Elena Cravens
Elena Cravens
Year: 2012
Faculty Advisor: Eric Richards

Functional dissection of the VIM1 protein and its role in cytosine methylation in Arabidopsis

Epigenetics is the study of chromatin modifications, such as cytosine methylation and histone modification, which affect gene expression. VARIANT IN METHYLATION 1 (VIM1) is an epigenetic regulator required for both maintenance of DNA methylation and centromeric heterochromatin compaction in Arabidopsis thaliana. The VIM1 protein has a methyl DNA binding SRA (SET- and RING-associated) domain, as well as a PHD(plant homeo-domain) and two RING (presumptive ubiquitin E3 ligase) domains. We hypothesized that the VIM1 protein SRA domain is involved in maintaining cytosine methylation in Arabidopsis but that the RING and PHD domains are dispensable. To test this hypothesis, PHD and RING point mutants were expressed in vim1 null mutants. We studied whether or not the centromeric repeats were fully methylated in transgenic plants expressing the mutated versions of VIM1 using DNA blots of genomic DNA digested with methylation-sensitive endonucleases. To test transgene expression of our point mutants, we looked at mRNA expression of VIM1 using RT-PCR. To supplement our experimental work on VIM1 domains, we studied natural variation of these domains using protein sequence alignments generated from the Arabidopsis 1001 genome database (http://signal.salk.edu/atg1001/3.0/gebrowser.php). Our research can lead to new knowledge about epigenetic mechanisms in plants. Furthermore, our research has implications for humans because VIM1 has a human homolog, UHRF1.

My Experience

As a PGRP intern at BTI, I was given the opportunity to learn more about plant biology on a molecular basis and practice new research techniques. The environment was very opened and supportive. Everybody in the Richards’ lab was very enthusiastic and welcoming. I know the skills and knowledge I gained over the summer will help me in future endeavors. The program exposed me to many different aspects of plant research separate from my project and gave me an accurate picture of what plant biology research entailed. Outside of lab, Ithaca is a great place to be over the summer. I have made strong connections and friends over the summer and I’m grateful for the opportunities the PGRP internship has given me.