Ian C Eperon

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Chair in Biochemistry

Tel: +44 (0)116 229 7012

Email: eci@le.ac.uk

 

 

 

 

 

Personal details

  • PhD with Dr Fred Sanger: MRC Laboratory of Molecular Biology, Cambridge University, 1981
  • SERC-NATO post-doctoral fellow with Joan Steitz, Yale University, USA, 1982 and 1983
  • Joined staff of Department of Biochemistry in 1984
  • Appointed Reader in Biochemistry from 1994
  • Awarded a Personal Chair in Biochemistry, 2000

Publications

  • Reichenbach, L.F., Agnew, C., Ahmad Sobri, A., Burton, N., Zaccai, N.R., Eperon, L.P., de Ornellas, S., Eperon, I.C., Brady, R.L., and Burley, G.A. (2016). Structural Basis for mis-pairing of an artificially expanded genetic information system. Chem (Cell Press) 1, 946-958.
  • Chen, L., Weinmeister, R., Kralovicova, J., Eperon, L.P., Vorechovsky, I., Hudson, A.J., and Eperon, I.C. (2017). Stoichiometries of U2AF35, U2AF65 and U2 snRNP reveal new early spliceosome assembly pathways. Nucleic Acids Research, published online prior to paper. (doi:10.1093/nar/gkw860).
  • Weldon, C., Behm-Ansmant, I., Hurley, L.H., Burley, G.A., Branlant, C., Eperon, I.C.,* and Dominguez, C.* (2017). Identification of G-quadruplexes in functional RNAs using 7-deaza-guanine. Nature Chemical Biology 13, 18-20 (doi: 10.1038/nchembio.2228). (* Joint senior authors).
  • Weldon, C., Eperon, I.C., and Dominguez, C. (2016). Do we know whether potential G-quadruplexes actually form in long functional RNA molecules? Biochemical Society Transactions 15, 1761-1768.
  • Feracci, M., Foot, J.N., Grellscheid, S.N., Danilenko, M., Stehle, R., Kang, H.S., Dalgleish, C., Meyer, N.H., Liu, Y., Sattler, M., Eperon, I.C., Elliott, D.J., & Dominguez, C. (2016). Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68. Nat. Commun. 7, 10355 (doi: 10.1038/ncomms10355).
  • Weinmeister, R., Freeman, E., Eperon, I.C., Stuart, A.M., & Hudson, A.J. (2015). Single-fluorophore detection in femtoliter droplets generated by flow focusing. ACS Nano 9, 9718-9730 (doi: 10.1021/acsnano.5b02422).
  • Smith, L.D., Dickinson, R.L., Lucas, C.M., Cousins, A., Malygin, A.A., Weldon, C., Perrett, A.J., Bottrill, A.R., Searle, M.S., Burley, G.A.,  & Eperon, I.C. (2014). A targeted oligonucleotide enhancer of SMN2 exon 7 splicing forms competing quadruplex and protein complexes in functional conditions. Cell Reports 9, 193-205 (doi: 10.1016/j.celrep.2014.08.051).
  • Smith, L.D., Lucas, C.M., and Eperon, I.C. (2013). Intron retention in the alternatively spliced region of RON results from weak 3’ splice site recognition. PLoS ONE 8(10): e77208. (doi:10.1371/journal.pone.0077208).
  • Schmid R, Grellscheid SN, Ehrmann I, Dalgleish C, Danilenko M, Paronetto MP, Pedrotti S, Grellscheid D, Dixon RJ, Sette C, Eperon IC, Elliott DJ (2013) The splicing landscape is globally reprogrammed during male meiosis. Nucleic Acids Res. 41, 10170-10184 ( DOI: 10.1093/nar/gkt811).
  • Gooding C, Edge C, Lorenz M, Coelho MB, Winters M, Kaminski CF, Cherny D, Eperon IC, Smith CWJ (2013) MBNL1 and PTB cooperate to repress splicing of Tpm exon 3. Nucleic Acids Research 41, 4765-4782 (DOI: 10.1093/nar/gkt168).
