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PubMed2005

Comparative analyses of genomic imprinting and CpG island-methylation in mouse Murr1 and human MURR1 loci revealed a putative imprinting control region in mice.

Human MURR1 is an orthologue of mouse Murr1 gene, which was previously reported to be imprinted only in adult brain with a maternal allele-predominant expression and to contain another imprinted gene, U2af1-rs1, in the first intron. Human MURR1 was found not to harbor the U2af1-rs1 orthologue and to be expressed biallelically in tissues, including adult brain. Three genes identified around Murr1 and their orthologues around MURR1 were expressed biallelically. These findings suggest that the mouse imprinting locus is limited to a small region and the introduction of U2af1-rs1 in mouse causes the imprinting of this locus. The CpG island (CGI) at U2af1-rs1 with maternal methylation was the only differentially methylated region among CGIs found in these loci. Detailed methylation analyses of the U2af1-rs1 CGI in germ cells led to identification of a region with oocyte-specific methylation. These results suggest that this region is the imprinting control region of the Murr1/U2af1-rs1 locus in mouse.

Adaptor Proteins, Signal Transducing↗
PubMed2004

Herbivore-induced plant vaccination. Part II. Array-studies reveal the transience of herbivore-specific transcriptional imprints and a distinct imprint from stress combinations.

Summary Microarray technology has given plant biologists the ability to simultaneously monitor changes in the expression of hundreds of genes, and yet, to date, this technology has not been applied to ecological phenomena. In native tobacco (Nicotiana attenuata), prior attack of sap-feeding mirids (Tupiocoris notatus) results in vaccination of the plant against subsequent attacks by chewing hornworms (Manduca sexta). This vaccination is mediated by a combination of direct and indirect defenses and tolerance responses, which act in concert with the attack preferences of a generalist predator. Here, we use microarrays enriched in herbivore-elicited genes with a principal components analysis (PCA) to characterize transcriptional 'imprints' of single, sequential, or simultaneous attacks by these two main herbivores of N. attenuata. The PCA identified distinctly different imprints left by individual attack from the two species after 24 h, but not after 5 days. Moreover, imprints of sequential or simultaneous attacks differed significantly from those of single attack, suggesting the existence of a distinct gene expression program responsive to the combination of biological stressors. A dissection of the transcriptional imprints revealed responses in direct and indirect defense genes that were well correlated with observed increases in defense metabolites. Attack from both herbivores elicits a switch from growth- to defense-related transcriptional processes, and herbivore-specific changes occur largely in primary metabolism and signaling cascades. PCA of these polygenic transcriptional imprints characterizes the ephemeral changes in the transcriptome that occur during the maturation of ecologically relevant phenotypic responses.

Animals↗
PubMed1995

Insulin-like growth factor II in uterine smooth-muscle tumors: maintenance of genomic imprinting in leiomyomata and loss of imprinting in leiomyosarcomata.

Uterine leiomyosarcomata, malignant smooth-muscle tumors that may arise from existing leiomyomata or directly from the myometrium, have been shown to oversecrete insulin-like growth factor II (IGF-II). It has been shown recently that the IGF-II gene (IGF2) is maternally imprinted in both mice and humans. Only the paternal allele of IGF2 is usually expressed, except in adult liver and in the central nervous system in which biallelic expression is seen. Recently, loss of IGF2 imprinting has been reported in Wilms' tumor and in several other malignancies, and it has been suggested that biallelic expression of the gene leads to overexpression of IGF-II peptide and increased mitogenic activity. Using the ApaI restriction enzyme polymorphism in exon 9 of IGF2, we examined the expression of IGF2 in five informative uterine leiomyosarcomata and found that IGF2 was expressed biallelically in two tumors. In contrast, five samples of normal myometrium and six informative benign uterine leiomyomata showed monoallelic expression of IGF2. The incidence of heterozygosity at this locus was markedly lower in patients with leiomyosarcoma (6%) than in the healthy population (42% heterozygous; P < 0.01). H19, a gene that is imprinted in normal tissues, was expressed monoallelically in all informative normal and neoplastic uterine tumors. In contrast, the IGF-II receptor gene was expressed from both alleles in all tissues examined, confirming the finding that the human IGF-II receptor gene is not imprinted in humans. This study provides further evidence that relaxation of IGF2 genomic imprinting occurs not only in childhood tumors but also in adult-onset tumors, and it suggests a novel epigenetic mechanism for oncogenesis throughout life.

