In vitro culture and somatic cell nuclear transfer affect imprinting of SNRPN gene in pre- and post-implantation stages of development in cattle

Background  

Embryo in vitro manipulations during early development are thought to increase mortality by altering the epigenetic regulation of some imprinted genes. Using a bovine interspecies model with a single nucleotide polymorphism, we assessed the imprinting status of the small nuclear ribonucleoprotein polypeptide N (SNRPN) gene in bovine embryos produced by artificial insemination (AI), in vitro culture (IVF) and somatic cell nuclear transfer (SCNT) and correlated allelic expression with the DNA methylation patterns of a differentially methylated region (DMR) located on the SNRPN promoter.     

Identification of a putative oocyte-specific small nuclear ribonucleoprotein polypeptide C in gibel carp

Previous studies have demonstrated that germinal vesicle of amphibian oocyte contains small nuclear ribonucleoprotein polypeptide C (SNRPC). In this study, a putative member of SNRPC was identified from Carassius auratus gibelio oocyte cDNA library. Its full-length cDNA has an open reading frame of 201 nt for encoding a peptide of 66 aa, a short 5'-UTR of 19 nt and a long 3'-UTR of 347 nt including a polyadenylation signal and poly- (A) tail, and the deduced amino acid sequence has 47% identity with the C-terminal of the zebrafish small nuclear ribonucleoprotein polypeptide C. Western blot analysis revealed its oocyte-specific expression. Immunofluorescence localization indicated that its gene product localized to numerous nucleoli within the oocytes and showed dynamic changes with the nucleoli during oocyte maturation. RT-PCR and Western blot analysis further revealed its constant presence in the oocytes and in the embryos until hatching. The data suggested that the newly identified CagOSNRPC might be a nucleolar protein.     

Human U1-70K ribonucleoprotein antigen gene: organization, nucleotide sequence, and mapping to locus 19q13.3

We have isolated and sequenced the gene encoding the human U1-70K snRNP protein. U1-70K is an RNA-binding protein that is a specific component of the U1 small nuclear ribonucleoprotein complex (snRNP) and constitutes the major anti-(U1) RNP autoimmune antigen. We have mapped the U1-70K gene to the distal portion of chromosome 19, at band q13.3. The gene is greater than 44 kb in size and consists of 11 exons. The general structure of the gene has been completely conserved during vertebrate evolution and accounts for the production of several different U1-70K mRNA species by alternative pre-mRNA splicing. Comparison of the predicted amino acid sequences of animal U1-70K proteins reveals a high degree of conservation, particularly in the region of the RNP consensus domain. Even more striking is the complete conservation of the nucleotide sequence of an alternative included/excluded exon containing an in-frame translational termination codon. This conservation also includes significant portions of the downstream intervening sequence. This extraordinary conservation at the nucleotide sequence level suggests that alternative splicing of this exon serves an important function, perhaps in regulating the production of functional U1-70K protein.     

Association between mRNA abundance of functional sperm function proteins and fertility of Holstein bulls

Although the existence of a complex population of mRNA in sperm is well documented, its role has not been completely elucidated. The objective of this study was to determine the relationship of mRNA abundance of sperm specific proteins and sire conception rates (SCR; a fertility index) in Holstein bulls. Samples of sperm from a single collection from commercial Holstein bulls (N = 34) were used to evaluate relative mRNA expression of adenylate kinase (AK) 1, integrin beta (IB) 5, Doppel, nerve growth factor, tissue inhibitors of metalloproteinases (TIMP) 2, lactate dehydrogenase C 1, small nuclear ribonucleoprotein polypeptide N, outer dense fiber 2, and phospholipase C zeta (PLCz) 1 in sperm. With the exception of lactate dehydrogenase C 1 and outer dense fiber 2, the mRNA abundances of these proteins were greater (P < 0.05) for high fertility (> +2 to ≤ 4 SCR) bulls compared with average (≥ 2 to ≤ +2) and low fertility (> −2 to ≤ −4) bulls. Of all the multivariate regression models tested, a combination of AK1, IB5, TIMP2, small nuclear ribonucleoprotein polypeptide N, and PLCz1 accounted for 97.4% of the variance in SCR scores. In the absence of PLCz1, the combination of AK1, IB5, Doppel, nerve growth factor, TIMP, and small nuclear ribonucleoprotein polypeptide N accounted for 96.6% of the variance in SCR scores. In addition, immunocytochemistry confirmed that the sperm-specific protein markers evaluated in this study were present in sperm. In conclusion, frozen-thawed semen from bulls with higher AK1, IB5, TIMP, small nuclear ribonucleoprotein polypeptide N 2 and PLCz1 mRNA abundances in the sperm had greater correlations with sire fertility index and may possess greater probabilities of siring calves.     

