Eric Miska

Research

Our research explores various aspects of RNA biology, epigenetics, inheritance mechanisms, and genome stability. Most of our ongoing research projects fall under one of these broader themes: RNA modifications and structure; Small- and non-coding RNA biology; RNA in communication and defense; Genomics, epigenomics, and Inheritance; Adaptive plasticity and evolution. Our projects span miRNA biology and pathology, miRNA mechanisms, piRNA biology and the germline, endo-siRNAs in epigenetic inheritance and environmental conditioning, small RNA evolution, and the role of RNAi in host pathogen interactions.

Lab members : Marc Ridyard, Fiona Goodman, Miguel V. Almeida, David Jordan, Harris (Charikleia) Papadopoulou, Jon Price, Chenming Zeng, Paula Milan-Rois, Bianca Pierattini, Jonathan Boudeman, Tsveta Kamenova, Leonardo Maffioloi, Juan Carlos Rueda Silva, Emma Walsh, Ulrika (Chengwei) Yuan

Recent publications :

• Shen A, Hencel K, Parker MT, Scott R, Skukan R, Adesina AS, Metheringham CL, Miska EA, Nam Y, Haerty W, Simpson GG, Akay A. U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs. Nucleic Acids Res. 2024 May 29:gkae447. doi: 10.1093/nar/gkae447. Epub ahead of print. PMID: 38808663
• Price JL, Ziv O, Pinckert ML, Lim A, Miska EA. rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments. Bioinformatics. 2024 Mar 29;40(4):btae193. doi: 10.1093/bioinformatics/btae193. PMID: 38597883
• Saredi G, Carelli FN, Rolland SGM, Furlan G, Piquet S, Appert A, Sanchez- Pulido L, Price JL, Alcon P, Lampersberger L, Déclais AC, Ramakrishna NB, Toth R, Macartney T, Alabert C, Ponting CP, Polo SE, Miska EA, Gartner A, Ahringer J, Rouse J. The histone chaperone SPT2 regulates chromatin structure and function in Metazoa. Nat Struct Mol Biol. 2024 Jan 18. doi: 10.1038/s41594-023-01204-3. Epub ahead of print. PMID: 38238586
• Jordan DJ, Miska EA. Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans. Mol Syst Biol. 2023 Nov 9;19(11):e11835. doi: 10.15252/msb.202311835. Epub 2023 Oct 18. PMID: 37850520
• Shen A, Hencel K, Parker MT, Scott R, Skukan R, Adesina AS, Metheringham CL, Miska EA, Nam Y, Haerty W, Simpson GG, Akay A. U6 snRNA m6A modification is required for accurate and efficient cis- and trans-splicing of C. elegansmRNAs. bioRxiv [Preprint]. 2023 Sep 16:2023.09.16.558044. doi: 10.1101/2023.09.16.558044. PMID: 37745402
• Stainthorp AK, Lin CC, Wang D, Medhi R, Ahmed Z, Suen KM, Miska EA, Whitehouse A, Ladbury JE. Regulation of microRNA expression by the adaptor protein GRB2. Sci Rep. 2023 Jun 16;13(1):9784. doi: 10.1038/s41598-023-36996-3. PMID: 37328606
• Bista I, Wood JMD, Desvignes T, McCarthy SA, Matschiner M, Ning Z, Tracey A, Torrance J, Sims Y, Chow W, Smith M, Oliver K, Haggerty L, Salzburger W, Postlethwait JH, Howe K, Clark MS, William Detrich H 3rd, Christina Cheng CH, Miska EA, Durbin R. Genomics of cold adaptations in the Antarctic notothenioid fish radiation. Nat Commun. 2023 Jun 9;14(1):3412. doi: 10.1038/s41467-023-38567-6. PMID: 37296119
