Faculty Research Page

Donald Rio

Donald Rio

Professor of Biochemistry, Biophysics and Structural Biology*
*Affiliate, Division of Biochemistry and Molecular Biology; Member, Center for Integrative Genetics; Richard and Rhoda Goldman Distinguished Chair in the Biological Sciences

Lab Homepage: http://mcb.berkeley.edu/labs/rio/

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Research Interests

The general interest of our laboratory is nucleic acid transactions, specifically, the mechanisms used to mobilize transposable DNA elements (a process called transposition) and how RNA binding proteins control patterns of alternative pre-mRNA splicing.  About half the human genome is composed of transposons; transposable DNA insertions have been linked to human disease gene mutations and chromosomal rearrangements and are thought to be important for genome and organismal evolution.  Our research focuses on the P element family of transposable elements found in the fruit fly, Drosophila melanogaster and more recently the vertebrate homologs of the P element transposase, THAP9.  P element transposition is related to retroviral DNA integration, such as HIV, and to the process by which immunoglobulin and T-cell receptor genes are rearranged in the vertebrate immune system [V(D)J recombination].  The P element system offers the ability to effectively combine the use of biochemical, genetic, molecular biological and proteomic approaches to study fundamental aspects of transposition mechanisms.  A second research area of research involves how patterns of alternative splicing of pre-mRNA are set up in a cell-type and tissue-specific manner, which is an important mechanism for the regulation of gene expression, evolution of organismal complexity in metazoans and leads to significant proteomic diversification.  Understanding how pre-mRNA splicing is controlled will be important since at least 40% of the known human and mouse disease gene mutations affect the splicing process.  Our studies deal with the interaction of proteins with RNA and DNA as well as the assembly, composition, structure, function and biochemical activities of these complex nucleoprotein machines.

Current Projects

Current Projects

Biochemistry of P element transposase, the mechanism of transposition and P element-related THAP 9 genes in humans and zebrafish. The 87kD P element-encoded transposase protein is required to catalyze P element transposition and belongs to a large polynucleotidyl transferase superfamily, that includes RNaseH, RuvC, retroviral integrases, transposases and the argonaute proteins.  Biochemical studies using the purified protein revealed that guanosine triphosphate (GTP) is an essential cofactor for the reaction.  Current studies involve the use of biochemical and cell-based assays, along with cryo-electron microscopy (cryo-EM) to investigate to the role(s) that GTP plays in transposition and the detailed assembly and reaction pathway of transposase on DNA.  Interestingly, the THAP9 gene in humans and zebrafish shares extensive sequence homology to the Drosophila P element transposase.  We have recently shown that both the human and zebrafish THAP9 proteins can mobilize P elements in human and Drosophila cells.

Figure 1

Cryo-EM structural model of the P element strand transfer complex.  A) overall structure showing protein and DNA. B) Unusal A-form DNA structure and refolded DNA at the transposon ends.  Taken from Ghanim et al. 2019.

RNA binding proteins and the control of alternative pre-mRNA splicing in Drosophila and humans.   The P element transposon pre-mRNA undergoes tissue-specific splicing and we showed that regulation of the third P element intron (IVS3) involves RNA binding proteins (PSI, hrp48, hrp36 and hrp38) that recognize an exonic splicing silencer (ESS) regulatory RNA element in the 5' exon adjacent to IVS3, resulting in splicing inhibition.  This RNA silencer element binds the splicing repressor protein PSI (P element somatic inhibitor) protein which directly interacts with U1 snRNP and modulates U1 snRNP binding to specific sites on the pre-mRNA.  We are using RNA-seq and bioinformatic analysis with the Junction Usage Model (JUM) software to identify changes in alternative splicing patterns and to identify and characterize new splicing silencers that use the hrp48 and PSI factors in cellular genes.  We are also interested in analyzing the splicing pattern changes in human cells in disease states using JUM.  This project involves genome editing mutations in the human splicing repressor hnRNPA1 that is mutated in ALS (Amyotrophic Lateral Sclerosis), a neurodegenerative disease and analyzing splicing pattern changes caused by the disease mutations.  We are also analyzing RNA-seq data from patient samples for splicing pattern changes in ALS and Parkinson’s disease to identify changes in gene expression correlated with disease state.

Selected Publications

Ghanim, G., Rio, D.C. and Karam Teixeira, Felipe. (2020).  Mechanism and regulation of P element transposition.  Open Biology, Open Biol. 2020 Dec;10(12):200244. doi: 10.1098/rsob.200244. Epub 2020 Dec 23. PMID: 33352068

Wang, Q., Conlon, E., Gao, J., Manley, J.L. and Rio, D.C. (2020).  Widespread intron retention impairs protein homeostasis in C9ORF72 ALS brains.  Genome Research, Genome Res. 2020 Dec;30(12):1705-1715. doi: 10.1101/gr.265298.120. Epub 2020 Oct 14. PMID: 33055097

Ghanim, G., Kellogg, E., Nogales, E. and Rio, D.C. (2019).  Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts.  Nature Struct. Mol. Biol. 26(11):1013-1022.

Wang, Q. and Rio, D.C. (2018).  The Junction Usage Model (JUM): A method for comprehensive annotation-free analysis of alternative pre-mRNA splicing patterns.  Proc. Natl. Acad. Sci. U.S.A. 115, E8181-E8190.

Lee, Y.J., Wang, Q. and Rio, D.C. (2018).  Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5.  Genes and Development, 32,1060-1074. doi: 10.1101/gad.316034.118.

Wang, Q., Abruzzi, K., Rosbash, M. and Rio, D.C. (2018).  Alternative splicing diversity and circadian cycling within discreet Drosophila neurons.  eLife, Jun 4;7. pii: e35618.

Teixeira, F.K., Okuniewska, M., Malone, C.D., Coux, R.-X., Rio, D.C. and Lehmann, R. (2017).  piRNA-mediated regulation of transposon alternative splicing in soma and germline. Nature 552, 268-272. 

Wang, Q., Taliaferro, J.M., Klibaite, U., Hilgers, V., Shaevitz, J. and Rio, D.C. (2016). The PSI-U1 snRNP interaction regulates neural pre-mRNA splicing to control Drosophila courtship.  Proc. Natl. Acad. Sci. U.S.A. 113, 5269-5274.

P transposable elements in Drosophila and other organisms.  Majumdar, S. and Rio, D.C. (2015).   ASM Press.  Online in:  Microbiol Spectr.  2015 Apr;3(2). pii: MDNA3-0004-2014.  Print:  Mobile DNA III.

Mechanisms and regulation of alternative pre-mRNA splicing. Lee, Y. and Rio, D.C. (2015). Ann. Rev. Biochem., 84, 291-323.

The human THAP9 gene encodes an active P element DNA transposase.  Majumdar, S., Singh, A. and Rio, D.C.  Science, 339, 446-448.  

Photo credit: Mark Hanson at Mark Joseph Studios.

Last Updated 2021-02-23