  • Zhou H, Janghra N, Mitrpant C, Dickinson R, Anthony K, Eperon I, Wilton S, Morgan J, Muntoni F (2013) A novel morpholino oligomer targeting ISS-N1 improves rescue of severe SMA transgenic mice. Human Gene Therapy 24, 1-12 (DOI:10.1089/hum.2012.211).
  • Roca X*, Krainer AR, Eperon IC* (2013). Pick one, but be quick: 5’ splice sites and the problems of too many choices. Genes & Development 27, 129-144 (DOI:10.1101/gad.209759.112).
  • Perrett AJ, Dickinson RL, Krpetić Z, Brust M, Lewis H, Eperon IC*, Burley GA* (2012) Conjugation of PEG and gold nanoparticles to increase the accessibility and valency of tethered RNA splicing enhancers. Chemical Science 4, 257-265 (DOI: 10.1039/C2SC20937C).
  • Lewis H, Perrett AJ, Burley GA*, Eperon IC* (2012). An RNA splicing enhancer that does not act by looping. Angewandte Chem. Int. Ed. 51, 9800-9803 (DOI: 10.1002/anie.201202932).
  • Eperon I (2012) New ways to nudge splicing. Nature Chemical Biology 8, 507-508.
  • Kafasla P, Mickleburgh I, Llorian M, Coelho M, Gooding C, Cherny D, Joshi A, Kotik-Kogan O, Curry S, Eperon I, Jackson R, Smith CWJ. (2012) Defining the roles and interactions of PTB. Biochem. Soc. Trans. 40, 815-820.
  • Hodson MJ, Hudson AJ, Cherny D, Eperon IC. (2012) The transition in spliceosome assembly from complex E to complex A purges surplus U1 snRNPs from alternative splice sites. Nucleic Acids Res. 40, 6850-6862. Featured article (top 5 %).
  • Fedorova OA, Moiseeva TN, Nikiforov AA, Tsimokha AS, Livinskaya VA, Hodson M, Bottrill A, Evteeva IN, Ermolayeva JB, Kuznetzova IM, Turoverov KK, Eperon I, Barlev NA. (2011). Proteomic analysis of the 20S proteasome (PSMA3)-interacting proteins reveals a functional link between the proteasome and mRNA metabolism. Biochem. Biophys. Res. Comm. 416, 258-265.
  • Owen N, Zhou H, Malygin A, Sangha J, Smith LD, Muntoni F, Eperon IC (2011). Design principles for bifunctional targeted oligonucleotide enhancers of splicing. Nucleic Acids Res., 39, 7194-7208.
  • Cherny D, Gooding C, Eperon GE, Coelho MB, Bagshaw CR, Smith CWJ, Eperon IC (2010) Stoichiometry of a regulatory splicing complex revealed by single molecule analyses. EMBO J. 29, 2161 - 2172.
  • Ghigna C, De Toledo M, Valacca C, Bonomi S, Gallo G, Apicella M, Eperon I, Tazi J, Biamonti G (2010). Pro-metastatic splicing of Ron proto-oncogene mRNA can be reversed: therapeutic potential of bifunctional oligonucleotides and indoles. RNA Biology 7, 1-9.
  • Cherny DI, Eperon IC, Bagshaw CR. (2009). Probing complexes with single fluorophores: factors contributing to dispersion of FRET in DNA/RNA duplexes. Eur. Biophys. J.38, 395-405.
  • Malygin A, Parakhnevitch NM, Ivanov AV, Eperon IC, Karpova GG. (2007). Human ribosomal protein S13 regulates expression of its own gene at the splicing step by a feedback mechanism. Nuc. Acids Res. 35, 6414-6423.
  • Dixon RJ, Eperon IC, Samani NJ. (2007). Complementary intron sequence motifs associated with human exon repetition: a role for intragenic, inter-transcript interactions in gene expression. Bioinformatics 23, 150-155.
  • Nasim MT, Eperon IC. (2006). A double-reporter splicing assay for determining splicing efficiency in mammalian cells. Nature Protocols 1, 1022-1028.
