Alex S. Flynt

Assistant Professor

Research in my lab broadly investigates the role of RNA biology in post-transcriptional gene regulation with a major focus on the biogenesis and function of non-coding, small regulatory RNAs. These molecules are most famously known as the effectors of RNAi and have pervasive roles in negative regulation of gene expression and defense against invasive genetic elements (i.e. viruses and transposons). Three main small RNA classes are recognized:  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. Moreover, manipulation of this process has led to genetic technologies used widely in eukaryotes for research, biotechnology, and therapies. To study these molecules, my group takes a multidisciplinary approach that combines genetics, biochemistry, and bioinformatics with a major emphasis on the use of genome-wide datasets. As described below, the lab engages a diverse set of research projects that address questions related to human genetics, invertebrate genome evolution, and practical application of RNAi.

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 project in the lab is to identify novel pathways and the factors involved in atypical miRNA maturation. Our approach is to use genetic tools in Drosophilaand cell culture systems to dissect processes involved in the production of these miRNAs. This work also extends to identification of animal phenotypes to understand the utility of atypical miRNAs in gene regulatory networks.

Another area of interest is characterizing evolution of small RNA biology in different animals. In these projects, we focus on evolutionary divergent nodes in animal phyla where RNAi mechanisms have departed from behaviors worked out in well-studied model organisms. To identify novel biogenesis process we lean on high throughput sequencing approaches, which allow reconstruction of enzymatic activities that generate different classes of small RNAs. Discoveries from these project have implications for animal genome evolution, and technology development.

A third focus is translational research into RNAi technology. Unlike other genetic manipulation methods, RNAi offers control of gene expression through environmental exposure. One exciting application is the use of RNAi to manage agricultural pests, and other economically significant organisms. My lab uses its expertise in RNA processing to understand the metabolism of RNAs following ingestion/exposure by invertebrates. These efforts include collaboration with material scientists to develop polymers that promote uptake through penetration of biological membranes.



Mosharrof Mondal, Kody Mansfield, and Alex Flynt (2018) siRNAs and piRNAs Collaborate for Transposon Control in the Two-Spotted Spider Mite. RNA rna.065839.118 doi:10.1261/rna.065839.118

Keith H. Parsons, Mosharrof H. Mondal, Charles L. McCormick, and Alex S. Flynt (2018) Guanidinium-Functionalized Interpolyelectrolyte Complexes Enabling RNAi in Resistant Insect Pests. Biomacromolecules 19 (4), 1111-1117 DOI: 10.1021/acs.biomac.7b01717

Mondal M, Klimov P, Flynt AS (2018) Rewired RNAi-mediated genome surveillance in house dust mites. PLOS Genetics 14(1): e1007183.

Jaaved Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hussein Mondal, Matthew DeCruz, Adam Siepel, and Eric C. Lai (2017) Deep experimental profiling of microRNA diversity, deployment, and evolution across the Drosophila genus. Genome Res. 28: 52-65 doi:10.1101/gr.226068.117

Partha Pratim Sengupta, Jared N. Gloria, Marcus K. Parker, Alex S. Flynt (2016) A Polyaniline-based Sensor of Nucleic Acids. JOVE, Issue 117; doi: 10.3791/54590

Keith H. Parsons, Andrew C. Holley, Gabrielle A. Munn, Alex S. Flynt, and Charles L. McCormick. (2016) Block ionomer complexes consisting of siRNA and aRAFT-synthesized hydrophilic-block-catonic copolymers II: the influence of catonic block charge density on gene suppression. Polym. Chem., 6044-6054

Sengupta P, Gloria, JN, Amato DN, Amato DV, Patton DL, Murali B, and Flynt AS. (2015) Utilizing Intrinsic Properteis of Polyanaline to Detect Nucleic Acid Hybridization through UV-Enhanced Electrostatic Interaction. Biomacromolecules. 16(10), 3217-3225

Amato DN, Amato DV, Narayanan J, Donovan BR, Doughlas JR, Walley SE, Flynt AS, Patton DL. (2015) Functional, Composite Polythioether Nanoparticles via Thiol-Alkyne Photopolymerization in Miniemulsion. Chemm Commun (Camb) 51(54): 10910-3

Amato DV, Amato DN, Flynt AS, Patton DL. Fuctional, sub-100 nm polymer nanoparticles via thiol-ene miniemulsion photopolymerization. (2015) Poly Chem 1759-9954 DOI:

Wen J, Mohammed J, Bortolamiol-Bect D, Tsai H, Robine N, Westholm J, Ladewig E, Dai Q, Okamura K, Flynt AS, Zhange D, Andrews J, Cherbas L, Kaufman T, Cherbas P, Seipel A, and Lai EC. (2014) Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines. Genome Research 24 1236-1250.

Mohammed J, Bortolamiol-Becet D, Flynt AS, Gronau I, Siepel A, Lai EC. (2014) Adaptive evolution of testis-specific, recently-evolved, clustered miRNAs in Drosophila. RNA 20(8).

Mohammed J, Flynt AS, Seipel A, Lai EC. (2013) The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA 19(9) 1295-308

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. 

Ladewig E, Flynt AS, Okamura K, Westholm JO, Lai EC. (2012) Discovery of Hundreds of Mirtrons in Mouse and Human Small RNA data. Genome Research, 22, 1634-1645.

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

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.

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.

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 of the Xenopus Eye. Mech Dev, 126(10): 804-16.

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.

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.

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.

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.

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.

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.