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Results for “Long noncoding RNA”
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Analysis of the methylation status of imprinted genes based on methylation-specific polymerase chain reaction combined with denaturing high-performance liquid chromatography.
A procedure for the analysis of the methylation status of imprinted genes is described. The method offers a rapid and reliable alternative to conventional methods such as Southern blots and methylation-specific polymerase chain reaction (PCR) (i.e., allele-specific methylation-specific PCR). The efficient resolution of the differentially methylated alleles is demonstrated for three human imprinted genes: SNRPN, LIT1 (alias KCNQ1OT1), and H19. Abnormal imprinting of SNRPN is associated with the Angelman/Prader-Willi syndromes, and that of LIT1 and H19 with the Beckwith-Wiedemann syndrome. The method is based on methylation-specific PCR followed by denaturing high-performance liquid chromatography (MSP/DHPLC). Briefly, genomic DNA is initially subjected to an in vitro bisulfite treatment, whereby unmethylated cytosines are deaminated. Subsequent PCR amplifications, using primers specific for modified DNA, are aimed at DNA segments that show parent-of-origin-specific methylation. PCR conditions are chosen that allow an efficient amplification of both alleles. The PCR products representing the two alleles are identical in size; they differ, however, at a number of positions within the amplified DNA segment. The DHPLC analysis allows very efficient resolution of the two populations of PCR products, providing qualitative and quantitative results.
Multiple elements within the Xic regulate random X inactivation in mice.
In female mammals, the majority of the genes on one of the two X-chromosomes are silenced by a process referred to as X-chromosome inactivation. The X-inactivation center (Xic), a complex genomic region on the X-chromosome which controls this process, contains the Xist gene encoding an untranslated RNA which plays a central role in the establishment of the transcriptional repression. The Xic encrypts a sophisticated program which coordinates X inactivation with sex and embryonic development. The present article reviews our current knowledge of the regulatory elements lying within the mouse Xic and of the mechanisms underlying random X inactivation.
A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation.
Xist is required for X inactivation. To study the initiation of X inactivation, we have generated a full-length mouse Xist cDNA transgene and an inducible expression system facilitating controlled Xist expression in ES cells and differentiated cultures. In ES cells, transgenic Xist RNA was stable and caused long-range transcriptional repression in cis. Repression was reversible and dependent on continued Xist expression in ES cells and early ES cell differentiation. By 72 hr of differentiation, inactivation became irreversible and independent of Xist. Upon differentiation, autosomal transgenes did not effect counting, but transgenic Xist RNA induced late replication and histone H4 hypoacetylation. Xist had to be activated within 48 hr of differentiation to effect silencing, suggesting that reversible repression by Xist is a required initiation step that might occur during normal X inactivation in female cells.
Xite, X-inactivation intergenic transcription elements that regulate the probability of choice.
Allelic expression differences contribute to phenotypic variation. In X chromosome inactivation (XCI), unfavorable XCI ratios promote X-linked disease penetrance in females. During XCI, one X is randomly silenced by Xist. X chromosome choice is determined by asymmetric expression of Tsix whose antisense action represses Xist. Here, we discover a cis element in the mouse X-inactivation center that regulates Tsix. Xite harbors intergenic transcription start sites and DNaseI hypersensitive sites with allelic differences. At the onset of XCI, deleting Xite downregulates Tsix in cis and skews XCI ratios, suggesting that Xite promotes Tsix persistence on the active X. Truncating Xite RNA is inconsequential, indicating that Xite action does not require intact transcripts. We propose that allele-specific Xite action promotes Tsix asymmetry and generates X chromosome inequality. Therefore, Xite is a candidate for the Xce, the classical modifier of XCI ratios.
Homology models for the PERB11 multigene family.
