torque teno viruses (TTV), parvoviruses, adenoviruses, hepatitis B virus, polyomaviruses, herpesviruses, and papillomaviruses. Detection of viral RNA splicing for active viral gene expression in a clinical sample is a nucleic acid-based detection. The interpretation of the detected viral RNA splicing results is straightforward without concern for carry-over DNA contamination, because the spliced RNA is smaller than its corresponding DNA template. Although many methods can be used, a simple method to detect viral RNA splicing is reverse transcription-polymerase chain reaction (RT-PCR). In principle, the detection of spliced RNA transcripts by RT-PCR depends on amplicon selection and primer design. The most common approach is the amplification over the intron regions by a set of primers in flanking exons. A larger product than the predicted size of smaller, spliced RNA is in general an unspliced RNA or contaminating viral genomic DNA. A spliced mRNA always gives a smaller RT-PCR product than its unspliced RNA due to removal of intron sequences by RNA splicing. The contaminating viral DNA can be determined by a minus RT amplification (PCR). Alternatively, specific amplification of a spliced RNA can be obtained by using an exon-exon junction primer because the sequence at exon-exon junction is not present in the unspliced RNA nor in viral genomic DNA.
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17
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Kim YE, Park C, Kim KE, Kim KK. Histone and RNA-binding protein interaction creates crosstalk network for regulation of alternative splicing. Biochem Biophys Res Commun 2018; 499:30-36. [PMID: 29551686 DOI: 10.1016/j.bbrc.2018.03.101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 03/13/2018] [Indexed: 12/18/2022]
Abstract
Alternative splicing is an essential process in eukaryotes, as it increases the complexity of gene expression by generating multiple proteins from a single pre-mRNA. However, information on the regulatory mechanisms for alternative splicing is lacking, because splicing occurs over a short period via the transient interactions of proteins within functional complexes of the spliceosome. Here, we investigated in detail the molecular mechanisms connecting alternative splicing with epigenetic mechanisms. We identified interactions between histone proteins and splicing factors such as Rbfox2, Rbfox3, and splicing factor proline and glutamine rich protein (SFPQ) by in vivo crosslinking and immunoprecipitation. Furthermore, we confirmed that splicing factors were bound to specific modified residues of histone proteins. Additionally, changes in histone methylation due to histone methyltransferase inhibitor treatment notably affected alternative splicing in selected genes. Therefore, we suggested that there may be crosstalk mechanisms connecting histone modifications and RNA-binding proteins that increase the local concentration of RNA-binding proteins in alternative exon loci of nucleosomes by binding specific modified histone proteins, leading to alternative splicing. This crosstalk mechanism may play a major role in epigenetic processes such as histone modification and the regulation of alternative splicing.
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Affiliation(s)
- Yong-Eun Kim
- Department of Biochemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Kyoon Eon Kim
- Department of Biochemistry, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, Chungnam National University, Daejeon, 34134, Republic of Korea.
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18
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Deep intronic variation in splicing regulatory element of the ERCC8 gene associated with severe but long-term survival Cockayne syndrome. Eur J Hum Genet 2018; 26:527-536. [PMID: 29422660 DOI: 10.1038/s41431-017-0009-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/19/2017] [Accepted: 08/31/2017] [Indexed: 01/08/2023] Open
Abstract
Cockayne syndrome is an autosomal recessive multisystem disorder characterized by intellectual disability, microcephaly, severe growth failure, sensory impairment, peripheral neuropathy, and cutaneous sensitivity. This rare disease is linked to disease-causing variations in the ERCC6 (CSB) and ERCC8 (CSA) genes. Various degrees of severity have been described according to age at onset and survival, without any clear genotype-phenotype correlation. All types of nucleotide changes have been observed in CS genes, including splice variations mainly affecting the splice site consensus sequences. We report here the case of two brothers from a consanguineous family presenting a severe but long-term survival phenotype of Cockayne syndrome. We identified in the patients a homozygous deep intronic nucleotide variation causing the insertion of a cryptic exon in the ERCC8 (CSA) transcript, by modifying intronic regulatory elements important for exon definition. The pathogenesis of the nucleotide variant NG_009289.1(NM_000082.3):c.173+1119G>C was validated in vitro with a reporter minigene system. To our knowledge, these are the first Cockayne patients described with this kind of disease-causing variation, though molecular mechanism underlying early onset symptoms and unexpected slow raise of progression of the disease remain to be elucidated.
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19
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Zhang Z, Cao W, Edery I. The SR protein B52/SRp55 regulates splicing of the period thermosensitive intron and mid-day siesta in Drosophila. Sci Rep 2018; 8:1872. [PMID: 29382842 PMCID: PMC5789894 DOI: 10.1038/s41598-017-18167-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/06/2017] [Indexed: 11/24/2022] Open
Abstract
Similar to many diurnal animals, Drosophila melanogaster exhibits a mid-day siesta that is more robust as temperature increases, an adaptive response that aims to minimize the deleterious effects from exposure to heat. This temperature-dependent plasticity in mid-day sleep levels is partly based on the thermal sensitive splicing of an intron in the 3′ untranslated region (UTR) of the circadian clock gene termed period (per). In this study, we evaluated a possible role for the serine/arginine-rich (SR) splicing factors in the regulation of dmpi8 splicing efficiency and mid-day siesta. Using a Drosophila cell culture assay we show that B52/SRp55 increases dmpi8 splicing efficiency, whereas other SR proteins have little to no effect. The magnitude of the stimulatory effect of B52 on dmpi8 splicing efficiency is modulated by natural variation in single nucleotide polymorphisms (SNPs) in the per 3′ UTR that correlate with B52 binding levels. Down-regulating B52 expression in clock neurons increases mid-day siesta and reduces dmpi8 splicing efficiency. Our results establish a novel role for SR proteins in sleep and suggest that polymorphisms in the per 3′ UTR contribute to natural variation in sleep behavior by modulating the binding efficiencies of SR proteins.
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Affiliation(s)
- Zhichao Zhang
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.,Institute of Animal Genetics and Breeding, Sichuan Agriculture University, Huimin Road 211#, Chengdu, Sichuan Province, 611130, P. R. China
| | - Weihuan Cao
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.,Human Genetics Institute of New Jersey, Nelson Biology Laboratories, 604 Allison Road, Piscataway, NJ, 08854, USA
| | - Isaac Edery
- Department of Molecular Biology and Biochemistry, Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, 08854, USA.
