Dr Michela Raponi, PhD - University of Southampton - Career Track Postdoctoral Research Fellow

Dr Michela Raponi

PhD

University of Southampton

Career Track Postdoctoral Research Fellow

United Kingdom

Main Specialties: Oncology

Additional Specialties: RNA splicing, Breast Cancer, Genes Regulation, Evolution

Dr Michela Raponi, PhD - University of Southampton - Career Track Postdoctoral Research Fellow

Dr Michela Raponi

PhD

Introduction

Primary Affiliation: University of Southampton - United Kingdom

Specialties:

Additional Specialties:

Publications

20Publications

258Reads

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353PubMed Central Citations

BRCA1 exon 11 a model of long exon splicing regulation.

RNA Biol 2014 18;11(4):351-9. Epub 2014 Mar 18.

University of Southampton; Southampton, United Kingdom.

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http://dx.doi.org/10.4161/rna.28458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075520PMC
January 2015
50 Reads
4 Citations
4.974 Impact Factor

RBFOX2 protein domains and cellular activities.

Biochem Soc Trans.

RBFOX2 (RNA-binding protein, Fox-1 homologue 2)/RBM9 (RNA-binding-motif protein 9)/RTA (repressor of tamoxifen action)/HNRBP2 (hexaribonucleotide-binding protein 2) encodes an RNA-binding protein involved in tissue specific alternative splicing regulation and steroid receptors transcriptional activity. Its ability to regulate specific splicing profiles depending on context has been related to different expression levels of the RBFOX2 protein itself and that of other splicing regulatory proteins involved in the shared modulation of specific genes splicing. However, this cannot be the sole explanation as to why RBFOX2 plays a widespread role in numerous cellular mechanisms from development to cell survival dependent on cell/tissue type. RBFOX2 isoforms with altered protein domains exist. In the present article, we describe the main RBFOX2 protein domains, their importance in the context of splicing and transcriptional regulation and we propose that RBFOX2 isoform distribution may play a fundamental role in RBFOX2-specific cellular effects.

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August 2014
10 Reads

BRCA1 EXON 11, a CERES (composite regulatory element of splicing) element involved in splice regulation.

Int J Mol Sci 2014 Jul 23;15(7):13045-59. Epub 2014 Jul 23.

Human Development and Health, University of Southampton, Southampton SO16 6YD, UK.

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http://dx.doi.org/10.3390/ijms150713045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139890PMC
July 2014
55 Reads
3 Citations
2.862 Impact Factor

Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11.

PLoS One 2012 16;7(5):e37255. Epub 2012 May 16.

Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0037255PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3353946PMC
September 2012
8 Reads
7 Citations
3.234 Impact Factor

Systematic screening of FBN1 gene unclassified missense variants for splice abnormalities.

Clin Genet.

Defects at the level of pre-mRNA splicing are a common source of genetic mutation but such mutations are not always easy to identify from DNA sequence data alone. Clinical practice has only recently begun to incorporate analysis for this type of abnormality. Some base changes at the DNA level currently viewed as unclassified variants or missense mutations may influence RNA splicing. To address this problem for fibrillin 1 (FBN1) gene missense mutations we have carried out RNA analysis and in silico analysis with splice site prediction programs on 40 cases with 36 different mutations. Direct analysis of RNA from blood was performed by cDNA preparation, PCR amplification of specific FBN1 fragments, gel electrophoresis and sequencing of the PCR products. Of the 36 missense base changes, direct RNA analysis identified 2 which caused an abnormality of splicing. In silico analysis using five splice site prediction programs did not always accurately predict the splicing seen by direct RNA analysis. In conclusion, some apparent missense mutations have an effect on splicing which can be identified by direct RNA analysis, however, in silico analysis of splice sites is not always accurate, should be carried out with more than one prediction program and results should be used with caution.

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September 2012
6 Reads

BRCA1 exon 11 alternative splicing, multiple functions and the association with cancer.

Biochem Soc Trans 2012 Aug;40(4):768-72

Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.

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http://dx.doi.org/10.1042/BST20120140DOI Listing
August 2012
9 Reads
15 Citations
3.194 Impact Factor

Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11.

