Nucleosomes positioning around transcriptional start site of tumor suppressor (Rbl2/p130) gene in breast cancer

Abstract

Dynamic positioning of nucleosomes is pivotal in determining level of genes expression especially on or around transcription start site (TSS) of a gene. Purpose of the current study was to determine nucleosome position around TSS of Rbl2/p130. We investigated Rbl2/p130 expression in connection to nucleosome positions around its TSS among breast tumors and their adjacent normal control tissues (ANCT) using micrococcal nuclease (MNAse) digestion assay and ChIP-PCR analysis. Three fold reduced Rbl2/p130 expression in these tumor tissues were noticed compared to their control tissues. DNA obtained from MNAse digested chromatin was used as PCR template. Region between - 137 to + 140 around TSS was scanned using 3 primer pairs (P1 = - 137 to + 69; P2 = - 90 to + 69; P3 = - 33 to + 140). ~ 66% breast tumors and ~ 26% ANCT samples were positive for P1. The difference was found statistically significant (p = 0.000) with an odd ratio (OD) of 9.143, suggesting that nucleosome formation in this region is ~ 9 times more probable in tumor samples. ~ 73% of the tumor and 60% ANCT were positive for P2, which although is significant (p = 0.035) with OD = 3.250, but less preferable than P1. However, P3 was not found to be a preferred area for nucleosome occupancy (p = 0.670; OD = 1.2). Negative correlations for nucleosome positions were observed especially for P1. Our results indicate that nucleosome are present slightly downstream of TSS in routine, while in case of breast carcinogenesis nucleosomes slides 55 bases upstream of the TSS, aligning + 1 position at the center of nucleosome, hence hindering access to the transcriptional machinery.

The Epigenetic Regulatory Protein CBX2 Promotes mTORC1 Signalling and Inhibits DREAM Complex Activity to Drive Breast Cancer Cell Growth

“…The DREAM complex represses E2F target gene expression and inhibits cell cycle progression, ultimately causing cell senescence [ 31 ]. RBL2 has been shown to suppress tumour growth in vivo [ 41 ], and downregulation of RBL2 has been reported in a number of cancers [ 42 , 43 , 44 , 45 , 46 ]. In BCa, epigenetic silencing at the RBL2 transcriptional start site has been reported, although the proteins mediating this repression have not been identified [ 45 , 46 ].…”

“…RBL2 has been shown to suppress tumour growth in vivo [ 41 ], and downregulation of RBL2 has been reported in a number of cancers [ 42 , 43 , 44 , 45 , 46 ]. In BCa, epigenetic silencing at the RBL2 transcriptional start site has been reported, although the proteins mediating this repression have not been identified [ 45 , 46 ]. We found an enrichment of CBX2 at the RBL2 gene promoter, which suggests that CBX2-associated cPRC1 could directly repress RBL2 expression.…”

Harvestman: A framework for hierarchical feature learning and selection from whole genome sequencing data

“…Ensembl also identifies genomic regions with predicted functional roles, including transcription start sites, enhancers, and promoters, or those that are associated with known peptides. These regions are collectively referred to as 'biological regions' or 'peptides' accordingly, and variation in such sites have also been tied to cancer among other diseases (Farman, Iqbal, Azam, & Saeed, 2018;Hua et al, 2018;Rhie et al, 2018).…”

ZCMM: A Novel Method Using Z-Curve Theory- Based and Position Weight Matrix for Predicting Nucleosome Positioning

“…By modulating the accessibility of genomic regions to regulatory proteins, it was observed that the packaging of DNA around the histone octamer plays important roles in many biological processes [7,8]. Most studies on nucleosome function have indicated that nucleosomes are involved in chromatin formation [9], antagonistic transcription factors [10,11], and regulating gene expression [12,13].…”