Research
Cis-acting control of epigenetic states
There is a lot of information known about where DNA methylation and histone modifications lie in the mammalian genome, but almost nothing is known about how they get there. Critical enzymes needed to place these marks have been identified, but the enzymes don't act randomly in the genome; there are some essential instructions that tell them where to act. What provides those instructions? The process of transcription provides a useful analogy to appreciate this question:
We know a lot about where genes are located, the mRNAs transcribed from them, the promoters and other regulatory sequences that direct transcription and soluble transcription factors that act at those regulatory sequences. But in the epigenetics field, though there are rapidly accumulating data describing the locations of epigenetic modifications and the soluble factors that are able to place them, there are at most three known regulatory sequences that can program or direct local placement of those marks.
Our lab has identified one of them at the Rasgrf1 locus in mouse that is able to program the local DNA methylation state. Now we seek to understand how that methylation programmer works. Some of our papers in this area are:
Lindroth, A. M., Park, Y. J., McLean, C. M., Dokshin, G. A., Persson, J. M., Herman, H., Pasini, D., Miro, X., Donohoe, M. E., Lee, J. T., Helin, K., and Soloway, P. D. (2008) "Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus" PLoS Genetics 4:(8), e1000145
Holmes, R., and Soloway, P. D. (2006) "Regulation of imprinted DNA methylation" Cytogenet Genome Res 113:(1-4), 122-129
Holmes, R., Chang, Y., and Soloway, P. D. (2006) "Timing and Sequence Requirements Defined for Embryonic Maintenance of Imprinted DNA Methylation at Rasgrf1" Mol Cell Biol 26:(24), 9564-9570
Yoon, B.-J., Herman, H., Hu, B., Park, Y. J., Lindroth, A. M., Bell, A., West, A. G., Chang, Y., Stablewski, A., Piel, J. C., Loukinov, D. I., Lobanenkov, V., and Soloway, P. D. (2005) "Rasgrf1 Imprinting is Regulated by a CTCF-dependent Methylation-Sensitive Enhancer Blocker" Mol Cell Biol 25:(24), 11184–11190
Herman, H., Lu, M., Anggraini, M., Sikora, A., Chang, Y., Yoon, B. J., and Soloway, P. D. (2003) "Trans allele methylation and paramutation-like effects in mice" Nat Genet 34:(2), 199-202
Yoon, B. J., Herman, H., Sikora, A., Smith, L. T., Plass, C., and Soloway, P. D. (2002) "Regulation of DNA methylation of Rasgrf1" Nat Genet 30:(1), 92-96
The identity of new imprinted genes:
Our earlier studies that identified the DNA methylation programming element at Rasgrf1 took advantage of the fact that Rasgrf1 is an imprinted locus. Imprinted genes undergo predictable and distinct patterns of epigenetic programming on the two parental alleles. This made it possible to hunt for the sequences that are needed for programming. We are undertaking genome wide approaches to identify new imprinted loci, which will provide new tools for characterizing epigenetic programming events. We have just begun publishing in this area:
McLean, C. M., Eilerston, K. E., Bustamante, C. D., and Soloway, P. D. (Submitted) "Successful Computational Prediction of Novel Imprinted Genes From Epigenomic Features"
Wang, X., Sun, Q., McGrath, S. D., Mardis, E. R., Soloway, P. D., and Clark, A. G. (2008) "Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain" PLoS ONE 3:(12), e3839
Epigenomic analyses on a nanoscale device:
Existing methods for performing genome wide epigenomic analyses rely on chromatin immunoprecipitations (ChIP) analyzed on a microarray (chip) or by deep sequencing (seq). ChIP-chip and ChIP-seq approaches have been extraordinarily useful, but they suffer from inherent limitations: (1) they require abundant materials, making analysis of single embryos, rare populations of cells or microdissected material impossible; (2) they query only one epigenetic mark at a time, making simultaneous analysis of multiple epigenetic marks impossible. In collaboration with Harold Craighead's lab in Engineering Physics, we are developing methods to overcome these limitations. Our results are not yet published. This work was recently funded by the NIH Epigenomics Road Map initiative.