Base Sequence↗
PubMed2006

Differential regulation of imprinting in the murine embryo and placenta by the Dlk1-Dio3 imprinting control region.

Genomic imprinting is an epigenetic mechanism controlling parental-origin-specific gene expression. Perturbing the parental origin of the distal portion of mouse chromosome 12 causes alterations in the dosage of imprinted genes resulting in embryonic lethality and developmental abnormalities of both embryo and placenta. A 1 Mb imprinted domain identified on distal chromosome 12 contains three paternally expressed protein-coding genes and multiple non-coding RNA genes, including snoRNAs and microRNAs, expressed from the maternally inherited chromosome. An intergenic, parental-origin-specific differentially methylated region, the IG-DMR, which is unmethylated on the maternally inherited chromosome, is necessary for the repression of the paternally expressed protein-coding genes and for activation of the maternally expressed non-coding RNAs: its absence causes the maternal chromosome to behave like the paternally inherited one. Here, we characterise the developmental consequences of this epigenotype switch and compare these with phenotypes associated with paternal uniparental disomy of mouse chromosome 12. The results show that the embryonic defects described for uniparental disomy embryos can be attributed to this one cluster of imprinted genes on distal chromosome 12 and that these defects alone, and not the mutant placenta, can cause prenatal lethality. In the placenta, the absence of the IG-DMR has no phenotypic consequence. Loss of repression of the protein-coding genes occurs but the non-coding RNAs are not repressed on the maternally inherited chromosome. This indicates that the mechanism of action of the IG-DMR is different in the embryo and the placenta and suggests that the epigenetic control of imprinting differs in these two lineages.

Animals↗
PubMed2005

Quantitative prediction of imprinting factor of molecularly imprinted polymers by artificial neural network.

Artificial neural network (ANN) implementing the back-propagation algorithm was applied for the calculation of the imprinting factors (IF) of molecularly imprinted polymers (MIP) as a function of the computed molecular descriptors of template and functional monomer molecules and mobile phase descriptors. The dataset used in our study were obtained from the literature and classified into two distinctive datasets on the basis of the polymer's morphology, irregularly sized MIP and uniformly sized MIP datasets. Results revealed that artificial neural network was able to perform well on datasets derived from uniformly sized MIP (n = 23, r = 0.946, RMS = 2.944) while performing poorly on datasets derived from irregularly sized MIP (n = 75, r = 0.382, RMS = 6.123). The superior performance of the uniformly sized MIP dataset over the irregularly sized MIP dataset could be attributed to its more predictable nature owing to the consistency of MIP particles, uniform number and association constant of binding sites, and minimal deviation of the imprinted polymers. The ability to predict the imprinting factor of imprinted polymer prior to performing actual experimental work provide great insights on the feasibility of the interaction between template-functional monomer pairs.

Neural Networks, Computer↗
PubMed1989

Imprint cytology of non-Hodgkin's lymphomas based on a study of 212 immunologically characterized cases: correlation of touch imprints with tissue sections.