BACKGROUND: PERB11 is a multicopy polymorphic gene family found in association with HLA Class I genes within the major histocompatibility complex (MHC). Although its function is unknown, PERB11 has sequence similarities to HLA Class I and other related proteins. To explore the possible functional roles for PERB11, homology models have been constructed using both HLA Class I and Class I-like protein structures as templates. RESULTS: The models show that PERB11.1 appears to have an unusual distribution of charged residues that potentially give the molecule a distinct polarity. Furthermore, a cluster of negatively charged residues in the traditional P2 site may form a novel binding site for a positively charged ligand such as a metal ion or complex. Other charged residues line the floor and walls of the cleft and are able to form salt bridges, reminiscent of the closed cleft of the Class I-like mouse neonatal Fc receptor structure. The closely related PERB11.2 family has a different arrangement of charged residues in the cleft, but these residues are still able to form salt bridges. Unlike HLA Class I, the majority of polymorphic positions in the PERB11 family occur outside the cleft and on the surface of the molecule. CONCLUSIONS: Homology models for PERB11 suggest that the structure is capable of associating with beta2 microglobulin or a similar molecule. Furthermore, not all of the potential glycosylation sites suggested by the PERB11 sequences appear viable. Importantly, the models suggest that the molecule has a less accessible cleft than HLA Class I and is not, therefore, able to bind peptides. Other small ligands, including metal ions, might be bound, however.
Haploidization to produce human embryos: a new frontier for micromanipulation.
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Establishment of histone h3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 polycomb group complexes.
Previous studies have implicated the Eed-Enx1 Polycomb group complex in the maintenance of imprinted X inactivation in the trophectoderm lineage in mouse. Here we show that recruitment of Eed-Enx1 to the inactive X chromosome (Xi) also occurs in random X inactivation in the embryo proper. Localization of Eed-Enx1 complexes to Xi occurs very early, at the onset of Xist expression, but then disappears as differentiation and development progress. This transient localization correlates with the presence of high levels of the complex in totipotent cells and during early differentiation stages. Functional analysis demonstrates that Eed-Enx1 is required to establish methylation of histone H3 at lysine 9 and/or lysine 27 on Xi and that this, in turn, is required to stabilize the Xi chromatin structure.
SETting the stage. Eed-Enx1 leaves an epigenetic signature on the inactive X chromosome.
Despite evidence implicating the Polycomb group protein, Eed (embryonic ectoderm development protein) in imprinted X inactivation, a similar role in random X inactivation in the embryo has remained an open question. Brockdorff and colleagues now report that Eed, along with its binding partner Enx1, transiently associates with the inactive X chromosome (Xi) and likely contributes to the epigenetic signature and long-term stability of the Xi heterochromatin.
The mouse Xist gene: a model for studying the gametic imprinting phenomenon.
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Preferential loss of heterozygosity of chromosome 7 loci in simian virus 40 t/T antigen-induced mouse hepatocellular carcinomas does not involve H-ras mutations.
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A clinical, cytogenetic and molecular study of 47 females with r(X) chromosomes.
We studied 47 patients with a 45,X/46,X,r(X) karyotype to identify phenotypic differences between these patients and 45,X patients, and to determine whether these differences could be explained by the status of genes within the ring. Only 2 patients had the 'severe' r(X) phenotype, and both were consistent with this resulting from functional disomy of genes normally subject to X inactivation. A further 7 patients also carried active rings but these patients did not have a more severe phenotype than those whose rings were inactivated, probably because their rings were smaller and did not contain the (as yet unidentified) genes whose functional disomy is particularly damaging. Patients with a r(X) did not show clear physical differences when compared with a 45,X series, except for a possible reduction in the frequency of oedema in those whose r(X) had an Xq breakpoint distal to DXS128E, at Xq13.2. Thus some protection from oedema may be provided by the presence of two copies of Xq13.2.
Ring-X chromosomes: their cognitive and behavioural phenotype.
We tested the cognitive abilities and educational attainments of 47 patients with a ring X chromosome, to evaluate the extent to which these variables correlated with failure of r(X) inactivation and with mosaicism. We found possession of a r(X) chromosome was associated with an increased risk of significant learning difficulties, and with associated behavioural maladjustment, compared with 45,X Turner females. Nearly a third had been educated outside mainstream schools. The proportion of cells in peripheral blood containing an inactivated r(X) chromosome was negatively correlated with nonverbal IQ. The parental origin of the normal chromosome did not appear to affect adjustment or abilities. In a minority of r(X) cases associated with mental retardation, there had been a failure to inactivate the ring, due to loss of the XIST locus. However, failure of X-inactivation was not necessarily associated with a severe phenotype. The degree of impairment in IQ depended on the size of the active ring, and hence was proportionate to the number of (as yet unidentified) genes whose functional disomy affected brain development and functioning.
Molecular correlates of the murine Xce locus.
