Genome-wide identification and comprehensive analysis of transcriptionsl desert regions
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Date
2009
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Publisher
University of the Western Cape
Abstract
The initiation of transcription in mammalian genomes predominatly occurs
at 5' promoter regions, however increasingly initiation events have been
observed within introns, coding exons and 3' UTRs. Nevertheless there are
large segments of mammalian genomes that are not prone to transcription
initiation. These locations can be understood to be 'transcription initiation
deserts'. It is challenging and useful to demarcate these segments or
locations of the genome. The availability of a huge number of transcript data
has provided an opportunity to develop a methodology to predict and
annotate these genomic segments.
A comprehensive collection of data for Homo sapiens ard Mus musculus,
consisting of CAGE tags and other evidence for the existence of
ffanscription was used to develop a methodology that allows the annotation
of locations of mammalian genomes as those that are highly likely to initiate
tanscription and those that are unlikely to harbour transcription start sites
(TSSs). The algorithm allows the recognition of TSSs with 100%
sensitivity, which makes it the superior choice over other existing
algorithms for promoter prediction for the task of annotating TSS deserts.
Description
Philosophiae Doctor - PhD