1. Can we identify the gene regulatory networks that drive early embryogenesis?
2. How do these networks function, how do they evolve?
(C. elegans, C. briggsae)
1. What is the function of microRNAs/piRNAs/RBPsduring regeneration/stem cell biology?
2. What are the molecular mechanisms that maintain totipotencyof stem cells?
1. How do RBPs/microRNAsrecognize their targets?
2. What is the molecular function of RBPs/microRNAs?
3. Can we make a testable theory that models site occupancy, site specificity together with RBP and target mRNA copy number?
(human cell lines + other systems)
A major lesson from recent genomics is that metazoans share to a large degree the same repertoire of protein encoding genes. It is thought that differences between cells within species, between species, or between healthy and diseased animals are in many cases due to differences in when, where and how genes are turned on or off. Gene regulatory information is to a large degree hardwired into the non-coding parts of the genome. Our lab focuses on decoding transcriptional regulation (identification and characterization of targets of transcription factors in non-coding DNA) and post-transcriptional control mediated by a class of small, non-coding RNAs (microRNAs). microRNAs are a recently discovered large class of regulatory genes, present in virtually all metazoans. They have been shown to bind to specific cis-regulatory sites in the 3' untranslated regions (3' UTRs) of protein-encoding mRNAs and, by unknown mechanisms, repress protein production of their target mRNAs. Our understanding of the biological function of animal microRNAs is just beginning to emerge, but it is clear that microRNAs are regulating or are involved in a large variety of biological processes and human diseases, such as developmental timing, long-term memory, signalling, homeostasis of key metabolic gene products such as cholesterol, apoptosis, onset of cancer, Tourett's syndrome, and others. Our predictions are tested experimentally, in collaboration with other labs or within our own wet lab.
Example 1: microRNAs
In recent years we have explored the function of microRNAs. For example, we have developed one of the first microRNA target finding algorithms (Rajewsky and Socci 2004) and could show that microRNAs very likely regulate thousands of genes within vertebrates, flies, and nematodes (Krek et al Nat Genetics 2005, Grun et al 2005 PLoS CB 2005, Lall et al Curr. Biol. 2006). We have further helped to elucidate the function of microRNAs in pancreatic beta cells (insulin secretion, Poy et al Nature 2004) and in liver (cholesterol levels, Krutzfeldt et al Nature 2005). More recently, we have shown that microRNAs can leave cell type specific mRNA expression signatures on hundreds of genes (Sood et al PNAS 2006), and that human genotyped SNP data can be used to explicitly demonstrate and quantify the contribution of microRNA targets to human fitness (Chen and Rajewsky, Nature Genetics 2006). All microRNA target predictions of our algorithm PicTar can be accessed at our searchable PicTar website. For recent reviews see: Rajewsky, Nature Genetics 2006; Chen and Rajewsky, Nature Reviews Genetics 2007.
Example 2: Analysis of Deep Sequencing Data
We are experimentally creating cDNA libraries suitable for deep sequencing, and are developing algorithms to analyze the massive output ("454", Illumina, SOLiD ...), including mRNA-Seq, small RNA deep sequencing, ChIP-Seq, ...
Example 3: Small RNAs, Stem Cells, and Regeneration
With kind support of Alejandro Sanchez (HHMI, University of Utah), we are setting up Planaria (tripoblasts, fresh-water flatworms) as a model system in our lab. Planaria have remarkable regeneration abilities: cutting the roughly 1cm long, complex animal into ~300 pieces will lead to ~300 healthy regenerated planaria. This regeneration is mediated by totipotent adult stem cells. It has been shown that genes in the small RNA pathway are required for regeneration. We are investigating (also in collaboration with the John Kim lab, University of Michigan) the function of small RNAs during planarian regeneration.