The let-7 tumor suppressor microRNAs are known for their regulation of oncogenes, while the RNA-binding proteins Lin28a/b promote malignancy by inhibiting let-7 biogenesis. We have uncovered unexpected roles for the Lin28/let-7 pathway in regulating metabolism. When overexpressed in mice, both Lin28a and LIN28B promote an insulin-sensitized state that resists high-fat-diet induced diabetes. Conversely, muscle-specific loss of Lin28a or overexpression of let-7 results in insulin resistance and impaired glucose tolerance. These phenomena occur, in part, through the let-7-mediated repression of multiple components of the insulin-PI3K-mTOR pathway, including IGF1R, INSR, and IRS2. In addition, the mTOR inhibitor, rapamycin, abrogates Lin28a-mediated insulin sensitivity and enhanced glucose uptake. Moreover, let-7 targets are enriched for genes containing SNPs associated with type 2 diabetes and control of fasting glucose in human genome-wide association studies. These data establish the Lin28/let-7 pathway as a central regulator of mammalian glucose metabolism.

The Lin28/let-7 Axis Regulates Glucose Metabolism

Lin28: primal regulator of growth and metabolism in stem cells.

Genomic imprinting is a form of epigenetic regulation that results in the expression of either the maternally or paternally inherited allele of a subset of genes (Ramowitz and Bartolomei 2011). This imprinted expression of transcripts is crucial for normal mammalian development. In humans, loss-of-imprinting of specific loci results in a number of diseases exemplified by the reciprocal growth phenotypes of the Beckwith-Wiedemann and Silver-Russell syndromes, and the behavioral disorders Angelman and Prader-Willi syndromes (Kagami et al. 2008; Buiting 2010; Choufani et al. 2010; Eggermann 2010; Kelsey 2010; Mackay and Temple 2010). In addition, aberrant imprinting also contributes to multigenic disorders associated with various complex traits and cancer (Kong et al. 2009; Monk 2010).

Imprinted loci contain differentially methylated regions (DMRs) where cytosine methylation marks one of the parental alleles, providing cis-acting regulatory elements that influence the allelic expression of surrounding genes. Some DMRs acquire their allelic methylation during gametogenesis, when the two parental genomes are separated, resulting from the cooperation of the de novo methyltransferase DNMT3A and its cofactor DNMT3L (Bourc'his et al. 2001; Hata et al. 2002). These primary, or germline imprinted DMRs are stably maintained throughout somatic development, surviving the epigenetic reprogramming at the oocyte-to-embryo transition (Smallwood et al. 2011; Smith et al. 2012). To confirm that an imprinted DMR functions as an imprinting control region (ICR), disruption of the imprinted expression upon genetic deletion of that DMR, either through experimental targeting in mouse or that which occurs spontaneously in humans, is required. A subset of DMRs, known as secondary DMRs, acquire methylation during development and are regulated by nearby germline DMRs in a hierarchical fashion (Coombes et al. 2003; Lopes et al. 2003; Kagami et al. 2010).

With the advent of large-scale, base-resolution methylation technologies, it is now possible to discriminate allelic methylation dictated by sequence variants from imprinted methylation. Yet our knowledge of the total number of imprinted DMRs in humans, and their developmental dynamics, remains incomplete, hampered by genetic heterogeneity of human samples.

Here we present high-resolution mapping of human imprinted methylation. We performed whole-genome-wide bisulfite sequencing (WGBS) on leukocyte-, brain-, liver-, and placenta-derived DNA samples to identify partially methylated regions common to all tissues consistent with imprinted DMRs. We subsequently confirmed the partial methylated states in tissues using high-density methylation microarrays. The parental origin of methylation was determined by comparing microarray data for DNA samples from reciprocal genome-wide uniparental disomy (UPD) samples, in which all chromosomes are inherited from one parent (Lapunzina and Monk 2011), and androgenetic hydatidiform moles, which are created by the fertilization of an oocyte lacking a nucleus by a sperm that endoreduplicates. The use of uniparental disomies and hydatidiform moles meant that our analyses were not subjected to genotype influences, enabling us to characterize all known imprinted DMRs at base-pair resolution and to identify 21 imprinted domains, which we show are absent in mice. Lastly, we extended our analyses to determine the methylation profiles of all imprinted DMRs in sperm, stem cells derived from parthenogenetically activated metaphase-2 oocyte blastocytes (phES) (Mai et al. 2007; Harness et al. 2011), and stem cells (hES) generated from both six-cell blastomeres and the inner cell mass of blastocysts, delineating the extent of embryonic reprogramming that occurs at these loci during human development.

