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SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster

View Article: PubMed Central - PubMed

ABSTRACT

Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373.

No MeSH data available.


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SMAR1 binds and targets distinct genes from various biological pathways depending on p53 status.(A) Functional categorization of SMAR1 target genes using DAVID Functional Annotation tool in HCT116 p53+/+ data set and (B) HCT116 p53−/− data set. (C) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53+/+ by anti-p53 antibody and (D) anti-SMAR1 antibody. For convenience, RP11-271C24.2 and RP11-419C23.1 have been labeled as C24.2 and C23.1 respectively. (E) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53−/− by anti-SMAR1 antibody. (F) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53+/+ cell line. (G) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53−/− cell line.
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f3: SMAR1 binds and targets distinct genes from various biological pathways depending on p53 status.(A) Functional categorization of SMAR1 target genes using DAVID Functional Annotation tool in HCT116 p53+/+ data set and (B) HCT116 p53−/− data set. (C) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53+/+ by anti-p53 antibody and (D) anti-SMAR1 antibody. For convenience, RP11-271C24.2 and RP11-419C23.1 have been labeled as C24.2 and C23.1 respectively. (E) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53−/− by anti-SMAR1 antibody. (F) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53+/+ cell line. (G) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53−/− cell line.

Mentions: As this study was the first of its kind to unravel novel and global gene targets of SMAR1, we were interested in understanding the diverse roles of SMAR1 via control of different downstream target genes. The SMAR1 gene targets in both the data sets as predicted by ChIP-seq analysis were subjected to DAVID Functional Annotation tools15. The target genes were then broadly classified into functional categories and selected for critical analysis. The DAVID functional analysis suggested that the SMAR1 gene targets in both the data sets belonged to a broad range of biological processes, viz., splicing, protein and histidine metabolism, pulmonary disorders, viral infection, insulin and calcium signalling, 3′UTR mediated translation regulation, cancer and metastasis, etc. (Fig. 3A,B). A distinct category of microRNA and long non-coding RNA (lncRNA) genes were also predicted to be targeted by SMAR1 (Supplementary Fig. S5).


SMAR1 binds to T(C/G) repeat and inhibits tumor progression by regulating miR-371-373 cluster
SMAR1 binds and targets distinct genes from various biological pathways depending on p53 status.(A) Functional categorization of SMAR1 target genes using DAVID Functional Annotation tool in HCT116 p53+/+ data set and (B) HCT116 p53−/− data set. (C) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53+/+ by anti-p53 antibody and (D) anti-SMAR1 antibody. For convenience, RP11-271C24.2 and RP11-419C23.1 have been labeled as C24.2 and C23.1 respectively. (E) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53−/− by anti-SMAR1 antibody. (F) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53+/+ cell line. (G) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53−/− cell line.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5037395&req=5

f3: SMAR1 binds and targets distinct genes from various biological pathways depending on p53 status.(A) Functional categorization of SMAR1 target genes using DAVID Functional Annotation tool in HCT116 p53+/+ data set and (B) HCT116 p53−/− data set. (C) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53+/+ by anti-p53 antibody and (D) anti-SMAR1 antibody. For convenience, RP11-271C24.2 and RP11-419C23.1 have been labeled as C24.2 and C23.1 respectively. (E) The gene promoters with p53 binding motif in juxtaposition of SMAR1 binding peaks were amplified in chromatin immunoprecipitate of HCT116 p53−/− by anti-SMAR1 antibody. (F) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53+/+ cell line. (G) Quantitative real-time PCR analysis of these gene targets upon overexpression and knockdown of SMAR1 in HCT116 p53−/− cell line.
Mentions: As this study was the first of its kind to unravel novel and global gene targets of SMAR1, we were interested in understanding the diverse roles of SMAR1 via control of different downstream target genes. The SMAR1 gene targets in both the data sets as predicted by ChIP-seq analysis were subjected to DAVID Functional Annotation tools15. The target genes were then broadly classified into functional categories and selected for critical analysis. The DAVID functional analysis suggested that the SMAR1 gene targets in both the data sets belonged to a broad range of biological processes, viz., splicing, protein and histidine metabolism, pulmonary disorders, viral infection, insulin and calcium signalling, 3′UTR mediated translation regulation, cancer and metastasis, etc. (Fig. 3A,B). A distinct category of microRNA and long non-coding RNA (lncRNA) genes were also predicted to be targeted by SMAR1 (Supplementary Fig. S5).

View Article: PubMed Central - PubMed

ABSTRACT

Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIP-sequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-373.

No MeSH data available.


Related in: MedlinePlus