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For: Erkelenz S, Theiss S, Otte M, Widera M, Peter JO, Schaal H. Genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Nucleic Acids Res 2014;42:10681-97. [PMID: 25147205 PMCID: PMC4176321 DOI: 10.1093/nar/gku736] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
Number Cited by Other Article(s)
1
Roesmann F, Müller L, Klaassen K, Heß S, Widera M. Interferon-Regulated Expression of Cellular Splicing Factors Modulates Multiple Levels of HIV-1 Gene Expression and Replication. Viruses 2024;16:938. [PMID: 38932230 PMCID: PMC11209495 DOI: 10.3390/v16060938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]  Open
2
Kramárek M, Souček P, Réblová K, Grodecká L, Freiberger T. Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. Nucleic Acids Res 2024;52:5959-5974. [PMID: 38426935 PMCID: PMC11162779 DOI: 10.1093/nar/gkae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]  Open
3
Sanoguera-Miralles L, Llinares-Burguet I, Bueno-Martínez E, Ramadane-Morchadi L, Stuani C, Valenzuela-Palomo A, García-Álvarez A, Pérez-Segura P, Buratti E, de la Hoya M, Velasco-Sampedro EA. Comprehensive splicing analysis of the alternatively spliced CHEK2 exons 8 and 10 reveals three enhancer/silencer-rich regions and 38 spliceogenic variants. J Pathol 2024;262:395-409. [PMID: 38332730 DOI: 10.1002/path.6243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/28/2023] [Indexed: 02/10/2024]
4
Zhang H, Xin M, Lin L, Chen C, Balestra D, Ding Q. Pleiotropic effects of different exonic nucleotide changes at the same position contribute to hemophilia B phenotypic variation. J Thromb Haemost 2024;22:975-989. [PMID: 38184202 DOI: 10.1016/j.jtha.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
5
Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024;35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
6
Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024;51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
7
Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023;51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023]  Open
8
Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023;24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023]  Open
9
Canson DM, O’Mara TA, Spurdle AB, Glubb DM. Splicing annotation of endometrial cancer GWAS risk loci reveals potentially causal variants and supports a role for NF1 and SKAP1 as susceptibility genes. HGG ADVANCES 2023;4:100185. [PMID: 36908940 PMCID: PMC9996439 DOI: 10.1016/j.xhgg.2023.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023]  Open
10
Barbosa P, Savisaar R, Carmo-Fonseca M, Fonseca A. Computational prediction of human deep intronic variation. Gigascience 2022;12:giad085. [PMID: 37878682 PMCID: PMC10599398 DOI: 10.1093/gigascience/giad085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023]  Open
11
Leman R, Parfait B, Vidaud D, Girodon E, Pacot L, Le Gac G, Ka C, Ferec C, Fichou Y, Quesnelle C, Aucouturier C, Muller E, Vaur D, Castera L, Boulouard F, Ricou A, Tubeuf H, Soukarieh O, Gaildrat P, Riant F, Guillaud‐Bataille M, Caputo SM, Caux‐Moncoutier V, Boutry‐Kryza N, Bonnet‐Dorion F, Schultz I, Rossing M, Quenez O, Goldenberg L, Harter V, Parsons MT, Spurdle AB, Frébourg T, Martins A, Houdayer C, Krieger S. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. Hum Mutat 2022;43:2308-2323. [PMID: 36273432 PMCID: PMC10946553 DOI: 10.1002/humu.24491] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023]
12
Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022;23:482. [PMID: 36376793 PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]  Open
13
Familial history and prevalence of BRCA1, BRCA2 and TP53 pathogenic variants in HBOC Brazilian patients from a public healthcare service. Sci Rep 2022;12:18629. [PMID: 36329109 PMCID: PMC9633799 DOI: 10.1038/s41598-022-23012-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]  Open
14
