Mechanisms and regulation of microRNA function and metabolism in mammalian cells
Epigenetic control of gene expression and post-transcriptional silencing of genes by RNA interference (RNAi) and miRNAs have emerged recently as extraordinarily important and interesting areas of molecular biology. These reactions greatly contribute to the developmental and tissue specificity of gene expression, and also exemplify a key role of hundreds of novel non-coding RNAs in the regulation of gene expression. Our research is focused on mechanistic and regulatory aspects of miRNA function and miRNA metabolism in mammalian cells. miRNAs are ~21-nt RNAs involved in the regulation of development, differentiation, and many other fundamental processes; hundreds of different miRNAs are encoded in the genomes of metazoa. miRNAs generally imperfectly base-pair to the mRNA 3'-UTR and inhibit protein synthesis by either repressing mRNA translation or causing mRNA deadenylation and degradation.
miRNA-mediated regulation is a complex process involving many different proteins and intersecting with other cellular pathways. miRNAs function in the form of miRNPs (also known as miRISC), with Argonaute and GW182 proteins being the most important protein components. Biogenesis of miRNAs is also a complex reaction. It involves two enzymes of the RNase III family, Dicer and Drosha. In addition, many accessory factors regulate miRNA biosynthesis at different steps. miRNAs are generally assumed to have a very long half-life but our recent studies indicate that in some cells, in particular in neurons, miRNAs turn over very fast and that miRNA turnover is a subject of sophisticated regulation.
For more personal account of my scientific activity, see the “Reflections” article "Traversing the RNA World", published in J. Biol. Chem. (2017) 292: 8122-8133.
Filipowicz W. (2017) Traversing the RNA WorldJ Biol Chem 292:8122- 8135
Krol J, Krol I, Alvarez CP, Fiscella M, Hierlemann A, Roska B, Filipowicz W. (2015) A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architectureNat Commun. 6:7305-17
de la Mata M, Gaidatzis D, Vitanescu M, Stadler MB, Wentzel C, Scheiffele P, Filipowicz W, Grosshans H. (2015) Potent degradation of neuronal miRNAs induced by highly complementary targetsEMBO Rep. 16:500-11
Ozgur S, Basquin J, Kamenska A, Filipowicz W, Standart N, Conti E. (2015) Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT ComplexCell Rep. 13:703-11
Mathys H, Basquin J, Ozgur S, Czarnocki-Cieciura M, Bonneau F, Aartse A,j Dziembowski A, Nowotny M, Conti E, and Filipowicz. (2014) Structural and biochemical insights into the role of the CCR4-NOT complex and DDX6 ATPase in microRNA-mediated repressionMol Cell 54, 751-765
Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B. (2014) miRNAs 182 and 183 are necessary to maintain adult cone photoreceptor outer segments and visual functionNeuron 83: 586-600
Loedige I, Gaidatzis D, Sack R, Meister G, Filipowicz W. (2013) The mammalian TRIM-NHL protein TRIM71/LIN-41 is a repressor of mRNA functionNucleic Acids Res. 41:518-32
Doyle M, Badertscher L, Jaskiewicz L, Güttinger S, Jurado S, Hugenschmidt T, Kutay U, Filipowicz W. (2013) The double-stranded RNA binding domain of human Dicer functions as a nuclear localization signalRNA 19(9):1238-52
Bethune J, Artus-Revel C, and Filipowicz W. (2012) Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cellsEMBO Reports, 13:716-23.
Krol J, Loedige I, Filipowicz W (2011) Regulation of miRNA Biogenesis, Function and DecayNat Rev Genet 11, 597-615
Chekulaeva M, Mathys H, Zipprich JT, Attig J, Colic M, Parker R, Filipowicz W (2011) MicroRNA repression involves GW182-mediated recruitment of CCR4-NOT through conserved W-containing motifsNat Struct Mol Biol 18:1218-26
Fabian MR, Sonenberg N, Filipowicz W (2010) Regulation of mRNA translation and stability by microRNAsAnnu Rev Biochem 79:351-79
Krol J, Busskamp V, Markiewicz I, Stadler MB, Ribi S, Richter J, Duebel J, Bicker S, Fehling HJ, Schübeler D, Oertner TG, Schratt G, Bibel M, Roska B, Filipowicz W (2010) Characterization of microRNAs induced by light adaptation in mouse retina reveals rapid turnover as a common property of neuronal microRNACell 141:618-31
Fabian MR, Mathonnet G, Sundermeier T, Mathys H, Zipprich JT, Svitkin YV, Rivas F, Jinek M, Wohlschlegel J, Doudna JA, Chen CA, Shyu AB, Yates III JR, Hannon GJ, Filipowicz W, Duchaine TF, Sonenberg N (2009) Mammalian miRNA RISC recruits CAF1 and PABP to effect PABP-dependent deadenylationMol Cell 35:868-80
Trabucchi M, Briata P, Garcia-Mayoral M, Haase AD, Filipowicz W, Ramos A, Gherzi R, Rosenfeld MG (2009) The RNA-binding protein KSRP Promotes the Biogenesis of a Subset of miRNAsNature 459:1010-1014
Sarasin-Filipowicz M, Krol J, Markiewicz I, Heim M, Filipowicz W (2009) Decreased levels of microRNA miR-122 in hepatitis C patients with poor response to interferon therapyNature Med 15:31-33
Filipowicz W, Bhattacharyya SN, Sonenberg N (2008) Mechanisms of post-transcriptional regulation by microRNAs: Are the answers in sight?Nature Rev Genet 9:102-114
Sinkkonen L, Hugenschmidt T, Berninger P, Gaidatzis D, Mohn F, Artus-Revel C, Zavolan M, Svoboda P, Filipowicz W (2008) MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cellsNature Struct Mol Biol 15:259-267
Bhattacharyya S, Habermacher R, Martine U, Closs EI, Filipowicz W (2006) Relief of microRNA-mediated translational repression in human cells subjected to stressCell 125:1111-1124
Pillai R, Bhattacharyya S, Artus C, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W (2005) Inhibition of translational initiation by let-7 microRNA in human cellsScience 309:1573-1576
Zhang H, Kolb FA, Jaskiewicz L, Westhof E, Filipowicz W (2004) Single processing center models for human Dicer and bacterial RNase IIICell 118:57-68