Integrative In-Silico Evaluation of Features on BRCA1 Cis Regulatory Element
Author(s): Apeksha Arun Bhandarkar, Smeeta Shrestha
Genomic cis regulatory elements support the gene transcriptional landscape which fine tune spatiotemporal gene expression via interaction with different transcription factors and co modulators during development. These regulatory elements are poorly conserved, highly heterogenous with limited understanding of their role in gene expression. Here we use a well-known human tumor suppressor gene, Breast Cancer Type 1 (BRCA1) and UCSC human genome browser database to report the in-silico putative cis regulatory enhancer element and its features. We report a 2kb double elite enhancer, GH17J043079 located within intron 12 of the BRCA1 gene. The enhancer interacts with NBR1, NBR2, TMEM106A and RPL27 and VAT1 gene promoters. GH17J043079 showed histone activity in human embryonic stem cells, cancerous cells, housed transcription factors specific to liver cells and was enriched with Alu elements, indicative of ability for potential gene rearrangements. Additionally, it contained eQTLs, rs4793197, rs8176190, rs8176192, rs8176193 and rs8176194 with disparity in allele frequency across populations. Our in-silico review on the features present within GH17J043079 element in BRCA1 helps to postulate an intricate transcription regulation. Such candidate based analysis of features within cis regulatory element on a gene can help elucidate intricate genomic architecture, gene regulation and its impact on complex disorders.