Angelman syndrome (AS) is a human genetic disorder characterized by mental retardation, seizures, inappropriate laughter, abnormal galt, tremor and ataxia. There is strong genetic evidence that the disorder is associated with a maternally expressed, imprinted gene mapping to chromosome 15q11-13. Affected patients demonstrate varied molecular abnormalities, including large maternal deletions, uniparental paternal disomy (UPD). Imprinting mutations and loss of function mutations of E6-associated-protein (E6-AP) ubiquitin-protein ligase (UBE3A). All of these abnormalities are associated with loss of maternal expression of UBE3A. Although mutations in UBE3A cause AS, indicating that maternal-specific expression of UBE3A is essential for a normal phenotype, evidence for maternal-specific expression of UBE3A has been lacking. Using mice with partial paternal UPD encompassing Ube3a to differentiate maternal and paternal expression, we found by in situ hybridization that expression of Ube3a in Purkinje cells, hippocampal neurons and mitral cells of the olfactory bulb in UPD mice was markedly reduced compared to non-UPD littermates. In contrast, expression of Ube3a in other regions of the brain was only moderately or not at all reduced in UPD mice. The major phenotypic features of AS correlate with the loss of maternal-specific expression of Ube3a in hippocampus and cerebellum as revealed in the mouse model.

Imprinted genes tend to occur in clusters. We have identified a cluster in distal mouse chromosome (Chr) 2, known from early genetic studies to contain both maternally and paternally imprinted, but unspecified, genes. Subsequently, one was identified as Gnas, which encodes a G protein ␣ subunit, and there is clinical and biochemical evidence that the human homologue GNAS1, mutated in patients with Albright hereditary osteodystrophy, is also imprinted. We have used representational difference analysis, based on parent-of-origin methylation differences, to isolate candidate imprinted genes in distal Chr 2 and found two oppositely imprinted genes, Gnasxl and Nesp. Gnasxl determines a variant G protein ␣ subunit associated with the trans-Golgi network and Nesp encodes a secreted protein of neuroendocrine tissues. Gnasxl is maternally methylated in genomic DNA and encodes a paternal-specific transcript, whereas Nesp is paternally methylated with maternal-specific expression. Their reciprocal imprinting may offer insight into the distal Chr 2 imprinting phenotypes. Remarkably, Gnasxl, Nesp, and Gnas are all part of the same transcription unit; transcripts for Gnasxl and Nesp are alternatively spliced onto exon 2 of Gnas. This demonstrates an imprinting mechanism in which two oppositely imprinted genes share the same downstream exons.

Mouse embryos with duplications of whole maternal (parthenogenetic and gynogenetic) or paternal (androgenetic) genomes show reciprocal phenotypes and do not develop to term. Genetic complementation has identified the distal region of chromosome 7 (Chr 7) as one of the regions for which both a maternal and paternal chromosome copy are essential for normal development, presumably because of the presence of imprinted genes whose expression is dependent on their parental origin. Embryos with the maternal duplication and paternal deficiency of distal Chr 7 are growth retarded and die around day 16 of gestation; the reciprocal paternal duplication embryos die at an unidentified earlier stage. We report here the incorporation of cells with the paternal duplication into chimaeras, resulting in a striking growth enhancement of the embryos. One gene located on mouse distal Chr 7 (ref. 5) is the insulin-like growth factor 2 (Igf2) gene, an embryonic mitogen. In embryos with the maternal duplication of distal Chr 7, the two maternal alleles of the Igf2 gene are repressed. The presence of two paternal alleles of this gene in many cells is probably responsible for the growth enhancement observed in chimaeras. We propose that there are other imprinted genes in this Chr 7 region. We also compare the imprinting of this subgenomic region with phenotypes resulting from the duplication of the whole parental genome in parthenogenones and androgenones.

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...