At least ten genes define the imprinted Dlk1-Dio3 cluster on mouse chromosome 12qF1

Spatiotemporal expression pattern of Mirg, an imprinted non-coding gene, during mouse embryogenesis

Recent research has revealed that the maternal non-coding RNA genes (Gtl2, Rian and Mirg) from the Dlk1-Dio3 imprinted cluster are closely related to the full development potential of the induced pluripotent stem cells (iPSCs). Transcriptional silencing of these genes failed to generate all-iPSC mice, indicating their significant contribution to embryogenesis. However, except for Gtl2, little information regarding these genes has been acquired in this cluster. In the present study, we analyzed the spatiotemporal expression patterns of Mirg during mouse embryogenesis. Using in situ hybridization and quantitative PCR, we demonstrated that Mirg non-coding RNA exhibited sustained expression throughout mouse embryogenesis from E8.5 to E18.5. Strong expression was detected in the central nervous system (E9.5-E15.5) and various skeletal muscles (E13.5 and E15.5), and the subcellular localization appeared to be in the nuclei. The pituitary and adrenal gland also showed high expression of Mirg, but, unlike the skeletal muscles and the neural circuitry, the signals were not concentrated in the nuclei. In the major internal organs, Mirg maintained low expression during embryogenesis (E12.5-E18.5) whereas in the liver and the developing lung, Mirg was expressed with a gradually decreasing trend and a gradually raising trend, respectively. These findings indicate that temporal regulation of Mirg expression may be required during specific stages and in specific tissues during embryonic development.

Nonallelic transcriptional roles of CTCF and cohesins at imprinted loci

The cohesin complex holds sister chromatids together and is essential for chromosome segregation. Recently, cohesins have been implicated in transcriptional regulation and insulation through genome-wide colocalization with the insulator protein CTCF, including involvement at the imprinted H19/Igf2 locus. CTCF binds to multiple imprinted loci and is required for proper imprinted expression at the H19/Igf2 locus. Here we report that cohesins colocalize with CTCF at two additional imprinted loci, the Dlk1-Dio3 and the Kcnq1/Kcnq1ot1 loci. Similar to the H19/Igf2 locus, CTCF and cohesins preferentially bind to the Gtl2 differentially methylated region (DMR) on the unmethylated maternal allele. To determine the functional importance of the binding of CTCF and cohesins at the three imprinted loci, CTCF and cohesins were depleted in mouse embryonic fibroblast cells. The monoallelic expression of imprinted genes at these three loci was maintained. However, mRNA levels for these genes were typically increased; for H19 and Igf2 the increased level of expression was independent of the CTCF-binding sites in the imprinting control region. Results of these experiments demonstrate an unappreciated role for CTCF and cohesins in the repression of imprinted genes in somatic cells.

Establishment of paternal allele-specific DNA methylation at the imprinted mouse Gtl2 locus

The monoallelic expression of imprinted genes is controlled by epigenetic factors including DNA methylation and histone modifications. In mouse, the imprinted gene Gtl2 is associated with two differentially methylated regions: the IG-DMR, which serves as a gametic imprinting mark at which paternal allele-specific DNA methylation is inherited from sperm, and the Gtl2-DMR, which acquires DNA methylation on the paternal allele after fertilization. The timeframe during which DNA methylation is acquired at secondary DMRs during post-fertilization development and the relationship between secondary DMRs and imprinted expression have not been well established. In order to better understand the role of secondary DMRs in imprinting, we examined the methylation status of the Gtl2-DMR in pre- and post-implantation embryos. Paternal allele-specific DNA methylation of this region correlates with imprinted expression of Gtl2 during post-implantation development but is not required to implement imprinted expression during pre-implantation development, suggesting that this secondary DMR may play a role in maintaining imprinted expression. Furthermore, our developmental profile of DNA methylation patterns at the Cdkn1c- and Gtl2-DMRs illustrates that the temporal acquisition of DNA methylation at imprinted genes during post-fertilization development is not universally controlled.

Differential genomic imprinting and expression of imprinted microRNAs in testes-derived male germ-line stem cells in mouse

BACKGROUND

Testis-derived male germ-line stem (GS) cells, the in vitro counterpart of spermatogonial stem cells (SSC), can acquire multipotency under appropriate culture conditions to become multipotent adult germ-line stem (maGS) cells, which upon testicular transplantation, produce teratoma instead of initiating spermatogenesis. Consequently, a molecular marker that can distinguish GS cells from maGS cells would be of potential value in both clinical and experimental research settings.

