Abstract 1075: Multiple alternative promoters and a long non-coding RNA constitute the complex regulatory region of the cancer and drug resistance associated gene B4GALT1
Authors: AlOBAIDE MOHAMMED A. , Alobydi Hytham , Abdelsalam Abdelsalam , Zhang Ruiwen , Srivenugopal Kalkunte S. 
Published: August 2015

Abstract
Background: The B4GALT1 (β-1,4-galactosyltransferase) gene, overexpressed in human cancers is highly implicated in tumor progression and metastasis. Used as a prototype in genomic analyses, it shows significant variations in the transcript origination sites in normal and cancer tissues. Little is known on the regulation of B4GALT1 transcription and regulatory regions involved. Objectives: To characterize the alternative promoters and the regulatory elements of B4GALT1 and gain further insight into its cancer and tissue-specific transcription. Methods: The genomic criteria of the bidirectional loci, B4GALT1 and B4GALT1-AS1 (encoding a long non-coding antisense RNA; lncRNA) and their promoters were searched in the NCBI-GenBank, UCSC Genome Bioinformatics, Ensembl, TRED, EDP, PEDB and MPromDb databases to specify the map locations and identify the transcription factor binding sites (TSS), namely the TATA-8 (TATAWAWR) and TATA-532 (HWHWWWWR, excluding: HTYTTTWR, CAYTTTWR, MAMAAAAR, CTYAAAAR) elements, INR (YYANWYY), CCAAT and its inverted sequence, BRE (SSRCGCC) and DPE (RGWCGTG) sequences. Several bioinformatic tools were used to retrieve the promoter sequences, identify and flip the forward or reverse strands in search for specific sequences and quantitate the dinucleotide base-stacking energy values (Kcal/mol/dimer) indicative of the helix stability and strength of protein binding. Results: 13 alternative promoters were identified in the databases B4GALT1. Six of these resided within 1.454 kb forming a complex transcriptional regulatory unit we refer to as the TR1-PE1; this unit had all characteristics known for bidirectional transcription of divergent genes, B4GALT1 and B4GALT1-AS1. The TR1-PE1 sequence harbored CpG Island and several types of TFBSs, INR, BRE, ERE, TCCAA and TATA-532. The dinucleotide base-stacking energy along TR1-PE1 showed variable values, indicating a differential stability along the sequence. The INR sequences were found mainly along sequences with lower dinucleotide base-stacking energy values, whereas BRE sequences were observed in regions with higher values. Two highly conserved (TG)18 repeats were identified in non-overlapping B4ALT1 promoter located 9.744 kb from 3′ TR1-PE1 side, which enhance transcription especially when they are located closer to the promoter. The transcripts of B4GALT1 and B4GALT1-AS1 are of different lengths, one of B4GALT1-AS1 transcripts showed a 66% complementarity with the primary B4GALT1 transcript. Conclusions: The unique expression of the B4GALT1 in malignant and non-malignant tissues is controlled by a differential usage of alternative and bidirectional promoters along with post-transcriptional regulation by the antisense lncRNA and possible involvement of (TG)18 repeats, which in turn govern the cell-matrix interactions, malignant progression and anticancer sensitivity.
Citation Format: MOHAMMED A. AlOBAIDE, Hytham Alobydi, Abdelsalam Abdelsalam, Ruiwen Zhang, Kalkunte S. Srivenugopal. Multiple alternative promoters and a long non-coding RNA constitute the complex regulatory region of the cancer and drug resistance associated gene B4GALT1. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1075. doi:10.1158/1538-7445.AM2015-1075