Bertone Group Research

Background

Much of our previous work has entailed the development of novel microarray platforms for genomic and proteomic analyses, extending these technologies beyond conventional array-based gene expression profiling and toward the global analysis of complex biological systems. Related platforms include chromosome- and genome-scale DNA tiling arrays for the discovery of novel functional elements in eukaryotes [1], and protein-based microarrays for the large-scale characterisation of biochemical activities [2].

DNA tiling arrays are designed for the interrogation of large regions of genomic sequence in an unbiased fashion, allowing the identification of novel transcribed RNAs and cis-regulatory elements in eukaryotes. This approach represents a conceptual departure from traditional gene-based arrays which focus exclusively on coding sequences, and its implementation has required significant technological advances in polymer synthesis and array fabrication, as well as the development of new array design algorithms and data analysis methods [3].

Comprehensive tiling arrays have recently been constructed to represent the entire non-repetitive sequence of both strands of the human genome [4]. These systems are now being used for high-resolution analyses of gene transcription and regulation, thereby annotating the genomes determined through large-scale sequencing efforts. Hybridisation to various RNA sources has identified thousands of previously unannotated transcripts, and chromatin profiling experiments are revealing a vast network of transcription factor binding sites and chromatin modifications across the human genome [5].

Differentiation and Development

Our research group investigates the cellular and molecular processes underlying mammalian stem cell differentiation and lineage commitment. Stem cells maintain a unique state of self-renewal, whereby they are capable of producing identical daughter cells, and pluripotency, or the ability to differentiate into specialised progenitors whose fates are more restricted. These properties are fundamental to cellular diversification and growth patterning during embryogenesis and development, as well as the initiation of cellular repair processes throughout adult life.

A primary focus of our research is to map the global transcriptomic and proteomic activity of neural and embryonic stem cells during various stages of differentiation and lineage commitment in tissue culture. This work involves the application of sophisticated genomic, proteomic and computational analyses, combined with new advances in cell culture methods to establish pure undifferentiated stem cell lines for investigation. Experimental projects are realised in part through collaborative research programmes established with laboratories in the Cambridge area and elsewhere, and computational analyses are performed by our group in the design of these experiments and the interpretation of results.

We are also involved in large-scale analyses of microarray-based gene expression experiments comparing numerous stem cell lines with differentiated tissues, in collaboration with the Genomics and Regulatory Systems Group headed by Nick Luscombe. The analysis of these experiments is expected to be an ongoing project, as we incorporate results from disparate sources when new data become available. Another interest lies in the integration of data from related work on epigenetic imprinting and gene suppression studies, through our interactions with the EBI Epigenomics team led by Ewan Birney as a joint initiative between EMBL-EBI and the Wellcome Trust Sanger Institute. This work is expected to provide key insights into the effects of chromatin modification on the determination of cell fate.

Selected References