Alex S. Flynt

Assistant Professor

Research in my lab broadly investigates the role of RNA biology in post-transcriptional gene regulation. Current projects are focused on the biogenesis and function of non-coding, small regulatory RNAs. These molecules are most famously known as the effectors of RNAi and can be placed in three classes:  microRNAs (miRNAs), small-interfering RNAs (siRNAs), and Piwi associated RNAs (piRNAs). While all mature small regulatory RNAs are 18-30 nucleotides long and associate with members of the Argonaute protein family, each class has distinct maturation pathways and functions. To study these molecules my lab takes a multidisciplinary approach that combines genetics, biochemistry, and bioinformatics. A major emphasis in our approach is the use of genome-wide datasets. Described below are a couple of the lab's active projects.

miRNAs are a nearly ubiquitous feature of animal genomes, are important developmental regulators, and have been implicated in many diseases. An interesting aspect of miRNA biology is that their biogenesis is heterogeneous, exhibiting a number of alternate pathways. A current focus of the lab is to identify novel pathways and the factors involved in miRNA maturation. Our approach is to use genetic screens based on atypical miRNAs in cell culture and Drosophila. These miRNAs require extra processing and thus are likely to be sensitized to changes in biogenesis dynamics.

Another area of interest is to identify adaptations in siRNA biology in different species. The term "siRNA" is a catch-all typically used to describe small RNAs derived from exogenous sources, such as those produced from synthetic RNAs introduced by researchers. However, processing of these molecules in disparate species can vary widely. Our lab is interested in siRNAs generated from long double-stranded RNA in invertebrates. RNAi is predominantly used in anti-viral defense in these animals, and therefore subject to strong selective pressures to compete with viral novelty. Indeed, siRNA biology is remarkably different between these clades. Understanding the differences will lead to improved strategies for genetic manipulation, and shed light on anti-viral defense strategies in these organisms.



(1) Mohammed J, Flynt AS, Seipel A, Lai EC. (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA. Jul 23.

(2) Jin Z, Flynt AS, Lai EC. (2013) Drosophila piwi mutants exhibit germline stem cell tumors that are sustained by elevated Dpp signaling. Curr Biol 5;23(15) 1442-8.

(3) Ladewig E, Okamura K, Flynt AS, Westholm, JO, Lai EC. (2012) Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Research 22, 1634-1645.

(4) Yao J, Hennessey T, Flynt AS, Lai EC, Beal MF, Lin MT. (2010) MicroRNA-related cofilin abnormality in Alzheimer’s disease. PLoS One, 16;5(12):e15546.

(5) Flynt AS, Greimann JC, Chung W, Lima CC, and Lai EC. (2010) Drosophila 3’ tailed-mirtrons generate microRNAs via splicing and exosome-mediated trimming. Mol Cell, 38(6): 900-7.

(6)Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, and Lai EC. (2010) Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat Genet, 42(1): 6-9.

(7)Qiu R, Liu K, Liu Y, Mo W, Flynt AS, Patton JG, Kar A, Wu JY, He R. (2009) The role of miR-124a in early development in early development of the Xenopus Eye. Mech Dev, 126(10): 804-16.

(8) Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, and Patton JG. (2009) miR-8 microRNAs regulate the response to stress in Zebrafish embryos. J Cell Biol (Cover article), 185(1): 115-27.

(9)Flynt AS, Liu N, Martin R, Lai EC. (2009) Dicing of viral replication intermediates during silencing of latent Drosophila viruses. Proc Natl Acad Sci USA, 106(13): 5270-5.

(10) Li N, Flynt AS, Kim HR, Solnica-Krezel L, and Patton JG. (2008) Dispatched homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites.  Nucleic Acids Res, 36(13): 4277-85.

(11)Thatcher EJ, Flynt AS, Li N, and Patton JG. (2007) miRNA expression analysis during normal Zebrafish development and following inhibition of the hedgehog and notch signaling pathways. Developmental Dynamics, 236(8): 2172-2180.

(12) Tillman JE, Yuan J, Gu G, Fazli L, Ghosh R, Flynt AS, Gleave M, Rennie PS, and Kasper S. (2007) DJ-1 binds androgen receptor directly and mediates its activity in hormonally treated prostate cancer cells. Cancer Res, 67(10): 4630-4637. 

(13) Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, and Patton JG. (2007) Zebrafish miR-214 modulates hedgehog signaling to specify muscle cell fate. Nature Genetics, 39(2): 259-263.

(14) Ryther RCC, Flynt AS, Harris BD, Phillips JA III, and Patton JG. (2004) Splicing of GH1 is regulated by multiple enhancers whose mutation produces a dominant-negative GH isoform that can be degraded by allele-specific siRNA. Endocrinology, 145(6):  2988-2996.

Review Articles and Book Chapters

(1)  Flynt AS, and Lai EC. (2011)  RNAi in Xenopus: look before you leap. Genes and Development 25(11): 1105-8.

(2) Flynt AS, and Patton JG. (2010) Crosstalk between planar cell polarity signaling and miR-8 control NHERF-1 mediated actin reorganization. Cell Cycle 26;9(2)

(3) Flynt AS, and Lai EC, (2008) Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat Rev Genet, 9(11): 831-42.

(4) Flynt AS, Thatcher EJ, and Patton JG. (2009) RNA interference and microRNAs in zebrafish. In:  Regulation of Gene Expression by Small RNAs. Rossi JJ and Gaur R. editors. CRC Press.

(5) Ryther RCC, Flynt AS, Phillips JA III, and Patton JG. (2004) siRNA therapeutics; big potential from small RNAs. Gene Therapy, 12: 5-11.