Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells

Gao, Fei; Ji, Guanyu; Gao, Zhaowei; Han, Xu; Ye, Mingzhi; Yuan, Zhimei; Luo, Huijuan; Huang, Xiaojun; Natarajan, Karthikraj; Wang, Jun; Yang, Huanming; Zhang, Xiuqing

doi:10.1016/j.ygeno.2013.12.006

Cited by 39 publications

(20 citation statements)

References 41 publications

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“…5e). The co-existence of H3K27me3 and H3K4me3 is the classical bivalent mark for developmentally regulated genes but it is also present in differentiated cell lines36; Repo-Man is significantly enriched at sites encompassing these markers.…”

Section: Resultsmentioning

confidence: 99%

Repo-Man/PP1 regulates heterochromatin formation in interphase

et al. 2017

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Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment. Using a novel proteogenomic approach, we show that Repo-Man is enriched at subtelomeric regions together with H2AZ and H3.3 and that depletion of Repo-Man alters the peripheral localization of a subset of these regions and alleviates repression of some polycomb telomeric genes. This study shows a role for a mitotic phosphatase in the regulation of the epigenetic landscape and gene expression in interphase.

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Section: Resultsmentioning

confidence: 99%

Repo-Man/PP1 regulates heterochromatin formation in interphase

et al. 2017

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“…In both SPLAT and Accel-NGS Methyl-Seq data, we found some degree of coverage decline in CpG islands and in very GC rich promoter regions, which is a common characteristic of many types WGBS data (Supplementary Data). Notably, the library preparation cost for SPLAT (<10 $/sample) is less than one tenth of the cost for any of the commercial WGBS methods, making SPLAT a particularly attractive method also for bisulphite sequencing of smaller genomes such as Arabidopsis and for applications such as ChIP-bisulphite sequencing (ChIP-BS-seq) (43,44) where the cost of library preparation per sample approaches the cost of sequencing. The post bisulphite adaptor tagging (PBAT) method, which is the only other alternative protocol for post bisulphite WGBS library preparation that has been described in a peer-reviewed journal, has the advantage of producing amplification free libraries from low amounts of DNA.…”

Section: Discussionmentioning

confidence: 99%

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

Raine

Manlig

Wahlberg

et al. 2016

Nucleic Acids Research

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Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.

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“…RNA-seq and BS-seq data for HEK293 [23] and KIRC cell lines [24, 25] were obtained from the GEO (http://www.ncbi.nlm.nih.gov/geo/, GSE68938, GSE51867, GSE64451, GSE44866).…”

Section: Methodsmentioning

confidence: 99%

A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma

et al. 2016

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The PVT1 lncRNA has recently been involved in tumorigenesis by affecting the protein stability of the MYC proto-oncogene. Both MYC and PVT1 reside in a well-known cancer-risk locus and enhanced levels of their products have been reported in different human cancers. Nonetheless, the extension and relevance of the MYC-PVT1 deregulation in tumorigenesis has not yet been systematically addressed.Here we performed a pan-cancer analysis of matched copy number, transcriptomic, methylation, proteomic and clinicopathological profiles for almost 7000 patients from 17 different cancers represented in the TCGA cohorts. Among all cancers types, kidney renal clear cell carcinoma (KIRC) showed the strongest upregulation of PVT1 and increased levels of both MYC and PVT1 correlated with the clinical outcome. PVT1 misregulation in KIRC is mostly associated to promoter hypomethylation rather than locus amplification. Furthermore, we found an association between MYC levels and PVT1 expression, which impacted on MYC-target genes.Collectively, our study discloses the role of PVT1 as a novel prognostic factor and as a molecular target for novel therapeutic interventions in renal carcinoma.

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Direct ChIP-bisulfite sequencing reveals a role of H3K27me3 mediating aberrant hypermethylation of promoter CpG islands in cancer cells

Cited by 39 publications

References 41 publications

Repo-Man/PP1 regulates heterochromatin formation in interphase

Repo-Man/PP1 regulates heterochromatin formation in interphase

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

A pan-cancer analysis of MYC-PVT1 reveals CNV-unmediated deregulation and poor prognosis in renal carcinoma

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