The murine Xce locus, first identified by Bruce Cattanach, influences the primary choice of the X chromosome to be inactivated. Methylation of a GC-rich region (DXPas34) that includes multiple 34 bp repeats and lies some 15 kb 3' to Xist has been shown to vary with Xce haplotype. The degree of methylation on the active X chromosome at this locus represents one of the few molecular correlates of Xce action currently available. Data relating to the specificity and other characteristics of this association are presented.
Expression of hTERT and hTR in cis reconstitutes and active human telomerase ribonucleoprotein.
Telomeres in eukaryotic cells are generally synthesized and maintained by the ribonucleoprotein (RNP) telomerase. This enzyme is composed of at least two subunits, the telomerase reverse transcriptase (TERT) and the telomerase RNA. Human telomerase activity can be reconstituted in vitro by the expression of the telomerase protein catalytic subunit (hTERT) in the presence of recombinant human telomerase RNA (hTR) in a rabbit reticulocyte lysate (RRL) system. The hTERT and hTR subunits are independently expressed in vivo, and little is known about the mechanism of their assembly. To facilitate recombinant telomerase RNP formation and reconstitution, we engineered a construct, termed hTERT-hTR cis, in which the 3' end of the hTERT coding sequence was extended by the addition of the sequence encoding hTR. Expression of the hTERT-hTR cis construct in vitro (in RRL) and in vivo (in the yeast Saccharomyces cerevisiae) produced hTERT-hTR transcripts of the predicted size. Active human telomerase was reconstituted by hTERT-hTR cis expression in both RRL and S. cerevisiae. Assembly of functional human telomerase by the bicistronic expression of the protein and RNA components may facilitate the overexpression and reconstitution of this enzyme in heterologous systems.
De novo methylation of nucleosomal DNA by the mammalian Dnmt1 and Dnmt3A DNA methyltransferases.
In the cell, DNA is wrapped on histone octamers, which reduces its accessibility for DNA interacting enzymes. We investigated de novo methylation of nucleosomal DNA in vitro and show that the Dnmt3a and Dnmt1 DNA methyltransferases efficiently methylate nucleosomal DNA without dissociation of the histone octamer from the DNA. In contrast, the prokaryotic SssI DNA methyltransferase and the catalytic domain of Dnmt3a are strongly inhibited by nucleosomes. We also found that full-length Dnmt1 and Dnmt3a bind to nucleosomes much stronger than their isolated catalytic domains, demonstrating that the N-terminal parts of the MTases are required for the interaction with nucleosomes. Variations of the DNA sequence or the histone tails did not significantly influence the methylation activity of Dnmt3a. The observation that mammalian methyltransferases directly modify nucleosomal DNA provides an insight into the mechanisms by which histone tail and DNA methylation patterns can influence each other because the DNA methylation pattern can be established while histones remain associated to the DNA.
Patterns of ENOD40 gene expression in stem-borne nodules of Sesbania rostrata.
At the base of adventitious root primordia, located on the stem of the tropical legume Sesbania rostrata, nitrogen-fixing nodules are formed upon inoculation with the microsymbiont Azorhizobium caulinodans. This pattern of nodule development presents features of indeterminate and determinate nodules in early and later stages, respectively. A S. rostrata cDNA clone homologous to early nodulin ENOD40 genes was isolated from a cDNA library of developing stem nodules. SrENOD40-1 contained the conserved regions I and II of other ENOD40 genes. By reverse transcriptase PCR, enhanced SrENOD40-1 expression was observed in the adventitious root primordia between 4 and 8 h after inoculation with A. caulinodans. In situ hybridization showed that SrENOD40-1 transcripts, present around the central vascular bundle of the uninfected root primordia, were strongly enhanced upon induction of nodule development. De novo SrENOD40-1 expression was observed in the initiating and growing nodule primordia and around vascular bundles. When cell type specification sets in, the expression became pronounced in cells derived from the meristematic regions. In other parts of the plant, weak SrENOD40-1 expression was associated with vascular bundles and was observed in leaf and stipule primordia.
The soybean ENOD40(2) promoter is active in Arabidopsis thaliana and is temporally and spatially regulated.
The ENOD40 gene is induced early during Rhizobium-legume symbiosis and has probably a primary role in the nodule organogenesis. In this paper we show that the 1.7 kb 5'-flanking region of the GmENOD40(2) is able to drive the expression of a gusA-int marker in transgenic Arabidopsis thaliana. The promoter activity is developmentally regulated and the major activity is detected in the root and in the stigma.