  • Dixon RJ, Eperon IC, Hall L, Samani NJ. (2005). A genome-wide survey demonstrates widespread non-kinear mRNA in expressed sequences from multiple species. Nuc. Acids Res. 33, 5904-5913.
  • Nasim MT, Eperon IC, Wilkins BM, Brammar WJ. (2004). The activity of a single-stranded promoter of plasmid ColIb-P9 depends on its secondary structure. Molecular Microbiology 53, 405-417.
  • Rigatti R, Jia J-H, Samani NJ, Eperon IC. (2004). Exon repetition: a major pathway for processing mRNA of some genes is allele-specific. Nuc. Acids Res. 32, 441-446.
  • Eperon IC, Muntoni F. (2003). Response to Buratti et al.: Can a 'patch' in a skipped exon make the pre-mRNA splicing machine run better? Trends Mol. Med. 9, 233-234.
  • Skordis LA, Dunckley MG, Yue B-G, Eperon IC, Muntoni F. (2003). Bifunctional antisense oligonucleotides provide a trans-acting splicing enhancer that stimulates SMN2 gene expression in patient fibroblasts. Proc. Natl Acad. Sci. USA 100, 4114-4119.
  • Nasim MT, Chernova TK, Chowdhury HM, Yue B-G, Eperon IC. (2003). HnRNP G and Tra2beta: opposite effects on splicing matched by antagonism in RNA binding. Hum. Mol. Gen. 12, 1337-1348.
  • Stover CM, Lynch NJ, Dahl MR, Hanson S, Takahashi M, Frankenberger M, Ziegler-Heitbrock L, Eperon IC, Thiel S, Schwaeble WJ. (2003). Murine serine proteases MASP-1 and MASP-3, components of the lectin pathway activation complex of complement, are encoded by a single structural gene. Genes and Immunity 4, 374-384.
  • Nasim MI, Chowdhury HM, Eperon IC. (2002). A double reporter assay for detecting changes in the ratio of spliced and unspliced mRNA in mammalian cells. Nuc. Acids Res. 30, e109 (6 pages).
  • Eperon IC, Makarova O, Mayeda A, Munroe SH, Caceres JF, Hayward DG, Krainer AR. (2000). Selection of alternative 5' splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1. Mol. Cell. Biol. 20, 8303-8318.
  • Elliott DJ, Venables JP, Newton C, Lawson D, Boyle S, Eperon IC, Cooke HJ. (2000). An evolutionary conserved germ cell-specific hnRNP is encoded by a retrotransposed gene. Hum. Mol. Gen. 9, 2117-2124. (September 2000, front cover).
  • Venables JP, Elliott DJ, Makarova OV, Makarov EM, Cooke HJ, Eperon IC. (2000). RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2b and affect splicing. Hum. Mol. Gen. 9, 685-694.
  • Chew SL, Baginsky L, Eperon IC. (2000). An exonic splicing silencer in the testis-specific DNA ligase III beta exon. Nucleic Acids Res. 27, 402-410.
  • Venables JP, Vernet C, Chew SL, Elliott DJ, Cowmeadow RB, Wu J, Cooke HJ, Artzt K, Eperon IC. (1999). T-STAR/E TOILE: a novel relative of SAM68 that interacts with an RNA-binding protein implicated in spermatogenesis. Hum. Mol. Gen. 8, 959-969.
  • Frantz SA, Thiara AS, Lodwick D, Eperon IC, Samani NJ. (1999). Exon repetition in mRNA. Proc. Natl Acad. Sci. USA 96, 5400-5405.
  • Venables JP, Eperon IC. (1999). The roles of RNA-binding proteins in spermatogenesis and male infertility. Curr. Op. Gen. Dev. 9, 346-354.
  • O'Mullane L, Eperon IC. (1998). The pre-mRNA 5' cap determines whether U6 small nuclear RNA succeeds U1 small nuclear ribonucleoprotein particle at 5' splice sites. Mol. Cell. Biol. 18, 7510-7520.
