ANRIL Promoter DNA Methylation: A Perinatal Marker for Later Adiposity

Karen A Lillycrop ,Rebecca Clarke-Harris,Emma Garratt,Mark A Hanson,Ai Ling Teh,Yonghui Wu,Fabian Yap,Keith M Godfrey,Yung Seng Lee,Xinyi Lin,Paula Costello,Yong-Cai Chua,Philip C Calder,Yap Seng Chong,Cyrus Cooper,Robert Murray,Graham C Burdge,Joanna D Holbrook,Peter D Gluckman,Philip Titcombe,Caroline E Childs,Neerja Karnani,Samantha J Liew ,Sheila J Barton ,Rae‐Chi Huang ,Carolina Parás Chávez ,Clara Yujing Cheong ,Bhuvaneshwari D/O Shunmuganathan ,Lawrence J Beilin ,James Hopkins ,Eloïse Cook ,Nicholas C Harvey ,Hazel Inskip ,Phillip E Melton

doi:10.1016/j.ebiom.2017.03.037

Abstract

Experimental studies show a substantial contribution of early life environment to obesity risk through epigenetic processes. We examined inter-individual DNA methylation differences in human birth tissues associated with child's adiposity. We identified a novel association between the level of CpG methylation at birth within the promoter of the long non-coding RNA ANRIL (encoded at CDKN2A) and childhood adiposity at age 6-years. An association between ANRIL methylation and adiposity was also observed in three additional populations; in birth tissues from ethnically diverse neonates, in peripheral blood from adolescents, and in adipose tissue from adults. Additionally, CpG methylation was associated with ANRIL expression in vivo, and CpG mutagenesis in vitro inhibited ANRIL promoter activity. Furthermore, CpG methylation enhanced binding to an Estrogen Response Element within the ANRIL promoter. Our findings demonstrate that perinatal methylation at loci relevant to gene function may be a robust marker of later adiposity, providing substantial support for epigenetic processes in mediating long-term consequences of early life environment on human health.

Highlights

Fixed variations in a number of genes have been linked to obesity (Frayling et al, 2007; Loos et al, 2008; Thorleifsson et al, 2009), K
To identify perinatal epigenetic biomarkers associated with later adiposity, we carried out a discovery scan of DNA methylation in the promoters of all refseq genes in umbilical cord DNA, comparing locus specific DNA methylation levels at birth with differences in percentage (%) fat mass in the children aged 6 years (Fig. 1A; Table S2)
The DNA replication and repair pathway included Differentially Methylated Regions (DMRs) linked with Cyclin dependent Kinase 2A inhibitor (CDKN2A), cyclin D (CCND1), flap structure-specific endonuclease 1 (FEN1), proliferating cell nuclear antigen (PCNA) and A-kinase anchor protein 8 (AKAP8) (Fig. 1B)

Summary

Introduction

Fixed variations in a number of genes have been linked to obesity (Frayling et al, 2007; Loos et al, 2008; Thorleifsson et al, 2009), K. We identified an association between the methylation level at birth of CpG loci within the promoter of ANRIL (antisense noncoding RNA in the INK4 locus), a 3.8 kb non-coding RNA transcribed from the CDKN2A gene locus, and variation in total and %fat mass at 6 years. We observed this association in cord tissue from ethnically diverse neonates from the Growing Up in Singapore with Healthy Outcomes (GUSTO) cohort (n = 187), in peripheral blood from adolescents (n = 812) in the Western Australian Pregnancy (RAINE) cohort, and in adipose tissue from adults (n = 81) from the UK BIOCLAIMS cohort. We identified an Estrogen Receptor-α (ERα) containing protein complex that binds to this region in a methylation specific manner and regulates transcription from this locus

Methods

Results

Conclusion