METHODS AND FINDINGS

Using mouse as a model system, here we show that, similar to sperm, expression of imprinted and paternally expressed miRNAs (miR-296-3p, miR-296-5p, miR-483) were consistently higher (P<0.001), while those of imprinted and maternally expressed miRNA (miR-127, miR-127-5p) were consistently lower (P<0.001) in GS cells than in control embryonic stem (ES) cells. DNA methylation analyses of imprinting control regions (ICR), that control the expression of all imprinted miRNAs in respective gene clusters (Gnas-Nespas DMR, Igf2-H19 ICR and Dlk1-Dio3 IG-DMR), confirmed that imprinted miRNAs were androgenetic in GS cells. On the other hand, DNA methylation of imprinted miRNA genes in maGS cells resembled those of ES cells but the expression pattern of the imprinted miRNAs was intermediate between those of GS and ES cells. The expression of imprinted miRNAs in GS and maGS cells were also altered during their in vitro differentiation and varied both with the differentiation stage and the miRNA.

CONCLUSIONS

Our data suggest that GS cells have androgenetic DNA methylation and expression of imprinted miRNAs which changes to ES cell-like pattern upon their conversion to maGS cells. Differential genomic imprinting of imprinted miRNAs may thus, serve as epigenetic miRNA signature or molecular marker to distinguish GS cells from maGS cells.

Molecular structure of bovine Gtl2 gene and DNA methylation status of Dlk1-Gtl2 imprinted domain in cloned bovines

Somatic cell nuclear transfer (SCNT) is an inefficient process, which is due to incomplete reprogramming of the donor nucleus. DNA methylation of imprinted genes is essential to the reprogramming of the somatic cell nucleus in SCNT. Dlk1-Gtl2 imprinted domain has been widely studied in mouse and human. However, little is known in bovine, possibly because of limited appropriate sequences of bovine. In our study, we first isolated the cDNA sequence and found multiple transcript variants occurred in bovine Gtl2 gene, which was conserved among species. A probably 110-kb-long Dlk1-Gtl2 imprinted domain was detected on bovine chromosome 21. We identified the putative Gtl2 DMR and IG-DMR corresponding to the mouse and human DMRs and assessed the methylation status of the two DMRs and Dlk1 5' promoter in lungs of deceased SCNT bovines that died within 48h after birth and the normal controls. In cloned bovines, Gtl2 DMR exhibited hypermethylation, which was similar to controls. However, the methylation status of IG-DMR and Dlk1 5' promoter in clones was significantly different from controls, with severe loss of methylation in IG-DMR and hypermethylation in the Dlk1 5' promoter region. Our data suggested that abnormal methylation patterns of IG-DMR may lead to the abnormal expression of Gtl2 and Dlk1 5' hypermethylated promoter is associated with the aberrant development of lungs of cloned bovines, which consequently may contribute to the low efficiency of SCNT.

Imprinting and expression analysis of a non-coding RNA gene in the mouse Dlk1-Dio3 domain

The Dlk1-Dio3 imprinted domain not only is implicated growth and development of the embryo and placenta, but also affects adult metabolism and brain function. In this study, we identified the imprinting status of a mouse non-coding RNA gene, B830012L14Rik, mapped to the Dlk1-Dio3 domain by the polymorphism- and sequencing-based approach. Imprinting analysis showed that the gene was expressed maternally at E15.5, E18.5 and postnatal day 1 mice. Two transcripts of approximately 1.9 and 3.5 kb were detected by northern blot. Furthermore, we examined the spatiotemporal expression patterns of the gene during the mouse development. In situ hybridization analysis showed that B830012L14Rik was mainly expressed in forebrain, pituitary, cartilage primordium of spinal column, lung and liver at E13.5 and E15.5. The results of real-time quantitative RT-PCR showed that the B830012L14Rik expression in brain, heart, lung and liver was higher at E15.5 than at E12.5 and E18.5. Furthermore, the gene expression increased progressively in brain from E12.5 to E15.5 whereas decreased from E15.5 to E19.5. This study may provide further insights into the imprinting, genomic features and expression regulation of the Dlk1-Dio3 imprinted cluster.

microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer

The human genome is replete with long non-coding RNAs (lncRNA), many of which are transcribed and likely to have a functional role. Microarray analysis of >23,000 lncRNAs revealed downregulation of 712 (~3%) lncRNA in malignant hepatocytes, among which maternally expressed gene 3 (MEG3) was downregulated by 210-fold relative to expression in non-malignant hepatocytes. MEG3 expression was markedly reduced in four human hepatocellular cancer (HCC) cell lines compared with normal hepatocytes by real-time PCR. RNA in situ hybridization showed intense cytoplasmic expression of MEG3 in non-neoplastic liver with absent or very weak expression in HCC tissues. Enforced expression of MEG3 in HCC cells significantly decreased both anchorage-dependent and -independent cell growth, and induced apoptosis. MEG3 promoter hypermethylation was identified by methylation-specific PCR and MEG3 expression was increased with inhibition of methylation with either 5-Aza-2-Deoxycytidine, or siRNA to DNA Methyltransferase (DNMT) 1 and 3b in HCC cells. MiRNA-dependent regulation of MEG3 expression was studied by evaluating the involvement of miR-29, which can modulate DNMT 1 and 3. Overexpression of mir-29a increased expression of MEG3. GTL2, the murine homolog of MEG3, was reduced in liver tissues from hepatocyte-specific miR-29a/b1 knock-out mice compared with wild-type controls. These data show that methylation-dependent tissue-specific regulation of the lncRNA MEG3 by miR-29a may contribute to HCC growth and highlight the inter-relationship between two classes of non-coding RNA, miRNAs and lncRNAs, and epigenetic regulation of gene expression.

Mouse ES and iPS cells can form similar definitive endoderm despite differences in imprinted genes

The directed differentiation of iPS and ES cells into definitive endoderm (DE) would allow the derivation of otherwise inaccessible progenitors for endodermal tissues. However, a global comparison of the relative equivalency of DE derived from iPS and ES populations has not been performed. Recent reports of molecular differences between iPS and ES cells have raised uncertainty as to whether iPS cells could generate autologous endodermal lineages in vitro. Here, we show that both mouse iPS and parental ES cells exhibited highly similar in vitro capacity to undergo directed differentiation into DE progenitors. With few exceptions, both cell types displayed similar surges in gene expression of specific master transcriptional regulators and global transcriptomes that define the developmental milestones of DE differentiation. Microarray analysis showed considerable overlap between the genetic programs of DE derived from ES/iPS cells in vitro and authentic DE from mouse embryos in vivo. Intriguingly, iPS cells exhibited aberrant silencing of imprinted genes known to participate in endoderm differentiation, yet retained a robust ability to differentiate into DE. Our results show that, despite some molecular differences, iPS cells can be efficiently differentiated into DE precursors, reinforcing their potential for development of cell-based therapies for diseased endoderm-derived tissues.

The functional role of long non-coding RNA in human carcinomas

Long non-coding RNAs (lncRNAs) are emerging as new players in the cancer paradigm demonstrating potential roles in both oncogenic and tumor suppressive pathways. These novel genes are frequently aberrantly expressed in a variety of human cancers, however the biological functions of the vast majority remain unknown. Recently, evidence has begun to accumulate describing the molecular mechanisms by which these RNA species function, providing insight into the functional roles they may play in tumorigenesis. In this review, we highlight the emerging functional role of lncRNAs in human cancer.

Developmental control of imprinted expression by macro non-coding RNAs

Genomic imprinting is a developmentally regulated epigenetic phenomenon. The majority of imprinted genes only show parent-of-origin specific expression in a subset of tissues or at defined developmental stages. In some cases, imprinted expression is controlled by an imprinted macro non-coding RNA (ncRNA) whose expression pattern and repressive activity does not necessarily correlate with that of the genes whose imprinted expression it controls. This suggests that developmentally regulated factors other than the macro ncRNA are involved in establishing or maintaining imprinted expression. Here, we review how macro ncRNAs control imprinted expression during development and differentiation and consider how this impacts on target choice in epigenetic therapy.

Expression of non-coding RNA AB063319 derived from Rian gene during mouse development

The regulatory functions of many non-coding RNAs (ncRNAs) were widely recognized. However, there are very few publications on long intronic ncRNAs. The transcriptional hierarchy driving a large amount of long and short ncRNAs originated from the maternal chromosome is not clarified in the Dlk1-Dio3 imprinted clusters of mouse distal chromosome 12. Here, we only focused on the previously identified long ncRNA AB063319 which derives from the large imprinted gene Rian and contains three retained introns of Rian, and tried to unsderstand this ncRNAs part of biological functions. We used in situ hybridization and quantitative real-time RT-PCR (QRT-PCR) to characterize the spatiotemporal expression pattern of AB063319 during mouse development. The in situ hybridization results showed that AB063319 was prominently expressed in the brain at embryonic day 10.5 (E10.5) and E11.5, and abundantly expressed in brain, muscle, liver, lung and neuroendocrine tissues at E15.5. Furthermore, quantitative analyses results showed that AB063319 was gradually up-regulated from E9.5 to E18.5 and down-regulated at E19.5 during the mouse embryonic development, and AB063319 was highly expressed in tongue and brain at E12.5, E15.5 and E18.5. Alternatively, AB063319 expression was also predominantly detected in tongue and brain at mouse postnatal day 6 (P6) by semi-quantitative RT-PCR. These results indicated that AB063319, as a stable transcriptional ncRNA, might play the important roles in the morphogenesis of diverse organs and tissues, especially associated with brain and muscle development at mouse embryonic and postnatal stages.

