Speaker: Xiaohui Xie
BroadInstitute, MIT
Friday, March 2, 2007
11:00 am - 12:00 pm
EBU3b 1202

ABSTRACT
Among the 3 billion bases contained in the human genome, only 1.5% are well characterized, primarily in the form of protein-coding genes. One of the main challenges in genomics is to understand the function of the other 98.5% of the genome. Comparison of the human genome to several other related genomes has revealed that these regions harbor a strikingly large number of highly conserved noncoding elements, accounting for over two-thirds of the portion of the human genome under selection.

And yet the function of these conserved noncoding elements (CNEs) remains largely unknown. We also know little about their evolutionary origins, or the molecular mechanisms that have preserved them through millions of years' evolution. I will describe computational methods for systematically dissecting the function of the CNEs. Using statistical analysis and comparative genomics, we have uncovered hundreds of novel regulatory motifs within the CNEs, matching hundreds of thousands of conserved instances in the genome. These motifs form distinct classes, including transcriptional regulatory elements, small RNA genes, micro RNA targeting sites, and chromatin barriers.

I will also describe an effort to characterize the evolution of regulatory sequences. I will propose the creative role of transposable elements as a major force for duplicating and dispersing regulatory elements in the human genome. Comparison of metatherian and eutherian genomes reveals that over 15% of the eutherian CNEs arose from sequence inserted by transposons.

In a few years, genome sequences of over 50 mammals will become available. I will discuss how these data will empower the methods I have described, and provide us an opportunity to unravel all information coded in the human genome.

BIO
Xiaohui Xie is a computational biologist working at the BroadInstitute of the Massachusetts Institute of Technology. His research interests are in computational genomics and regulatory motif finding in particular. Dr. Xie received his M.S. in CS from MIT, Ph.D. in Computational Neurosciences from MIT, where he continued as a postdoc with Eric Lander.