A protein associated with small nuclear ribonucleoprotein particles recognizes the 3' splice site of premessenger RNA

A HeLa cell nuclear extract active in splicing of pre-mRNA has been fractionated to identify the component that interacts with the 3' splice site. The activity that binds this region in an RNAase T1 protection assay copurifies with a 70 kd protein which is recognized by anti-Sm antibodies. Protein blots probed with labeled mRNA precursors either containing or lacking an intact 3' splice site reveal that the 70 kd polypeptide can bind pre-mRNA after immobilization on nitrocellulose and that it shows a preference for sequences located between the 3' splice junction and the site of lariat formation. Cofractionation during chromatography and immunoprecipitation by anti-2,2,7-trimethylguanosine antibodies demonstrate that the 3' splice site binding component associates with small nuclear ribonucleoprotein particles in low (1 mM) but not high (15 mM) Mg++ concentrations.     

Imprinting mutations suggested by abnormal DNA methylation patterns in familial Angelman and Prader-Willi syndromes.

The D15S9 and D15S63 loci in the Prader-Willi/Angelman syndrome region on chromosome 15 are subject to parent-of-origin-specific DNA methylation. We have found two Prader-Willi syndrome families in which the patients carry a maternal methylation imprint on the paternal chromosome. In one of these families, the patients have a small deletion encompassing the gene for the small nuclear ribonucleoprotein polypeptide N, which maps 130 kb telomeric to D15S63. Furthermore, we have identified a pair of nondeletion Angelman syndrome sibs and two isolated Angelman syndrome patients who carry a paternal methylation imprint on the maternal chromosome. These Angelman and Prader-Willi syndrome patients may have a defect in the imprinting process in 15q11-13. We propose a model in which a cis-acting mutation prevents the resetting of the imprinting signal in the germ line and thus disturbs the expression of imprinted genes in this region.     

A murine monoclonal antibody recognizes the 13,000 molecular weight polypeptide of the Sm small nuclear ribonucleoprotein complex

Antibodies to the Sm antigen are closely associated with the rheumatic disease systemic lupus erythematosus (SLE). The Sm antigen exists in the cell as part of a ribonucleoprotein complex containing at least 10 polypeptides and five small nuclear RNA. The major immunoreactive Sm species are three polypeptides of m.w. 27,000, 26,000, and 13,000. By using an MRL/1 mouse, a strain which spontaneously produces a disease with many of the characteristics of human SLE, we have produced an anti-Sm hybridoma specific for the 13,000 m.w. Sm polypeptide. This monoclonal antibody is sufficient to allow for the rapid bulk isolation of the entire class of Sm snRNP, and can be used sequentially with an anti-(U1)RNP monoclonal antibody to subfractionate the Sm snRNP particles.     

A subset of small nuclear ribonucleoprotein particle antigens is a component of the nuclear matrix

We have assessed whether antigenic proteins associated with small nuclear ribonucleoprotein particles (snRNP) are associated with the nuclear matrix. Immunofluorescence studies showed that a subset of these particles (those reactive with anti-Sm antisera) were associated with the nuclear matrix, while a different set of particles (those reactive with anti-La antisera) were not associated with the nuclear matrix. Immunoprecipitation experiments showed that three specific polypeptide components of the snRNP reactive with the anti-Sm antisera were significantly enriched in nuclear matrix proteins.     

Structure, chromosomal localization and evolutionary conservation of the gene encoding human U1 snRNP-specific A protein.

Three specific proteins, called A, 70K and C, are present in the U1 small nuclear ribonucleoprotein (snRNP) particle, in addition to the common proteins. The human U1 snRNP-specific A protein is, apart from a proline-rich region, highly similar to the U2 snRNP-specific protein B". To examine the homologous regions at the genomic level, we isolated and characterized the human U1-A gene. The human U1-A protein appears to be encoded by a single-copy gene and its locus has been mapped to the q arm of chromosome 19. The gene, about 14-16 kb in length, consists of six exons. The regions homologous to the U2-B" gene are not limited to single exons and are mostly not confined by exon-exon junctions in the corresponding U1-A mRNA. However, the proline-rich region of U1-A, absent in U2-B", is encoded by a single exon, suggesting a specific function for this domain of U1-A. The region of the cap site and upstream sequences contain interesting similarities to the promoter region of other snRNP protein-encoding genes and several housekeeping genes, in particular the vertebrate ribosomal protein-encoding genes. Hybridization experiments with various vertebrate genomic DNAs revealed that U1-A sequences are evolutionarily conserved in all tested vertebrate genomes, except for chicken, duck and pigeon. The divergence of these avian genomes is probably typical for the class of birds.     

