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Results for “structural genomics”

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At least 469 records · Page 26Linked to original sources

PubMed1999

Genomic structure, chromosomal mapping, and expression pattern of human DCAMKL1 (KIAA0369), a homologue of DCX (XLIS).

Human DCAMKL1, also known as KIAA0369, is a homologue of DCX (Xq22. 3), a gene associated with X-linked lissencephaly and subcortical band heterotopia. This suggests that DCAMKL1 may play a role in neuronal migration. The gene also shows similarity to Ca2+/calmodulin-dependent protein kinases. We have determined its genomic structure, regional mapping, and expression pattern in human tissues. DCAMKL1 consists of at least 18 exons ranging from 58 to 3359 bp in length. We have characterized the exon/intron borders, and primers were designed to amplify each individual exon for mutation analysis. DCAMKL1 was mapped to chromosome 13q13 by fluorescence in situ hybridization. Northern blot analysis showed DCAMKL1 to be predominantly expressed in human fetal brain as a major transcript of about 5.8 kb.

Brain↗

PubMed2006

Genomic structure and gene order of swine chromosome 7q1.1-->q1.2.

To clarify the structure of the porcine genomic region that contains quantitative trait loci (QTL) related to fat, we constructed a bacterial artificial chromosome (BAC) contig of the region from DST to SRPK1 on porcine chromosome 7 and performed low-redundancy 'skim' shotgun sequencing of the clones that composed a minimum tiling path of the contig. This analysis revealed that the gene order from VPS52 to SRPK1 is conserved between human and swine and that comparison with the human sequence identified a rearrangement in the swine genome at the proximal end of VPS52. Analysis of the nucleotide sequences of three BAC clones that included the rearrangement point demonstrated that COL21A1 and DST, which were not present in the corresponding human region, were located adjacent to the rearrangement point. These results provide useful information about the genomic region containing QTL for fat in pigs and help to clarify the structure of the so-called 'extended-class II' region distal to the porcine major histocompatibility complex class II region.

Adipose Tissue↗

PubMed2002

Genomic structure and embryonic expression of estrogen receptor beta a (ERbetaa) in zebrafish (Danio rerio).

Estrogenic steroid hormones mediate complex actions important in both embryonic and adult life. The hormones signal through ligand-inducible transcription factors known as estrogen receptors (ERs). In this study, we have isolated a zebrafish estrogen receptor with homology to human estrogen receptor beta (ERbeta). This zebrafish ERbeta (ERbetaa) has a conserved genomic structure of eight coding exons with boundaries similar to those of human ERbeta. The coding exon structures of two other zebrafish estrogen receptors (ERalpha and ERbetab) are presented as well. We also analyzed 3.3 kb of the promoter region and identified numerous putative transcription factor binding sites, including SP1 and ER half sites. Zebrafish ERbetaa message RNA is maternally loaded, but quickly degraded after fertilization, as detected by reverse transcriptase polymerase chain reaction. ERbetaa transcripts are detected again between 24 and 48 h post fertilization. These results indicate that ERbeta has been highly conserved during evolution and is likely used during later embryogenesis in zebrafish. Future identification of the expression levels and patterns of this and other estrogen receptors in zebrafish will allow a better understanding of estrogen signaling during embryogenesis.

Amino Acid Sequence↗

PubMed1999

Cloning of the cyclin A1 genomic structure and characterization of the promoter region. GC boxes are essential for cell cycle-regulated transcription of the cyclin A1 gene.

Cyclin A1 is a recently cloned cyclin with high level expression in meiotic cells in the testis. However, it is also frequently expressed at high levels in acute myeloid leukemia. To elucidate the regulation of cyclin A1 gene expression, we cloned and analyzed the genomic structure of cyclin A1. It consists of 9 exons within 13 kilobase pairs. The TATA-less promoter initiates transcription from several start sites with the majority of transcripts beginning within a 4-base pair stretch. A construct containing a fragment from -190 to +145 showed the highest transcriptional activity. Transfection of cyclin A1 promoter constructs into S2 Drosophila cells demonstrated that Sp1 is essential for the activity of the promoter. Sp1, as well as Sp3, bound to four GC boxes between nucleotides -130 and -80 as observed by gel shift analysis. Mutations in two or more of the four GC boxes decreased promoter activity by >80%. The promoter was found to be cell cycle-regulated with highest activities found in late S and G2/M phase. Further analyses suggested that cell cycle regulation was accomplished by periodic repression of the GC boxes in G1 phase. Taken together, our data show that cyclin A1 promoter activity critically depends on four GC boxes, and members of the Sp1 family appear to be involved in directing expression of cyclin A1 in both a tissue- and cell cycle-specific manner.

