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PubMed1994

Physical mapping of 5S rDNA loci by direct-cloned biotinylated probes in barley chromosomes.

5S rDNA loci have been mapped on barley chromosomes by in situ hybridization using five reciprocal translocation lines. Two kinds of DNA probes covering either the 5S rDNA coding region or the 5S rDNA coding and flanking noncoding regions were used. They were prepared by direct cloning from interphase nuclei and simultaneous direct labeling in PCR. Four 5S rDNA loci were detected in a haploid genome by the 5S rDNA coding region, whereas in addition, the four or six 5S rDNA related sites, depending on the variety used, were revealed by the probe covering the flanking region. The four 5S rDNA loci revealed and mapped on the barley chromosomes: 2 (2I), 3 (3I), 1 (7I), and 4 (4I) were designated 5SRrn-I1, 5SRrn-I2, 5SRrn-I3 and 5SRrn-I4, respectively, in descending order of copy number of 5S rRNA genes.

Base Sequence↗

PubMed2006

Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues.

MicroRNAs are small approximately 22 nucleotide-long noncoding RNAs capable of controlling gene expression by inhibiting translation. Alignment of human microRNA stem-loop sequences (mir) against a recent draft sequence assembly of the bovine genome resulted in identification of 334 predicted bovine mir. We sequenced five tissue-specific cDNA libraries derived from the small RNA fractions of bovine embryo, thymus, small intestine, and lymph node to validate these predictions and identify new mir. This strategy combined with comparative sequence analysis identified 129 sequences that corresponded to mature microRNAs (miR). A total of 107 sequences aligned to known human mir, and 100 of these matched expressed miR. The other seven sequences represented novel miR expressed from the complementary strand of previously characterized human mir. The 22 sequences without matches displayed characteristic mir secondary structures when folded in silico, and 10 of these retained sequence conservation with other vertebrate species. Expression analysis based on sequence identity counts revealed that some miR were preferentially expressed in certain tissues, while bta-miR-26a and bta-miR-103 were prevalent in all tissues examined. These results support the premise that species differences in regulation of gene expression by miR occur primarily at the level of expression and processing.

Animals↗

PubMedDate not supplied

Mutations of transforming growth factor beta 1 type II receptor, BAX, and insulin-like growth factor II receptor genes in microsatellite unstable cell lines.

Inactivation of the DNA mismatch repair (MMR) system allows the genome to accumulate mutations because of failure to correct mispairing of nucleotides and slippage mistakes at microsatellite sequences (termed microsatellite instability ¿MSI¿). While most mutations are acquired in noncoding regions by virtue of its larger share of DNA, mutations may occur in exons of genes that contain microsatellite sequences. The type II receptor for TGF beta 1 (TGF beta RII), the insulin-like growth factor II receptor (IGFIIR), and the proapoptotic gene BAX have been shown to contain mononucleotide microsatellites, and in MSI tumors, mutations may occur in these sequences late in the multistep carcinogenesis pathway. Here, we characterize 9 cell lines for MSI and mutations in TGF beta RII, BAX, and IGFIIR by PCR-based assays. The MMR-proficient cell lines SW480 and HT29 demonstrate stability at microsatellite sequences and do not have mutations in TGF beta RII, BAX, or IGFIIR. The MMR-deficient cell lines LoVo, SW48, LS174t, and HCT116 all demonstrate MSI and have only mutant alleles of TGF beta RII. Additionally, SW48 cells were heterozygous for wild-type and mutant IGFIIR. While LoVo and LS174t cells possessed only mutant BAX alleles, HCT116 was heterozygous and SW48 had only the wild-type allele. The MMR-deficient ovarian cell line 2774 demonstrated MSI, but showed only wild-type TGF beta RII, IGFIIR, and BAX alleles. In HCT116+ch2 cells, there was no genotypic change from the hMLH1-mutated HCT116 cells. In HCT116+ch3 cells, MSI was corrected, and this cell line became heterozygous for mutant and wild-type TGF beta RII because wild-type hMLH1 and TGF beta RII are both located on chromosome 3. Thus, the presence of a defective MMR system correlates with MSI, and the wild-type allele of TGF beta RII was absent in all microsatellite unstable colon cell lines, whereas the absence of wild-type BAX occurred in only two colon cell lines. In ovarian cancer cells with MSI, mutations in TGF beta RII, BAX, and IGFIIR may be unimportant in the genesis of this tumor.

