"Reconstructing 3-D Shapes of Chromosomes from Hi-C Data"
April 5, 2011 @ 3:30 - 4:30 pm
Jun Liu, Ph.D., Harvard University
Location: Blockley Hall - Room 701
TITLE: Reconstructing 3-D Shapes of Chromosomes from Hi-C Data
How human chromatin fits into a nucleus approximately ten micrometers in diameter remains largely unresolved. Understanding how chromosomes fold may provide insights into transcription regulation, and therefore functional state of the cell. A recent technology named Hi-C offers an opportunity to gain an unbiased view of chromatin organization in the nucleus. It usesproximity ligation of cross-linked DNA with a biotin linker, which is used to pull down the fragments, followed by high-throughput sequencing. The observed counts are modeled by a Poisson distribution with rate inversely related to the spacial distance between two chromosomal locations. We build a Bayesian model equipped with advanced MCMC techniques to reconstruct the3-D shapes of the chromosome as well as estimating the sequencing efficiencyof each chromosomal region. The biological implications of the constructed structures are consistent with the recent published results regarding chromosome formations.
Based on the joint with Ming Hu, Ke Deng, and Steve Z Qin.