Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene

Brandon J Thomas,Aaron A Golden,Karol Bomsztyk,John M Greally,Niklas Krumm,Eric D Rubio,Pilib Ó Broin,Piri Welcsh,Anton Krumm

doi:10.1186/1756-8935-4-14

Abstract

BackgroundRandom monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (IGF2), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the IGF2 gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II.ResultsUsing array-based chromatin immunoprecipitation, we identified 293 genomic loci that are associated with both CTCF and histone H3 trimethylated at lysine 9 (H3K9me3). A comparison of their genomic positions with those of previously published monoallelically expressed genes revealed no significant overlap between allele-specifically expressed genes and colocalized CTCF/H3K9me3. To analyze the contributions of CTCF and H3K9me3 to gene regulation in more detail, we focused on the monoallelically expressed IGF2BP1 gene. In vitro binding assays using the CTCF target motif at the IGF2BP1 gene, as well as allele-specific analysis of cytosine methylation and CTCF binding, revealed that CTCF does not regulate mono- or biallelic IGF2BP1 expression. Surprisingly, we found that RNA polymerase II is detected on both the maternal and paternal alleles in B lymphoblasts that express IGF2BP1 primarily from one allele. Thus, allele-specific control of RNA polymerase II elongation regulates the allelic bias of IGF2BP1 gene expression.ConclusionsColocalization of CTCF and H3K9me3 does not represent a reliable chromatin signature indicative of monoallelic expression. Moreover, association of individual alleles with both active (H3K4me3) and silent (H3K27me3) chromatin modifications (allelic bivalent chromatin) or with RNA polymerase II also fails to identify monoallelically expressed gene loci. The selection of individual alleles for expression occurs in part during transcription elongation.

Highlights

Random monoallelic expression contributes to phenotypic variation of cells and organisms
Using ChIP-chip, we identified CTCF binding sites by tiling through the nonrepetitive portion of the genome in 100-bp intervals
40% of the CTCF/ H3K9me3 loci mapped to intergenic regions, 51% mapped to intragenic domains and 9% mapped to promoter regions, a distribution similar to that of the 8,462 CTCF loci (44%, 51% and 10% respectively)

Summary

Introduction

Random monoallelic expression contributes to phenotypic variation of cells and organisms. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (IGF2), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the IGF2 gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II. The importance of genomic imprinting has recently been highlighted by RNA sequencing studies that demonstrated widespread allelic differences in gene thought [7] These new findings illustrate the scale and complexity of genomic allele-specific expression. The best-characterized locus with strict monoallelic imprinted gene expression is the region containing the insulin-like growth factor 2 (IGF2) and H19 genes [8] The regulation of this locus relies on the imprinting control region (ICR), which acquires DNA methylation on the paternal allele during normal development of the male germline. The unmethylated ICR on the maternal allele recruits CTCF, effectively preventing promoter-enhancer interactions and maintaining repression of the maternal IGF2 gene

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