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Activity Number: 418
Type: Contributed
Date/Time: Wednesday, August 9, 2006 : 10:30 AM to 12:20 PM
Sponsor: Section on Statistical Computing
Abstract - #306303
Title: Linker DNA Length Preference in Human Chromatin Revealed by a Two-State Duration Hidden Markov Model
Author(s): Guei-Feng Tsai*+ and Ji-Ping Wang and Jonathan Widom
Companies: Northwestern University and Northwestern University and Northwestern University
Address: , , 60208,
Keywords: dinucleosome ; linker DNA ; hidden Markov model ; duration
Abstract:

The nucleosome is the repeating subunit of chromatin, formed by a short stretch of DNA, 147bp in length, wrapping around four pairs of histones. The linker DNA that connects two neighboring nucleosomes may favor particular values for a given cell type of a given organism to facilitate chromatin forming. The data we have contains 1002 experimentally obtained human dinucleosome DNA sequences. Each sequence roughly covers two nucleosomes in the two ends with a linker DNA in between, while their exact positions are undetermined. We develop a two state duration Hidden Markov model to determine the optimal path of nulceosome-linker-nucleosome structure under certain biochemical constraints. Our results show that the linker length distribution does favor a series of values roughly space by 5 or 10 bps in a range between 10 bp and 120 bps.

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