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20
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Ullah F, Hamilton M, Reddy ASN, Ben-Hur A. Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genomics 2018; 19:21. [PMID: 29304739 PMCID: PMC5756433 DOI: 10.1186/s12864-017-4393-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 12/15/2017] [Indexed: 11/29/2022] Open
Abstract
Background Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular. Results In this study we use publicly available DNase I-seq data in arabidopsis and rice to investigate the relationship between IR and chromatin structure. We find that IR events are highly enriched in DHSs in both species. This implies that chromatin is more open in retained introns, which is consistent with a kinetic model of the process whereby higher speeds of transcription in those regions give less time for the spliceosomal machinery to recognize and splice out those introns co-transcriptionally. The more open chromatin in IR can also be the result of regulation mediated by DNA-binding proteins. To test this, we performed an exhaustive search for footprints left by DNA-binding proteins that are associated with IR. We identified several hundred short sequence elements that exhibit footprints in their DNase I-seq coverage, the telltale sign for binding events of a regulatory protein, protecting its binding site from cleavage by DNase I. A highly significant fraction of those sequence elements are conserved between arabidopsis and rice, a strong indication of their functional importance. Conclusions In this study we have established an association between IR and chromatin accessibility, and presented a mechanistic hypothesis that explains the observed association from the perspective of the co-transcriptional nature of splicing. Furthermore, we identified conserved sequence elements for DNA-binding proteins that affect splicing. Electronic supplementary material The online version of this article (10.1186/s12864-017-4393-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fahad Ullah
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Michael Hamilton
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Anireddy S N Reddy
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, 80523, CO, USA
| | - Asa Ben-Hur
- Computer Science Department, Colorado State University, 1873 Campus Delivery, Fort Collins, 80523, CO, USA.
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21
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Ke S, Anquetil V, Zamalloa JR, Maity A, Yang A, Arias MA, Kalachikov S, Russo JJ, Ju J, Chasin LA. Saturation mutagenesis reveals manifold determinants of exon definition. Genome Res 2017; 28:11-24. [PMID: 29242188 PMCID: PMC5749175 DOI: 10.1101/gr.219683.116] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 11/27/2017] [Indexed: 11/24/2022]
Abstract
To illuminate the extent and roles of exonic sequences in the splicing of human RNA transcripts, we conducted saturation mutagenesis of a 51-nt internal exon in a three-exon minigene. All possible single and tandem dinucleotide substitutions were surveyed. Using high-throughput genetics, 5560 minigene molecules were assayed for splicing in human HEK293 cells. Up to 70% of mutations produced substantial (greater than twofold) phenotypes of either increased or decreased splicing. Of all predicted secondary structural elements, only a single 15-nt stem–loop showed a strong correlation with splicing, acting negatively. The in vitro formation of exon-protein complexes between the mutant molecules and proteins associated with spliceosome formation (U2AF35, U2AF65, U1A, and U1-70K) correlated with splicing efficiencies, suggesting exon definition as the step affected by most mutations. The measured relative binding affinities of dozens of human RNA binding protein domains as reported in the CISBP-RNA database were found to correlate either positively or negatively with splicing efficiency, more than could fit on the 51-nt test exon simultaneously. The large number of these functional protein binding correlations point to a dynamic and heterogeneous population of pre-mRNA molecules, each responding to a particular collection of binding proteins.
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Affiliation(s)
- Shengdong Ke
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Vincent Anquetil
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jorge Rojas Zamalloa
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Alisha Maity
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Anthony Yang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Mauricio A Arias
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Sergey Kalachikov
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
| | - James J Russo
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, New York 10027, USA
| | - Lawrence A Chasin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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22
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Tan JH, Fraser AG. The combinatorial control of alternative splicing in C. elegans. PLoS Genet 2017; 13:e1007033. [PMID: 29121637 PMCID: PMC5697891 DOI: 10.1371/journal.pgen.1007033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 11/21/2017] [Accepted: 09/19/2017] [Indexed: 12/31/2022] Open
Abstract
Normal development requires the right splice variants to be made in the right tissues at the right time. The core splicing machinery is engaged in all splicing events, but which precise splice variant is made requires the choice between alternative splice sites—for this to occur, a set of splicing factors (SFs) must recognize and bind to short RNA motifs in the pre-mRNA. In C. elegans, there is known to be extensive variation in splicing patterns across development, but little is known about the targets of each SF or how multiple SFs combine to regulate splicing. Here we combine RNA-seq with in vitro binding assays to study how 4 different C. elegans SFs, ASD-1, FOX-1, MEC-8, and EXC-7, regulate splicing. The 4 SFs chosen all have well-characterised biology and well-studied loss-of-function genetic alleles, and all contain RRM domains. Intriguingly, while the SFs we examined have varied roles in C. elegans development, they show an unexpectedly high overlap in their targets. We also find that binding sites for these SFs occur on the same pre-mRNAs more frequently than expected suggesting extensive combinatorial control of splicing. We confirm that regulation of splicing by multiple SFs is often combinatorial and show that this is functionally significant. We also find that SFs appear to combine to affect splicing in two modes—they either bind in close proximity within the same intron or they appear to bind to separate regions of the intron in a conserved order. Finally, we find that the genes whose splicing are regulated by multiple SFs are highly enriched for genes involved in the cytoskeleton and in ion channels that are key for neurotransmission. Together, this shows that specific classes of genes have complex combinatorial regulation of splicing and that this combinatorial regulation is critical for normal development to occur. Alternative splicing (AS) is a highly regulated process that is crucial for normal development. It requires the core splicing machinery, but the specific choice of splice site during AS is controlled by splicing factors (SFs) such as ELAV or RBFOX proteins that bind to specific sequences in pre-mRNAs to regulate usage of different splice sites. AS varies across the C. elegans life cycle and here we study how diverse SFs combine to regulate AS during C. elegans development. We selected 4 RRM-containing SFs that are all well studied and that have well-characterised loss-of-function genetic alleles. We find that these SFs regulate many of the same targets, and that combinatorial interactions between these SFs affect both individual splicing events and organism-level phenotypes including specific effects on the neuromuscular system. We further show that SFs combine to regulate splicing of an individual pre-mRNA in two distinct modes—either by binding in close proximity or by binding in a defined order on the pre-mRNA. Finally, we find that the genes whose splicing are most likely to be regulated by multiple SFs are genes that are required for the proper function of the neuromuscular system. These genes are also most likely to have changing AS patterns across development, suggesting that their splicing regulation is highly complex and developmentally regulated. Taken together, our data show that the precise splice variant expressed at any point in development is often the outcome of regulation by multiple SFs.