The classification of non-Hodgkin's lymphomas (NHLs) has been traditionally based on analysis of histologic sections and has been supplemented more recently by immunologic marker studies. It was the purpose of the present study to illustrate, side-by-side, sections and Romanowsky-stained imprints from the same surgical specimen from practically all categories of immunophenotyped NHLs, including rare and atypical variants that were difficult to classify from the histologic sections alone. Our results indicate that imprint cytology may reveal nuclear and cytoplasmic details not discernible in even the best tissue sections and that it may be selectively helpful in contributing to the classification of NHLs. Our results also show that the relative value of imprint cytology in the classification of malignant lymphomas varies greatly among categories. Specifically, we have found that imprints assist in three ways: the recognition of plasmacytoid features in small cell lymphocytic lymphomas, the recognition of plasmacytoid immunoblastic lymphoma, and the differentiation between NHLs which may be difficult to distinguish histologically. These include (1) small lymphocytic lymphoma versus lymphocytic lymphoma of intermediate differentiation, (2) true histiocytic malignancies versus large cell malignant lymphomas with abundant cytoplasm and/or phagocytosis, (3) anaplastic myeloma versus plasmacytoid immunoblastic lymphoma, (4) large noncleaved versus plasmacytoid immunoblastic lymphoma, (5) lymphoblastic lymphoma versus diffuse small cleaved cell lymphoma, and (6) lymphoblastic lymphoma versus small noncleaved cell lymphoma. Lymph node imprints are easy to prepare and readily interpretable by those experienced in the study of abnormal blood and bone marrow films. Their value as an ancillary methodology aimed at optimal accuracy in the classification of NHLs should be recognized.

Humans↗
PubMed2002

Alternative non-coding splice variants of Nespas, an imprinted gene antisense to Nesp in the Gnas imprinting cluster.

The Gnas locus on mouse Chr 2 represents a unique cluster of overlapping imprinted genes. Three of these in the order Nesp--Gnasxl--Gnas are transcribed in the sense direction with Nesp having maternal-specific expression, Gnasxl having paternal expression, and Gnas as being biallelically expressed in most tissues. A fourth imprinted gene, Nespas, is paternally expressed, lies antisense to Nesp, and expresses an unspliced transcript. Large unspliced antisense transcripts are emerging as a feature of imprinted gene clusters, and such non-coding RNAs may have a cis-regulatory function. Here we show that, in addition to an unspliced form of Nepas, we can detect five alternatively spliced forms of Nespas up to 1.4 kb in length that are non-coding. The splice variants are paternally expressed; they start approximately 2 kb upstream of Gnasxl in a region of maternal methylation and end 2.5 kb beyond the ATG of Nesp. These variants do not correspond to exons of the human antisense transcript although they start in the same region; the Nespas transcript, like its human counterpart, is spliced in various alternative patterns. The identification of a set of small spliced imprinted transcripts in the human and now in the mouse suggests that these antisense transcripts are functionally important.

Alternative Splicing↗
PubMed2000

The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1.

The gene encoding the insulin-like growth-factor type-2 receptor (Igf2r) is maternally expressed and imprinted. A CpG island in Igf2r intron 2 that carries a maternal-specific methylation imprint was shown in a transgenic model to be essential for Igf2r imprinting and for the production of an antisense RNA from the paternal allele. We report here that the endogenous region2 is the promoter for this antisense RNA (named Air, for antisense Igf2r RNA) and that the 3' end lies 107,796 bp distant in an intron of the flanking, but non-imprinted, gene Mas1.

Base Sequence↗
PubMed1998

Genomic imprinting, development and disease--is pre-eclampsia caused by a maternally imprinted gene?

Several genes in conserved clusters are expressed from only the maternal or the paternal allele. The other allele has been genetically silenced ('imprinted') by its passage through one sex. Many known imprinted genes have effects on embryonic or trophoblast growth or fetal development, and mutation or loss of the single active copy causes diseases such as Prader-Willi, Angelmann and Beckwith-Wiederman syndromes. Imprinted genes show an unusual mode of inheritance, since mutant genes have an effect on the phenotype only if they come from the parent from which they are expressed. This may explain some conditions which appear to be heritable but show an inconsistent pattern in affected families. Of particular interest is pre-eclampsia/eclampsia, the most serious complication of pregnancy, which has some features suggesting that it results from fetal expression of the mutant gene, but others which imply it results from maternal expression. This could be resolved by proposing that the condition is due to mutation in a paternally imprinted, maternally active gene which must be expressed by the fetus in order to establish a normal placenta in the first pregnancy.

