Regulation of alternative polyadenylation by genomic imprinting

Abstract

Maternally and paternally derived alleles can utilize different promoters, but allele-specific differences in cotranscriptional processes have not been reported. We show that alternative polyadenylation sites at a novel murine imprinted gene (H13) are utilized in an allele-specific manner. A differentially methylated CpG island separates polyA sites utilized on maternal and paternal alleles, and contains an internal promoter. Two genetic systems show that alleles lacking methylation generate truncated H13 transcripts that undergo internal polyadenylation. On methylated alleles, the internal promoter is inactive and elongation proceeds to downstream polyadenylation sites. This demonstrates that epigenetic modifications can influence utilization of alternative polyadenylation sites.Supplemental material is available at http://www.genesdev.org.Received January 28, 2008; revised version accepted March 10, 2008. Transcription by RNA polymerase II (Pol II) requires multiple linked steps, including the assembly of an initiation complex, promoter release, elongation followed by splicing, polyadenylation (polyA), and dissociation of the polymerase complex from the template DNA. Each step provides an opportunity for the cell to regulate gene expression, either by changing the abundance or availability of mRNAs or by generating variant gene products. Epigenetic modifications to DNA and histones can influence transcription at the initiation stage by altering the accessibility of promoter sequences to initiation complex components (Kass et al. 1997a,b). Following initiation, regions of heterochromatin can subtly impede the progress of an elongating polymerase complex, reducing transcriptional output (Lorincz et al. 2004). However, it is not clear whether epigenetic modifications downstream from a promoter can lead to variant gene products through alternative polyadenylation or splicing.Polyadenylation, the addition of multiple adenyl residues to the 3Ј end of a newly synthesized transcript, confers stability and is required for nuclear export (Huang and Carmichael 1996;Jacobson and Peltz 1996). This occurs following cleavage of the newly synthesized pre-mRNA, typically 15-30 nucleotides downstream from a conserved hexamer motif (usually AAUAAA or AUUAAA) (Proudfoot and Brownlee 1976;Zhao et al. 1999). A large proportion of human genes utilize more than one polyadenylation (polyA) site (Tian et al. 2005), making alternative polyadenylation a major source of transcriptional diversity. The mechanisms governing alternative polyA site selection in mammalian cells have been studied in detail at only a small number of loci; notably the immunoglobulin heavy chain (Takagaki and Manley 1998) and calcitonin/CGRP genes (Lou et al. 1998). In both cases, polyA site selection is cell typespecific and is regulated by changes in the concentration of diffusible RNA processing factors (Lou et al. 1998;Takagaki and Manley 1998).Imprinted genes are differentially expressed on maternally and paternally derived alleles and are estimated to com...

Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia

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