Annotation of genomics data using bidirectional hidden Markov models unveils variations in Pol II transcription cycle.

ABSTRACT: DNA replication, transcription and repair involve the recruitment of protein complexes that change their composition as they progress along the genome in a directed or strand-specific manner. Chromatin immunoprecipitation in conjunction with hidden Markov models (HMMs) has been instrumental in understanding these processes, as they segment the genome into discrete states that can be related to DNA-associated protein complexes. However, current HMM-based approaches are not able to assign forward or reverse direction to states or properly integrate strand-specific (e.g., RNA expression) with non-strand-specific (e.g., ChIP) data, which is indispensable to accurately characterize directed processes. To overcome these limitations, we introduce bidirectional HMMs which infer directed genomic st

SUBMITTER: Zacher B 

PROVIDER: S-EPMC4300491 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature