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Sergei Filichkin

Sergei Filichkin

 Assistant Professor (Senior Research),
Ph.D. 1984, Krasnodar Polytechnic Institute, USSR



Office/Lab:Cordley 3060
Phone: 541-737-5269/5230

Research Area

General : Plant genomics.

Specific interests : Circadian rhythms. Alternative splicing.

Description of Research

•  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.

Related Links

Todd Mockler - Danforth Plant Science Center

Steve Kay - University of Southern California, Dornsife


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