Modulation of lymphocyte nuclear matrix organization in vivo by 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole: an autoradiographic and immunofluorescence study

Assembly of active nuclei in lymphocytes stimulated by mitogen is paralleled by the elaboration of a structurally and biochemically complex nuclear matrix (NM). To examine the dynamics of individual NM polypeptide components during blastogenesis, we have applied immunofluorescence labelling with anti-NM antibodies to concanavalin A-stimulated mouse splenocytes. Whereas peripherin and PI2 antigens did not reorganize during stimulation, labelling of PI1 and small nuclear ribonucleoprotein (snRNP) antigens increased markedly in intensity and redistributed in concert with the previously reported NM restructuring. Double-labelling showed, furthermore, that snRNPs and the internal staining component of PI1 were largely co-localized. As an approach to studying the role of RNA and RNA synthesis in NM organization, we have further examined the effects of the inhibitor of RNA synthesis, 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole (DRB), on NM antigen distribution. The rapid inhibition of 3H-uridine incorporation by DRB was accompanied by coordinate aggregation of snRNPs and of the internal PI1 component into large, brightly stained patches. Both 3H-uridine incorporation levels and antigen localization were readily reversed upon removal of DRB. We conclude that NM antigens behave independently during nuclear and NM assembly and that NM organization, as reflected by NM antigen distribution, is modulated by con A- and DRB-induced alterations in RNA synthesis. We propose, furthermore, that the PI1 antigen plays a role in RNA metabolism, and is possibly involved in RNA transport to the nuclear periphery.     

Molecular characterization of porcine NECD, SNRPN and UBE3A genes and imprinting status in the skeletal muscle of neonate pigs

Imprinted genes are expressed monoallelically depending on their parental origin, and play important roles in embryo survival and postnatal growth regulation. In this study, we characterized the porcine NECD (necdin), SNRPN (small nuclear ribonucleoprotein polypeptide N) and UBE3A (UBE3A ubiquitin protein ligase E3A) genes, analyzed their expression in nine tissues including liver, lung, small intestine, skeletal muscle, heart, kidney, spleen, inguinal lymph nodes and fat, and also examined their imprinting status in the skeletal muscle of neonate pigs. Results indicated that these three genes were highly homologous between pigs and cattle, being 95.02?% in nucleotide and 99.17?% in amino acid with the cattle SNRPN gene, and 96.46?% in nucleotide and 98.63?% in amino acid with the cattle UBE3A gene, respectively. The three genes were expressed in all the tissues investigated. Three single nucleotide polymorphisms (SNPs) in the coding region of these genes, i.e. g.263G>C, g.402T>C and g.340A>G for porcine NECD, SNRPN and UBE3A genes, respectively, were revealed; and imprinting analysis with which indicated that, in the skeletal muscle of neonate pigs, both NECD and SNRPN were maternally imprinted, while UBE3A was not imprinted.     

Associations of small nuclear RNAs in human cells

Several observations have been made about the associations of small nuclear RNAs (snRNAs) in human cells. When nuclear RNA was extracted with phenol and chloroform under standard nondenaturing conditions, the proportion of the nuclear snRNA content that cosedimented with high molecular weight RNA was very low. These results do not support the proposal that it is a large percentage of the cellular snRNA content that is involved in relatively stable base-paired interactions with heterogeneous nuclear RNA at any given time. The various small nuclear ribonucleoprotein particles (snRNPs), in which the snRNAs are found in the cell, appear to differ substantially in their sedimentation rates under conditions of physiological ionic strength. Using anti-RNP and anti-Sm antibodies to analyze various subcellular fractions, we found that most, if not all, of the U1 snRNA cellular content is associated with the polypeptide(s) bearing the RNP determinant (in interphase and mitotic cells) and with the polypeptide(s) carrying the Sm determinant (in mitotic cells).     

Prader-Willi syndrome: Methylation study or fluorescence in situ hybridization first?

Prader-Willi syndrome (PWS) is neurogenetic disorder involving the imprinting mechanism at 15q11-13 region. We report a 4-year-old girl who was referred to our laboratory to be investigated for clinical obesity, mental deficiency and respiratory problems. The patient was born for non-consanguineous and healthy biological parents. After normal pregnancy, the patient was delivered by cesarean section at full term, with a birth weight of 2500 g, and the height and head circumference were unknown. In neonatal stage, she presented severe hypotonia with feeding problems. Her developmental progress was delayed. She walked and developed speech at the age of 3 years. Since the age of 3 years, she presented severe dental problems. Methylation study had confirmed the diagnosis, and for detecting etiology, fluorescence in situ hybridization using probes for small nuclear ribonucleoprotein polypeptide N (SNRPN), which map inside the chromosomal region 15q11-15q13, was necessary to confirm the 15q11-15q13 deletion of paternal chromosome 15, which is the predominant genetic defect in PWS. In conclusion, we report this case with an objective to reinforce the necessity of analysis of DNA methylation within the 15q11-13 region, which is an important tool for the correct diagnosis among children presenting with neonatal hypotonia, mental deficiency and obesity.     