  • Dunckley MG, Manoharan M, Villiet P, Eperon IC, Dickson G. (1998). Modification of splicing in the dystrophin gene in cultured mdx muscle cells by antisense oligoribonucleotides. Hum. Mol. Gen. 7, 1083-1090.
  • Elliott DJ, Oghene K, Makarov G, Makarova O, Hargreave TB, Chandley AC, Eperon IC, Cooke HJ. (1998). Dynamic changes in the subnuclear organisation of pre-mRNA splicing proteins and RBM during human germ cell development. J. Cell Sci. 111, 1255-1265.
  • Dunckley M, Eperon IC, Dickson G. (1997). Modulation of splicing in the DMD gene by antisense oligonucleotides. Nucleotides and Nucleotides 16, 1665-1668.
  • Vekony MA, Holder JE, Lee AI, Horrocks C, Eperon IC, Camp RDR. (1997). Selective simplification of T-cell receptor variable region species is demonstrable but not essential in early lesions of psoriasis vulgaris: analysis by anchored polymerase chain reaction and hypervariable region size spectratyping. J. Invest. Dermatol. 109, 5-13.
  • Willmott CJR, Critchlow SE, Eperon IC, Maxwell A. (1994) The complex of DNA gyrase and quinolone drugs with DNA forms a barrier to transcription by RNA polymerase. J. Mol. Biol. 242, 351-363.
  • Eperon IC, Krainer AR. (1994) Splicing of Messenger RNA Precursors. In RNA Processing: a Practical Approach, eds Hames, D., and Higgins, S. Oxford University Press, pp. 57-101.
  • Eperon IC, Ireland DC, Smith RA, Mayeda A, Krainer AR. (1993) Pathways for selection of 5' splice sites by U1 snRNPs and SF2/ASF. EMBO J. 12, 3607-3617.
  • Hamshere M, Eperon IC. (1993) Applications of gene transfer for analysis of pre-mRNA splicing. Journal of Tissue Culture Methods 15, 99-107.
  • Graham IR, Hamshere M, Eperon IC. (1992) Alternative splicing of a human alpha-tropomyosin muscle-specific exon: Identification of determining sequences. Mol. Cell. Biol. 12, 3872-3882.
  • Waites GT, Graham IR, Jackson P, Millake DB, Patel B, Blanchard AD, Weller P, Eperon IC, Critchley DR. (1991). Mutually-exclusive splicing of calcium-binding domain exons in chick alpha-actinin. J. Biol. Chem. 267, 6263-6271.
  • Hamshere M, Dickson G, Eperon I. (1991). The muscle-specific domain of mouse N-CAM: structure and alternative splicing patterns. Nuc. Acids Res. 19, 4709-4716.
  • Garde J, Bell SC, Eperon IC. (1991) Multiple forms of mRNA encoding human pregnancy-associated endometrial alpha 2-globulin, a beta-lactoglobulin homologue. Proc. Natl. Acad. Sci. USA 88, 2456-2460.
  • Skilton H, Eperon IC, Rivett JA. (1991). Co-purification of a small RNA species with multicatalytic proteinase (proteasome) from rat liver. FEBS Lett. 279, 351-355.
  • Cunningham SA, Else AJ, Potter BVL, Eperon IC. (1991). The influences of separation and adjacent sequences on the use of alternative 5' splice sites. J. Mol. Biol. 217, 265-281.
  • Lear AL, Eperon LP, Wheatley IM, Eperon IC. ( 1990). A hierarchy for 5' splice site preference determined in vivo. J. Mol. Biol. 211, 103-115.
  • Eperon LP, Graham IR, Griffiths AD, Eperon IC. (1988) The effects of RNA secondary structure on alternative splicing of pre-mRNA: is folding limited to a region behind the transcribing RNA polymerase? Cell 54, 393-401.
