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Results for “structural genomics”

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PubMed1997

Chromosomal localization and partial genomic structure of the human peroxisome proliferator activated receptor-gamma (hPPAR gamma) gene.

We determined the chromosomal localization and partial genomic structure of the coding region of the human PPAR gamma gene (hPPAR gamma), a nuclear receptor important for adipocyte differentiation and function. Sequence analysis and long PCR of human genomic DNA with primers that span putative introns revealed that intron positions and sizes of hPPAR gamma are similar to those previously determined for the mouse PPAR gamma gene[13]. Fluorescent in situ hybridization localized hPPAR gamma to chromosome 3, band 3p25. Radiation hybrid mapping with two independent primer pairs was consistent with hPPAR gamma being within 1.5 Mb of marker D3S1263 on 3p25-p24.2. These sequences of the intron/exon junctions of the 6 coding exons shared by hPPAR gamma 1 and hPPAR gamma 2 will facilitate screening for possible mutations. Furthermore, D3S1263 is a suitable polymorphic marker for linkage analysis to evaluate PPAR gamma's potential contribution to genetic susceptibility to obesity, lipoatrophy, insulin resistance, and diabetes.

Adipose Tissue↗

PubMed1996

Genomic structure and chromosomal localization of the mouse CDEI-binding protein CDEBP (APLP2) gene and promoter sequences.

The genomic structure of the mouse gene encoding the CDEBP protein has been established. The protein was initially identified on the basis of its ability to bind the CDEI motif (GTCACATG). The same locus has been independently described under the name APLP2, on the basis of sequence similarities with the Amyloid Precursor Protein (APP). The exon-intron distribution of Cdebp appears strikingly similar to that of the App gene in the regions encoding the conserved domains, with a divergent structure in the other parts. The transcription start site has been localized, and sequences with promoter activity have been identified immediately upstream of it by their ability to direct the expression of a reporter luciferase gene in transfected cells. This region is devoid of either TATA or CAAT boxes. The gene has been mapped to mouse chromosome 9 by in situ hybridization on metaphase chromosomes.

Animals↗

PubMed1991

Chromosome rearrangement by ectopic recombination in Drosophila melanogaster: genome structure and evolution.

Ectopic recombination between interspersed repeat sequences generates chromosomal rearrangements that have a major impact on genome structure. A survey of ectopic recombination in the region flanking the white locus of Drosophila melanogaster identified 25 transposon-mediated rearrangements from four parallel experiments. Eighteen of the 25 were generated from females carrying X chromosomes heterozygous for interspersed repeat sequences. The cytogenetic and molecular analyses of the rearrangements and the parental chromosomes show: (1) interchromosomal and intrachromosomal recombinants are generated in about equal numbers; (2) ectopic recombination appears to be a meiotic process that is stimulated by the interchromosomal effect to about the same degree as regular crossing over; (3) copies of the retrotransposon roo were involved in all of the interchromosomal exchanges; some copies were involved much more frequently than others in the target region; (4) homozygosis for interspersed repeat sequences and other sequence variations significantly reduced ectopic recombination.

Animals↗

PubMed2004

Comparative genomic structure of prokaryotes.

Recent advances in DNA-sequencing technologies have made available an enormous resource of data for the study of bacterial genomes. The broad sample of complete genomes currently available allows us to look at variation in the gross features and characteristics of genomes while the detail of the sequences reveal some of the mechanisms by which these genomes evolve. This review aims to describe bacterial genome structures according to current knowledge and proposed hypotheses. We also describe examples where mechanisms of genome evolution have acted in the adaptation of bacterial species to particular niches.

Bacteria↗

PubMed2000

Genomic structure and multiple single-nucleotide polymorphisms (SNPs) of the thiopurine S-methyltransferase (TPMT) gene.