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Affiliation(s)
- June H. Tan
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON, Canada
| | - Andrew G. Fraser
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON, Canada
- * E-mail:
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23
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Brillen AL, Schöneweis K, Walotka L, Hartmann L, Müller L, Ptok J, Kaisers W, Poschmann G, Stühler K, Buratti E, Theiss S, Schaal H. Succession of splicing regulatory elements determines cryptic 5΄ss functionality. Nucleic Acids Res 2017; 45:4202-4216. [PMID: 28039323 PMCID: PMC5397162 DOI: 10.1093/nar/gkw1317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/19/2016] [Indexed: 12/25/2022] Open
Abstract
A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5’ end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bβ-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3’ exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3’ exon end definition.
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Affiliation(s)
- Anna-Lena Brillen
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Katrin Schöneweis
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Lara Walotka
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Linda Hartmann
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Müller
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Johannes Ptok
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Wolfgang Kaisers
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, BMFZ, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany.,Institute for Molecular Medicine, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, 34149 Trieste, Italy
| | - Stephan Theiss
- Institute of Clinical Neuroscience and Medical Psychology, Heinrich-Heine-University Düsseldorf, 40225
| | - Heiner Schaal
- Institute for Virology, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
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24
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Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O'Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O'Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Sci Transl Med 2017; 9:eaal5209. [PMID: 28424332 PMCID: PMC5548421 DOI: 10.1126/scitranslmed.aal5209] [Citation(s) in RCA: 444] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/29/2017] [Indexed: 12/21/2022]
Abstract
Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.
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Affiliation(s)
- Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Jamie L Marshall
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Taru Tukiainen
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Monkol Lek
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Leigh B Waddell
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sarah A Sandaradura
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Gina L O'Grady
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Elicia Estrella
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hemakumar M Reddy
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Fengmei Zhao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ben Weisburd
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Daniel Birnbaum
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anna Sarkozy
- Dubowitz Neuromuscular Centre, University College London Institute of Child Health, London WC1N 1EH, U.K
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hernan Gonorazky
- Division of Neurology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Kristl Claeys
- Department of Neurology, University Hospitals Leuven and University of Leuven (Katholieke Universiteit Leuven), Leuven 3000, Belgium
| | - Himanshu Joshi
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Adam Bournazos
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Emily C Oates
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Roula Ghaoui
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Mark R Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia 6009, Australia
| | - Nigel G Laing
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, Perth, Western Australia 6009, Australia
- Harry Perkins Institute of Medical Research, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ana Topf
- John Walton Muscular Dystrophy Research Centre, MRC (Medical Research Council) Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, U.K
| | - Peter B Kang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kathryn N North
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Melbourne, Victoria 3052, Australia
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, MRC (Medical Research Council) Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, U.K
| | - James J Dowling
- Division of Neurology, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London Institute of Child Health, London WC1N 1EH, U.K
| | - Nigel F Clarke
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Sandra T Cooper
- School of Paediatrics and Child Health, University of Sydney, Sydney, New South Wales 2006, Australia
- Institute for Neuroscience and Muscle Research, Kids Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales 2145, Australia
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA.
- Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
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25
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Yan Q, Xia X, Sun Z, Fang Y. Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes. PLoS Genet 2017; 13:e1006663. [PMID: 28273088 PMCID: PMC5362245 DOI: 10.1371/journal.pgen.1006663] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/22/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription in a direct or indirect manner to maintain the proper expression of genes and development. SR proteins were identified to be important splicing factors. This work generated mutants of different subfamilies of the classic Arabidopsis SR proteins. Genetic analysis revealed that loss of the function of SC35/SCL proteins influences the plant development. This study revealed SC35/SCL proteins regulate alternative splicing, preferentially bind a specific RNA motif, interact with NRPB4, and affect the transcription of a subset of genes. This study further revealed that SC35/SCL proteins control flowering by regulating the splicing and transcription of FLC. These results shed light on the functions of SR proteins in plants.
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Affiliation(s)
- Qingqing Yan
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xi Xia
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhenfei Sun
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yuda Fang
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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26
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Calvello R, Panaro MA, Salvatore R, Mitolo V, Cianciulli A. Conservation/Mutation in the Splice Sites of Mitochondrial Solute Carrier Genes of Vertebrates. J Mol Evol 2016; 83:147-155. [PMID: 27766348 DOI: 10.1007/s00239-016-9762-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
The "canonical" introns begin by the dinucleotide GT and end by the dinucleotide AG. GT, together with a few downstream nucleotides, and AG, with a few of the immediately preceding nucleotides, are thought to be the strongest splicing signals (5'ss and 3'ss, respectively). We examined the composition of the intronic initial and terminal hexanucleotides of the mitochondrial solute carrier genes (SLC25A's) of zebrafish, chicken, mouse, and human. These genes are orthologous and we selected the transcripts in which the arrangement of exons and introns was superimposable in the species considered. Both 5'ss and 3'ss were highly polymorphic, with 104 and 126 different configurations, respectively, in our sample. In the line of evolution from zebrafish to chicken, as well as in that from zebrafish to mammals, the average nucleotide conservation in the four variable nucleotides was about 50 % at 5' and 40 % at 3'. In the divergent evolution of mouse and human, the conservation was about 80 % at 5' and 70 % at 3'. Despite these changes, the splicing signals remain strong enough to operate at the same site. At both 5' and 3', the frequency of a nucleotide at a given position in the zebrafish sequence is positively correlated with its conservation in chicken and mammals, suggesting that selection continued to operate in birds and mammals along similar lines.
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Affiliation(s)
- Rosa Calvello
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126, Bari, Italy
| | - Maria A Panaro
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126, Bari, Italy.
| | - Rosaria Salvatore
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126, Bari, Italy
| | - Vincenzo Mitolo
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126, Bari, Italy
| | - Antonia Cianciulli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126, Bari, Italy
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27
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Abstract
Examples of associations between human disease and defects in pre-messenger RNA splicing/alternative splicing are accumulating. Although many alterations are caused by mutations in splicing signals or regulatory sequence elements, recent studies have noted the disruptive impact of mutated generic spliceosome components and splicing regulatory proteins. This review highlights recent progress in our understanding of how the altered splicing function of RNA-binding proteins contributes to myelodysplastic syndromes, cancer, and neuropathologies.
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Affiliation(s)
- Benoit Chabot
- Centre of Excellence in RNA Biology, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
| | - Lulzim Shkreta
- Centre of Excellence in RNA Biology, Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec J1E 4K8, Canada
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28
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mCarts: Genome-Wide Prediction of Clustered Sequence Motifs as Binding Sites for RNA-Binding Proteins. Methods Mol Biol 2016; 1421:215-26. [PMID: 26965268 DOI: 10.1007/978-1-4939-3591-8_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are critical components of post-transcriptional gene expression regulation. However, their binding sites have until recently been difficult to determine due to the apparent low specificity of RBPs for their target transcripts and the lack of high-throughput assays for analyzing binding sites genome wide. Here we present a bioinformatics method for predicting RBP binding motif sites on a genome-wide scale that leverages motif conservation, RNA secondary structure, and the tendency of RBP binding sites to cluster together. A probabilistic model is learned from bona fide binding sites determined by CLIP and applied genome wide to generate high specificity binding site predictions.
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29
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Gracida X, Norris AD, Calarco JA. Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:229-61. [DOI: 10.1007/978-3-319-29073-7_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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31
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Guo L, Liu CM. A single-nucleotide exon found in Arabidopsis. Sci Rep 2015; 5:18087. [PMID: 26657562 PMCID: PMC4674806 DOI: 10.1038/srep18087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/11/2015] [Indexed: 01/09/2023] Open
Abstract
The presence of introns in gene-coding regions is one of the most mysterious evolutionary inventions in eukaryotic organisms. It has been proposed that, although sequences involved in intron recognition and splicing are mainly located in introns, exonic sequences also contribute to intron splicing. The smallest constitutively spliced exon known so far has 6 nucleotides, and the smallest alternatively spliced exon has 3 nucleotides. Here we report that the Anaphase Promoting Complex subunit 11 (APC11) gene in Arabidopsis thaliana carries a constitutive single-nucleotide exon. In vivo transcription and translation assays performed using APC11-Green Fluorescence Protein (GFP) fusion constructs revealed that intron splicing surrounding the single-nucleotide exon is effective in both Arabidopsis and rice. This discovery warrants attention to genome annotations in the future.
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Affiliation(s)
- Lei Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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32
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Kralovicova J, Patel A, Searle M, Vorechovsky I. The role of short RNA loops in recognition of a single-hairpin exon derived from a mammalian-wide interspersed repeat. RNA Biol 2015; 12:54-69. [PMID: 25826413 PMCID: PMC4615370 DOI: 10.1080/15476286.2015.1017207] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Splice-site selection is controlled by secondary structure through sequestration or approximation of splicing signals in primary transcripts but the exact role of even the simplest and most prevalent structural motifs in exon recognition remains poorly understood. Here we took advantage of a single-hairpin exon that was activated in a mammalian-wide interspersed repeat (MIR) by a mutation stabilizing a terminal triloop, with splice sites positioned close to each other in a lower stem of the hairpin. We first show that the MIR exon inclusion in mRNA correlated inversely with hairpin stabilities. Employing a systematic manipulation of unpaired regions without altering splice-site configuration, we demonstrate a high correlation between exon inclusion of terminal tri- and tetraloop mutants and matching tri-/tetramers in splicing silencers/enhancers. Loop-specific exon inclusion levels and enhancer/silencer associations were preserved across primate cell lines, in 4 hybrid transcripts and also in the context of a distinct stem, but only if its loop-closing base pairs were shared with the MIR hairpin. Unlike terminal loops, splicing activities of internal loop mutants were predicted by their intramolecular Watson-Crick interactions with the antiparallel strand of the MIR hairpin rather than by frequencies of corresponding trinucleotides in splicing silencers/enhancers. We also show that splicing outcome of oligonucleotides targeting the MIR exon depend on the identity of the triloop adjacent to their antisense target. Finally, we identify proteins regulating MIR exon recognition and reveal a distinct requirement of adjacent exons for C-terminal extensions of Tra2α and Tra2β RNA recognition motifs.
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Affiliation(s)
- Jana Kralovicova
- a University of Southampton; Faculty of Medicine ; Southampton , UK
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Li H, Hou S, Hao T, Azam S, Liu C, Shi L, Lei H. HuR antagonizes the effect of an intronic pyrimidine-rich sequence in regulating WT1 +/-KTS isoforms. RNA Biol 2015; 12:1364-71. [PMID: 26512748 DOI: 10.1080/15476286.2015.1102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
WT1 + KTS and -KTS isoforms only differ in 3 amino acids in protein sequence but show significant functional difference. The +/-KTS isoforms were generated by alternative usage of 2 adjacent 5' splice sites at RNA level, however, how these 2 isoforms are regulated is still elusive. Here we report the identification of an intronic pyrimidine-rich sequence that is critical for the ratio of +/-KTS isoforms, deletion or partial replacement of the sequence led to full/significant shift to -KTS isoform. To identify trans-factors that can regulate +/-KTS isoforms via the binding to the element, we performed RNP assembly using in vitro transcribed RNA with or without the pyrimidine-rich sequence. Mass spectrometry analysis of purified RNPs showed that the element associated with many splicing factors. Co-transfection of these factors with WT1 reporter revealed that HuR promoted the production of -KTS isoform at the reporter level. RNA immuno-precipitation experiment indicated that HuR interacted with the pyrimidine-rich element in WT1 intron 9. We further presented evidence that transient or stable over-expression of HuR led to enhanced expression of endogenous -KTS isoform. Moreover, knockdown of HuR resulted in decreased expression of endogenous -KTS isoform in 293T, SW620, SNU-387 and AGS cell lines. Together, these data indicate that HuR binds to the pyrimidine-rich sequence and antagonize its effect in regulating WT1 +/-KTS isoforms.
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Affiliation(s)
- Hui Li
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China.,c Equal contribution
| | - Shuai Hou
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China.,c Equal contribution
| | - Tian Hao
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Sikandar Azam
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Caigang Liu
- b Breast Disease and Reconstruction Center; Breast Cancer Key Lab of Dalian; the Second Hospital of Dalian Medical University ; Dalian , P.R. China
| | - Lei Shi
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
| | - Haixin Lei
- a Institute of Cancer Stem Cell; Cancer Center; Dalian Medical University ; Dalian , P.R. China
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Badr E, Heath LS. CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements. BMC Bioinformatics 2015; 16:285. [PMID: 26337677 PMCID: PMC4559876 DOI: 10.1186/s12859-015-0698-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a post-transcriptional regulatory mechanism for gene expression regulation. Splicing decisions are affected by the combinatorial behavior of different splicing factors that bind to multiple binding sites in exons and introns. These binding sites are called splicing regulatory elements (SREs). Here we develop CoSREM (Combinatorial SRE Miner), a graph mining algorithm to discover combinatorial SREs in human exons. Our model does not assume a fixed length of SREs and incorporates experimental evidence as well to increase accuracy. CoSREM is able to identify sets of SREs and is not limited to SRE pairs as are current approaches. RESULTS We identified 37 SRE sets that include both enhancer and silencer elements. We show that our results intersect with previous results, including some that are experimental. We also show that the SRE set GGGAGG and GAGGAC identified by CoSREM may play a role in exon skipping events in several tumor samples. We applied CoSREM to RNA-Seq data for multiple tissues to identify combinatorial SREs which may be responsible for exon inclusion or exclusion across tissues. CONCLUSION The new algorithm can identify different combinations of splicing enhancers and silencers without assuming a predefined size or limiting the algorithm to find only pairs of SREs. Our approach opens new directions to study SREs and the roles that AS may play in diseases and tissue specificity.