Müller L, Ptok J, Nisar A, Antemann J, Grothmann R, Hillebrand F, Brillen AL, Ritchie A, Theiss S, Schaal H. Modeling splicing outcome by combining 5'ss strength and splicing regulatory elements. Nucleic Acids Res 2022;50:8834-8851. [PMID: 35947702 PMCID: PMC9410876 DOI: 10.1093/nar/gkac663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/23/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]  Open
15
Holcomb DD, Jankowska KI, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins. STAR Protoc 2022;3:101648. [PMID: 36052345 PMCID: PMC9345850 DOI: 10.1016/j.xpro.2022.101648] [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] [Indexed: 12/14/2022]  Open
16
Splicing mutations in the CFTR gene as therapeutic targets. Gene Ther 2022;29:399-406. [PMID: 35650428 PMCID: PMC9385490 DOI: 10.1038/s41434-022-00347-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
17
Müller L, Moskorz W, Brillen AL, Hillebrand F, Ostermann PN, Kiel N, Walotka L, Ptok J, Timm J, Lübke N, Schaal H. Altered HIV-1 mRNA Splicing Due to Drug-Resistance-Associated Mutations in Exon 2/2b. Int J Mol Sci 2021;23:ijms23010156. [PMID: 35008581 PMCID: PMC8745674 DOI: 10.3390/ijms23010156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 12/02/2022]  Open
18
Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021;43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
19
Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021;4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023]  Open
20
Let It Go: HIV-1 cis-Acting Repressive Sequences. J Virol 2021;95:e0034221. [PMID: 33980600 DOI: 10.1128/jvi.00342-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
21
An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism. Sci Rep 2021;11:14015. [PMID: 34234248 PMCID: PMC8263618 DOI: 10.1038/s41598-021-93390-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]  Open
22
Moles-Fernández A, Domènech-Vivó J, Tenés A, Balmaña J, Diez O, Gutiérrez-Enríquez S. Role of Splicing Regulatory Elements and In Silico Tools Usage in the Identification of Deep Intronic Splicing Variants in Hereditary Breast/Ovarian Cancer Genes. Cancers (Basel) 2021;13:cancers13133341. [PMID: 34283047 PMCID: PMC8268271 DOI: 10.3390/cancers13133341] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022]  Open
23
Bueno-Martínez E, Sanoguera-Miralles L, Valenzuela-Palomo A, Lorca V, Gómez-Sanz A, Carvalho S, Allen J, Infante M, Pérez-Segura P, Lázaro C, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. RAD51D Aberrant Splicing in Breast Cancer: Identification of Splicing Regulatory Elements and Minigene-Based Evaluation of 53 DNA Variants. Cancers (Basel) 2021;13:2845. [PMID: 34200360 PMCID: PMC8201001 DOI: 10.3390/cancers13112845] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/01/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022]  Open
24
Ptok J, Müller L, Ostermann PN, Ritchie A, Dilthey AT, Theiss S, Schaal H. Modifying splice site usage with ModCon: Maintaining the genetic code while changing the underlying mRNP code. Comput Struct Biotechnol J 2021;19:3069-3076. [PMID: 34136105 PMCID: PMC8178101 DOI: 10.1016/j.csbj.2021.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/22/2022]  Open
25
Hotspot exons are common targets of splicing perturbations. Nat Commun 2021;12:2756. [PMID: 33980843 PMCID: PMC8115636 DOI: 10.1038/s41467-021-22780-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/24/2021] [Indexed: 11/08/2022]  Open
26
Functional Analysis of the PCCA and PCCB Gene Variants Predicted to Affect Splicing. Int J Mol Sci 2021;22:ijms22084154. [PMID: 33923806 PMCID: PMC8073151 DOI: 10.3390/ijms22084154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/29/2021] [Accepted: 04/12/2021] [Indexed: 12/03/2022]  Open
27
Holcomb D, Alexaki A, Hernandez N, Hunt R, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Gene variants of coagulation related proteins that interact with SARS-CoV-2. PLoS Comput Biol 2021;17:e1008805. [PMID: 33730015 PMCID: PMC8007013 DOI: 10.1371/journal.pcbi.1008805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/29/2021] [Accepted: 02/15/2021] [Indexed: 12/30/2022]  Open
28
