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Analysis of Urea Cycle Gene Transcription Regulation using Bioinformatic Software and Patient Sequences
Author(s) -
LaBella Abigail Leavitt,
Feeney Timothy,
Heibel Sandra,
Tuchman Mendel,
Caldovic Ljubica
Publication year - 2011
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.25.1_supplement.564.8
Subject(s) - computational biology , urea cycle , transcription (linguistics) , transcription factor , gene , software , biology , genetics , computer science , programming language , linguistics , philosophy , amino acid , arginine
Conversion of nitrogenous waste to urea via the urea cycle is regulated by factors that respond to nitrogen load to prevent toxic ammonia buildup. Six enzymes, N‐acetylglutamate synthase, carbamylphosphate synthetase, ornithine transcarbamylase (OTC), argininosuccinate synthase, argininosuccinate lyase and arginase 1 (ARG1) are essential for ureagenesis. Most urea cycle disorders result from mutations in coding regions or splice sites, but regulatory region changes may also contribute. To analyze urea cycle transcriptional regulation we used Cis‐Element Over Representation (CLOVER) software to find transcription factor binding motifs in conserved regions. Candidate binding sites for Estrogen Receptor and BRCA1 were found in the ARG1 promoter. Binding will be verified using an avidin‐agarose pull down assay and western blotting. We also screened patients with OTC deficiency that lack typical mutations, for changes in OTC regulatory regions. We identified three single nucleotide substitutions as disease‐causing candidates in the OTC promoter; two in a known HNF‐4 binding site and one in a conserved region of unknown function. These changes were absent in 800 alleles from persons of Caucasian, Hispanic and African decent. Bioinformatic detection and molecular verification of regulatory factors is critical to understanding the urea cycle and for better diagnosis of disease.