Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/28336
Title: Identifying and characterizing cis-regulatory elements in the human genome
Authors: LEE PING ALISON
Keywords: comparative genomics; conserved noncoding elements
Issue Date: 8-Jun-2009
Source: LEE PING ALISON (2009-06-08). Identifying and characterizing cis-regulatory elements in the human genome. ScholarBank@NUS Repository.
Abstract: Comparative genomics is a powerful approach for identifying conserved <i>cis</i>-regulatory elements in the human genome. Since functional sequences evolve slower than surrounding neutrally evolving regions, <i>cis</i>-regulatory elements can be identified as conserved noncoding elements (CNEs) in comparisons of human and other vertebrate genomes. The objective of my study is to identify all putative <i>cis</i>-regulatory elements associated with transcription factor (TF)-encoding genes in the human genome by comparison with pufferfish (<i>Takifugu rubripes</i>; "fugu") sequences. I have built a database of all TF-encoding genes in human, mouse and fugu and predicted CNEs (&ge;65% identity over 50 bp) associated with orthologous genes. The human-fugu CNEs identified show a significant overlap with experimentally validated transcription factor binding sites, and are significantly associated with TF-encoding genes that are involved in regulating development, in particular development of the central nervous system. Expression profiling based on publicly available expression data, shows that genes that express most highly in central nervous system tissues are enriched with CNEs. Through functional assays in transgenic mice, several CNEs are shown to act as transcriptional enhancers at a specific developmental stage. An online database has been constructed to catalog the human, mouse and fugu TF-encoding genes, and their associated CNEs. This database, named TFCONES (http://tfcones.fugu-sg.org/), would be useful to researchers interested in studying the regulation of TF-encoding genes and understanding gene regulatory networks in vertebrates.
URI: http://scholarbank.nus.edu.sg/handle/10635/28336
Appears in Collections:Ph.D Theses (Open)

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