/pdf/genome-wide-parent-of-origin-dna-methylation-analysis-2lsudc173u.pdf

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

Genomic imprinting is an important regulatory mechanism that silences one of the parental copies of a gene. To systematically characterize this phenomenon, we analyze tissue specificity of imprinting from allelic expression data in 1582 primary tissue samples from 178 individuals from the Genotype-Tissue Expression (GTEx) project. We characterize imprinting in 42 genes, including both novel and previously identified genes. Tissue specificity of imprinting is widespread, and gender-specific effects are revealed in a small number of genes in muscle with stronger imprinting in males. IGF2 shows maternal expression in the brain instead of the canonical paternal expression elsewhere. Imprinting appears to have only a subtle impact on tissue-specific expression levels, with genes lacking a systematic expression difference between tissues with imprinted and biallelic expression. In summary, our systematic characterization of imprinting in adult tissues highlights variation in imprinting between genes, individuals, and tissues.

/pdf/the-landscape-of-genomic-imprinting-across-diverse-adult-52od1pq8it.pdf

The landscape of genomic imprinting across diverse adult human tissues

The ever growing complexity of placental epigenetics - role in adverse pregnancy outcomes and fetal programming.

Genomic imprinting characterizes genes with a monoallelic expression, which is dependent on the parental origin of each allele. Approximately 150 imprinted genes are known to date, in humans and mice but, though computational searches have tried to extract intrinsic characteristics of these genes to identify new ones, the existing list is probably far from being comprehensive. We used a high-throughput strategy by diverting the classical use of genotyping microarrays to compare the genotypes of mRNA/cDNA vs. genomic DNA to identify new genes presenting monoallelic expression, starting from human placental material. After filtering of data, we obtained a list of 1,082 putative candidate monoallelic SNPs located in more than one hundred candidate genes. Among these, we found known imprinted genes, such as IPW, GRB10, INPP5F and ZNF597, which contribute to validate the approach. We also explored some likely candidates of our list and identified seven new imprinted genes, including ZFAT, ZFAT-AS1, GLIS3, NTM, MAGI2, ZC3H12Cand LIN28B, four of which encode zinc finger transcription factors. They are, however, not imprinted in the mouse placenta, except for Magi2. We analyzed in more details the ZFAT gene, which is paternally expressed in the placenta (as ZFAT-AS1, a non-coding antisense RNA) but biallelic in other tissues. The ZFAT protein is expressed in endothelial cells, as well as in syncytiotrophoblasts. The expression of this gene is, moreover, downregulated in placentas from complicated pregnancies. With this work we increase by about 10% the number of known imprinted genes in humans.

https://www.tandfonline.com/doi/pdf/10.4161/epi.21495

A genome-wide approach reveals novel imprinted genes expressed in the human placenta

We identified, through a genome-wide search for new imprinted genes in the human placenta, DSCAM (Down Syndrome Cellular Adhesion Molecule) as a paternally expressed imprinted gene. Our work revealed the presence of a Differentially Methylated Region (DMR), located within intron 1 that might regulate the imprinting in the region. This DMR showed a maternal allele methylation, compatible with its paternal expression. We showed that DSCAM is present in endothelial cells and the syncytiotrophoblast layer of the human placenta. In mouse, Dscam expression is biallelic in foetal brain and placenta excluding any possible imprinting in these tissues. This gene encodes a cellular adhesion molecule mainly known for its role in neurone development but its function in the placenta remains unclear. We report here the first imprinted gene located on human chromosome 21 with potential clinical implications.

/pdf/a-genome-wide-search-for-new-imprinted-genes-in-the-human-1c2vyijj6g.pdf

Amélie Pinard

Papers

A genome-wide approach reveals novel imprinted genes expressed in the human placenta

A genome-wide search for new imprinted genes in the human placenta identifies DSCAM as the first imprinted gene on chromosome 21.

DSCAM, un nouveau gène soumis à empreinte parentale