PLoS One

BACKGROUND: Alternative splicing across exon 11 produces several BRCA1 isoforms. Their proportion varies during the cell cycle, between tissues and in cancer suggesting functional importance of BRCA1 splicing regulation around this exon. Although the regulatory elements driving exon 11 splicing have never been identified, a selective constraint against synonymous substitutions (silent nucleotide variations that do not alter the amino acid residue sequence) in a critical region of BRCA1 exon 11 has been reported to be associated with the necessity to maintain regulatory sequences. METHODOLOGY/PRINCIPAL FINDINGS: Here we have designed a specific minigene to investigate the possibility that this bias in synonymous codon usage reflects the need to preserve the BRCA1 alternative splicing program. We report that in-frame deletions and translationally silent nucleotide substitutions in the critical region affect splicing regulation of BRCA1 exon 11. CONCLUSIONS/SIGNIFICANCE: Using a hybrid minigene approach, we have experimentally validated the hypothesis that the need to maintain correct alternative splicing is a selective pressure against translationally silent sequence variations in the critical region of BRCA1 exon 11. Identification of the trans-acting factors involved in regulating exon 11 alternative splicing will be important in understanding BRCA1-associated tumorigenesis.

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May 2012
6 Reads

Novel Tandem Duplication in Exon 1 of the SNURF/SNRPN Gene in a Child with Transient Excessive Eating Behaviour and Weight Gain.

Mol Syndromol

A deletion in 15q11.2 involving the SNURF/SNRPN gene is the typical finding in patients with Prader-Willi syndrome. Apart from translocations disrupting this gene, no other mutation types have been described so far. We report a patient in whom a small duplication in exon 1 of the SNURF/SNRPN gene was diagnosed which is predicted to interrupt only SNURF expression. The patient was investigated due to overgrowth, increased appetite and developmental delay in childhood. This duplication was inherited from her father who carries the duplication on his paternal chromosome 15 and also had transient excessive eating behaviour as an adolescent. RNA studies showed that the duplication introduces a premature stop codon in SNURF.

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January 2012
6 Reads

Prediction of single-nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6.

Hum Mutat 2011 Apr 8;32(4):436-44. Epub 2011 Mar 8.

University of Southampton School of Medicine, Southampton, United Kingdom.

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http://dx.doi.org/10.1002/humu.21458DOI Listing
April 2011
13 Reads
23 Citations
5.144 Impact Factor

An intronic mutation in MLH1 associated with familial colon and breast cancer.

Fam. Cancer

Single base substitutions can lead to missense mutations, silent mutations or intronic mutations, whose significance is uncertain. Aberrant splicing can occur due to mutations that disrupt or create canonical splice sites or splicing regulatory sequences. The assessment of their pathogenic role may be difficult, and is further complicated by the phenomenon of alternative splicing. We describe an HNPCC patient, with early-onset colorectal cancer and a strong family history of colorectal and breast tumors, who harbours a germ line MLH1 intronic variant (IVS9 c.790 +4A>T). The proband, together with 2 relatives affected by colorectal-cancer and 1 by breast cancer, have been investigated for microsatellite instability, immunohistochemical MMR protein staining, direct sequencing and Multiplex Ligation-dependent Probe Amplification. The effect of the intronic variant was analyzed both by splicing prediction software and by hybrid minigene splicing assay. In this family, we found a novel MLH1 germline intronic variant (IVS9 c.790 +4A>T) in intron 9, consisting of an A to T transversion, in position +4 of the splice donor site of MLH1. The mutation is associated with the lack of expression of the MLH1 protein and MSI in tumour tissues. Furthermore, our results suggest that this substitution leads to a complete skip of both exon 9 and 10 of the mutant allele. Our findings suggest that this intronic variant plays a pathogenic role.

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March 2011
6 Reads

Expanding the tuberous sclerosis phenotype: mild disease caused by a TSC1 splicing mutation.

J Neurol Neurosurg Psychiatry 2010 Mar;81(3):350-2

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http://dx.doi.org/10.1136/jnnp.2009.179689DOI Listing
March 2010
1 Read
2 Citations
6.810 Impact Factor

Alternative splicing: good and bad effects of translationally silent substitutions.

FEBS J. 2010 Feb;277(4):836-40.