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Affiliation(s)
- Eman Badr
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA.
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Badr E, Heath LS. Identifying splicing regulatory elements with de Bruijn graphs. J Comput Biol 2015; 21:880-97. [PMID: 25393830 DOI: 10.1089/cmb.2014.0183] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Splicing regulatory elements (SREs) are short, degenerate sequences on pre-mRNA molecules that enhance or inhibit the splicing process via the binding of splicing factors, proteins that regulate the functioning of the spliceosome. Existing methods for identifying SREs in a genome are either experimental or computational. Here, we propose a formalism based on de Bruijn graphs that combines genomic structure, word count enrichment analysis, and experimental evidence to identify SREs found in exons. In our approach, SREs are not restricted to a fixed length (i.e., k-mers, for a fixed k). As a result, we identify 2001 putative exonic enhancers and 3080 putative exonic silencers for human genes, with lengths varying from 6 to 15 nucleotides. Many of the predicted SREs overlap with experimentally verified binding sites. Our model provides a novel method to predict variable length putative regulatory elements computationally for further experimental investigation.
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Affiliation(s)
- Eman Badr
- Department of Computer Science, Virginia Tech , Blacksburg, Virginia
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Identification and Validation of Evolutionarily Conserved Unusually Short Pre-mRNA Introns in the Human Genome. Int J Mol Sci 2015; 16:10376-88. [PMID: 25961948 PMCID: PMC4463651 DOI: 10.3390/ijms160510376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/13/2015] [Accepted: 04/13/2015] [Indexed: 11/29/2022] Open
Abstract
According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism.
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Pan K, Lee JTH, Huang Z, Wong CM. Coupling and coordination in gene expression processes with pre-mRNA splicing. Int J Mol Sci 2015; 16:5682-96. [PMID: 25768347 PMCID: PMC4394499 DOI: 10.3390/ijms16035682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/28/2015] [Accepted: 03/04/2015] [Indexed: 12/13/2022] Open
Abstract
RNA processing is a tightly regulated and highly complex pathway which includes transcription, splicing, editing, transportation, translation and degradation. It has been well-documented that splicing of RNA polymerase II medicated nascent transcripts occurs co-transcriptionally and is functionally coupled to other RNA processing. Recently, increasing experimental evidence indicated that pre-mRNA splicing influences RNA degradation and vice versa. In this review, we summarized the recent findings demonstrating the coupling of these two processes. In addition, we highlighted the importance of splicing in the production of intronic miRNA and circular RNAs, and hence the discovery of the novel mechanisms in the regulation of gene expression.
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Arias MA, Lubkin A, Chasin LA. Splicing of designer exons informs a biophysical model for exon definition. RNA (NEW YORK, N.Y.) 2015; 21:213-229. [PMID: 25492963 PMCID: PMC4338349 DOI: 10.1261/rna.048009.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
Pre-mRNA molecules in humans contain mostly short internal exons flanked by longer introns. To explain the removal of such introns, exon recognition instead of intron recognition has been proposed. We studied this exon definition using designer exons (DEs) made up of three prototype modules of our own design: an exonic splicing enhancer (ESE), an exonic splicing silencer (ESS), and a Reference Sequence (R) predicted to be neither. Each DE was examined as the central exon in a three-exon minigene. DEs made of R modules showed a sharp size dependence, with exons shorter than 14 nt and longer than 174 nt splicing poorly. Changing the strengths of the splice sites improved longer exon splicing but worsened shorter exon splicing, effectively displacing the curve to the right. For the ESE we found, unexpectedly, that its enhancement efficiency was independent of its position within the exon. For the ESS we found a step-wise positional increase in its effects; it was most effective at the 3' end of the exon. To apply these results quantitatively, we developed a biophysical model for exon definition of internal exons undergoing cotranscriptional splicing. This model features commitment to inclusion before the downstream exon is synthesized and competition between skipping and inclusion fates afterward. Collision of both exon ends to form an exon definition complex was incorporated to account for the effect of size; ESE/ESS effects were modeled on the basis of stabilization/destabilization. This model accurately predicted the outcome of independent experiments on more complex DEs that combined ESEs and ESSs.
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Affiliation(s)
- Mauricio A Arias
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Ashira Lubkin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Lawrence A Chasin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Soemedi R, Vega H, Belmont JM, Ramachandran S, Fairbrother WG. Genetic variation and RNA binding proteins: tools and techniques to detect functional polymorphisms. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:227-66. [PMID: 25201108 DOI: 10.1007/978-1-4939-1221-6_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
At its most fundamental level the goal of genetics is to connect genotype to phenotype. This question is asked at a basic level evaluating the role of genes and pathways in genetic model organism. Increasingly, this question is being asked in the clinic. Genomes of individuals and populations are being sequenced and compared. The challenge often comes at the stage of analysis. The variant positions are analyzed with the hope of understanding human disease. However after a genome or exome has been sequenced, the researcher is often deluged with hundreds of potentially relevant variations. Traditionally, amino-acid changing mutations were considered the tractable class of disease-causing mutations; however, mutations that disrupt noncoding elements are the subject of growing interest. These noncoding changes are a major avenue of disease (e.g., one in three hereditary disease alleles are predicted to affect splicing). Here, we review some current practices of medical genetics, the basic theory behind biochemical binding and functional assays, and then explore technical advances in how variations that alter RNA protein recognition events are detected and studied. These advances are advances in scale-high-throughput implementations of traditional biochemical assays that are feasible to perform in any molecular biology laboratory. This chapter utilizes a case study approach to illustrate some methods for analyzing polymorphisms. The first characterizes a functional intronic SNP that deletes a high affinity PTB site using traditional low-throughput biochemical and functional assays. From here we demonstrate the utility of high-throughput splicing and spliceosome assembly assays for screening large sets of SNPs and disease alleles for allelic differences in gene expression. Finally we perform three pilot drug screens with small molecules (G418, tetracycline, and valproic acid) that illustrate how compounds that rescue specific instances of differential pre-mRNA processing can be discovered.
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Affiliation(s)
- Rachel Soemedi
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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Gong SG. Isoforms of Receptors of Fibroblast Growth Factors. J Cell Physiol 2014; 229:1887-95. [DOI: 10.1002/jcp.24649] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Accepted: 04/10/2014] [Indexed: 01/12/2023]
Affiliation(s)
- Siew-Ging Gong
- Faculty of Dentistry; University of Toronto; Toronto Ontario Canada
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Siala O, Rebai A, Fakhfakh F. Slight variations in the SC35 ESE sequence motif among human chromosomes: a computational approach. Gene 2014; 545:102-10. [PMID: 24792892 DOI: 10.1016/j.gene.2014.04.075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 11/26/2022]
Abstract
Gene expression is initiated by the binding of transcription factors to cis-regulatory modules such as enhancer elements binding to the Serine/Arginine proteins. Recently, we noticed an increased ability to identify the location as well as the motifs of enhancers using genome-wide information on spliceosomal factor occupancy, cofactor recruitment and chromatin modifications. In this study, we have undertaken a large-scale genomic analysis in an attempt to uncover if the exonic splicing enhancer motif binding to the SC35 and the SRp40 SR proteins is conserved among several groups of human genes. For the SRp40, the results showed that the ESE consensus is conserved among human genes. Concerning the SC35 SR protein, results showed an ESE motif conserved among human tissues and between different levels of muscular cell differentiation and within the same chromosome. However, this motif displays subtle discrepancies between genes localized in different chromosomes. These results emphasize the presence of different translational isoforms of the SFRS2 gene encoding for the SC35, or different post-translational protein maturations in different chromosomes, confirming that chromatin structure is another layer of gene regulation. These links between chromatin pattern and splicing give further mechanistic support to functional interconnections between splicing, transcription and chromatin structure, and raise the intriguing possibility of the existence of a memory for splicing patterns to be inherited through epigenetic modifications.
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Affiliation(s)
- Olfa Siala
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Avenue Majida Boulila, 3029 Sfax, Tunisia.
| | - Ahmed Rebai
- Unit of Bioinformatics and Biostatistics, Centre of Biotechnology of Sfax, Sfax 3038, Tunisia.
| | - Faiza Fakhfakh
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Avenue Majida Boulila, 3029 Sfax, Tunisia.
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Lo C, Kakaradov B, Lokshtanov D, Boucher C. SeeSite: Characterizing Relationships between Splice Junctions and Splicing Enhancers. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:648-656. [PMID: 26356335 DOI: 10.1109/tcbb.2014.2304294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RNA splicing is a cellular process driven by the interaction between numerous regulatory sequences and binding sites, however, such interactions have been primarily explored by laboratory methods since computational tools largely ignore the relationship between different splicing elements. Current computational methods identify either splice sites or other regulatory sequences, such as enhancers and silencers. We present a novel approach for characterizing co-occurring relationships between splice site motifs and splicing enhancers. Our approach relies on an efficient algorithm for approximately solving Consensus Sequence with Outliers , an NP-complete string clustering problem. In particular, we give an algorithm for this problem that outputs near-optimal solutions in polynomial time. To our knowledge, this is the first formulation and computational attempt for detecting co-occurring sequence elements in RNA sequence data. Further, we demonstrate that SeeSite is capable of showing that certain ESEs are preferentially associated with weaker splice sites, and that there exists a co-occurrence relationship with splice site motifs.
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Kosiorek M, Podszywalow-Bartnicka P, Zylinska L, Pikula S. NFAT1 and NFAT3 cooperate with HDAC4 during regulation of alternative splicing of PMCA isoforms in PC12 cells. PLoS One 2014; 9:e99118. [PMID: 24905014 PMCID: PMC4048221 DOI: 10.1371/journal.pone.0099118] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/10/2014] [Indexed: 02/07/2023] Open
Abstract
Background The bulk of human genes undergo alternative splicing (AS) upon response to physiological stimuli. AS is a great source of protein diversity and biological processes and is associated with the development of many diseases. Pheochromocytoma is a neuroendocrine tumor, characterized by an excessive Ca2+-dependent secretion of catecholamines. This underlines the importance of balanced control of calcium transport via regulation of gene expression pattern, including different calcium transport systems, such as plasma membrane Ca2+-ATPases (PMCAs), abundantly expressed in pheochromocytoma chromaffin cells (PC12 cells). PMCAs are encoded by four genes (Atp2b1, Atp2b2, Atp2b3, Atp2b4), whose transcript products undergo alternative splicing giving almost 30 variants. Results In this scientific report, we propose a novel mechanism of regulation of PMCA alternative splicing in PC12 cells through cooperation of the nuclear factor of activated T-cells (NFAT) and histone deacetylases (HDACs). Luciferase assays showed increased activity of NFAT in PC12 cells, which was associated with altered expression of PMCA. RT-PCR experiments suggested that inhibition of the transcriptional activity of NFAT might result in the rearrangement of PMCA splicing variants in PC12 cells. NFAT inhibition led to dominant expression of 2x/c, 3x/a and 4x/a PMCA variants, while in untreated cells the 2w,z/b, 3z,x/b,c,e,f, and 4x/b variants were found as well. Furthermore, chromatin immunoprecipitation experiments showed that NFAT1-HDAC4 or NFAT3-HDAC4 complexes might be involved in regulation of PMCA2x splicing variant generation. Conclusions We suggest that the influence of NFAT/HDAC on PMCA isoform composition might be important for altered dopamine secretion by PC12 cells.