Thiopurine S-methyltransferase (TPMT) catalyzes the S-methylation of drugs such as azathiopurine, 6-mercaptopurine, and 6-thioguanine, which are widely prescribed for immunosuppressive or cytotoxic applications. We report here the entire genomic structure of the TPMT gene and the presence of 30 single-nucleotide polymorphisms (SNPs) within that structure. The gene spans a genomic region about 27kb long and consists of nine exons. By screening its entire genomic sequence for SNPs in 48 Japanese chromosomes by direct DNA sequencing, we detected 1 SNP in the 870-bp promoter region, 26 SNPs in introns, and 3 SNPs in the 3' untranslated region (3'UTR) for investigating correlations between TPMT genotypes and the side-effects caused by thiopurine drugs.

Humans↗

PubMed1997

Genomic structure of the human PLCD1 (phospholipase C delta 1) locus on 3p22-->p21.3.

A large-scale sequencing analysis of genomic DNA in the vicinity of homozygous deletion on chromosome 3p found in a lung cancer cell line disclosed that the gene encoding phospholipase C delta 1 (PLCD1) is located just distal to the region removed by the deletion We report the genomic structure of this gene, which consists of 15 exons and spans about 22 kb, and its precise localization to chromosome 3p22-->p21.3.

Alternative Splicing↗

PubMed2000

Genomic structure and fine mapping of the two human filamin gene paralogues FLNB and FLNC and comparative analysis of the filamin gene family.

The genomic structure of the filamin gene paralogues FLNB and FLNC was determined and related to FLNA. FLNB consists of 45 exons and 44 introns and spans approximately 80 kb of genomic DNA. FLNC is divided into 48 exons and 47 introns and covers approximately 29.5 kb of genomic DNA. A previously unknown intron was found in FLNA. The comparison of all three filamin gene paralogues revealed a highly conserved exon-intron structure with significant differences in the exons 32 of all paralogues encoding the hinge I region, as well as the insertion of a novel exon 40A in FLNC only. Gene organization does not correlate with the domain structures of the respective proteins. To improve candidate gene cloning approaches, FLNB was precisely mapped at 3p14 in an interval of 0.81 cM between WI3771 and WI6691 and FLNC at 7q32 in an interval of 2.07 cM between D7S530 and D7S649.

Animals↗

PubMed2024

Rok from B. subtilis: Bridging genome structure and transcription regulation.

Bacterial genomes are folded and organized into compact yet dynamic structures, called nucleoids. Nucleoid orchestration involves many factors at multiple length scales, such as nucleoid-associated proteins and liquid-liquid phase separation, and has to be compatible with replication and transcription. Possibly, genome organization plays an intrinsic role in transcription regulation, in addition to classical transcription factors. In this review, we provide arguments supporting this view using the Gram-positive bacterium Bacillus subtilis as a model. Proteins BsSMC, HBsu and Rok all impact the structure of the B. subtilis chromosome. Particularly for Rok, there is compelling evidence that it combines its structural function with a role as global gene regulator. Many studies describe either function of Rok, but rarely both are addressed at the same time. Here, we review both sides of the coin and integrate them into one model. Rok forms unusually stable DNA-DNA bridges and this ability likely underlies its repressive effect on transcription by either preventing RNA polymerase from binding to DNA or trapping it inside DNA loops. Partner proteins are needed to change or relieve Rok-mediated gene repression. Lastly, we investigate which features characterize H-NS-like proteins, a family that, at present, lacks a clear definition.

Bacillus subtilis↗

PubMed2005

Structural genomics analysis of alternative splicing and application to isoform structure modeling.

Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge of alternatively spliced variants is derived mainly from mRNA transcripts, and very little is known about their protein tertiary structures. We carried out a large-scale analysis of known alternatively spliced variants at both protein sequence and structure levels and have shown that threading is, in general, a viable approach for modeling structures of alternatively spliced variants. An examination of alternative splicing at the protein sequence level revealed that the size of splicing events follows the power law distribution and the majority of splicing isoforms harbor only one or two alternations. We examined alternative splicing in the context of protein 3D structures and found that the boundaries of alternative splicing events generally happen in coil regions of secondary structures and exposed residues and the majority of the sequences involved in splicing are located on the surface of proteins. In light of these findings, we then proceeded to demonstrate that threading represents a useful tool for structure prediction of alternative splicing isoforms and addressed the fold stability issue of threading-based structure prediction by molecular dynamics simulation. Our analysis and the insights gained have helped to establish a viable method for structure prediction of alternatively spliced isoforms at the genome scale.