FEBS J.

Nucleotide variations that do not alter the protein-coding sequence have been routinely considered as neutral. In light of the developments we have seen over the last decade or so in the RNA processing and translational field, it would be proper when assessing these variants to ask if this change is neutral, good or bad. This question has been recently partly addressed by genome-wide in silico analysis but significantly fewer cases by laboratory experimental examples. Of particular relevance is the effect these mutations have on the pre-mRNA splicing pattern. In fact, alterations in this process may occur as a consequence of translationally silent mutations leading to the expression of novel splicing isoforms and/or loss of an existing one. This phenomenon can either generate new substrates for evolution or cause genetic disease when aberrant isoforms altering the essential protein function are produced. In this review we briefly describe the current understanding in the field and discuss emerging directions in the study of the splicing mechanism by integrating disease-causing splicing mutations and evolutionary changes.

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February 2010
7 Reads

Low U1 snRNP dependence at the NF1 exon 29 donor splice site.

FEBS J 2009 Apr;276(7):2060-73

Department of Pathology, University of Cambridge, UK.

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http://dx.doi.org/10.1111/j.1742-4658.2009.06941.xDOI Listing
April 2009
8 Reads
4 Citations
4.001 Impact Factor

Polypyrimidine tract binding protein regulates alternative splicing of an aberrant pseudoexon in NF1.

FEBS J 2008 Dec 1;275(24):6101-8. Epub 2008 Nov 1.

Human Genetics Division, University of Southampton, UK.

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http://dx.doi.org/10.1111/j.1742-4658.2008.06734.xDOI Listing
December 2008
27 Reads
7 Citations
4.001 Impact Factor

Can donor splice site recognition occur without the involvement of U1 snRNP?

Biochem Soc Trans 2008 Jun;36(Pt 3):548-50

Human Genetics Division, University of Southampton, Duthie Building (Mailpoint 808), Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.

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http://dx.doi.org/10.1042/BST0360548DOI Listing
June 2008
1 Read
2 Citations
3.194 Impact Factor

Reduced splicing efficiency induced by synonymous substitutions may generate a substrate for natural selection of new splicing isoforms: the case of CFTR exon 12.

Nucleic Acids Res 2007 15;35(2):606-13. Epub 2006 Dec 15.

International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy.

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http://dx.doi.org/10.1093/nar/gkl1087DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802620PMC
March 2007
6 Reads
6 Citations
9.112 Impact Factor

Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization.

Hum Mutat. 2006 Mar;27(3):294-5.

Hum Mutat.

Genomic variations with no apparent effect ("neutral polymorphisms") may have a significant effect on splicing. The effect of this type of mutation is difficult to spot, unless a functional assay is undertaken. In our study, DNA sequencing of a patient with clinically defined neurofibromatosis type 1 (NF1) showed only a single polymorphism in intron 30 due to an A>G transition 279 nucleotides from the 3' splice site. Using a minigene splicing assay we conclusively show that this change produces a cryptic exon with a 3' SS defined by the nucleotide change and the unexpected activation of a very weak 5'SS. Further site directed mutagenesis studies aimed at identifying the signals involved in the cryptic exon inclusion were carried out. Interestingly we find that particular characteristics of the cryptic 5' SS are essential for its inclusion. Significantly an additional single nucleotide change disrupting the cryptic 5'ss consensus sequence rescues the effect of the pathogenetic mutation resulting in normal splicing.

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March 2006
6 Reads

Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution.

Proc Natl Acad Sci U S A 2005 May 19;102(18):6368-72. Epub 2005 Apr 19.

International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy.

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http://dx.doi.org/10.1073/pnas.0502288102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088389PMC
May 2005
14 Reads
79 Citations
9.810 Impact Factor

A centrosomal mechanism involving CDK5RAP2 and CENPJ controls brain size.

Nat Genet 2005 Apr 27;37(4):353-5. Epub 2005 Mar 27.

Molecular Medicine Unit, University of Leeds, St. James's University Hospital, Beckett Street, Leeds LS9 7TF, UK.

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http://dx.doi.org/10.1038/ng1539DOI Listing
April 2005
27 Reads
183 Citations
29.352 Impact Factor