DBBS graduate programs                                                                                  Molecular Genetics and Genomics Program
Molecular Microbiology and Microbial Pathogenesis Program
Developmental, Regenerative and Stem Cell Biology Program

Research Interests

RNA interference (RNAi)-related mechanisms participate in diverse epigenetic phenomena. Few are more extreme than the genome remodeling of the ciliate Tetrahymena thermophila. This organism eliminates nearly 15 megabases of its germline DNA from the somatic nucleus during its development. Our lab aims to understand the regulation of this massive genome reorganization using a combination of genetic, molecular, and cellular biology approaches to uncover how ~6000 DNA segments are selectively excised. Our current model is built on the observations that bi-directional germline transcription leads to the generation of 28-30 base RNA molecules (scan RNAs) that then target specific chromatin modification(s) to the homologous locus. The DNA rearrangement machinery recognizes the modified chromatin state and eliminates the targeted DNA segment. These studies will certainly provide fundamental insight into RNAi-related mechanisms that direct chromatin modifications that are critical for transcriptional gene silencing and heterochromatin formation in eukaryotes. Underlying this proposal is a goal to understand how RNA molecules can communicate genetic information between the parental and developing genomes, which has great potential to reveal novel roles for RNA in epigenetic programming. Additionally, we believe many of the DNA segments targeted for elimination are important for germline chromosome structure, and thus understanding how the cell specifically recognizes these sequences will contribute general knowledge of mechanisms ensuring chromosome stability that are essential to prevent aberrant rearrangements.

Photo caption: Nuclear development occurs during Tetrahymena mating. Shown here is a conjugating pair shortly before the genome reorganization initiates. The DNA deletion protein, Pdd1p, fused to green fluorescent protein, is localized on the chromatin of the large, developing somatic nuclei.

Selected Publications

Malone C.D., A. M. Anderson, J. A. Motl, C. H. Rexer, and  D. L. Chalker. (2005) Germline transcripts are processed by a Dicer-like protein that is essential for developmentally programmed genome rearrangements of Tetrahymena thermophila. Mol. Cell. Biology 25(20):9151-64.

Charles H. Rexer and D L. Chalker. (2007) Lia1p, a Novel Protein Required during Nuclear Differentiation for Genome-Wide DNA Rearrangements in Tetrahymena thermophila.  Eukaryotic Cell 6(8):1320-1329

Malone CD, Falkowska KA, Li AY, Galanti SE, Kanuru RC, LaMont EG, Mazzarella KC, Micev AJ, Osman MM, Piotrowski NK, Suszko JW, Timm AC, Xu MM, Liu L, Chalker DL. (2008) Nucleus-specific importin alpha proteins and nucleoporins regulate protein import and nuclear division in the binucleate Tetrahymena thermophila. Eukaryot Cell. 7:1487-99

Chalker DL, Meyer E, Mochizuki K. (2013) Epigenetics of ciliates. Cold Spring Harb Perspect Biol. 2013 Dec 1;5(12):a017764. doi: 10.1101/cshperspect.a017764. PMID: 24296171

Shieh AW, and DL Chalker (2013) LIA5 Is Required for Nuclear Reorganization and Programmed DNA Rearrangements Occurring during Tetrahymena Macronuclear Differentiation. PLoS One. 2013 Sep 17;8(9):e75337. PMID: 24069402

Schwope RM and DL Chalker (2014) Mutations in Pdd1 reveal distinct requirements for its chromo- and chromoshadow domains in directing histone methylation and heterochromatin elimination. Eukaryotic Cell 2014, 13(2):190-201. PMID: 24297443

Horrell SA, Chalker DL. (2014) LIA4 encodes a chromoshadow domain protein required for genomewide DNA rearrangements in Tetrahymena thermophila. Eukaryot Cell. 2014 Oct;13(10):1300-11.