Animals↗
PubMed1999

Loss of imprinting of a paternally expressed transcript, with antisense orientation to KVLQT1, occurs frequently in Beckwith-Wiedemann syndrome and is independent of insulin-like growth factor II imprinting.

Genomic imprinting plays a fundamental role in cancer and some hereditary diseases, including Beckwith-Wiedemann syndrome (BWS), a disorder of prenatal overgrowth and predisposition to embryonal malignancies such as Wilms tumor. We have previously shown that the KVLQT1 gene on chromosomal band 11p15 is imprinted, with expression of the maternal allele, and that the maternal allele is disrupted in rare BWS patients with balanced germ-line chromosomal rearrangements. We now show that an antisense orientation transcript within KVLQT1, termed LIT1 (long QT intronic transcript 1) is expressed normally from the paternal allele, from which KVLQT1 transcription is silent, and that in the majority of patients with BWS, LIT1 is abnormally expressed from both the paternal and maternal alleles. Eight of sixteen informative BWS patients (50%) showed biallelic expression, i.e., loss of imprinting (LOI) of LIT1. Similarly, 21 of 36 (58%) BWS patients showed loss of maternal allele-specific methylation of a CpG island upstream of LIT1. Surprisingly, LOI of LIT1 was not linked to LOI of insulin-like growth factor II (IGF2), which was found in 2 of 10 (20%) BWS patients, even though LOI of IGF2 occurs frequently in Wilms and other tumors, and in some patients with BWS. Thus, LOI of LIT1 is the most common genetic alteration in BWS. We propose that 11p15 harbors two imprinted gene domains-a more centromeric domain including KVLQT1 and p57(KIP2), alterations in which are more common in BWS, and a more telomeric domain including IGF2, alterations in which are more common in cancer.

Beckwith-Wiedemann Syndrome↗
PubMed2000

An imprinted transcript, antisense to Nesp, adds complexity to the cluster of imprinted genes at the mouse Gnas locus.

The Gnas locus in distal mouse chromosome (Chr) 2 is emerging as a complex genomic region. It contains three imprinted genes in the order Nesp-Gnasxl-Gnas. Gnas encodes a G protein alpha-subunit, and Nesp and Gnasxl encode proteins of unknown function expressed in neuroendocrine tissue. Together, these genes form a single transcription unit because transcripts of Nesp and Gnasxl are alternatively spliced onto exon 2 of Gnas. Nesp and Gnasxl are expressed from opposite parental alleles, with Nesp encoding a maternal-specific transcript and Gnasxl encoding a paternal-specific transcript. We now identify a further imprinted transcript in this cluster. Reverse transcription-PCR analysis of Nesp expression in 15. 5-days-postcoitum embryos carrying only maternal or paternal copies of distal Chr 2 revealed an isoform that is exclusively paternally, rather than maternally, expressed. Strand-specific reverse transcription-PCR showed that this form is an antisense transcript. The existence of a paternally expressed antisense transcript was confirmed by Northern blot analysis. The sequence is contiguous with genomic sequence downstream of Nesp and encompasses Nesp exons 1 and 2 and an intervening intron. We propose that Nespas is an additional control element in the imprinting region of mouse distal Chr 2; it adds further complexity to the Gnas-imprinted gene cluster.

Animals↗
PubMed1999

gamma2-COP, a novel imprinted gene on chromosome 7q32, defines a new imprinting cluster in the human genome.