Somatic nucleus reprogramming is significantly improved by m-carboxycinnamic acid bishydroxamide, a histone deacetylase inhibitor

Somatic cell nuclear transfer (SCNT) has shown tremendous potential for understanding the mechanisms of reprogramming and creating applications in the realms of agriculture, therapeutics, and regenerative medicine, although the efficiency of reprogramming is still low. Somatic nucleus reprogramming is triggered in the short time after transfer into recipient cytoplasm, and therefore, this period is regarded as a key stage for optimizing SCNT. Here we report that CBHA, a histone deacetylase inhibitor, modifies the acetylation status of somatic nuclei and increases the developmental potential of mouse cloned embryos to reach pre- and post-implantation stages. Furthermore, the cloned embryos treated by CBHA displayed higher efficiency in the derivation of nuclear transfer embryonic stem cell lines by promoting outgrowths. More importantly, CBHA increased blastocyst quality compared with trichostatin A, another prevalent histone deacetylase inhibitor reported previously. Use of CBHA should improve the productivity of SCNT for a variety of research and clinical applications, and comparisons of cells with different levels of pluripotency and treated with CBHA versus trichostatin A will facilitate studies of the mechanisms of reprogramming.

Regulatory RNAs in brain function and disorders

Regulatory RNAs are being increasingly investigated in neurons, and important roles in brain function have been revealed. Regulatory RNAs are non-protein-coding RNAs (npcRNAs) that comprise a heterogeneous group of molecules, varying in size and mechanism of action. Regulatory RNAs often exert post-transcriptional control of gene expression, resulting in gene silencing or gene expression stimulation. Here, we review evidence that regulatory RNAs are implicated in neuronal development, differentiation, and plasticity. We will also discuss npcRNA dysregulation that may be involved in pathological states of the brain such as neurodevelopmental disorders, neurodegeneration, and epilepsy.

Cloning of avian Delta-like 1 homolog gene: the biallelic expression of Delta-like 1 homolog in avian species

Delta-like 1 homolog (Dlk1) is a paternally expressed imprinted gene in mammals, regulating development and differentiation of adipose and muscle. The Dlk1 genes of the quail and turkey were cloned and analyzed in their properties of amino acid sequences, alternative splicing, and genetic distances from other species. In addition, because Dlk1 is located in the cluster of up to 10 imprinted genes in mammals, the genomic structure of the cluster was investigated in the chicken. Furthermore, the imprinting status of the avian Dlk1 gene was also determined here. The numbers of coding sequences of the quail and turkey Dlk1 were the same as chicken Dlk1 in nucleotide (1,161 bp) and amino acid (386 amino acids) sequences. The amino acid similarities were more than 96% with predicted conserved domains including the signal sequence, 6 epidermal growth factor-like domains, and a transmembrane domain. As in the chicken, the alternative splicing of Dlk1 transcripts was not observed in the turkey and quail. Phylogenetic analysis revealed that the chicken and turkey Dlk1 were closer than the chicken and quail. Comparative analysis of the gene clusters containing the Dlk1 gene revealed that Yy1, Wars, Wdr25, Begain, Dlk1, Dio3, and Ppp2r5c were found in the cluster of the chicken genome, but 3 genes (Meg3, Rtl1, and Meg8) between Dlk1 and deiodinase, iodothyronine, type III (Dio3) were not found. Several SNP in the genomic DNA sequences of the fifth exon were identified in chickens and quail. Sequencing analysis of reverse transcription-PCR products of Dlk1 revealed that adipose and muscle from chickens and quail heterozygous for these SNP produce Dlk1 transcripts from both alleles, demonstrating biallelic expression of Dlk1 in the avian species. These results clearly demonstrate that avian Dlk1 is not imprinted and its expression might be regulated in a different manner from mammals.

The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep

Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.

