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Title: Identification and characterization of CIS-regulatory elements for vertebrate developmental control genes
Keywords: enhancers, EGFP, CNEs, zebrafish, transcription factors, development,
Issue Date: 27-Jul-2009
Citation: SUMANTRA CHATTERJEE (2009-07-27). Identification and characterization of CIS-regulatory elements for vertebrate developmental control genes. ScholarBank@NUS Repository.
Abstract: Identifying DNA sequences (enhancers) that direct the precise spatial and temporal expression of developmental control genes remains a significant challenge in the annotation of vertebrate genomes. Locating these sequences, which in many cases lie at a great distance from the transcription start site, has been a major obstacle in deciphering gene regulation. The completion of a number of vertebrate genome sequences with its unprecedented coverage and resolution, as well as the concurrent development of genomic alignment, visualization, and analytical bioinformatics tools, has made large scale genomic sequence comparisons between diverse species, not only possible but an increasingly popular approach for the discovery of putative cis- regulatory elements. Here we present a novel study which integrates comparative genomics at four different genomic loci, with medium throughput functional assays to identify a list of conserved non-coding sequences to test for regulatory activity in important genes which control the specification and development of various tissue types in vertebrates. We also performed detailed biochemical tests to locate and validate a functional enhancer that did not show any sequence level constraint between species. Our results clearly indicate that high level of functional conservation of genes is not necessarily associated with sequence conservation of their regulatory elements. We show that irrespective of tissue type the gene expresses in, sequence conservation does not hold the key to elucidate all its enhancers. Moreover, non-conserved non-coding elements may have significant role in cis -regulation. Our study proves unambiguously the pressing need to bring together multiple approaches to locate and validate the functional elements in the genome so that we can fully decipher how the genome functions.
Appears in Collections:Ph.D Theses (Open)

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