Genome-wide DNA methylation analysis in cohesin mutant human cell lines

Jinglan Liu, Zhe Zhang, Masashige Bando, Takehiko Itoh, Matthew A. Deardorff, Jennifer R. Li, Dinah Clark, Maninder Kaur, Kondo Tatsuro, Antonie Debra Kline, Celia Chang, Hugo Vega, Laird G. Jackson, Nancy B. Spinner, Katsuhiko Shirahige, Ian D. Krantz

Research output: Contribution to journalArticle

Abstract

The cohesin complex has recently been shown to be a key regulator of eukaryotic gene expression, although the mechanisms by which it exerts its effects are poorly understood. We have undertaken a genome-wide analysis of DNA methylation in cohesin-deficient cell lines from probands with Cornelia de Lange syndrome (CdLS). Heterozygous mutations in NIPBL, SMC1A and SMC3 genes account for ~65% of individuals with CdLS. SMC1A and SMC3 are subunits of the cohesin complex that controls sister chromatid cohesion, whereas NIPBL facilitates cohesin loading and unloading. We have examined the methylation status of 27 578 CpG dinucleotides in 72 CdLS and control samples. We have documented the DNA methylation pattern in human lymphoblastoid cell lines (LCLs) as well as identified specific differential DNA methylation in CdLS. Subgroups of CdLS probands and controls can be classified using selected CpG loci. The X chromosome was also found to have a unique DNA methylation pattern in CdLS. Cohesin preferentially binds to hypo-methylated DNA in control LCLs, whereas the differential DNA methylation alters cohesin binding in CdLS. Our results suggest that in addition to DNA methylation multiple mechanisms may be involved in transcriptional regulation in human cells and in the resultant gene misexpression in CdLS.

Original languageEnglish (US)
Article numbergkq346
Pages (from-to)5657-5671
Number of pages15
JournalNucleic Acids Research
Volume38
Issue number17
DOIs
Publication statusPublished - May 6 2010

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ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this

Liu, J., Zhang, Z., Bando, M., Itoh, T., Deardorff, M. A., Li, J. R., ... Krantz, I. D. (2010). Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Research, 38(17), 5657-5671. [gkq346]. https://doi.org/10.1093/nar/gkq346