The sequencing of eukaryotic genomes revealed that a remarkably small fraction is occupied by protein-coding sequences (2% in human). Surprisingly, protein-coding sequences occupy a similarly small percentage of the total diversity of transcriptional output. The genome generates incredibly complex populations of non-coding RNAs. What is the role of these non-coding RNAs? Over the past decade, it has become clear that small regulatory RNAs are key regulators of multiple biological processes, including transcription, translation and mRNA stability. Many non-coding RNAs such as ribosomal and spliceosomal RNAs are well known, and these act at key steps of gene expression. Others, like the recently discovered miRNAs modulate gene expression by regulating stability and translation of multiple protein-coding mRNAs. But even beyond these known non-coding RNAs, there is a vast number of species still awaiting characterization. We are interested in identifying and dissecting the role of other, less characterized small non-coding RNAs. We are focusing on two classes of small non-coding RNAs: 1) the recently described genic small RNAs and 2) piwi-interacting, or piRNAs
1) Dissecting the biogenesis and role of small genic RNAs: We have recently described and characterized a new class of small RNAs that map to the promoter regions and the bodies of protein coding genes. These small RNAs as a class seem conserved in multiple organisms including flies and humans. Our data implies that they at least in part are processed from long mature transcripts through cleavage and a subsequent capping mechanism possibly by a recently identified cytoplasmic capping complex. While their function is still unclear, several lines of evidence indicate that genic small RNAs or the act of their transcription per se regulates the expression of the protein-coding genes to which they are linked. We are interested in elucidating the exact processes, through which these small RNAs are generated and the regulatory pathways involved in their biogenesis. In particular we are trying to elucidate the role of the cytoplasmic capping complex and diverse RNA degradation pathways in their cleavage and capping. In parallel we are focusing on determining the role of these small RNAs. Due to sequence homology to their "host gene", they have a great potential to regulate the expression of protein coding genes, but at which level this regulation might occur is still unclear. We are using different biochemical and cell biological approaches to identify at which step of gene expression and how they are involved. While current work focuses on the genic small RNAs we continue to pursue the characterization of the transcriptional complexity of the mammalian genomes through genome-wide analysis of other cellular RNA populations.
2) Identifying the role of piRNAs in epigenetic regulation: Another recently discovered class of the small RNA are Piwi-interacting or piRNAs. The piRNA pathway, functions in the germline to repress transposon activity, thereby maintaining genomic integrity. Perturbation of this pathway leads to dysfunctional gonads and sterility in both Drosophila and mouse. However, the exact mechanism by which the piRNA pathway protects the genome remains poorly understood. There is increasing evidence that one of the protein partners of piRNAs (Piwi in flies, Miwi2 in mice) has an important function in the germline nucleus. We are investigating the nuclear function of Piwi by analyzing its interaction with chromatin. We are trying to identify genomic loci to which Piwi binds and compare those with the distribution of active and repressive epigenetic marks.