  • Griffiths AD, Potter BVL, Eperon IC. (1988). Substitution of pre-mRNA with phosphorothioate linkages reveals a new splicing-related reaction. J. Biol. Chem. 263, 12295-12304.
  • Eperon IC. (1988) M13 cloning and dideoxy sequencing. In Gene Cloning and Analysis: a Laboratory Guide (ed. G.J. Boulnois), pp. 107-122, Blackwell Scientific.
  • Eperon IC. (1988) Oligonucleotide Mutagenesis. Ibid., pp. 123-128.
  • Eperon IC. (1988) Mapping RNA. Ibid., pp. 129-136.
  • Turnbull-Ross AD, Else AJ, Eperon IC. (1988) The dependence of splicing efficiency on the length of 3' exon. Nucl. Acids Res. 16, 395-411.
  • Deeney CMM, Eperon IC, Potter BVL. (1987) Self-splicing of tetrahymena rRNA can proceed with phosphorothioate substitution at the splice sites. Nucl. Acids Res. Symposium Series No. 18, 277-280.
  • Griffiths AD, Potter BVL, Eperon IC. (1987) Stereospecificity of nucleases towards phosphorothioate-substituted RNA: stereochemistry of transcription by T7 RNA polymerase. Nucl. Acids Res. 15, 4145-4162.
  • Price GJ, Jones P, Davison MD, Patel B, Eperon IC, Critchley DR. (1987) Isolation and characterization of a vinculin cDNA from chick-embryo fibroblasts. Biochem. J. 245, 595-603.
  • Eperon LP, Estibeiro JP, Eperon IC. (1986) The role of nucleotide sequences in splice site selection in eukaryotic pre-messenger RNA. Nature 324, 280-282.
  • Skinner JA, Eperon IC. (1986) Misincorporation by AMV reverse transcriptase shows strong dependence on the combination of template and substrate nucleotides. Nucl. Acids Res. 14, 6945-6964.
  • Eperon IC. (1986) Rapid preparation of bacteriophage DNA for sequence analysis in sets of 96 clones, using filtration. Analyt. Biochem. 156, 406-412.
  • Eperon IC. (1986) M13 vectors with T7 polymerase promoters : transcription limited by oligonucleotides. Nucl. Acids Res. 14, 2830.
  • Eperon IC, Janssen JWG, Hoeijmakers JHJ, Borst P. (1983). The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs. Nucl. Acids Res. 11, 105-125.
  • Anderson, S, de Bruijn, MH, Coulson, AR, Eperon, IC, Sanger, F, and Young, IG (1982) The complete sequence of bovine mitochondrial DNA: Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156, 683-717.
  • Anderson, S, Bankier, AT, Barrell, BG, de Bruijn, MH, Coulson, AR, Drouin, J, Eperon, IC, Nierlich, DP, Roe, BA, Sanger, F, Schreier, PH, Smith, AJ, Staden, R, and Young, IG (1981). The sequence and organisation of the human mitochondrial genome. Nature 290, 457-467.
  • de Bruijn, MH, Schreier, PH, Eperon, IC, Barrell, BG, Chen, EY, Armstrong, PW, Wong, JF, and Roe, BA (1980). A mammalian mitochondrial serine transfer RNA lacking "dihydrouridine" loop and stem. Nucl. Acids Res. 8, 5213-5222.
  • BG Barrell et al. (1980). Sequence of mammalian mitochondrial DNA. In Proceedings of the 31st Mosbacher Colloquium. Springer-Verlag.
  • Barrell, BG, Anderson, S, Bankier, AT, de Bruijn, MH, Chen, E, Coulson, AR, Drouin, J, Eperon, IC, Nierlich, DP, Roe, BA, Sanger, F, Schreier, PH, Smith, AJ, Staden, R, and Young, IG (1980). Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc. Nat. Acad. Sci. USA 77, 3164-3166.
  • Eperon IC, Anderson S, Nierlich DP. (1980). Distinctive sequence of human mitochondrial ribosomal RNA genes. Nature 298, 460-467.