Base Pair Mismatch↗

PubMed2002

RNA-protein interactions that regulate pre-mRNA splicing.

Splicing of nuclear precursor messenger RNAs is an important and ubiquitous type of gene regulation in metazoans. Splicing joins the coding sequences called exons by removing the intervening noncoding sequences, introns, from primary transcripts. Alternative splicing generates an enormous repertoire of functional diversity by producing multiple RNAs and proteins from a single gene. In fact, recent genome sequences from several organisms suggest that splicing regulation is likely to provide an important source of functional diversity in more complex organisms. Because splice sites are short sequences at the ends of introns, the functional splice sites have to be distinguished from an excessively large number of sequences in the primary transcripts that resemble a splice site. Furthermore, alternative splice sites have to be correctly chosen at appropriate times. Thus, selection of proper splice sites remains a daunting biological problem. This review focuses on a few examples in which the molecular and biochemical basis for splice site selection is better understood.

Alternative Splicing↗

PubMed1996

High incidence of loss of heterozygosity and abnormal imprinting of H19 and IGF2 genes in invasive cervical carcinomas. Uncoupling of H19 and IGF2 expression and biallelic hypomethylation of H19.

The few imprinted genes characterized so far include the insulin-like growth factor-2 gene (IGF2) coding for a foetal growth factor and the H19 gene whose normal function is unknown but which is likely to act as an RNA with an antitumour effect. IGF2 is expressed by the paternal allele and H19 by the maternal allele. This reciprocal expression is quite interesting because both H19 and IGF2 genes are located close to each other on chromosome 11p15.5 in a region subject to loss of heterozygosity (LOH). Moreover, loss of imprinting (LOI) or biallelic expression has been proposed as an epigenetic mechanism for tumorigenesis in a variety of human cancers including Wilms' tumour. In this study we report the LOH, LOI and methylation status of H19 and IGF2 genes in 29 invasive cervical carcinomas of different clinical stages. Fourteen (48%) and 13 (45%) tumours were heterozygous for H19 and IGF2 respectively. LOH for H19 and IGF2 genes were found in 2 of 14 (14%) and 3 of 13 (23%) informative tumours, respectively. LOI of H19 and IGF2 was detected in 2 of 12 (17%) and 5 of 10 (50%) tumours with no LOH, respectively. More interestingly, monoallelic expression of the otherwise silent H19 allele (allele switch) was observed in 2 of 12 (17%) tumours and biallelic expression of IGF2 was detected in one specimen of normal cervix adjacent to the tumour. The expressing H19 allele, and to a lower degree also the silent allele, were hypomethylated in tumours suggesting that demethylation of both H19 alleles may be associated with an early step of imprinting alteration. In cervical cancer H19 and IGF2 expressions could be independently regulated. In conclusion, our data suggest that H19 and IGF2 genes, via deletions and/or abnormal imprinting, could play a crucial role in a large proportion (58%) of cervical cancers where they may be associated with disease progression.

Alleles↗

PubMed2000

Genomic structure and expression of human KCNJ9 (Kir3.3/GIRK3).

The human KCNJ9 (Kir 3.3, GIRK3) is a member of the G-protein-activated inwardly rectifying potassium (GIRK) channel family. Here we describe the genomic organization of the KCNJ9 locus on chromosome 1q21-23 as a candidate gene for Type II diabetes mellitus in the Pima Indian population. The gene spans approximately 7.6 kb and contains one noncoding and two coding exons separated by approximately 2.2 and approximately 2.6 kb introns, respectively. We identified 14 single nucleotide polymorphisms (SNPs), including one that predicts a Val366Ala substitution, and an 8 base-pair (bp) insertion/deletion. Our expression studies revealed the presence of the transcript in various human tissues including pancreas, and two major insulin-responsive tissues: fat and skeletal muscle. The characterization of the KCNJ9 gene should facilitate further studies on the function of the KCNJ9 protein and allow evaluation of the potential role of the locus in Type II diabetes.