• Manley BF, Lotharukpong JS, Barrera-Redondo J, Llewellyn T, Yildirir G, Sperschneider J, Corradi N, Paszkowski U, Miska EA, Dallaire A. A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis. G3 (Bethesda). 2023 Jun 1;13(6):jkad077. doi: 10.1093/g3journal/jkad077. PMID: 36999556
• Lampersberger L, Conte F, Ghosh S, Xiao Y, Price J, Jordan D, Matus DQ, Sarkies P, Beli P, Miska EA, Burton NO. Loss of the E3 ubiquitin ligases UBR-5 or HECD-1 restores Caenorhabditis elegans development in the absence of SWI/SNF function. Proc Natl Acad Sci U S A. 2023 Jan 31;120(5):e2217992120. doi: 10.1073/pnas.2217992120. Epub 2023 Jan 23. PMID: 36689659
• Karin O, Miska EA, Simons BD. Epigenetic inheritance of gene silencing is maintained by a self-tuning mechanism based on resource competition. Cell Syst. 2023 Jan 18;14(1):24-40.e11. doi: 10.1016/j.cels.2022.12.003. PMID: 36657390
• Ramakrishna NB, Battistoni G, Surani MA, Hannon GJ, Miska EA. Mouse primordial germ-cell-like cells lack piRNAs. Dev Cell. 2022 Dec 5;57(23):2661-2668.e5. doi: 10.1016/j.devcel.2022.11.004. PMID: 36473462
• Navarro IC, Suen KM, Bensaddek D, Tanpure A, Lamond A, Balasubramanian S, Miska EA. Identification of putative reader proteins of 5-methylcytosine and its derivatives in Caenorhabditis elegans RNA. Wellcome Open Res. 2022 Nov 17;7:282. doi: 10.12688/wellcomeopenres.17893.1. PMID: 37475875
• Efstathiou S, Ottens F, Schütter LS, Ravanelli S, Charmpilas N, Gutschmidt A, Le Pen J, Gehring NH, Miska EA, Bouças J, Hoppe T. ER-associated RNA silencing promotes ER quality control. Nat Cell Biol. 2022 Dec;24(12):1714-1725. doi: 10.1038/s41556-022-01025-4. Epub 2022 Dec 5. PMID: 36471127
• Carruthers M, Edgley DE, Saxon AD, Gabagambi NP, Shechonge A, Miska EA, Durbin R, Bridle JR, Turner GF, Genner MJ. Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes. Mol Biol Evol. 2022 Nov 3;39(11):msac251. doi: 10.1093/molbev/msac251. PMID: 36376993
• Vernaz G, Hudson AG, Santos ME, Fischer B, Carruthers M, Shechonge AH, Gabagambi NP, Tyers AM, Ngatunga BP, Malinsky M, Durbin R, Turner GF, Genner MJ, Miska EA. Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish. Nat Ecol Evol. 2022 Dec;6(12):1940-1951. doi: 10.1038/s41559-022-01894-w. Epub 2022 Oct 20. PMID: 36266459
• Clark B, Elkin J, Marconi A, Turner GF, Smith AM, Joyce D, Miska EA, Juntti SA, Santos ME. Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera. R Soc Open Sci. 2022 Apr 20;9(4):220077. doi: 10.1098/rsos.220077. PMID: 35601449
• Georgakopoulos-Soares I, Parada GE, Wong HY, Medhi R, Furlan G, Munita R, Miska EA, Kwok CK, Hemberg M. Alternative splicing modulation by G-quadruplexes. Nat Commun. 2022 May 3;13(1):2404. doi: 10.1038/s41467-022-30071-7. PMID: 35504902
• Almeida MV, Vernaz G, Putman ALK, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet. 2022 Jun;38(6):529-553. doi: 10.1016/j.tig.2022.02.009. Epub 2022 Mar 17. PMID: 35307201
• Riehl K, Riccio C, Miska EA, Hemberg M. TransposonUltimate: software for transposon classification, annotation and detection. Nucleic Acids Res. 2022 Mar 2:gkac136. doi: 10.1093/nar/gkac136. Epub ahead of print. PMID: 35234904.
