In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects

Lastella, Patrizia; Concetta Surdo, Nicoletta; Resta, Nicoletta; Guanti, Ginevra; Stella, Alessandro
January 2006
BMC Genomics;2006, Vol. 7, p1
Academic Journal
Background: Abnormalities of pre-mRNA splicing are increasingly recognized as an important mechanism through which gene mutations cause disease. However, apart from the mutations in the donor and acceptor sites, the effects on splicing of other sequence variations are difficult to predict. Loosely defined exonic and intronic sequences have been shown to affect splicing efficiency by means of silencing and enhancement mechanisms. Thus, nucleotide substitutions in these sequences can induce aberrant splicing. Web-based resources have recently been developed to facilitate the identification of nucleotide changes that could alter splicing. However, computer predictions do not always correlate with in vivo splicing defects. The issue of unclassified variants in cancer predisposing genes is very important both for the correct ascertainment of cancer risk and for the understanding of the basic mechanisms of cancer gene function and regulation. Therefore we aimed to verify how predictions that can be drawn from in silico analysis correlate with results obtained in an in vivo splicing assay. Results: We analysed 99 hMLH1 and hMSH2 missense mutations with six different algorithms. Transfection of three different cell lines with 20 missense mutations, showed that a minority of them lead to defective splicing. Moreover, we observed that some exons and some mutations show cell-specific differences in the frequency of exon inclusion. Conclusion: Our results suggest that the available algorithms, while potentially helpful in identifying splicing modulators especially when they are located in weakly defined exons, do not always correspond to an obvious modification of the splicing pattern. Thus caution must be used in assessing the pathogenicity of a missense or silent mutation with prediction programs. The variations observed in the splicing proficiency in three different cell lines suggest that nucleotide changes may dictate alternative splice site selection in a tissue-specific manner contributing to the widely observed phenotypic variability in inherited cancers.


Related Articles

  • Restoration of Mismatch Repair Functions in Human Cell Line Nalm-6, Which Has High Efficiency for Gene Targeting. Suzuki, Tetsuya; Ukai, Akiko; Honma, Masamitsu; Adachi, Noritaka; Nohmi, Takehiko // PLoS ONE;Apr2013, Vol. 8 Issue 4, p1 

    Gene targeting is a powerful approach in reverse genetics. The approach has been hampered in most of human cell lines, however, by the poor targeting efficiency. Nalm-6, a human pre-B acute lymphoblastic leukemia cell line, exhibits exceptionally high gene targeting efficiency and is used in DNA...

  • Genomic deletions of MSH2 and MLH1 in colorectal cancer families detected by a novel mutation detection approach. Gille, J.J.P.; Hogervorst, F.B.L.; Pals, G; Wijnen, J Th; van Schooten, R J; Dommering, C J; Meijer, G A; Craanen, M E; Nederlof, P M; de Jong, D; McElgunn, C J; Schouten, J P; Menko, F H // British Journal of Cancer;10/7/2002, Vol. 87 Issue 8, p892 

    Hereditary non-polyposis colorectal cancer is an autosomal dominant condition due to germline mutations in DNA-mismatch-repair genes, in particular MLH1, MSH2 and MSH6. Here we describe the application of a novel technique for the detection of genomic deletions in MLH1 and MSH2. This method,...

  • Pooled-DNA sequencing identifies novel causative variants in PSEN1, GRN and MAPT in a clinical early-onset and familial Alzheimer's disease Ibero-American cohort. Sheng Chih Jin; Pastor, Pau; Cooper, Breanna; Cervantes, Sebastian; Benitez, Bruno A.; Razquin, Cristina; Goate, Alison; Cruchaga, Carlos // Alzheimer's Research & Therapy;2012, Vol. 4 Issue 4, p34 

    Introduction: Some familial Alzheimer's disease (AD) cases are caused by rare and highly-penetrant mutations in APP, PSEN1, and PSEN2. Mutations in GRN and MAPT, two genes associated with frontotemporal dementia (FTD), have been found in clinically diagnosed AD cases. Due to the dramatic...

  • Genetic Modulation of CD44 Expression by Intragraft Fibroblasts. Wu, Gordon D.; Hong Wang; Hui Zhu; Yao He; Barr, Mark L.; Klein, Andrew S. // Journal of Biochemistry;Nov2008, Vol. 144 Issue 5, p571 

    This study investigated the genetic composition and the functional implication of CD44 species expressed by intragraft fibroblasts. An LEW-to-F344 heart transplant model of chronic rejection was used. Intragraft fibroblasts recovered from the chronically rejecting allografts displayed a 4.5-fold...

  • Nucleotide sequence comparisons between several strains and isolates of human cytomegalovirus reveal alternate start codon usage. Brondke, H.; Schmitz, B.; Doerfler, W. // Archives of Virology;Nov2007, Vol. 152 Issue 11, p2035 

    Mutations abound in all viral populations, which are thus rendered adaptable to changes in environmental conditions. Human cytomegalovirus (HCMV) is an important human pathogen for investigating nucleotide sequence variations because they can affect its potential to cause disease. We have...

  • Cancer: Mutations close in on gene regulation. Aerts, Stein; Cools, Jan // Nature;7/4/2013, Vol. 499 Issue 7456, p35 

    The article discuses discovery of several sequences in adult acute myeloid leukemia. The researchers at the Cancer Genome Atlas Research Network have discovered DNA sequences, transcribed messenger RNA sequences and microRNA sequences along with DNA modification caused by methylation in such...

  • Exome Analyses of Long QT Syndrome Reveal Candidate Pathogenic Mutations in Calmodulin-Interacting Genes. Shigemizu, Daichi; Aiba, Takeshi; Nakagawa, Hidewaki; Ozaki, Kouichi; Miya, Fuyuki; Satake, Wataru; Toda, Tatsushi; Miyamoto, Yoshihiro; Fujimoto, Akihiro; Suzuki, Yutaka; Kubo, Michiaki; Tsunoda, Tatsuhiko; Shimizu, Wataru; Tanaka, Toshihiro // PLoS ONE;7/1/2015, Vol. 10 Issue 7, p1 

    Long QT syndrome (LQTS) is an arrhythmogenic disorder that can lead to sudden death. To date, mutations in 15 LQTS-susceptibility genes have been implicated. However, the genetic cause for approximately 20% of LQTS patients remains elusive. Here, we performed whole-exome sequencing analyses on...

  • Integrating Transcriptome and Genome Re-Sequencing Data to Identify Key Genes and Mutations Affecting Chicken Eggshell Qualities. Zhang, Quan; Zhu, Feng; Liu, Long; Zheng, Chuan Wei; Wang, De He; Hou, Zhuo Cheng; Ning, Zhong Hua // PLoS ONE;May2015, Vol. 10 Issue 5, p1 

    Eggshell damages lead to economic losses in the egg production industry and are a threat to human health. We examined 49-wk-old Rhode Island White hens (Gallus gallus) that laid eggs having shells with significantly different strengths and thicknesses. We used HiSeq 2000 (Illumina) sequencing to...

  • Naive Bayes for microRNA target predictions machine learning for microRNA targets. Malik Yousef; Segun Jung; Andrew V. Kossenkov; Louise C. Showe; Michael K. Showe // Bioinformatics;Nov2007, Vol. 23 Issue 22, p2987 

    Motivation: Most computational methodologies for miRNA:mRNA target gene prediction use the seed segment of the miRNA and require cross-species sequence conservation in this region of the mRNA target. Methods that do not rely on conservation generate numbers of predictions, which are too large to...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics