DNA Methylation of Alternative Promoters Directs Tissue Specific Expression of Epac2 Isoforms

Abstract

Epac 1 and Epac 2 (Epac1/2; exchange factors directly activated by cAMP) are multidomain proteins that mediate cellular responses upon activation by the signaling molecule cAMP. Epac1 is ubiquitously expressed, whereas Epac2 exhibits a restricted expression pattern. The gene encoding Epac2 gives rise to at least three protein isoforms (Epac2A, Epac2B and Epac2C) that exhibit confined tissue and cell specific expression profiles. Here, we describe alternative promoter usage for the different isoforms of Epac2, and demonstrate that the activity of these promoters depend on the DNA methylation status. Bisulfite sequencing demonstrated that the level of methylation of the promoters in different tissues correlates with Epac2 isoform expression. The presented data indicate that the tissue-specific expression of the Epac2 isoforms is epigenetically regulated, and identify tissue-specific differentially methylated promoter regions within the Epac2 locus that are essential for its transcriptional control.

Cyclic AMP Sensor EPAC Proteins and Their Role in Cardiovascular Function and Disease

“…6,7 In contrast, the epigenetical regulation of Rapgef4 alternative promoters leads to a restricted expression pattern of EPAC2 isoforms. 13 EPAC2B, which is similar to EPAC1 in domain structure, is detected in the adrenal gland and the endocrine pancreas, whereas EPAC2C mRNA was reported only in the liver. 12,14 Nonstandard Abbreviations and Acronyms Compelling evidence indicates that EPAC1 and EPAC2 expression levels change throughout development.…”

“…Rapgef3 transcription leads to the synthesis of one 4-kb long mRNA, whereas alternative promoter usage and differential splicing of Rapgef4 generate 3 different EPAC2 isoforms (named EPAC2A, EPAC2B, and EPAC2C). 12,13 EPAC1 and EPAC2 exhibit distinct expression profiles that may vary depending on developmental stages and pathophysiological situations. EPAC1 is nearly ubiquitously expressed with high levels of expression in the heart, blood vessels, uterus, kidney, and central nervous system.…”

DNA Methylation Influences the Expression of DICER-LIKE4 Isoforms, Which Encode Proteins of Alternative Localization and Function

“…A few studies in plants and mammals have suggested that promoter methylation changes might influence alternative mRNA isoform transcription Hoivik et al, 2013;Connolly et al, 2011), a possibility we therefore examined for DCL4 transcriptional start sites (TSSs). Analysis of the DCL4 locus revealed a discrete methylation patch affecting cytosines in CG, CHG, and CHH contexts immediately upstream of the coding sequence (Stroud et al, 2013) (Figure 1C; Supplemental Figure 2).…”

“…DNA methylation control of alternative TSS expression is a fascinating concept that is just starting to emerge: Only two such examples are available in metazoans (Hoivik et al, 2013;Connolly et al, 2011), and two imprinted genes were recently shown to undergo this type of regulation in rice (Oryza sativa) endosperm, although the functional significance of alternative TSS isoforms was not elucidated in this instance . While expression studies on RdDM mutants did not detect profound gene expression changes (Reinders et al, 2009;Stroud et al, 2014), such studies would have unlikely revealed subtle changes in TSS usage such as DCL4 Δ and DCL4 NLS .…”

The Steroidogenic Acute Regulatory Protein (StAR)

“…SF-1 is highly expressed in steroidogenic cell types where it functions to help control the tissue-specific expression of genes involved in the steroid hormone biosynthesis pathway [90,91]. Additionally, gene knockout studies in mice showed that SF-1 is critical for development and differentiation of the endocrine and reproductive systems, demonstrating it has multiple functions [92].…”