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Affiliation(s)
- Michalina Kosiorek
- Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre PAS, Warsaw, Poland
| | | | - Ludmila Zylinska
- Department of Molecular Neurochemistry, Medical University, Lodz, Poland
| | - Slawomir Pikula
- Department of Biochemistry, Nencki Institute of Experimental Biology, Warsaw, Poland
- * E-mail:
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Podlaha O, De S, Gonen M, Michor F. Histone modifications are associated with transcript isoform diversity in normal and cancer cells. PLoS Comput Biol 2014; 10:e1003611. [PMID: 24901363 PMCID: PMC4046914 DOI: 10.1371/journal.pcbi.1003611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/26/2014] [Indexed: 11/29/2022] Open
Abstract
Mechanisms that generate transcript diversity are of fundamental importance in eukaryotes. Although a large fraction of human protein-coding genes and lincRNAs produce more than one mRNA isoform each, the regulation of this phenomenon is still incompletely understood. Much progress has been made in deciphering the role of sequence-specific features as well as DNA-and RNA-binding proteins in alternative splicing. Recently, however, several experimental studies of individual genes have revealed a direct involvement of epigenetic factors in alternative splicing and transcription initiation. While histone modifications are generally correlated with overall gene expression levels, it remains unclear how histone modification enrichment affects relative isoform abundance. Therefore, we sought to investigate the associations between histone modifications and transcript diversity levels measured by the rates of transcription start-site switching and alternative splicing on a genome-wide scale across protein-coding genes and lincRNAs. We found that the relationship between enrichment levels of epigenetic marks and transcription start-site switching is similar for protein-coding genes and lincRNAs. Furthermore, we found associations between splicing rates and enrichment levels of H2az, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3, H3K36me3, H3K79me2, and H4K20me, marks traditionally associated with enhancers, transcription initiation, transcriptional repression, and others. These patterns were observed in both normal and cancer cell lines. Additionally, we developed a novel computational method that identified 840 epigenetically regulated candidate genes and predicted transcription start-site switching and alternative exon splicing with up to 92% accuracy based on epigenetic patterning alone. Our results suggest that the epigenetic regulation of transcript isoform diversity may be a relatively common genome-wide phenomenon representing an avenue of deregulation in tumor development. Traditionally, the regulation of gene expression was thought to be largely based on DNA and RNA sequence motifs. However, this dogma has recently been challenged as other factors, such as epigenetic patterning of the genome, have become better understood. Sparse but convincing experimental evidence suggests that the epigenetic background, in the form of histone modifications, acts as an additional layer of regulation determining how transcripts are processed. Here we developed a computational approach to investigate the genome-wide prevalence and the level of association between the enrichment of epigenetic marks and transcript diversity generated via alternative transcription start sites and splicing. We found that the role of epigenetic patterning in alternative transcription start-site switching is likely to be the same for all genes whereas the role of epigenetic patterns in splicing is likely gene-specific. Furthermore, we show that epigenetic data alone can be used to predict the inclusion pattern of an exon. These findings have significant implications for a better understanding of the regulation of transcript diversity in humans as well as the modifications arising during tumor development.
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Affiliation(s)
- Ondrej Podlaha
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, Colorado, United States of America
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
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da Glória VG, Martins de Araújo M, Mafalda Santos A, Leal R, de Almeida SF, Carmo AM, Moreira A. T cell activation regulates CD6 alternative splicing by transcription dynamics and SRSF1. THE JOURNAL OF IMMUNOLOGY 2014; 193:391-9. [PMID: 24890719 DOI: 10.4049/jimmunol.1400038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The T cell-surface glycoprotein CD6 is a modulator of cellular responses and has been implicated in several autoimmune diseases such as multiple sclerosis, rheumatoid arthritis, and psoriasis. During Ag presentation, CD6 is targeted to the immunological synapse in a ligand binding-dependent manner, in which CD6 domain 3 directly contacts CD166, expressed on the APC. T cell activation results in the induction of CD6Δd3, an alternatively spliced isoform that lacks the ligand-binding domain and thus no longer localizes at the immunological synapse. In this study, we investigated the molecular mechanisms regulating the expression of CD6Δd3 upon human primary T cell activation. Using chromatin immunoprecipitation, we observed an increase in RNA polymerase II occupancy along the CD6 gene and augmented CD6 transcription. We showed that activation leads to transcription-related chromatin modifications, revealed by higher CD6 acetylation levels. Modulation of chromatin conformation using a histone deacetylase inhibitor that increases transcription rate causes an increase of exon 5 skipping. We further showed that the splicing factor SRSF1 binds to a regulatory element in CD6 intron 4, activating exon 5 splicing and promoting exon 5 inclusion. Concomitant with T cell activation-induced exon 5 skipping, we observed a downregulation of SRSF1. Using RNA immunoprecipitation, we showed that in activated T cells, SRSF1 recruitment to the CD6 transcript is impaired by increased chromatin acetylation levels. We propose that upon T cell activation, SRSF1 becomes limiting, and its function in CD6 exon 5 splicing is countered by an increase in CD6 transcription, dependent on chromatin acetylation.
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Affiliation(s)
- Vânia G da Glória
- Grupo Regulação Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal
| | - Mafalda Martins de Araújo
- Grupo Activação Celular e Expressão Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal; Instituto de Investigação em Ciências da Vida e da Saude, Escola de Ciências da Saude, Universidade do Minho, Braga 4710-057, Portugal; ICVS/3B's Laboratório Associado, Braga/Guimarães 4806-909, Portugal
| | - Ana Mafalda Santos
- Grupo Activação Celular e Expressão Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal
| | - Rafaela Leal
- Grupo Regulação Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade Lisboa, Lisboa 1649-028, Portugal; and
| | - Alexandre M Carmo
- Grupo Activação Celular e Expressão Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal; Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto 4050-313, Portugal
| | - Alexandra Moreira
- Grupo Regulação Genética, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto 4150-180, Portugal;
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Liu C, Karam R, Zhou Y, Su F, Ji Y, Li G, Xu G, Lu L, Wang C, Song M, Zhu J, Wang Y, Zhao Y, Foo WC, Zuo M, Valasek MA, Javle M, Wilkinson MF, Lu Y. The UPF1 RNA surveillance gene is commonly mutated in pancreatic adenosquamous carcinoma. Nat Med 2014; 20:596-8. [PMID: 24859531 PMCID: PMC4048332 DOI: 10.1038/nm.3548] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 03/27/2014] [Indexed: 12/15/2022]
Abstract
Pancreatic adenosquamous carcinoma (ASC) is an enigmatic and aggressive tumor that has a worse prognosis and higher metastatic potential than its adenocarcinoma counterpart. Here we report that ASC tumors frequently harbor somatically acquired mutations in the UPF1 gene, which encodes the core component of the nonsense-mediated RNA decay (NMD) pathway. These tumor-specific mutations alter UPF1 RNA splicing and perturb NMD, leading to upregulated levels of NMD substrate mRNAs. UPF1 mutations are, to our knowledge, the first known unique molecular signatures of pancreatic ASC.
