Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes.

Benedetta Izzi,Kathleen Freson,Katrien Cludts,Marc Hoylaerts,Fabrizia Noro

doi:10.3390/ijms19041069

Abstract

Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2, RRNAD1, MRLP24, HDGF and PRCC, using available promoter capture Hi-C datasets. These genes are involved in ribosome processing, protein synthesis, cell cycle and cell proliferation. We next studied the methylation and expression profile of these five genes in Human Umbilical Vein Endothelial Cells (HUVECs) and megakaryocyte precursors. While cell-specific PEAR1 methylation corresponded to variability in expression for four out of five genes, no methylation change was observed in their promoter regions across cell types. Our data suggest that PEAR1 cell-type specific methylation changes may control long distance interactions with other genes. Further studies are needed to show whether such interaction data might be relevant for the genome-wide association data that showed a role for non-coding PEAR1 variants in the same region and platelet function, platelet count and cardiovascular risk.

Highlights

The identification of long-range interactions between chromosome regions, separated by more than 100,000 bases led to the discovery of intra-chromosomal loops that juxtapose downstream enhancers close to several promoter regions
PEAR1 methylation was studied in megakaryocytes (MKs) and the endothelial cell lines Human Umbilical Endothelial cell (HUVECs) and Blood Outgrowth Endothelial cells (BOECs) for three different regions of the gene being the CpG Island 1 (PCGI1), the intron 1 (Pintron1) and the CpG Island 2 (PCGI2), as previously described [53] (Figure 1)
We here show that the PEAR1 regulatory region encompassing both the promoter CpG island (CGWI1e)haenrde stheowfirtsht aitntrhoenP-eEnAhaRn1cerer gouflathtoergyerneegpiornesentcsomwipthasssiignngifbicoatnhtltyhedipffreormenottmereCthpyGlatiisolnand (CpGrIo1f)ilaesndwhthene cfiormstpianrtirnogne-nendhotahnecleiarl oceflltshwe igthenMe Kpsr.eMseonrtesowveirt,hthsiisgrneigfiicoannitslyaldsoifhfeigrehnlyt cmoentnheycltaedtion protofiloetshewrhgeennecso,maspbaarisnegd eonndcohtrhoemlioalsocmellasl winittehraMctKiosn

Summary

Introduction

The identification of long-range interactions between chromosome regions, separated by more than 100,000 bases led to the discovery of intra-chromosomal loops that juxtapose downstream enhancers close to several promoter regions. Sequence-specific DNA-binding proteins may guide this process by directly repositioning these loci to relevant chromatin compartments [12,13,14,15,16] These architectural proteins (i.e., CTCF, cohesin, etc.) are genome-wide bound to promoter-genome interactions and may interfere with gene expression through several mechanisms [17,18,19,20,21] including those that depend on DNA methylation and, such long-distance control can be coordinated in a cell-specific manner. The function of trans or long-range actions of CpG methylation has been revealed by a genome-wide study, performed on various cancer types In this analysis, the correlation between DNA methylation at distal regulatory regions and long-range target gene expression was shown to be significantly stronger than the correlation with the nearby promoter methylation [30]

Methods

Results

Conclusion