3' Untranslated Regions↗

PubMed2005

The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): evidence for its evolution via gene duplication.

The translocation of tRNA genes has occurred frequently among multiple independent arthropod lineages. However, the mechanisms of such gene rearrangement are still unclear. In this study we sequenced the nearly complete mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Decapoda, Brachyura, Potamidae). Its size is relatively large (app. 24 kb) for higher animal mtDNA and is due to the presence of many intergenic noncoding sequences (IGNs), one of which is a large repeat region (>7.0 kb). Excluding the repeat region and the putative control region (514 bp), the total size of IGNs (1953 bp) is still the largest reported in arthropods. In comparison to the proposed ancestral arrangement for the insect-crustacean clade, G. dehaani displays changes in the positional order for three tRNA genes (trnQ, trnL(uur) and trnH). At the putative former and current locations for trnQ and trnH, there are IGNs with high similarities to corresponding sequences in the ancestral arrangement. This suggests the occurrence of partial duplication, followed by a loss of function for one copy of these two duplicated genes in G. dehaani. Furthermore, three trnLs (one trnL(uur) and two trnL(cun)s) are found in G. dehaani; their sequences are highly similar to each other (70.8-82.5%) and similar to the trnL(cun) of other arthropods. This suggests that duplication of trnL(cun) occurred at least twice, and the current trnL(uur) of G. dehaani arose by a subsequent anticodon alternation. These observations provide direct evidence for the "duplication-random loss" model for mtDNA gene rearrangement. Comparisons with other available Brachyuran data(http://www.ncbi.nlm.nih.gov/genomes/ORGANELLES/6657.html) suggest that two of the three tRNA translocations are unique in G. dehaani. For G. dehaani, where duplications have occurred but deletion of extra sequences is incomplete, the IGNs found at the ancestral or trans-locations are likely to be footprints of relatively recent mitochondrial genome evolution.

Animals↗

PubMed1992

Nuclear-encoded tobacco chloroplast ribosomal protein L24. Protein identification, sequence analysis of cDNAs encoding its cytoplasmic precursor, and mRNA and genomic DNA analysis.

Using a Nicotiana tabacum leaf cDNA library in the expression vector lambda gt11, two cDNAs encoding the full-length precursor polypeptide (M(r) 20,696) of tobacco chloroplast ribosomal protein L24 were identified and sequenced. These cDNAs encode a mature protein of 146 amino acids (M(r) 16,418) with a transit peptide of 41 amino acids (M(r) 4,278). The mature tobacco L24 protein has 78, 65, 45, and 35% sequence identity with ribosomal proteins L24 of pea, spinach, Bacillus subtilis, and Escherichia coli, respectively. The transit peptide of tobacco L24 is 54 and 57% identical with that of L24 chloroplast ribosomal proteins of pea and spinach, respectively. An expressed beta-galactosidase:L24 fusion protein, bound to nitrocellulose filters, was used as affinity matrix to purify monospecific antibody to L24 protein. Using this monospecific antibody protein L24 was identified among high performance liquid chromatography (HPLC)-purified tobacco chloroplast ribosome 50 S subunit proteins. The predicted amino terminus of the mature L24 protein was confirmed by partial sequencing of the HPLC-purified L24 protein. Northern blot analysis revealed a single mRNA band (0.85-0.90 kilobase) corresponding in size to full-length L24 cDNA. The presence of multiple genes for L24 is suggested by Southern blot hybridization and characterization of two cDNAs for L24 which only differ in their 3'-noncoding sequences.

Amino Acid Sequence↗

PubMed2000

The genomic structure of human olfactory receptor genes.