Alternative Splicing↗

PubMed1999

Genomic structure, 5' flanking sequences, and precise localization in 1P31.1 of the human prostaglandin F receptor gene.

This paper describes the genomic structure of the human Prostaglandin F receptor gene (FP) with its exon-intron borders and 5' flanking sequences. Furthermore, the location of the gene has been localized to a very small region on 1p31.1 using FISH and radiation hybrids analysis. The PGF receptor (FP) is highly expressed in mouse tissues especially in the corpora lutea in ovaries and in the kidney. Recently, it has been shown that homozygous knockout-mice lacking the gene for this receptor are unable to deliver normal fetuses at term. It might be speculated that the lack of the FP gene has the same effect in human as in mouse. Mutation analysis in families with difficulties in parturition would therefore be of high interest. The results presented here provides data necessary for further investigations of the FP gene.

Animals↗

PubMed1996

Isolation, genomic structure, and expression of human erythroid Krüppel-like factor (EKLF).

Erythroid Krüppel-like factor (EKLF) is an essential transcriptional activator that directs high-level expression of the adult beta-globin promoter by binding to its CACCC element, one of a trio of highly conserved sequences present in erythroid cell-specific promoters and enhancers. This report describes the isolation and characterization of the human homolog of murine EKLF. The human EKLF transcription unit shares a number of structural properties with its marine counterpart. Human EKLF is contained within 3 kb of genomic DNA, and its coding region is interrupted by two introns whose locations are conserved with the murine gene. The three zinc fingers share >90% sequence similarity with and are predicted to bind the same target sequence as the mouse EKLF. The rest of the protein is proline-rich and retains approximately 70% sequence similarity to the mouse gene. Human EKLF is expressed in bone marrow and HEL, JK1, and OCIM1 erythroleukemic cell lines but not in K562 nor in myeloid or lymphoid cell lines. These results indicate that the genomic structure and erythroid-restricted expression of EKLF are highly conserved between the murine and human homologues. Availability of human EKLF will enable initiation of studies to molecularly assess whether it is functionally compromised in those cases of beta-thalassemia that contain a normal beta-globin gene locus.

Amino Acid Sequence↗

PubMed1993

cDNA and genomic structures of arrowhead proteinase inhibitors.

Arrowhead double-headed proteinase inhibitors A and B consist of 150 amino acid residues with three disulfide bonds. Based on their primary structures, three cDNA fragments of the inhibitors were amplified in vitro by the PCR method using a constructed arrowhead cDNA library as a template. With the overlapping sequences, the full-length cDNA sequences of the inhibitors were then ascertained. The open reading frame encodes a pre-inhibitor, including a 24 residue signal peptide. The deduced amino acid sequences are consistent in principle with those determined by primary structure analysis, except that there are seven extra residues in the C-terminal part of the inhibitors, which might be cleaved off by proteinase post-processing immediately after protein synthesis. It is worth pointing out that cDNAs of both inhibitors A and B contain an 87 bp intron in the AAG codon of residue Lys-97. According to the elucidated cDNA sequences, the structural genes of inhibitors A and B were amplified using the total cDNA or genomic DNA of arrowhead as a PCR template. It was indicated that both the cDNA and genomic structures of inhibitors A and B have the same sequences.

Amino Acid Sequence↗

PubMed1997

Genomic structures of viral agents in relation to the biosynthesis of selenoproteins.

