Our laboratory studies the gene regulatory networks (GRNs) that control animal development and disease, with a particular emphasis on microRNAs (miRNAs) and other non-coding RNAs (ncRNAs). The long-term goal of our research is to determine the role of ncRNAs during embryonic development and how they integrate the complex network of gene regulation established by protein-coding genes. Work in our lab revolves around on two major topics: (1) the role of ncRNAs in the regulatory networks that control patterning of the mesoderm, and the specification of mesoderm derivatives (e.g. muscle and heart) in the fruitfly Drosophila melanogaster, and (2) the gene regulatory network that governs pancreatic endocrine cell differentiation in zebrafish (Danio rerio).
The role of ncRNAs in the regulatory networks that control the formation and differentiation of the mesoderm. Specification of the mesoderm in Drosophila starts with the formation, in the precellular embryo, of nuclear gradient of a protein called Dorsal (Dl). Peak levels of this protein in the ventral part of the embryo activates the expression of twist (twi), which encodes a bHLH transcription factor. Twist in turns activates the expression of target genes that are required at various steps of mesoderm development -e.g. T48 (invagination of mesoderm precursors during gastrulation), dMef2 (segmentation and specification of muscle types), and tinman (formation of the heart). Twist also controls the expression of miR-1, a mesoderm-specific microRNA whose sequence and function have been conserved in mammals. We used whole-genome tiling arrays to identify additional ncRNAs expressed in the mesoderm. In contrast to miR-1, which is broadly expressed in the mesoderm, two other ncRNAs identified in our screen are expressed in progressively more restricted cell types at later stages of development, suggesting distinct and/or combinatorial functions in the specification, differentiation and morphogenesis of mesoderm derivatives. Our current focus is to characterize the function of these new non-protein coding genes using a combination of genetics, embryology, genomics, molecular, cell biological and computational approaches.
The gene regulatory network that governs pancreatic endocrine cell differentiation. Over the last couple of years, the zebrafish has become a major model organism to study vertebrate organogenesis. Initial studies showed that, albeit some minor differences, the essential components (transcription factors and signaling molecules) involved in pancreas organogenesis in zebrafish and mammals are conserved. Nonetheless, the gene network underlying pancreas development in zebrafish and mammals is incomplete because mainly based on epistatic relationships inferred from knockout phenotypes. In addition, recent surveys of the embryonic expression of microRNAs during zebrafish development revealed at least two that appear to be pancreas-specific. The function of these miRNAs in pancreas formation is unknown.What are the genes directly regulated by some of the major transcription factors involved in pancreas organogenesis (i.e. Ptf1, Pdx, Hb9, Isl1, Pax6, Nk2.2,...)? What are the target cis-regulatory modules bound by those factors? Are target genes regulated by these factors combinatorially? What is the role of microRNAs expressed in the pancreatic anlage during zebrafish embryogenesis? We will address those questions using a combination of ChiP-Chip and SELEX assays, classical deletion studies, comparative genomics and other bioinformatics methods, as well as reverse genetics. The information obtained from these analyses will greatly improve our understanding of the complex network regulating pancreas formation and endocrine cell differentiation.
Zecchin E, Filippi A, Biemar F, Tiso N, Pauls S, Ellertsdottir E, Gnugge L, Bortolussi M, Driever W, Argenton F. Distinct delta and jagged genes control sequential segregation of pancreatic cell types from precursor pools in zebrafish. Dev Biol. (2007) 301:192-204.
Biemar F, Nix DA, Piel J, Peterson B, Ronshaugen M, Sementchenko V, Bell I, Manak JR, Levine MS. Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array. Proc Natl Acad Sci U S A. (2006) 103:12763-8.
Ronshaugen M, Biemar F, Piel J, Levine M, Lai EC. The Drosophila microRNA iab-4 causes a dominant homeotic transformation of halteres to wings. Genes Dev. (2005) 19:2947-52.
Biemar F, Zinzen R, Ronshaugen M, Sementchenko V, Manak JR, Levine MS. Spatial regulation of microRNA gene expression in the Drosophila embryo. Proc Natl Acad Sci U S A. (2005) 102:15907-11.
Mavropoulos A, Devos N, Biemar F, Zecchin E, Argenton F, Edlund H, Motte P, Martial JA, Peers B. sox4b is a key player of pancreatic alpha cell differentiation in zebrafish. Dev Biol. (2005) 285:211-23.
Biemar F, Argenton F, Schmidtke R, Epperlein S, Peers B, Driever W. Pancreas development in zebrafish: early dispersed appearance of endocrine hormone expressing cells and their convergence to form the definitive islet. Dev Biol. (2001) 230:189-203.