Ekaterina "Kate" Mirkin

Ekaterina "Kate" Mirkin

Lecturer
617-627-3726
Robinson Hall, Room 367
200 College Avenue, Medford, MA

Education

  • Postdoctoral fellow, Harvard University, 2006 - 2013
  • Ph.D., Molecular Genetics, University of Illinois at Chicago, 1999 - 2006
  • B.S./M.S., Molecular Biology, Moscow State University, Russia, 1994 - 1999

Expertise

Genetics

Research Interests

I am interested in chromosome biology, genome's structure and function, maintenance of genomic stability and nuclear architecture.

My graduate work focused on transcription-replication collisions in the cells of a bacterium, E. coli. As bacterial cells simultaneously replicate and transcribe their chromosome, occasional collisions between the replication forks and RNA polymerases can occur. Such collisions can affect both replication and transcription, as well as influence the structure of the genome in the course of evolution. I have shown that RNA polymerase inhibits the movement of the replication fork in vivo, if the replication fork approaches it in the head-on direction.

During my postdoctoral training, I was using baker's yeast S. cerevisiae as a model system to study interactions between parts of chromosomes. In the recent years, it has become clear that nuclear architecture plays an important role in gene expression and maintenance of genomic stability, but molecular mechanisms, which shape nuclear architecture, remain largely unknown. I have demonstrated that self-dimerizing ("sticky") proteins can act as tethers to physically bring parts of different chromosomes together.

Selected Publications and Presentations

Mirkin EV, Mirkin SM. (2014) To Switch or Not to Switch: At the Origin of Repeat Expansion Disease. Mol Cell. 53, 1-3.

Mirkin EV, Chang FS, Kleckner N. (2014) Protein-mediated chromosome pairing of repetitive arrays. J Mol Biol. 426, 550-557.

Mirkin EV, Chang FS, Kleckner N. (2013) Dynamic trans interactions in yeast chromosomes. PLoS ONE 8(9), e75895.

Mirkin EV, Mirkin SM. (2007) Replication fork stalling at natural impediments. Microbiol Molec Biol Rev. 71, 13-35.

Mirkin EV, Castro Roa D, Nudler E, Mirkin SM. (2006) Transcription regulatory elements are punctuation marks for DNA replication. Proc Natl Acad Sci. 103, 7276-7281.
(This article was highlighted in: A. Katsnelson (2006) Genome punctuation. J Cell Biol. 173, 643.)

Mirkin EV, Mirkin SM. (2005) Mechanisms of transcription - replication collisions in bacteria. Mol Cell Biol. 25, 888-895.

Bondar T, Mirkin EV, Ucker DS, Walden WE, Mirkin SM, and Raychaudhuri P. (2003) Schizosaccharomyces pombe Ddb1 is functionally linked to the replication checkpoint pathway. J Biol Chem. 278, 37006-37014.

Mirkin SM, Smirnova EV. (2002) Positioned to expand. Nat Genet. 31, 5-6.

Korobko IV, Korobko EV, Chupikova NI, Vanechkin MA, Smirnova EV, Kiselev SL, Georgiev GP. (2002) The use of the two-hybrid cloning in yeast for functional characterization of protein kinase MAK-V. Mol Biol (Mosk). 36, 491-495.

Krasilnikova MM, Smirnova EV, Krasilnikov AS, Mirkin SM. (2001) A new trick for an old dog: TraY binding to a homopurine-homopyrimidine run attenuates DNA replication. J Mol Biol. 313, 271-282.

Korobko EV, Smirnova EV, Kiselev SL, Georgiev GP, Korobko IV. (2000) Identification of a new alternative-splicing transcript of Rabaptin-5 interacting with protein kinase MAK-V. Dokl Biochem. 370, 1-3.

Teaching/Courses Taught

Biology 41: Genetics
Biology 13L: Cells and organisms, laboratory coordinator
Biology 260-02: Preparation of teaching assistants to lead laboratory sections