The genomes of both bacteria and eukaryotic organisms are known to encode selenoproteins, using the UGA codon for seleno-cysteine (SeC), and a complex cotranslational mechanism for SeC incorporation into polypeptide chains, involving RNA stem-loop structures. These common features and similar codon usage strongly suggest that this is an ancient evolutionary development. However, the possibility that some viruses might also encode selenoproteins remained unexplored until recently. Based on an analysis of the genomic structure of the human immunodeficiency virus HIV-1, we demonstrated that several regions overlapping known HIV genes have the potential to encode selenoproteins (Taylor et al. [31], J. Med. Chem. 37, 2637-2654 [1994]). This is provocative in the light of overwhelming evidence of a role for oxidative stress in AIDS pathogenesis, and the fact that a number of viral diseases have been linked to selenium (Se) deficiency, either in humans or by in vitro and animal studies. These include HIV-AIDS, hepatitis B linked to liver disease and cancer, Coxsackie virus B3, Keshan disease, and the mouse mammary tumor virus (MMTV), against which Se is a potent chemoprotective agent. There are also established biochemical mechanisms whereby extreme Se deficiency can induce a proclotting or hemorrhagic effect, suggesting that hemorrhagic fever viruses should also be examined for potential virally encoded selenoproteins. In addition to the RNA stem-loop structures required for SeC insertion at UGA codons, genomic structural features that may be required for selenoprotein synthesis can also include ribosomal frameshift sites and RNA pseudoknots if the potential selenoprotein module overlaps with another gene, which may prove to be the rule rather than the exception in viruses. One such pseudoknot that we predicted in HIV-1 has now been verified experimentally; a similar structure can be demonstrated in precisely the same location in the reverse transcriptase coding region of hepatitis B virus. Significant new findings reported here include the existence of highly distinctive glutathione peroxidase (GSH-Px)-related sequences in Coxsackie B viruses, new theoretical data related to a previously proposed potential selenoprotein gene overlapping the HIV protease coding region, and further evidence in support of a novel frameshift site in the HIV nef gene associated with a well-conserved UGA codon in the 1-reading frame.

Amino Acid Sequence↗

PubMed2003

Mycobacterium tuberculosis: a model system for structural genomics.

Over the past five years, genomics has had a major impact on Mycobacterium tuberculosis research. With the publication of the sequences of two virulent strains (H37Rv and CDC1551) and three closely related sequences, M. tuberculosis is becoming a model system for proteomics and structural genomics initiatives. Together with the promise of structures of proteins with novel folds, high-resolution structures of drug targets are providing the basis for rational inhibitor design, with the goal of the development of novel anti-tuberculars. In addition, this work is aiding scientists in the quest for an effective vaccine against this persistent pathogen.

Animals↗

PubMed2003

Genomic structure of the NtPDR1 gene, harboring the two miniature inverted-repeat transposable elements, NtToya1 and NtStowaway101.

Here we report the genomic structure including the promoter sequence and coding region of NtPDR1 (Nicotiana tabacum Pleiotropic Drug Resistance 1), which is an elicitor-responsive gene encoding an ATP binding cassette (ABC) transporter that might be involved in the defense response in tobacco, as we reported recently. The NtPDR1 gene consists of 20 exons and 19 introns. Among the introns, the first and fifth are much larger than the others and harbor typical miniature inverted-repeat transposable elements (MITEs). One of the MITE elements in the first intron, termed NtToya1, belongs to the Toya family that was recently described in rice, while the other element in the fifth intron, termed NtStowaway101, shows high homology with the Stowaway elements of the IS630-Tc1-mariner family. Many of the genes we found to harbor Toya and Stowaway elements in Nicotiana species by BLAST search are also involved in stress responses or plant-pathogen interactions. The existence of putative cis-elements (a GCC box, three W boxes, and several JA-responsive elements) in the promoter region supports our previous finding that this gene is strongly inducible by elicitation and methyljasmonate, and that this ABC transporter might be essential for plant defense responses. Furthermore, Southern blot analysis and PCR amplification of the introns harboring the MITE-like elements from genomic DNA of three Nicotiana species suggests that NtPDR1 originated from N. sylvestris.