The imprinted DLK1-MEG3 gene region on chromosome 14q32.2 alters susceptibility to type 1 diabetes

Genome-wide association (GWA) studies to map common disease susceptibility loci have been hugely successful, with over 300 reproducibly associated loci reported to date. However, these studies have not yet provided convincing evidence for any susceptibility locus subject to parent-of-origin effects. Using imputation to extend existing GWA datasets, we have obtained robust evidence at rs941576 for paternally inherited risk of type 1 diabetes (T1D; ratio of allelic effects for paternal versus maternal transmissions = 0.75; 95% confidence interval (CI) = 0.71-0.79). This marker is in the imprinted region of chromosome 14q32.2, which contains the functional candidate gene DLK1. Our meta-analysis also provided support at genome-wide significance for a T1D locus at chromosome 19p13.2. The highest association was at marker rs2304256 (odds ratio (OR) = 0.86; 95%CI = 0.82-0.90) in the TYK2 gene, which has previously been associated with systemic lupus erythematosus and multiple sclerosis.

Effect of DLK1 and RTL1 but not MEG3 or MEG8 on muscle gene expression in Callipyge lambs

Callipyge sheep exhibit extreme postnatal muscle hypertrophy in the loin and hindquarters as a result of a single nucleotide polymorphism (SNP) in the imprinted DLK1-DIO3 domain on ovine chromosome 18. The callipyge SNP up-regulates the expression of surrounding transcripts when inherited in cis without altering their allele-specific imprinting status. The callipyge phenotype exhibits polar overdominant inheritance since only paternal heterozygous animals have muscle hypertrophy. Two studies were conducted profiling gene expression in lamb muscles to determine the down-stream effects of over-expression of paternal allele-specific DLK1 and RTL1 as well as maternal allele-specific MEG3, RTL1AS and MEG8, using Affymetrix bovine expression arrays. A total of 375 transcripts were differentially expressed in callipyge muscle and 25 transcripts were subsequently validated by quantitative PCR. The muscle-specific expression patterns of most genes were similar to DLK1 and included genes that are transcriptional repressors or affect feedback mechanisms in beta-adrenergic and growth factor signaling pathways. One gene, phosphodiesterase 7A had an expression pattern similar to RTL1 expression indicating a biological activity for RTL1 in muscle. Only transcripts that localize to the DLK1-DIO3 domain were affected by inheritance of a maternal callipyge allele. Callipyge sheep are a unique model to study over expression of both paternal allele-specific genes and maternal allele-specific non-coding RNA with an accessible and nonlethal phenotype. This study has identified a number of genes that are regulated by DLK1 and RTL1 expression and exert control on postnatal skeletal muscle growth. The genes identified in this model are primary candidates for naturally regulating postnatal muscle growth in all meat animal species, and may serve as targets to ameliorate muscle atrophy conditions including myopathic diseases and age-related sarcopenia.

The genetic signatures of noncoding RNAs

The majority of the genome in animals and plants is transcribed in a developmentally regulated manner to produce large numbers of non-protein-coding RNAs (ncRNAs), whose incidence increases with developmental complexity. There is growing evidence that these transcripts are functional, particularly in the regulation of epigenetic processes, leading to the suggestion that they compose a hitherto hidden layer of genomic programming in humans and other complex organisms. However, to date, very few have been identified in genetic screens. Here I show that this is explicable by an historic emphasis, both phenotypically and technically, on mutations in protein-coding sequences, and by presumptions about the nature of regulatory mutations. Most variations in regulatory sequences produce relatively subtle phenotypic changes, in contrast to mutations in protein-coding sequences that frequently cause catastrophic component failure. Until recently, most mapping projects have focused on protein-coding sequences, and the limited number of identified regulatory mutations have been interpreted as affecting conventional cis-acting promoter and enhancer elements, although these regions are often themselves transcribed. Moreover, ncRNA-directed regulatory circuits underpin most, if not all, complex genetic phenomena in eukaryotes, including RNA interference-related processes such as transcriptional and post-transcriptional gene silencing, position effect variegation, hybrid dysgenesis, chromosome dosage compensation, parental imprinting and allelic exclusion, paramutation, and possibly transvection and transinduction. The next frontier is the identification and functional characterization of the myriad sequence variations that influence quantitative traits, disease susceptibility, and other complex characteristics, which are being shown by genome-wide association studies to lie mostly in noncoding, presumably regulatory, regions. There is every possibility that many of these variations will alter the interactions between regulatory RNAs and their targets, a prospect that should be borne in mind in future functional analyses.