Keith Giles, Ph.D.
||Shelby Biomedical Rsch Building
19th Street South
Birmingham, AL 35294-0024
Lab Research Focus:
In plants and animals, chromatin can be thought of as the entire genome plus all of the proteins that bind to it in vivo. By wrapping DNA around histone proteins (to form the nucleosome) and then packaging multiple nucleosomes together to form higher-order structures, the cell is able to condense 2 meters of DNA into a microscopic nucleus (Figure 1). Heterochromatin refers to the physically condensed and largely transcriptionally silent regions of the genome. The packaging of regions of the genome into heterochromatin is critical for many aspects of cell physiology, including: chromosome pairing and separation during mitosis, regulation of gene expression during development, regulation of DNA recombination, and the imprinting of maternal and/or paternal specific transcription patterns. Furthermore, the ability to form heterochromatin is responsible for the regulation of highly repetitive genetic elements that can lead to genomic instability if they are not controlled. The development of cancer can also be linked to the loss of heterochromatin-specific modifications at certain tumor suppressor genes.
The Giles' Lab is focused on understanding the molecular mechanisms of heterochromatin formation. Current projects are aimed at understanding the role of the RNA interference (RNAi) machinery in this process. The establishment of heterochromatin in the model organism S. pombe is critically dependent upon the RNA interference machinery. This process involves the processing of double stranded RNA into short interfering RNAs (siRNAs) by the enzyme Dicer. These siRNAs are then bound by a member of the Argonaute protein family and used to target the entire chromatin remodeling complex to the chromatin in -cis. Although less is known about animals, preliminary evidence suggests that the RNAi machinery is involved in the regulation of vertebrate chromatin structure. However, as is often the case, the situation is likely more complex than in S. pombe.
In chicken cells, the RNAi protein Argonaute 2 (cAgo2) localizes to a heterochromatin region upstream of the developmentally regulated globin locus. Chicken Argonaute 2 (cAgo2) is required for maintaining physically condensed chromatin, transcriptional silencing, and histone hypo-acetylation throughout this 16 kb long locus. Furthering the connection between the RNAi machinery and the control of vertebrate chromatin structure is the presence of siRNAs originating at the sites of cAgo2 localization. Current work involves investigation of the role and molecular mechanism of the RNAi machinery in human cells. Next generation sequencing techniques (ChIP-seq and RNA-seq) are being used to determine the function and molecular mechanisms of the RNAi machinery on a whole genome scale. Also of interest is the study of the protein-protein interactions made by the human RNAi machinery in the nucleus.
Although the study of RNAi and its relationship to chromatin structure is the current focus of the lab, projects aimed at increasing our understanding of chromatin structure and the regulation of gene expression in a broad sense are always of interest. Students interested in any of these projects should contact me directly to discuss more specifically.
Figure 1. The levels of chromatin compaction in the human genome. Taken from Felsenfeld and
Groudine, Nature, 2003.
Assistant Professor University of Alabama at Birmingham 2011
Post-Doctoral NIDDK/NIH 2011
PhD The Johns Hopkins University 2004
BS State University of New York at Buffalo 1999
1. Chromatin boundaries, insulators, and long-range interactions in the nucleus. Giles KE, Gowher, H, Ghirlando, R, Jin C, Felsenfeld, G. Cold Spring Harb Symp Quant Biol, 2010
2. Maintenance of a constitutive heterochromatin domain in vertebrates by a Dicer-dependent mechanism. Giles KE, Girlando R, Felsenfeld G. Nature Cell Biology, 2010
3. Retroviral splicing suppressor sequesters a 3' splice site in a 50S aberrant splicing complex. Giles KE, Beemon KL. Mol Cell Biol, 2005.
4. Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. Cabello-Villegas J, Giles KE, Soto AM, Yu P, Mougin A, Beemon KL, Wang YX. RNA, 2004.
5. Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. Giles KE, Caputi M, Beemon KL. RNA, 2004.