The genomic and cDNA structures were studied for eight human olfactory receptor (OR) genes within the chromosome 17p13.3 cluster. A common gene structure was revealed, which included an approximately 1-kb intronless coding region terminated by a signal for polyadenylation and a variable number of upstream noncoding exons. The latter were found to be alternatively spliced, giving rise to different isoforms of OR mRNA. While the initial exons mostly agreed with previous computer predictions and were conserved within OR subfamilies, other upstream exons were novel and idiosyncratic. In some cases, repetitive sequences were involved in the generation of splice sites and putative transcription control elements. Such gene structure is consistent with early repertoire enhancement by retrogene generation, which was likely followed by extensive genomic duplication. Each OR gene had a unique signature of transcription factor elements, consistent with a combinatorial expression control mechanism.

Alternative Splicing↗

PubMed1992

A poliovirus replicon containing the chloramphenicol acetyltransferase gene can be used to study the replication and encapsidation of poliovirus RNA.

A poliovirus replicon, FLC/REP, which incorporates the reporter gene chloramphenicol acetyltransferase (CAT) in place of the region encoding the capsid proteins VP4, VP2, and part of VP3 in the genome of poliovirus type 3, has been constructed. Transfection of cells indicates that the FLC/REP replicon replicates efficiently and that active CAT enzyme is produced as a CAT-VP3 fusion protein. The level of CAT activity in transfected cells broadly reflects the level of FLC/REP RNA. A series of mutations in the 5' noncoding region of poliovirus type 3 were introduced into FLC/REP, and their effects were monitored by a simple CAT assay. These experiments helped to define further the stem-loop structures in the 5' noncoding region which are essential for RNA replication. The CAT-containing poliovirus replicon could also be packaged into poliovirus capsids provided by helper virus and was stable as a subpopulation of virus particles over at least four passages. The location of the CAT gene in FLC/REP excluded the presence of an encapsidation signal in the region of the poliovirus genome comprising nucleotides 756 to 1805.

Amino Acid Sequence↗

PubMed1991

Cloning, sequence analysis, and expression in Escherichia coli of a gene coding for a beta-mannanase from the extremely thermophilic bacterium "Caldocellum saccharolyticum".

A lambda recombinant phage expressing beta-mannanase activity in Escherichia coli has been isolated from a genomic library of the extremely thermophilic anaerobe "Caldocellum saccharolyticum." The gene was cloned into pBR322 on a 5-kb BamHI fragment, and its location was obtained by deletion analysis. The sequence of a 2.1-kb fragment containing the mannanase gene has been determined. One open reading frame was found which could code for a protein of Mr 38,904. The mannanase gene (manA) was overexpressed in E. coli by cloning the gene downstream from the lacZ promoter of pUC18. The enzyme was most active at pH 6 and 80 degrees C and degraded locust bean gum, guar gum, Pinus radiata glucomannan, and konjak glucomannan. The noncoding region downstream from the mannanase gene showed strong homology to celB, a gene coding for a cellulase from the same organism, suggesting that the manA gene might have been inserted into its present position on the "C. saccharolyticum" genome by homologous recombination.

Amino Acid Sequence↗

PubMed2006

RNA world - the dark matter of evolutionary genomics.

For a long time, molecular evolutionary biologists have been focused on DNA and proteins, whereas RNA has lived in the shadow of its famous chemical cousins as a mere intermediary. Although this perspective has begun to change since genome-wide transcriptional profiling was successfully extended to evolutionary biology, it still echoes in evolutionary literature. In this mini-review, new developments of RNA biochemistry and transcriptomics are brought to the attention of evolutionary biologists. In particular, the unexpected abundance and functional significance of noncoding RNAs is briefly reviewed. Noncoding RNAs control a remarkable range of biological pathways and processes, all with obvious fitness consequences, such as initiation of translation, mRNA abundance, transposon jumping, chromosome architecture, stem cell maintenance, development of brain and muscles, insulin secretion, cancerogenesis and plant resistance to viral infections.

Animals↗

PubMed1990

Mutational analysis of the promoter region of the alpha 27 gene of herpes simplex virus 1 within the context of the viral genome.

