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, Archana Yerra, Miguel V. Almeida, Alexandra Dallaire, David Jordan, Melanie Heckwolf (visiting), Xiaodan Liu, Harris (Charikleia) Papadopoulou, Jon Price, Chenming Zeng, Ben Fisher, Lisa Lampersberger, Narendra Meena, Audrey Putman, Fu Xiang Quah, Juan Carlos Rueda Silva, Ulrika (Chengwei) Yuan
Recent publications :
- 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.