GSE70058
Role of SMAR1 in global gene regulation through interaction with tumor suppressor p53
Scaffold Matrix Attachment Region binding protein 1, SMAR1 has vital role to play as a general repressor of transcription. SMAR1 is known to retard cell cycle progression and delay tumor growth in mice. Further, it forms a ternary complex with p53-Mdm2 and inhibit p53-mediated transcription. Thus, SMAR1 can potentially alter p53 function and orchestrate different set of genes in p53-dependent and p53-independent manner. The present study aims to decipher the potential role of SMAR1 in global transcription regulation and to study role of p53 in the process. Towards this objective, chromatin immunoprecipitation combined Next-generation sequencing (ChIP-Seq) was performed using HCT116 and HCT116 p53-/- cell samples. The a-SMAR1 antibody was used for such ChIP experiments which was already tested by Wastern blot assays and found to be SMAR1 specific. The sequence data generated was then analyzed and the results obtained are (1) Higher genomic occupancy of SMAR1 in HCT116 (wild type) than HCT116 p53-/- (P53 null) data set (2) For peaks within ±5kb of TSS, SMAR1 had the highest predisposition to bind upstream of the TSS in close proximity, i.e., -1 to 0 kb that represents the promoter region of the gene (3) SMAR1 was found to target 5617 genes (unique in Wild type) , 8198 genes (unique in Null) and 1876 genes that were common in both the samples (4) In silico motif search indicated that SMAR1 binds to a dinucleotide T(C/G) repeat sequence (5) Functional Annotation of targets revealed that the predicted target genes are involved in apoptosis, epigenetics, cell cycle, cell signalling, neuronal genes, transcription, metabolism etc. The target also include noncoding RNAs genes such as microRNAs /lincRNAs. Overall design: Chromatin immunoprecipitation was carried out using ChIP grade a-SMAR1 antibody (immune fraction) and Rabbit IgG (mock) in HCT116 p53+/+ (Wild type)  and HCT116 p53-/- (null) cell lines. It was followed by massively parallel sequencing using Illumina GAIIx Analyzer.