In herpes simplex virus 1-infected cells, the first set of genes to be expressed (alpha genes) is induced by the alpha gene trans-inducing factor (alpha TIF), a virion structural protein. The cis-acting site in the 5' untranscribed domain of alpha genes was previously reported to be the sequence 5'-GYATGNTAATGARATTCYTTGNGGG noncoding (where Y is a pyrimidine, R is a purine, N is any base), which binds a host protein designated alpha H1 (also termed the octamer binding protein, OTF-1, Oct-1, etc.) and which, together with this and possibly other proteins, forms complexes with alpha TIF. To determine the role of the various components of this cis-acting site and of other sequences shared by the alpha genes, we constructed 17 mutants spanning 110 nucleotides of the promoter domain of the alpha 27 gene and made a series of chimeric genes. Each chimeric gene embodying one set of these mutations was inserted into the viral genome and measurements were made of (i) accumulated mRNA under conditions in which only alpha genes were expressed and (ii) the capacity of the mutated sequence to form complexes containing alpha TIF and alpha H1 proteins. We report that (i) transversions in the "TAAT" sequence abolished both complex formation and induction of the chimeric alpha gene, (ii) mutations in the octamer binding site sequence upstream from TAAT or of the downstream GARAT abolished alpha TIF complex formation and also reduced alpha mRNA accumulation, (iii) mutations in a "CAAT" box also reduced expression of mRNA without affecting the formation of DNA-protein complexes containing alpha TIF, and (iv) mutations in sequences immediately downstream from TAATGARAT and in a pair of GA-rich elements reduced alpha mRNA expression whereas mutations between these elements had no effect on the accumulation of the mRNA. The results are consistent with the conclusion that both the alpha H1 octamer binding site ATGNTAAT and the GARAT sequence play a significant role in the induction of alpha genes. For optimal gene expression, however, additional elements downstream from the GARAT sequence and in other regions of the alpha promoter must be present.

Animals↗

PubMed1997

Internal entry of ribosomes is directed by the 5' noncoding region of classical swine fever virus and is dependent on the presence of an RNA pseudoknot upstream of the initiation codon.

Bicistronic RNAs containing the 373-nucleotide-long 5' nontranslated region (NTR) of the classical swine fever virus (CSFV) genome as intercistronic spacer were used to show the presence of an internal ribosome entry site (IRES) in the 5' end of the CSFV genome. By coexpression of the poliovirus 2A protease it was demonstrated that the CSFV 5' NTR-driven translation is independent of the presence of functional eukaryotic initiation factor eIF-4F. Deletion analysis indicated that the 5' border of the IRES is located between nucleotides 28 and 66. The role of a proposed pseudoknot structure at the 3' end of the CSFV 5' NTR in IRES-mediated translation was investigated by site-directed mutagenesis. Mutant RNAs that had lost the ability to base pair in stem II of the pseudoknot were translationally inactive. Translation to wild-type levels could be restored through the introduction of compensatory complementary base changes that repaired base pairing in stem II. In addition, we showed that the AUG codon, which is located 7 nucleotides upstream of the polyprotein initiation site and is conserved in pestiviruses, could not be used to initiate translation. Also, an AUG codon introduced downstream of the polyprotein initiation site was not recognized as an initiation site by ribosomes. These data suggest that after internal entry on the CSFV 5' NTR, ribosomal scanning for the initiation codon is limited to a small region.

Animals↗

PubMed1994

The structure and organization of the human erythroid anion exchanger (AE1) gene.

The AE1 (anion exchanger, band 3) protein is expressed in erythrocytes and in the A-type intercalated cells of the kidney distal collecting tubule. In both cell types it mediates the electroneutral transport of chloride and bicarbonate ions across the lipid bilayer, and, in erythrocytes, it also serves as the critical attachment site of the peripheral membrane skeleton. We have characterized the human AE1 gene using overlapping clones isolated from a phage library of human genomic DNA. The gene spans approximately 20 kb and consists of 20 exons separated by 19 introns. The structure of the human AE1 gene corresponds closely with that of the previously characterized mouse AE1 gene, with a high degree of conservation of exon/intron junctions, as well as exon and intron nucleotide sequences. The putative upstream and internal promoter sequences of the human AE1 gene used in erythroid and kidney cells, respectively, are described. We also report the nucleotide sequence of the entire 3' noncoding region of exon 20, which was lacking in the published cDNA sequences. In addition, we have characterized 9 Alu repeat elements found within the body of the human AE1 gene that are members of 4 related subfamilies that appear to have entered the genome at different times during primate evolution.

