Although they carry the same genetic information, individual cells within a multi-cellular organism exhibit stunningly different phenotypes. This is a consequence of the expression of different subsets of the transcriptome and proteome in each cell type. The path from gene to protein has multiple steps, which offer many possibilities for regulation along the way.
While until recently it was believed that gene expression is regulated mainly at transcriptional level, recent studies have unveiled additional layers of complexity. The goal of the RNA Regulatory Networks (RRN) group is to use computational methods to discover and understand the regulatory networks leading to tissue-specific expression of protein forms.
For many years transcription factors held the center stage in the regulation of gene expression. This paradigm has changed with the discovery of Piwi-protein-associated small RNAs that regulate gene expression at either transcriptional or post-transcriptional level. Among these, the microRNAs (miRNAs) have initially been discovered in the worm Caenorhabditis elegans, but in recent years they have been found in the genomes of organisms as varied as viruses, plants and humans. miRNAs play essential roles in development, metabolism, immune responses, and they can either suppress or enhance specific pathogenic processes such as infections and cancer. By combining high-throughput experimental approaches with data analysis and computational modeling, the group of Mihaela Zavolan aims to uncover post-transcriptional regulatory circuits that control cellular differentiation.
Projects and Services
The vast volumes of data that are obtained with current technologies such as deep sequencing can only be interpreted with the help of computational tools. By developing such tools, the Zavolan group has contributed to the discovery of many miRNAs in animals, as well as in viruses. Because the function of most of the miRNAs that have been discovered is unknown, computational prediction of miRNA targets remains essential for guiding the experiments.
The Zavolan group used a comparative genomics approach to develop ElMMo, which is one of the most accurate miRNA target prediction programs currently available.They further studied target sites that are identified based on various types of measurements (evolutionary conservation, mRNA degradation or translational inhibition upon miRNA transfection or depletion) and uncovered several properties that are predictive for functional miRNA target sites. These properties are common to evolutionarily conserved miRNA target sites and to target sites that are associated with the degradation of target mRNAs, indicating that mRNA degradation is a common, important outcome of miRNA-target interaction. One of the most intriguing features of miRNA-dependent regulation is that most mRNAs that carry highly conserved miRNA target sites respond only mildly to changes in miRNA concentrations. It is therefore believed that miRNAs mostly „fine-tune“ gene expression. Understanding the mechanisms behind this fine-tuning function is one of the current projects of the group.
Given the still limited understanding of what constitutes a miRNA target, it is important to have an experimental method that allows identification of a large number of miRNA targets in a manner that is as unbiased as possible. The Zavolan group contributed to the development of a photoreactive nucleoside-enhanced crosslinking and immunoprecipitation (CLIP) method that enables isolation of miRNA targets on the basis of their being bound by miRNA-guided Argonaute proteins (collaboration with the group of Tom Tuschl, The Rockefeller University). Through further computational analyses of such Argonaute CLIP data the group aims to uncover miRNA-target interactions that are relevant for the progression of cancers.
Mammalian transcriptomes are extremely complex. Generation of a mature mRNA involves many steps (transcription initiation, splicing, 3’ end processing) that can be independently regulated to give rise to multiple transcripts with different properties. In different phases of their cycle, cells can for e.g. express transcript forms that translate into the same protein, but have different susceptibilities to post-transcriptional regulation. In collaboration with Walter Keller, professor emeritus at the Biozentrum, the Zavolan group is mapping binding sites of 3’ end processing factors transcriptome-wide in order to understand what configurations of interactions determine the choice of 3’ end processing site. This study will provide further insights into the interplay between post-transcriptional processes that regulate gene expression.
Websites for Further Information
RNA Regulatory Networks Group: http://www.biozentrum.unibas.ch/research/groups-platforms/overview/unit/zavolan/
Server for the ananlysis of binding sites of RNA-binding proteins: http://www.clipz.unibas.ch