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Sergei Filichkin Assistant Professor (Senior Research),
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General : Plant genomics.
Specific interests : Circadian rhythms. Alternative splicing.
• Circadian rhythms
Most species have evolved an endogenous circadian clock with a period of about 24 hrs that ensures internal biological processes are appropriately synchronized with the daily environmental cycles. Daily rhythms in gene expression regulate a wide variety of downstream events, including light perception and signaling, daily growth, reproductive development, photosynthetic capacity, and ensure that specific biological processes are phased to the correct times of day. Proper phasing of biological activities provides selective advantage for organisms in specific environments. We are interested in understanding how transcriptional networks control genome-wide phase-specific gene expression through binding to specific regulatory DNA cis elements and re-phase oscillating transcripts depending upon the external light/temperature conditions.
• Alternative splicing
Alternative pre-mRNA splicing is an important mechanism that serves as a regulatory step during development and differentiation in higher eukaryotes and can enhance proteome diversity by generating multiple protein isoforms. Recent genome-scale transcriptome mapping by high throughput sequencing demonstrated that the extent and the scope of alternative splicing in different species were profoundly underestimated. For example, estimates based on deep transcriptome sequencing suggested that up to 94% of human genes are alternatively spliced. It is also becoming increasingly clear that alternative splicing coupled with nonsense mediated mRNA decay (NMD) plays a role in regulating the levels of functional transcripts via a mechanism called regulated unproductive splicing and translation (RUST). The mechanisms of RUST and its role in plant development and protein homeostasis are not known. Our interest is to investigate the extent and the roles of alternative splicing in regulating of gene expression in plants. In particular, we are interested in abiotic stress-regulated unproductive alternative splicing as a specific response to environmental stress.
There are several reported instances when alternatively spliced circadian-associated plant genes can regulate abundance of their mRNA via a negative auto-regulatory feedback loop by production of NMD-targeted transcripts. We are interested in understanding the role of unproductive alternative splicing of circadian genes in auto- and global regulation of diurnally controlled rhythmical gene expression.
Todd Mockler - BPP/CGRB Oregon State University
Steve Kay - Scripps Research Institute
Filichkin , S.A. , Priest, H.D., Givan, S.A., Shen, R., Bryant, D.W., Fox, S.E., Wong, W-K., Mockler TC (2009). Deep transcriptome sequencing reveals a complex network of alternative splicing in plants. Genome Res . In revision.
Priest H., Filichkin , S.A. , Mockler, T.C. (2009) Cis -regulatory elements in plant cell signaling. Curr. Opin. Plant Biol . In press.
Fox, S.E., Filichkin , S.A. , Mockler T.C. 2009. Applications of ultra high throughput sequencing. In: Plant Systems Biology. Methods in Molecular Biology (Ed. D. A. Belostotsky). Humana Press. New York . 553 : 79-108.
Filichkin , S.A. , DiFazio, S.P., Brunner, A.M., Davis , J.M., Yang, Z.K., Kalluri, U.C., Arias, R.S., Etherington, E., Tuskan, G.A., Strauss, S.H. 2007. Efficiency of gene silencing in Arabidopsis : direct inverted repeats vs. transitive RNAi vectors. Plant Biotechnol. J . 5 : 615-626.
Filichkin , S.A. , Wu, Q., Busov, V.B., Meilan, R., Lanz-Garcia, C., Groover, A., Goldfarb, B., Ma, C., Dharmawardhana, P., Brunner, A.M., Strauss, S.H. 2006. Enhancer trapping in woody plants: Isolation of the ET304 gene encoding a putative AT-hook motif transcription factor and characterization of the expression patterns conferred by its promoter in transgenic Populus and Arabidopsis . Plant Sci . 174 : 206-216.
Arias, R.S., Filichkin , S.A. , Strauss, S.H. 2006. Divide and conquer: Plant cell cycle and development genes for plant transformation. Trends Biotechnol . 24 : 267-273.
Filichkin , S.A. , Meilan, R., Busov, V.B., Ma, C., Brunner, A.M., Strauss, S.H. 2006. Alcohol-inducible gene expression in transgenic Populus . Plant Cell Rep . 25 (7): 660-667.
Filichkin , S.A. , Slabaugh, M.B., Knapp, S.J. (2006). New FATB thioesterases from a high laurate Cuphea species: Functional and complementation analyses. Eur. J. Lipid Sci. Technol. 108 : 979-990.
Busov, V.B., Brunner, A.M., Meilan, R., Filichkin, S., Ganio, L., Gandhi, S., Strauss, S.H. 2005. Genetic transformation: a powerful tool for dissection of adaptive traits in trees. New Phytol . 167 : 9-18.
Filichkin , S.A. , Leonard, J.M., Monteros, A., Liu, P.P., Nonogaki, H. 2004. A novel endo- ß -mannanase gene LeMAN5 in tomato is associated with anther and pollen development. Plant Physiol. 134 : 1080-1087.
Filichkin , S.A. , Bransom, K.L., Goodwin, J.B., Dreher, T.W. 2000. The infectivities of turnip yellow mosaic virus genomes with altered tRNA mimicry are not dependent on compensating mutations in the viral replication protein. J. Virol. 74 (18): 8368-8375.
Young, M.J. and Filichkin , S.A. 1999. Luteovirus interactions with aphid vector cellular components. Trends Microbiol. 7 (9): 346-347.
Filichkin , S.A. , Brumfield, S., Filichkin, T.P., Young, M.J. 1997. In vitro interactions of the aphid endosymbiotic SymL chaperonin with barley yellow dwarf virus. J. Virol. 71 (1): 569-577.
Filichkin , S.A. , Lister, R.M., McGrath, P.F., Young, M.J. 1994. In vivo expression and mutational analysis of the barley yellow dwarf virus readthrough gene. Virol. 205 (1): 290-299.
Filichkin , S.A. , Gelvin, S.B. 1993. Formation of a putative relaxation intermediate during T-DNA processing directed by the Agrobacterium tumefaciens VirD1,D2 endonuclease. Mol. Microbiol . 8 : 915-926.
Gelvin, S.B. and Filichkin , S.A. 1993. Processing of the T-DNA from the Agrobacterium tumefaciens Ti plasmid. In: Molecular Mechanisms of Bacterial Virulence . Eds. C.J. Kado and J. H. Crosa. Kluwer Acad. Publ. , Netherlands , pp. 207-222.
Filichkin , S.A. , Gelvin, S.B. 1992. Effect of dimethyl sulfoxide concentration on specificity of primer matching in PCR. Biotechniques , 12 (6): 828-830.