We describe a novel imprinted gene, gamma 2-COP (nonclathrincoatprotein), identified in a search for expressed sequences in human chromosome 7q32 where the paternally expressed MEST gene is located. gamma 2-COP contains 24 exons and spans >50 kb of genomic DNA. Like MEST, gamma 2-COP is ubiquitously transcribed in fetal and adult tissues. In fetal tissues, including skeletal muscle, skin, kidney, adrenal, placenta, intestine, lung, chorionic plate and amnion, gamma 2-COP is imprinted and expressed from the paternal allele. In contrast to the monoallelic expression observed in these fetal tissues, biallelic expression was evident in fetal brain and liver and in adult peripheral blood. Biallelic expression in blood is supported by the demonstration of gamma 2-COP transcripts in lymphoblastoid cell lines with maternal uniparental disomy 7. Absence of paternal gamma 2-COP transcripts during embryonic development may contribute to Silver-Russell syndrome. However, on mutation scanning the only gamma 2-COP mutation detected was maternally derived. Amino acid comparison of gamma2-COP protein revealed close relation to gamma-COP, a subunit of the coatomer complex COPI, suggesting a role of gamma2-COP in cellular vesicle traffic. The existence of distinct coatomer complexes could be the basis for the functional heterogeneity of COPI vesicles in retrograde and anterograde transport and/or in cargo selection. Together, gamma 2-COP and MEST constitute a novel imprinting cluster in the human genome that may contain other, as yet unknown, imprinted genes.

Amino Acid Sequence↗
PubMed2001

Bidirectional action of the Igf2r imprint control element on upstream and downstream imprinted genes.

Imprinting of the maternally-expressed Igf2r gene is controlled by an intronic imprint control element (ICE) known as Region2 that contains the promoter of the noncoding Air RNA, whose transcript overlaps the silenced paternal Igf2r promoter in an antisense orientation. Two novel imprinted genes, Slc22a2 and Slc22a3 are described here that lie 110 and 155 kb 3' to Igf2r and that are not overlapped by the Air transcript but are regulated by the Igf2r-ICE, as previously shown for Igf2r. These results identify a new cluster of imprinted genes whose repression by the bidirectional action of the Region2-ICE is independent of transcript overlap by the Air RNA.

Animals↗
PubMed2003

Epigenetic properties and identification of an imprint mark in the Nesp-Gnasxl domain of the mouse Gnas imprinted locus.

The Gnas locus in the mouse is imprinted with a complex arrangement of alternative transcripts defined by promoters with different patterns of monoallelic expression. The Gnas transcript is subject to tissue-specific imprinted expression, Nesp is expressed only from the maternal allele, and Gnasxl is expressed only from the paternal allele. The mechanisms controlling these expression patterns are not known. To identify potential imprinting regulatory regions, particularly for the reciprocally expressed Nesp and Gnasxl promoters, we examined epigenetic properties of the locus in gametes, embryonic stem cells, and fetal and adult tissues. The Nesp and Gnasxl promoter regions are contained in extensive CpG islands with methylation of the paternal allele at Nesp and the maternal allele at Gnasxl. Parental allele-specific DNase I-hypersensitive sites were found at these regions, which correlate with hypomethylation rather than actual expression status. A germ line methylation mark was identified covering the promoters for Gnasxl and the antisense transcript Nespas. Prominent DNase I-hypersensitive sites present on paternal alleles in embryonic stem cells are contained within this mark. This is the second gametic mark identified at Gnas and suggests that the Nesp and Gnasxl promoters are under separate control from the Gnas promoter. We propose models to account for the regulation of imprinting at the locus.

Alleles↗
PubMed1993

Maternal-specific methylation of the imprinted mouse Igf2r locus identifies the expressed locus as carrying the imprinting signal.