Base Sequence↗

PubMed1995

Rat genomic structure of amidophosphoribosyltransferase, cDNA sequence of aminoimidazole ribonucleotide carboxylase, and cell cycle-dependent expression of these two physically linked genes.

Genomic structure of rat amidophosphoribosyltransferase (ATase; EC 2.4.2.14), which catalyzes the first committed step in de novo purine nucleotide synthesis, was determined by polymerase chain reaction (PCR)-based methods. There are 11 exons and all exon-intron boundaries were conserved among rat, human, and chicken ATase genes. A rat aminoimidazole ribonucleotide carboxylase (AIRC) cDNA encoding a bifunctional enzyme of AIRC (EC 4.1.1.21) at step 6 and SAICAR synthetase (EC 6.3.2.6) at step 7 in de novo purine nucleotide synthesis was cloned and sequenced. The size of the cloned rat AIRC cDNA was 1329 bp, and amino acid identity with human and chicken AIRC was 96 and 85%, respectively. The intergenic sequence using a phage clone and the PCR product disclosed that ATase and AIRC genes are physically linked with the 736 bp sequence between the translation start sites, and the determination of the transcriptional start sites by the primer extension assay for these genes disclosed that distance between the two major transcriptional start sites is 585 bp. The amount of mRNAs of both genes showed approx. 5-6-fold increase in G1/S phase of the cell cycle over those in G0 phase in synchronized rat 3Y1 fibroblasts.

Amidophosphoribosyltransferase↗

PubMed2002

Genomic structure, organization, and promoter region analysis of murine guanylyl cyclase/atrial natriuretic peptide receptor-A gene.

We have determined the complete genomic nucleotide sequence and analyzed the promoter region of murine guanylyl cyclase/natriuretic peptide receptor-A gene (Npr1,coding for NPRA). The gene spans about 17.8 kb and contains 22 exons interrupted by 21 introns. All the exon-intron boundaries possess the consensus GT/AG splice junctions. Four different types of short interspersed nuclear elements (ten mouse B1 elements, seven mouse B2-B4 elements, one ID and one MIR element) and one medium reiteration frequency repeats have been found in the non-coding regions of the gene. Eleven tandem repeats, including three in the promoter region of the gene, have been identified. The transcription start site, 362 bp upstream from the start codon, was determined by 5'- rapid amplification of cDNA ends. The 1.98 kb 5'-flanking region contains three potential SP1 binding sites and one inverted CCAAT box but lacks the TATA box. This region also contains several putative cis-acting motifs known to bind kidney specific nuclear protein HFH-3, cAMP-responsive element binding protein (CREB) and AP-4. In addition, the binding sites for a variety of transcription factors: AML-1 alpha, SRY, Nkx-2.5, LyF-1, p300, GATA-1/2, HNF-3 beta, c/EBP alpha/beta and USF have been localized in the promoter region of Npr1 gene. The analyses and characterization of the genomic structure of murine Npr1 gene should yield important insights into the species-specific regulation of this important gene family.

5' Flanking Region↗

PubMed2005

Plastid genome structure and loss of photosynthetic ability in the parasitic genus Cuscuta.

The genus Cuscuta (dodder) is composed of parasitic plants, some species of which appear to be losing the ability to photosynthesize. A molecular phylogeny was constructed using 15 species of Cuscuta in order to assess whether changes in photosynthetic ability and alterations in structure of the plastid genome relate to phylogenetic position within the genus. The molecular phylogeny provides evidence for four major clades within Cuscuta. Although DNA blot analysis showed that Cuscuta species have smaller plastid genomes than tobacco, and that plastome size varied significantly even within one Cuscuta clade, dot blot analysis indicated that the dodders possess homologous sequence to 101 genes from the tobacco plastome. Evidence is provided for significant rates of DNA transfer from plastid to nucleus in Cuscuta. Size and structure of Cuscuta plastid genomes, as well as photosynthetic ability, appear to vary independently of position within the phylogeny, thus supporting the hypothesis that within Cuscuta photosynthetic ability and organization of the plastid genome are changing in an unco-ordinated manner.

Cuscuta↗