Ssm1: DNA methylation and chromatin structure in a murine transgene

In recent years, epigenetics (the heritable storage of information not encoded in the primary DNA sequence) has moved to the forefront of biological inquiry. From the regulation of transcription to orchestrating cellular development epigenetics plays a pivotal role in the life of an organism. The discovery of Ssm1, a gene which controls the DNA methylation of a murine transgene in a strain and sequence specific manner, gives us a powerful tool to investigate epigenetic phenomena---particularly the relationships between DNA methylation, chromatin structural change, and transcription.; In this work we sought to understand whether Ssm1 directs a mouse strain dependent chromatin structure at the HRD transgenic locus in addition to its previously documented regulation of strain-specific DNA methylation. Further we wanted to understand the relationship these two factors would have with transgene expression. To this end we first used chromatin immunoprecipitation to assay the chromatin structure at HRD at several different developmental time points (represented by undifferentiated embryonic stem cells, partially and fully differentiated ES cells, and adult mice). Secondly we compared the relative timing of chromatin structural change at HRD with the establishment of DNA methylation. Finally we assayed transcription of the transgene and compared this to both chromatin structure and DNA methylation status.; In addition to investigating the epigenetic state of HRD, efforts were made to better understand the nature of Ssm1. First a BAC complementation assay was used in an effort to narrow the position of Ssm1 within the murine genome. Secondly, a particularly promising Ssm1 candidate was investigated by transfection into embryonic stems cells, and finally the timing of Ssm1 action was probed by newly transfecting HRD into ES cells.; Lastly, we analyzed the genomic region containing Ssm1 and in doing so discovered novel murine specific repetitive elements strongly associated with zinc-finger protein domains.; Further work characterizing Ssm1's effects on HRD epigenetic status and Ssm1 itself will allow us to better understand the mechanisms which establish and maintain epigenetic structures not only in mice but in other mammals and possibly in all vertebrates.