Characterization of the La (SS-B) antigen from several mammalian sources

The La or SS-B antigen is associated with rheumatic diseases, systemic lupus erythematosus, and Sjogren's syndrome, and is part of a larger ribonucleoprotein complex. Immunoaffinity chromatography allowed for the efficient separation of the La antigen from the bulk of the cellular proteins, with a minimum of protease exposure. Protein blot analysis of the affinity-isolated material indicated a major immunoreactive polypeptide of 50,000 m.w. A comparison of this antigen in a number of mammalian sources (human, rabbit, and rat) suggested strong conservation of the native polypeptide m.w. Likewise, in a direct comparison of this antigen from Epstein-Barr virus-infected cells in which there are distinct differences in the antigen-associated RNA species, the immunoreactive polypeptide species were of similar size. The La protein is readily susceptible to endogenous proteolysis, with the resulting generation of smaller, discrete polypeptides that still retain antigenicity. By using the La protein to monitor potential degradation, we have developed a simple two-step procedure to isolate the La-associated snRNP complex. The complexes thus isolated provide material suitable as a source of both the active antigen and of the functional ribonucleoprotein complex.     

Cloning of the cDNA for a human homolog of the rat PEP-19 gene and mapping to chromosome 21q22.2–q22.3

Exon trapping was used to identify fragments of genes on human chromosome 21. One trapped sequence, hmc18h10 (GenBank no. X88329), showed homology to a sequence (GenBank no. S65225) that includes the first three codons of the rat PEP-19 gene and 5′ untranslated leader region. We have cloned the corresponding cDNA for a human homolog of the rat PEP-19 gene and mapped it to the region between markers ERG and D21S56 of chromosome 21q22.2–q22.3. Rat PEP-19 is a neuron-specific polypeptide expressed in several regions of the central nervous system. It serves as a cell-specific marker in Purkinje cells and its expression is developmentally regulated in the cerebellum, but its precise function is unknown. It is also presently unknown whether overexpression of the PEP-19 gene is involved in certain phenotypes of Down syndrome. Received: 3 May 1996 / Revised: 2 July 1996     

Nanosecond electric pulses penetrate the nucleus and enhance speckle formation

Nanosecond electric pulses generate nanopores in the interior membranes of cells and modulate cellular functions. Here, we used confocal microscopy and flow cytometry to observe Smith antigen antibody (Y12) binding to nuclear speckles, known as small nuclear ribonucleoprotein particles (snRNPs) or intrachromatin granule clusters (IGCs), in Jurkat cells following one or five 10 ns, 150 kV/cm pulses. Using confocal microscopy and flow cytometry, we observed changes in nuclear speckle labeling that suggested a disruption of pre-messenger RNA splicing mechanisms. Pulse exposure increased the nuclear speckled substructures by ∼2.5-fold above basal levels while the propidium iodide (PI) uptake in pulsed cells was unchanged. The resulting nuclear speckle changes were also cell cycle dependent. These findings suggest that 10 ns pulses directly influenced nuclear processes, such as the changes in the nuclear RNA-protein complexes.     

Protein composition of nuclear ribonucleoprotein particles isolated from liver of rats in the early stages of feeding of 3'-methyl-4-dimethylaminoazobenzene and from hepatoma induced by the same carcinogen.

The feeding of carcinogenic 3'-methyl-4-dimethylaminoazobenzene (3'-MeDAB) in the early stages results in a change in the protein composition of the nuclear ribonucleoprotein particles of the rat liver. These particles are associated with newly synthesized RNA and it is assumed that they are involved in the processing and in the transport of this RNA. After 6 weeks of feeding of this azocarcinogen, the amount of one of the main polypeptides (apparent molecular weight 42 000) is decreased and after 10 weeks of feeding the particles are devoid of this polypeptide completely. Feeding of the non-carcinogenic p-aminoazobenzene (AB) is without any effect. The loss of this polypeptide is not characteristic for the malignant transformation. In the nuclear ribonucleoprotein particles isolated from hepatoma which has been induced by 3'-MeDAB this polypeptide is present in even higher proportion to other polypeptides than it is in particles isolated from liver cells of control animals. The 3'-MeDAB binds to the proteins of the liver nuclear ribonucleoprotein particles and interferes with the RNA processing. It is proposed that the changes in the composition of the protein moiety of the particles reflect changes in the population of liver cells leading finally to the selection of hepatoma cells which are resistant to the toxic effect of 3'-MeDAB on RNA processing.