Saint-Martin C, Cauchois-Le Mière M, Rex E, Soukarieh O, Arnoux JB, Buratti J, Bouvet D, Frébourg T, Gaildrat P, Shyng SL, Bellanné-Chantelot C, Martins A. Functional characterization of ABCC8 variants of unknown significance based on bioinformatics predictions, splicing assays, and protein analyses: Benefits for the accurate diagnosis of congenital hyperinsulinism. Hum Mutat 2021;42:408-420. [PMID: 33410562 DOI: 10.1002/humu.24164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/06/2020] [Accepted: 12/31/2020] [Indexed: 12/20/2022]
29
Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2021. [DOI: 10.1016/j.preteyeres.2020.100874 expr 921883647 + 833887994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
30
Martin N, Bergougnoux A, Baatallah N, Chevalier B, Varilh J, Baux D, Costes B, Fanen P, Raynal C, Sermet-Gaudelus I, Girodon E, Taulan-Cadars M, Hinzpeter A. Exon identity influences splicing induced by exonic variants and in silico prediction efficacy. J Cyst Fibros 2020;20:464-472. [PMID: 33341408 DOI: 10.1016/j.jcf.2020.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/22/2020] [Accepted: 12/03/2020] [Indexed: 01/09/2023]
31
Hoser SM, Hoffmann A, Meindl A, Gamper M, Fallmann J, Bernhart SH, Müller L, Ploner M, Misslinger M, Kremser L, Lindner H, Geley S, Schaal H, Stadler PF, Huettenhofer A. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biol 2020;21:299. [PMID: 33292386 PMCID: PMC7722341 DOI: 10.1186/s13059-020-02199-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/09/2020] [Indexed: 02/19/2023]  Open
32
Le Tertre M, Ka C, Raud L, Berlivet I, Gourlaouen I, Richard G, Uguen K, Chen JM, Férec C, Fichou Y, Le Gac G. Splicing analysis of SLC40A1 missense variations and contribution to hemochromatosis type 4 phenotypes. Blood Cells Mol Dis 2020;87:102527. [PMID: 33341511 DOI: 10.1016/j.bcmd.2020.102527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/09/2023]
33
Ptok J, Theiss S, Schaal H. VarCon: An R Package for Retrieving Neighboring Nucleotides of an SNV. Cancer Inform 2020;19:1176935120976399. [PMID: 33281441 PMCID: PMC7691889 DOI: 10.1177/1176935120976399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/01/2020] [Indexed: 11/24/2022]  Open
34
Humphrey S, Kerr A, Rattray M, Dive C, Miller CJ. A model of k-mer surprisal to quantify local sequence information content surrounding splice regions. PeerJ 2020;8:e10063. [PMID: 33194378 PMCID: PMC7648452 DOI: 10.7717/peerj.10063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/08/2020] [Indexed: 12/22/2022]  Open
35
Holcomb D, Alexaki A, Hernandez N, Laurie K, Kames J, Hamasaki-Katagiri N, Komar AA, DiCuccio M, Kimchi-Sarfaty C. Potential impact on coagulopathy of gene variants of coagulation related proteins that interact with SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32935103 DOI: 10.1101/2020.09.08.272328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
36
JMJD6 Regulates Splicing of Its Own Gene Resulting in Alternatively Spliced Isoforms with Different Nuclear Targets. Int J Mol Sci 2020;21:ijms21186618. [PMID: 32927736 PMCID: PMC7555845 DOI: 10.3390/ijms21186618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022]  Open
37
Kováčová T, Souček P, Hujová P, Freiberger T, Grodecká L. Splicing Enhancers at Intron-Exon Borders Participate in Acceptor Splice Sites Recognition. Int J Mol Sci 2020;21:ijms21186553. [PMID: 32911621 PMCID: PMC7554774 DOI: 10.3390/ijms21186553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 02/07/2023]  Open
38
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]
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Erkelenz S, Poschmann G, Ptok J, Müller L, Schaal H. Profiling of cis- and trans-acting factors supporting noncanonical splice site activation. RNA Biol 2020;18:118-130. [PMID: 32693676 DOI: 10.1080/15476286.2020.1798111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]  Open
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Canson D, Glubb D, Spurdle AB. Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 2020;41:1705-1721. [PMID: 32623769 DOI: 10.1002/humu.24074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