The mouse insulin-like growth factor type 2 receptor (Igf2r) is imprinted and expressed exclusively from the maternally inherited chromosome. To investigate whether methylation could function as the imprinting signal, we have cloned 130 kb from the Igf2r locus and searched for sequences methylated in a parental-specific manner. Two regions have been identified: region 1 contains the start of transcription and is methylated only on the silent paternal chromosome; region 2 is contained in an intron and is methylated only on the expressed maternal chromosome. Methylation of region 1 is acquired after fertilization, in contrast with the methylation of region 2, which is inherited from the female gamete. Methylation of region 2 may mark the maternal Igf2r locus in a manner that could act as an imprinting signal. These data suggest that the expressed locus carries a potential imprinting signal and imply that methylation is necessary for expression of the Igf2r gene.

Amino Acid Sequence↗
PubMed2006

Investigation of imprinting parameters and their recognition nature for quinine-molecularly imprinted polymers.

A series of molecularly imprinted polymers (MIPs) was prepared using quinine as the template molecules by bulk polymerization. The presence of monomer-template solution complexes in non-covalent MIPs systems has been verified by both fluorescence and UV-vis spectrometric detection. The influence of different synthetic conditions (porogen, functional monomer, cross-linkers, initiation methods, monomer-template ratio, etc.) on recognition properties of the polymers was investigated. Scatchard analysis revealed that two classes of binding sites were formed in the imprinted polymer. The corresponding dissociation constants were estimated to be 45.00 micromol l(-1) and 1.42 mmol l(-1), respectively, by utilizing a multi-site recognition model. The binding characteristics of the imprinted polymers were explored in various solvents using equilibrium binding experiments. In the organic media, results suggested that polar interactions (hydrogen bonding, ionic interactions, etc.) between acidic monomer/polymer and template molecules were mainly responsible for the recognition, whereas in aqueous media, hydrophobic interactions had a remarkable non-specific contribution to the overall binding. The specificity of MIP was evaluated by rebinding the other structurally similar compounds. The results indicated that the imprinted polymers exhibited an excellent stereo-selectivity toward quinine.

Adsorption↗
PubMed2006

Imprinted polymeric materials. Insight into the nature of prepolymerization complexes of quercetin imprinted polymers.

Molecular imprinting techniques have proved to be a highly accessible method for producing molecule-specific recognition materials for a variety of applications, ranging from sensing to catalysis and separations. In noncovalent imprinting, it is anticipated that polymerizable complexes are created in the prepolymerization solution via self-assembly of functional monomers and template molecules resulting from inherent chemical complementarity, which will ideally form binding sites within the cross-linked matrix after polymerization. On the basis of 1H NMR data and X-ray crystallographic evidence, we now infer a more important role for template self-association for the recognition properties of quercetin-imprinted polymers. While directly applicable to fundamental understanding of the molecular imprinting mechanism of this polyphenol, on a more generic scale, this work also demonstrates the utility of this strategy toward analyzing complex noncovalent interaction mechanisms between small molecules. These interactions are of particular interest for quercetin and other members of the flavone/flavonoid class of compounds, which are radical-scavenging polyphenols of substantial interest to biomedicine.

Journal Article↗
PubMed2004

Functional mimicry of the active site of carboxypeptidase a by a molecular imprinting strategy: cooperativity of an amidinium and a copper ion in a transition-state imprinted cavity giving rise to high catalytic activity.

A model for the natural enzyme carboxypeptidase A was prepared by molecular imprinting in synthetic polymers. An unusually high activity and efficiency for carbonate hydrolysis could be obtained by imprinting with a stable transition-state analogue template and introducing an amidinium group and a Cu2+ ion-binding site in a defined orientation to each other into the active site. With substrates having a very similar structure to the template, extraordinarily high enhancements of rates of 110 000-fold were obtained of catalyzed to uncatalyzed reaction kcat/kuncat . The efficiency kcat/Km of the molecularly imprinted catalysts compared to that of the nonimprinted control polymers containing the same functional groups was 790-fold higher, a clear indication of a very efficient imprinting procedure.

Amides↗