• edhi R, Price J, Furlan G, Gorges B, Sapetschnig A, Miska EA. RNA uridyl transferases TUT4/7 differentially regulate miRNA variants depending on the cancer cell type. RNA. 2022 Mar;28(3):353-370. doi: 10.1261/rna.078976.121. Epub 2021 Dec 23. PMID: 34949722.
• Ramakrishna NB, Murison K, Miska EA, Leitch HG. Epigenetic Regulation during Primordial Germ Cell Development and Differentiation. Sex Dev. 2021;15(5-6):411-431. doi: 10.1159/000520412. Epub 2021 Nov 30. PMID: 34847550.
• Dallaire A, Manley BF , Wilkens M, Bista I, Quan C, Evangelisti E, Bradshaw CR, Ramakrishna NB, Schornack S, Butter F, Paszkowski U, Miska EA. Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis. Genome Res. 2021 Nov 12;31(12):2290–302. doi: 10.1101/gr.275752.121. Epub ahead of print. PMID: 34772700;.
• Ramakrishna NB, Miska EA. Who watches the watchmen? RNAi pathway-derived ribosomal small RNAs burgeon in absence of piRNAs. Dev Cell. 2021 Aug 23;56(16):2269-2270. doi: 10.1016/j.devcel.2021.08.002. PMID: 34428395.
• Chandrasekaran V, Desai N, Burton NO, Yang H, Price J, Miska EA, Ramakrishnan V. Visualizing formation of the active site in the mitochondrial ribosome. Elife. 2021 Oct 5;10:e68806. doi: 10.7554/eLife.68806. PMID: 34609277; PMCID: PMC8492066.
• Vernaz G, Malinsky M, Svardal H, Du M, Tyers AM, Santos ME, Durbin R, Genner MJ, Turner GF, Miska EA. Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes. Nat Commun. 2021 Oct 7;12(1):5870. doi: 10.1038/s41467-021-26166-2. PMID: 34620871; PMCID: PMC8497601.
• Burton NO, Willis A, Fisher K, Braukmann F, Price J, Stevens L, Baugh LR, Reinke AW, Miska EA. Intergenerational adaptations to stress are evolutionarily conserved, stress-specific, and have deleterious trade-offs. Elife. 2021 Oct 8;10:e73425. doi: 10.7554/eLife.73425. Epub ahead of print. PMID: 34622777.
• Gapp K, Parada G E, Gross F, Corcoba A, Kaur J, Grau E, Hemberg M, Bohacek J, Miska EA. Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance. iScience, 2021,
  doi:10.1016/j.isci.2021.102870.
• Kranse O, Beasley H, Adams S, Pires-daSilva A, Bell C, Lilley CJ, Urwin PE, Bird D, Miska E, Smant G, Gheysen G, Jones J, Viney M, Abad P, Maier TR, Baum TJ, Siddique S, Williamson V, Akay A, Eves-van den Akker S. Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3 (Bethesda). 2021 Feb 9;11(2):jkaa058. doi: 10.1093/g3journal/jkaa058. PMID: 33585878.
• Berkyurek AC, Furlan G, Lampersberger L, Beltran T, Weick EM, Nischwitz E, Cunha Navarro I, Braukmann F, Akay A, Price J, Butter F, Sarkies P, Miska EA. The RNA polymerase II subunit RPB-9 recruits the integrator complex to terminate Caenorhabditis elegans piRNA transcription. EMBO J. 2021 Mar 1;40(5):e105565. doi: 10.15252/embj.2020105565. Epub 2021 Feb 3. PMID: 33533030; PMCID: PMC7917558.
• Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA, Hemberg M. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biol. 2021 Jan 22;22(1):43. doi: 10.1186/s13059-020-02246-2. PMID: 33482885; PMCID: PMC7821500.