Research

  • Single molecule studies on the molecular mechanisms of mammalian pre-mRNA splicing, splice site selection and the regulation of alternative splicing
  • Using our understanding of these processes to develop potential therapies for diseases

RNA splicing: single molecules to therapy

Ian Eperon

Almost all mammalian genes produce multiple isoforms of mRNA and protein by alternative splicing; this, not the number of genes, is the key to the evolution of complex eukaryotes. We are interested in the molecular mechanisms by which sites are selected and have made a number of contributions.

The very existence of extensive alternative splicing in mammals tells us something important: the splice site sequences are not very information-rich, and there are lots of candidate sites in the pre-mRNA. Some are used constitutively, some in specific circumstances, some only if the normal site is mutated, and others never. How is the RECOGNITION by specific factors turned into SELECTION of a site? Most nucleotides in or near some exons contribute to the use of an exon, presumably because they are bound by one or more of the many RNA-binding proteins that appear to compete for binding, with low and overlapping specificities. To understand recognition and selection, we need to understand what the pre-mRNA looks like: which proteins are bound, where, and in what numbers, and what effects they have on the behaviour of the RNA.
It became clear to me some years ago that splicing was too complicated for conventional molecular approaches to be very informative, and, in collaboration with Clive Bagshaw, we began a programme to develop single molecule methods for analysing splicing in nuclear extracts. Dmitry Cherny did the first single molecule experiments on mammalian splicing and showed that we could determine the numbers of regulatory proteins associated with each molecule of RNA in functional conditions (nuclear extracts). We are now in a position to address some of the most intractable problems.

Recent highlights

PTB (Cherny et al., 2010). In collaboration with Chris Smith and colleagues, Cambridge.

  • Established for the first time the numbers of molecules of a regulatory protein bound to pre-mRNA
  • 5-6 molecules of PTB bind 2 regions flanking repressed exon 3 of TM1
  • Modelling with known domain structures revealed  new insights into the arrangements of proteins on the RNA, and in particular suggested that for proteins with multiple RNA-binding domains, with similar RNA sequence specificities, the sites with the highest apparent affinity are those that enable the highest number of possible arrangements of the domains on the RNA .

5' SS SELECTION BY U1 snRNPs (Hodson et al., 2012)

  • Single molecule methods showed that in early complex E two U1 snRNPs bind pre-mRNA with 2 strong 5' splice sites.
  • This suggests U1 snRNPs bind independently and stochastically to alternative sites, not via recruitment of a single U1 snRNP as would be expected on the basis of existing models for complex E.
  • In complex A, only one is bound; there is a process associated with ATP-dependent complex A formation in which the surplus U1 is removed. This is linked to commitment to a specific 5' SS.
  • The results suggest models for selection of weak and strong sites:
  • The affinity-dependent selection among weak sites arises because the probability of a site being occupied by U1 is low and reflects the affinity.
  • The position effect (favouring the intron-proximal site) arises when there are alternative strong sites because both are occupied concomitantly.
  • Why is the intron-proximal site favoured? Calculations suggests that this is not the result of free diffusion of an RNA chain. A better match to our 1991 data on the effects of distance between the sites is seen if we model the exon as a RIGID rod. Does U1 or protein binding change the physical properties of an exon?

AN ENHANCER THAT DOES NOT ACT BY LOOPING (Lewis et al., 2012). This is a joint project with Glenn Burley and colleagues, Strathclyde.

  • The general model for the action of exonic splcing enhancers is that they act by looping of a free RNA chain (just as was expected for the selection of 5' splice sites when there is simultaneous occupancy by U1 snRNPs), but there was little evidence.
  • We placed an enhancer upstream of two alternative 5' splice sites; it shifted splicing to the nearest site.
  • We inserted a non-RNA flexible linker between the enhancer and the sites, using click chemistry. This abolished the effect of the enhancer.
  • The conclusion is that the enhancer must in some way exert its effects along the connecting RNA. As with the U1 work, does this suggest that protein complexes propagate along the exon from an enhancer (and make it more rigid, perhaps?).

 

We are developing the power of single molecule methods further in collaboration with Andrew Hudson (Chemistry, Leicester) to observe single molecule reactions in real time in a laser trap.
Defective or altered splice site selection is the cause of many genetic diseases and is required for diseases such as cancer. We developed a method some years ago, in collaboration with Francesco Muntoni, in ICH, UCL, to rescue the splicing of an exon in spinal muscular atrophy. We are optimizing this, trying to understand the reasons for its success, and applying the method to genes involved in cancer to switch splicing either to favour cell death (in collaboration with Cyril Dominguez, Leicester) or prevent invasiveness (collaboration with Guiseppe Biamonti, Pavia).

Supervision

I welcome enquiries from prospective PhD students interested in RNA splicing research, especially those with backgrounds in physics or physical chemistry.

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Contact Details

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Redfearn Lecture 2017

To Be Confirmed