Research Interests

 We work with the budding and fission yeasts (S.cerevisiae and Sz.pombe). Using a combination of high-throughput genetics, genomic analyses and biochemistry we investigate the role of chromatin in RNA Polymerase II (RNApII) transcription elongation, DNA Double-Strand Break (DSB) repair and chromosome stability. Our most recent publications in these fields include:

 

Fiedler et al (2009) Cell 136:952

Reversible protein phosphorylation is a signaling mechanism involved in all cellular processes. To create a systems view of the signaling apparatus in budding yeast, we generated an E-MAP (epistatic miniarray profile) comprised of 100,000 pair-wise, quantitative genetic interactions, including virtually all protein kinases and phosphatases and key cellular regulators. Quantitative genetic interaction mapping reveals factors working in compensatory pathways (negative genetic interactions; e.g. synthetic lethality) or those operating in linear pathways (positive genetic interactions; e.g. suppression). Within kinases, phosphatases, and their substrates, we found an enrichment of positive genetic interactions. To develop a global view of the signaling apparatus, we isolated “triplet genetic motifs” and assembled these into a higher-order map. The resulting network view provides new insights into signaling pathway regulation, and revealed a link between the cell cycle kinase, Cak1, the Fus3 MAP kinase, and a pathway that regulates chromatin integrity during transcription by RNA polymerase II. (PDF)

 

Ahn et al (2009) EMBO J 28:205

As RNA polymerase II (RNApII) transitions from initiation to elongation, Mediator and the basal transcription factors TFIID, TFIIA, TFIIH, and TFIIE remain at the promoter as part of a scaffold complex, whereas TFIIB and TFIIF dissociate. The yeast Ctk1 kinase associates with elongation complexes and phosphorylates serine 2 in the YSPTSPS repeats of the Rpb1 C-terminal domain, a modification that couples transcription to mRNA 3'-end processing. The higher eukaryotic kinase Cdk9 not only performs a similar function, but also functions at the 5'-end of genes in the transition from initiation to elongation. In strains lacking Ctk1, many basal transcription factors cross-link throughout transcribed regions, apparently remaining associated with RNApII until it terminates. Consistent with this observation, preinitiation complexes formed on immobilized templates with transcription extracts lacking Ctk1 leave lower levels of the scaffold complex behind after escape. Taken together, these results suggest that Ctk1 is necessary for the release of RNApII from basal transcription factors. Interestingly, this function of Ctk1 is independent of its kinase activity, suggesting a structural function of the protein. (PDF)
 

Fillingham et al (2008) Mol Cell Biol 28:4342

Acetylation of S.cerevisiae histone H3-K56 by the Histone AcetylTransferase (HAT) Rtt109 is important for repairing replication-associated lesions. Rtt109 purifies from yeast in complex with the histone chaperone Vps75, which stabilizes the HAT in vivo. A whole genome screen to identify genes whose deletions have synthetic genetic interactions with rtt109Δ suggests the HAT has functions in addition to DNA repair. We show that Rtt019 is also an H3-K9 HAT and its activity towards this substrate is stongly enhanced by Vps75. Vps75 and another histone chaperone, Asf1, are both required for H3-K9Ac by Rtt109 in vivo, whereas H3-K56Ac requires only Asf1. Asf1 also physically interacts with the nuclear Hat1 / Hat2 / Hif1 complex that acetylates H4-K5 and H4-K12. We suggest Asf1 is capable of assembling into chromatin H3-H4 dimers diacetylated on both H4-K5/12 and H3-K9/56. (PDF)

_______________________________________________________

Contact Details

Department of Cell Biology, Albert Einstein College of Medicine
Chanin 415A, 1300 Morris Park Avenue
Bronx, NY 10461, USA.
Email: mkeogh@aecom.yu.edu
Tel: 1-718-430 8796 (Office); 1-718-430 4787 (Lab)
Fax: 1-718-430 8574
AIM: mckeogh2004
Skype: michaelckeogh

_______________________________________________________