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Affiliation(s)
- Chen Liu
- 1] Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China. [2] Tongji University School of Life Science and Technology, Shanghai, China. [3]
| | - Rachid Karam
- 1] Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA. [2]
| | - YingQi Zhou
- 1] The Third General Surgery Department, Changhai Hospital, Second Military Medical University, Shanghai, China. [2]
| | - Fang Su
- 1] Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China. [2]
| | - Yuan Ji
- 1] Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China. [2]
| | - Gang Li
- The Third General Surgery Department, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - GuoTong Xu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - LiXia Lu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - ChongRen Wang
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - MeiYi Song
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - JingPing Zhu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - YiRan Wang
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - YiFan Zhao
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wai Chin Foo
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - MingXin Zuo
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark A Valasek
- Division of Anatomic Pathology, Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Miles F Wilkinson
- 1] Department of Reproductive Medicine, School of Medicine, University of California San Diego, La Jolla, California, USA. [2] Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
| | - YanJun Lu
- Clinical and Translational Cancer Research Center, The Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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47
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Suzuki H, Tsukahara T. A view of pre-mRNA splicing from RNase R resistant RNAs. Int J Mol Sci 2014; 15:9331-42. [PMID: 24865493 PMCID: PMC4100097 DOI: 10.3390/ijms15069331] [Citation(s) in RCA: 323] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/08/2014] [Accepted: 05/16/2014] [Indexed: 01/05/2023] Open
Abstract
During pre-mRNA splicing, exons in the primary transcript are precisely connected to generate an mRNA. Intron lariat RNAs are formed as by-products of this process. In addition, some exonic circular RNAs (circRNAs) may also result from exon skipping as by-products. Lariat RNAs and circRNAs are both RNase R resistant RNAs. RNase R is a strong 3' to 5' exoribonuclease, which efficiently degrades linear RNAs, such as mRNAs and rRNAs; therefore, the circular parts of lariat RNAs and the circRNAs can be segregated from eukaryotic total RNAs by their RNase R resistance. Thus, RNase R resistant RNAs could provide unexplored splicing information not available from mRNAs. Analyses of these RNAs identified repeating splicing phenomena, such as re-splicing of mature mRNAs and nested splicing. Moreover, circRNA might function as microRNA sponges. There is an enormous variety of endogenous circRNAs, which are generally synthesized in cells and tissues.
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Affiliation(s)
- Hitoshi Suzuki
- Center for Nano Materials and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
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48
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Feng J, Wilkinson M, Liu X, Purushothaman I, Ferguson D, Vialou V, Maze I, Shao N, Kennedy P, Koo J, Dias C, Laitman B, Stockman V, LaPlant Q, Cahill ME, Nestler EJ, Shen L. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol 2014; 15:R65. [PMID: 24758366 PMCID: PMC4073058 DOI: 10.1186/gb-2014-15-4-r65] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 04/22/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Increasing evidence supports a role for altered gene expression in mediating the lasting effects of cocaine on the brain, and recent work has demonstrated the involvement of chromatin modifications in these alterations. However, all such studies to date have been restricted by their reliance on microarray technologies that have intrinsic limitations. RESULTS We use next generation sequencing methods, RNA-seq and ChIP-seq for RNA polymerase II and several histone methylation marks, to obtain a more complete view of cocaine-induced changes in gene expression and associated adaptations in numerous modes of chromatin regulation in the mouse nucleus accumbens, a key brain reward region. We demonstrate an unexpectedly large number of pre-mRNA splicing alterations in response to repeated cocaine treatment. In addition, we identify combinations of chromatin changes, or signatures, that correlate with cocaine-dependent regulation of gene expression, including those involving pre-mRNA alternative splicing. Through bioinformatic prediction and biological validation, we identify one particular splicing factor, A2BP1(Rbfox1/Fox-1), which is enriched at genes that display certain chromatin signatures and contributes to drug-induced behavioral abnormalities. Together, this delineation of the cocaine-induced epigenome in the nucleus accumbens reveals several novel modes of regulation by which cocaine alters the brain. CONCLUSIONS We establish combinatorial chromatin and transcriptional profiles in mouse nucleus accumbens after repeated cocaine treatment. These results serve as an important resource for the field and provide a template for the analysis of other systems to reveal new transcriptional and epigenetic mechanisms of neuronal regulation.
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49
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Falanga A, Stojanović O, Kiffer-Moreira T, Pinto S, Millán JL, Vlahoviček K, Baralle M. Exonic splicing signals impose constraints upon the evolution of enzymatic activity. Nucleic Acids Res 2014; 42:5790-8. [PMID: 24692663 PMCID: PMC4027185 DOI: 10.1093/nar/gku240] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Exon splicing enhancers (ESEs) overlap with amino acid coding sequences implying a dual evolutionary selective pressure. In this study, we map ESEs in the placental alkaline phosphatase gene (ALPP), absent in the corresponding exon of the ancestral tissue-non-specific alkaline phosphatase gene (ALPL). The ESEs are associated with amino acid differences between the transcripts in an area otherwise conserved. We switched out the ALPP ESEs sequences with the sequence from the related ALPL, introducing the associated amino acid changes. The resulting enzymes, produced by cDNA expression, showed different kinetic characteristics than ALPL and ALPP. In the organism, this enzyme will never be subjected to selection because gene splicing analysis shows exon skipping due to loss of the ESE. Our data prove that ESEs restrict the evolution of enzymatic activity. Thus, suboptimal proteins may exist in scenarios when coding nucleotide changes and consequent amino acid variation cannot be reconciled with the splicing function.
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Affiliation(s)
- Alessia Falanga
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
| | - Ozren Stojanović
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Tina Kiffer-Moreira
- Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sofia Pinto
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - José Luis Millán
- Sanford Children's Health Research Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kristian Vlahoviček
- Bioinformatics Group, Department of Molecular Biology, Division of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway
| | - Marco Baralle
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, 34149 Trieste, Italy
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50
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Shen Y, Zhou Z, Wang Z, Li W, Fang C, Wu M, Ma Y, Liu T, Kong LA, Peng DL, Tian Z. Global dissection of alternative splicing in paleopolyploid soybean. THE PLANT CELL 2014; 26:996-1008. [PMID: 24681622 PMCID: PMC4001406 DOI: 10.1105/tpc.114.122739] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/05/2014] [Accepted: 03/12/2014] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) is common in higher eukaryotes and plays an important role in gene posttranscriptional regulation. It has been suggested that AS varies dramatically among species, tissues, and duplicated gene families of different sizes. However, the genomic forces that govern AS variation remain poorly understood. Here, through genome-wide identification of AS events in the soybean (Glycine max) genome using high-throughput RNA sequencing of 28 samples from different developmental stages, we found that more than 63% of multiexonic genes underwent AS. More AS events occurred in the younger developmental stages than in the older developmental stages for the same type of tissue, and the four main AS types, exon skipping, intron retention, alternative donor sites, and alternative acceptor sites, exhibited different characteristics. Global computational analysis demonstrated that the variations of AS frequency and AS types were significantly correlated with the changes of gene features and gene transcriptional level. Further investigation suggested that the decrease of AS within the genome-wide duplicated genes were due to the diminution of intron length, exon number, and transcriptional level. Altogether, our study revealed that a large number of genes were alternatively spliced in the soybean genome and that variations in gene structure and transcriptional level may play important roles in regulating AS.
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Affiliation(s)
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhengkui Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weiyu Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Mian Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanming Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ling-An Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - De-Liang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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