Amino Acid Sequence↗

PubMedDate not supplied

Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences.

To study the genomic divergence between human and chimpanzee, large-scale genomic sequence alignments were performed. The genomic sequences of human and chimpanzee were first masked with the RepeatMasker and the repeats were excluded before alignments. The repeats were then reinserted into the alignments of nonrepetitive segments and entire sequences were aligned again. A total of 2.3 million base pairs (Mb) of genomic sequences, including repeats, were aligned and the average nucleotide divergence was estimated to be 1.22%. The Jukes-Cantor (JC) distances (nucleotide divergences) in nonrepetitive (1.44 Mb) and repetitive sequences (0.86 Mb) are 1.14% and 1.34%, respectively, suggesting a slightly higher average rate in repetitive sequences. Annotated coding and noncoding regions of homologous chimpanzee genes were also retrieved from GenBank and compared. The average synonymous and nonsynonymous divergences in 88 coding genes are 1.48% and 0.55%, respectively. The JC distances in intron, 5' flanking, 3' flanking, promoter, and pseudogene regions are 1.47%, 1.41%, 1.68%, 0.75%, and 1.39%, respectively. It is not clear why the genetic distances in most of these regions are somewhat higher than those in genomic sequences. One possible explanation is that some of the genes may be located in regions with higher mutation rates.

Animals↗

PubMed1994

Cloning, sequence analysis and expression of the gene encoding the mouse bradykinin B2 receptor.

The bradykinin B2 receptor (B2R) mediates most of the biological effects of kinins. In the present study, we have cloned and sequenced the gene (B2R) from a mouse embryonic stem (ES) cell genomic library. Mouse B2R is 7 kb in length containing three exons of 0.3, 0.23 and 3.7 kb separated by two introns of 2.5 and 0.41 kb. The first and second exons are noncoding while the third exon contains the full-length coding region and a long 3' noncoding region. An ATG translation start codon, TGA stop codon and a polyadenylation signal (AATAAA) were identified in the third exon. B2R encodes a protein of 41,470 Da and 366 amino acids (aa) forming seven transmembrane (TM) domains. At the aa level, B2R shares 91 and 82% sequence identity with the rat and human B2R, respectively. In the 5' flanking region, a consensus TATA box, a putative cAMP-response element, a putative phorbol ester-response element, a putative AP-1-binding site and a putative IL-6-response element were identified. Southern blot analysis following reverse transcription and PCR showed that B2R is expressed in most mouse tissues, except the liver and spleen, which is consistent with the wide distribution of B2R activity as deduced from pharmacological studies.

Amino Acid Sequence↗

PubMed1999

Complete sequence determination of the mouse and human CTLA4 gene loci: cross-species DNA sequence similarity beyond exon borders.

CTLA4 (CD152), a receptor for the B7 costimulatory molecules (CD80 and CD86), is considered a fundamental regulator of T-cell activation. In this paper, we present the complete primary structure of the mouse and human CTLA4 gene loci. Sequence comparison between the mouse and the human CTLA4 gene loci revealed a high degree of sequence conservation both for homologous noncoding regions (65-78% identity) and for coding regions (72-98% identity), with an overall score of 71% over the entire length of the two genes. Of the CTLA4 genomic regions aligned, five simple repetitive elements were found in the mouse locus, whereas two simple repetitive sequences were localized on the human locus. RNA blot analysis of mouse and human primary tissues indicated that both CTLA4 and T-cell receptor transcripts were found in most organs with generally higher levels in lymphoid tissues. The conservation of CTLA4 gene patterning raises the possibility that constrained gene evolution of CTLA4 may be linked to conserved transcriptional control of this locus.

Abatacept↗