Regulatory dissection of the CBX5 and hnRNPA1 bi-directional promoter in human breast cancer cells reveals novel transcript variants differentially associated with HP1α down-regulation in metastatic cells

Abstract

BackgroundThe three members of the human heterochromatin protein 1 (HP1) family of proteins, HP1α, HP1β, and HPγ, are involved in chromatin packing and epigenetic gene regulation. HP1α is encoded from the CBX5 gene and is a suppressor of metastasis. CBX5 is down-regulated at the transcriptional and protein level in metastatic compared to non-metastatic breast cancer. CBX5 shares a bi-directional promoter structure with the hnRNPA1 gene. But whereas CBX5 expression is down-regulated in metastatic cells, hnRNAP1 expression is constant. Here, we address the regulation of CBX5 in human breast cancer.MethodsTransient transfection and transposon mediated integration of dual-reporter mini-genes containing the bi-directional hnRNPA1 and CBX5 promoter was performed to investigate transcriptional regulation in breast cancer cell lines. Bioinformatics and functional analysis were performed to characterize transcriptional events specifically regulating CBX5 expression. TSA treatment and Chromatin Immunoprecipitation (ChIP) were performed to investigate the chromatin structure along CBX5 in breast cancer cells. Finally, expression of hnRNPA1 and CBX5 mRNA isoforms were measured by quantitative reverse transcriptase PCR (qRT-PCR) in breast cancer tissue samples.ResultsWe demonstrate that an hnRNPA1 and CBX5 bi-directional core promoter fragment does not comprise intrinsic capacity for specific CBX5 down-regulation in metastatic cells. Characterization of transcriptional events in the 20 kb CBX5 intron 1 revealed existence of several novel CBX5 transcripts. Two of these encode consensus HP1α protein but used autonomous promoters in intron 1 by which HP1α expression could be de-coupled from the bi-directional promoter. In addition, another CBX5 transcriptional isoform, STET, was discovered. This transcript includes CBX5 exon 1 and part of intron 1 sequences but lacks inclusion of HP1α encoding exons. Inverse correlation between STET and HP1α coding CBX5 mRNA expression was observed in breast cancer cell lines and tissue samples from breast cancer patients.ConclusionWe find that HP1α is down-regulated in a mechanism involving CBX5 promoter downstream sequences and that regulation through alternative polyadenylation and splicing generates a transcript, STET, with potential importance in carcinogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12885-016-2059-x) contains supplementary material, which is available to authorized users.

Bioinformatic analysis of the expression and prognostic value of chromobox family proteins in human breast cancer

“…CBX5 was upregulated at the mRNA and protein levels in breast cancer cells compared with non-cancerous cells 29,30 . However, CBX5 was downregulated in highly invasive or metastatic breast cancer cell lines compared with weakly invasive or non-metastatic cells, which suggested that CBX5 is a metastatic suppressor in the invasion process 29,31,32 . The suppressor mechanism of CBX5 in invasion is unknown.…”

“…In this study, we used novel applications of bioinformatics to analyze four aspects of eight CBX proteins in breast cancer: expression pattern, clinicopathological parameters, prognostic value, and genetic alteration. Human HP1 proteins, HP1α/CBX5, HP1β/CBX1, and HPγ/CBX3, correlated with proliferation, invasion, and metastasis by regulating gene expression in human breast cancer cells 2,17,29 . CBX5 is the most studied HP1 protein, and CBX3 is barely examined.…”

“…Human HP1 proteins, HP1α/CBX5, HP1β/CBX1, and HPγ/CBX3, correlated with proliferation, invasion, and metastasis by regulating gene expression in human breast cancer cells 2 , 17 , 29 . CBX5 is the most studied HP1 protein, and CBX3 is barely examined.…”

Inflammatory related gene IKKα, IKKβ, IKKγ cooperates to determine liver cancer stem cells progression by altering telomere via heterochromatin protein 1-HOTAIR axis

“…Heterochromatin protein1 is involved in chromatin packing and epigenetic gene regulation [8]. The α, β and γ isoforms of HP1 selectively bind to methylated lysine 9 of histone H3 via their chromodomains [9].…”

Inflammatory factor receptor Toll‐like receptor 4 controls telomeres through heterochromatin protein 1 isoforms in liver cancer stem cell

“…5 Three members of the human heterochromatin protein 1 (HP1) family (HP1a, HP1b and HP1c) are involved in chromatin packing and epigenetic gene regulation. 6 Emerging evidence has shown that HP1a plays a unique biological role in breast cancer-related processes and particularly in epigenetic control mechanisms involved in aberrant cell proliferation and metastasis. 7 a, b and c proteins of HP1 family selectively bind to methylated lysine 9 of histone H3 via their chromo-domains.…”