41
Tubeuf H, Caputo SM, Sullivan T, Rondeaux J, Krieger S, Caux-Moncoutier V, Hauchard J, Castelain G, Fiévet A, Meulemans L, Révillion F, Léoné M, Boutry-Kryza N, Delnatte C, Guillaud-Bataille M, Cleveland L, Reid S, Southon E, Soukarieh O, Drouet A, Di Giacomo D, Vezain M, Bonnet-Dorion F, Bourdon V, Larbre H, Muller D, Pujol P, Vaz F, Audebert-Bellanger S, Colas C, Venat-Bouvet L, Solano AR, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Gaildrat P, Sharan SK, Martins A. Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System. Cancer Res 2020;80:3593-3605. [PMID: 32641407 DOI: 10.1158/0008-5472.can-20-0895] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
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Splicing mutations in inherited retinal diseases. Prog Retin Eye Res 2020;80:100874. [PMID: 32553897 DOI: 10.1016/j.preteyeres.2020.100874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 05/30/2020] [Accepted: 05/31/2020] [Indexed: 12/15/2022]
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Rong S, Buerer L, Rhine CL, Wang J, Cygan KJ, Fairbrother WG. Mutational bias and the protein code shape the evolution of splicing enhancers. Nat Commun 2020;11:2845. [PMID: 32504065 PMCID: PMC7275064 DOI: 10.1038/s41467-020-16673-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023]  Open
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Ribeiro M, Furtado M, Martins S, Carvalho T, Carmo-Fonseca M. RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy. Int J Mol Sci 2020;21:ijms21041329. [PMID: 32079122 PMCID: PMC7072897 DOI: 10.3390/ijms21041329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/27/2022]  Open
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Skittrall JP, Ingemarsdotter CK, Gog JR, Lever AML. A scale-free analysis of the HIV-1 genome demonstrates multiple conserved regions of structural and functional importance. PLoS Comput Biol 2019;15:e1007345. [PMID: 31545786 PMCID: PMC6791557 DOI: 10.1371/journal.pcbi.1007345] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/14/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022]  Open
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Rhine CL, Neil C, Glidden DT, Cygan KJ, Fredericks AM, Wang J, Walton NA, Fairbrother WG. Future directions for high-throughput splicing assays in precision medicine. Hum Mutat 2019;40:1225-1234. [PMID: 31297895 DOI: 10.1002/humu.23866] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 11/12/2022]
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Katneni UK, Liss A, Holcomb D, Katagiri NH, Hunt R, Bar H, Ismail A, Komar AA, Kimchi‐Sarfaty C. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. Mol Genet Genomic Med 2019;7:e840. [PMID: 31257730 PMCID: PMC6687662 DOI: 10.1002/mgg3.840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 06/10/2019] [Indexed: 12/27/2022]  Open
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Goina E, Musco L, Dardis A, Buratti E. Assessment of the functional impact on the pre-mRNA splicing process of 28 nucleotide variants associated with Pompe disease in GAA exon 2 and their recovery using antisense technology. Hum Mutat 2019;40:2121-2130. [PMID: 31301153 DOI: 10.1002/humu.23867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/11/2022]
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Souček P, Réblová K, Kramárek M, Radová L, Grymová T, Hujová P, Kováčová T, Lexa M, Grodecká L, Freiberger T. High-throughput analysis revealed mutations' diverging effects on SMN1 exon 7 splicing. RNA Biol 2019;16:1364-1376. [PMID: 31213135 DOI: 10.1080/15476286.2019.1630796] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
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Ptok J, Müller L, Theiss S, Schaal H. Context matters: Regulation of splice donor usage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019;1862:194391. [PMID: 31202784 DOI: 10.1016/j.bbagrm.2019.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 11/16/2022]
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