Projects - Future Plans

We aim to characterize, from a genome point of view, the interconnection of three cycles fundamental to living organisms. The project relies on ChIP-Seq, a method that will allow us to study not only transcription of the protein-coding genes, but transcription of pol II- and pol III-ncRNA genes. These RNAs have been often ignored before, simply because they were difficult or impossible to detect and analyze with previous techniques.

In future research we plan to continue the functional analysis of some of the specific transcription factors identified in Subproject 2, and for the most interesting ones we will want to test their role in cycle-cycle connections in the context of an entire organism, i.e. the mouse. Further, the results obtained will undoubtedly reveal the need to analyze additional factors for their genomic localization during the various phases of each cycle, and for their function in cultured mouse fibroblasts and liver.

We will also be interested in expanding the transcription maps described in Subproject I to include pol I and spRNAP-IV. Pol I is responsible for the synthesis of the large rRNA precursor whereas the recently discovered single polypeptide spRNAP-IV, a nuclear RNA polymerase expressed from an alternative transcript of the mitochondrial RNA polymerase gene, is responsible for the synthesis of a small subset of mRNA-encoding genes and perhaps other genes. A difficulty with the pol I analysis is the repeated configuration of rRNA genes and their flanking sequences. Nevertheless, our preliminary experiments with pol III genes indicate that we can exploit differences in flanking sequences to map accurately sequence tags from pol III ChIPs. It is possible that the flanking regions of transcribed pol I genes display enough differences that this will also be possible. Including these two additional polymerases will give us a complete view of the transcription activity at different stages of each cycle and may reveal unexpected exciting activities by, for example, spRNAP-IV.

As the project progresses and datasets become available, we will be able to put more and more emphasis on mathematical analysis of the data, network analysis, and modeling. We plan to develop collaborations with more researchers interested in modeling as needed.