Base Sequence↗

PubMed1995

Genomic structure, expression and mutational analysis of the P15 (MTS2) gene.

The P15 gene (MTS2) encodes a cyclin-dependent kinase (CDK) inhibitor with considerable sequence identity and biochemical similarity to the CDK inhibitor p16. It is closely linked to the P16 gene (MTS1) and is homozygously deleted in many tumor cell lines. These features suggest that p15 may be a tumor suppressor. We have determined the genomic structure of P15 and examined its pattern of mRNA expression. In addition, we have shown that ectopic expression of p15 inhibits growth of tumor-derived cell lines. We have also searched for P15 mutations in tumor cell lines and in 9p21-linked melanoma kindreds. Other than the previously described homozygous deletions, no mutations of P15 were found. Collectively, these observations suggest a role for p15 in growth regulation, but a limited role for p15 in tumor progression.

Base Sequence↗

PubMed1998

Determination of the genomic structure of the COL4A4 gene and of novel mutations causing autosomal recessive Alport syndrome.

Autosomal recessive Alport syndrome is a progressive hematuric glomerulonephritis characterized by glomerular basement membrane abnormalities and associated with mutations in either the COL4A3 or the COL4A4 gene, which encode the alpha3 and alpha4 type IV collagen chains, respectively. To date, mutation screening in the two genes has been hampered by the lack of genomic structure information. We report here the complete characterization of the 48 exons of the COL4A4 gene, a comprehensive gene screen, and the subsequent detection of 10 novel mutations in eight patients diagnosed with autosomal recessive Alport syndrome. Furthermore, we identified a glycine to alanine substitution in the collagenous domain that is apparently silent in the heterozygous carriers, in 11.5% of all control individuals, and in one control individual homozygous for this glycine substitution. There has been no previous finding of a glycine substitution that is not associated with any obvious phenotype in homozygous individuals.

Alanine↗

PubMed1996

Genomic structure of HOXD13 gene: a nine polyalanine duplication causes synpolydactyly in two unrelated families.

Synpolydactyly (SPD) is a limb malformation that shows a characteristic manifestation in both hands and feet. This condition is inherited as an autosomal dominant trait with reduced penetrance. We have recently mapped this locus centromeric to the HOXD8 intragenic marker and suggested the HOXD13 gene as a potential candidate for this condition. The genomic structure of HOXD13 established in this study consists of two exons that encodes a polypeptide of 335 amino acids. The downstream exon at the 3' end of this gene contains the homeodomain sequences that are highly conserved. Sixty-three bp upstream of this exon lies a stretch of intronic CA-repeats that proved to be polymorphic in two different populations. The upstream exon encodes 75% of the entire protein and contains a stretch of 15 normal alanines at its 5' end. Sequence comparison at this position in the homozygous affected individuals identified a total of 24 alanine residues that resulted from a duplication of nine polyalanines. In two unrelated SPD families, this duplication was directly transmitted from the affected parents to their affected, but not unaffected, offspring; in one family its size has remained constant for at least 150 years spanning over seven generations. The presence of this duplication confirmed the status of four normal gene carriers, one incomplete penetrance and two affected individuals who were recombinants for HOXD8 or HOXD13-CA repeat markers. This duplication was not present in 150 chromosomes of unrelated healthy subjects of two different populations.

Adolescent↗

PubMed1999

Human TRH-degrading ectoenzyme cDNA cloning, functional expression, genomic structure and chromosomal assignment.

Thyrotropin-Releasing Hormone (TRH) is an important extracellular signal substance that acts as a stimulator of hormone secretion from adenohypophyseal target cells and fulfills many criteria for the function of a neuromodulator/neurotransmitter within the central and peripheral nervous systems. The inactivation of TRH-signals is catalysed by a highly specific ectoenzyme. Here, we characterize the human TRH-degrading ectoenzyme (TRH-DE) by primary sequence, functional expression, genomic structure and chromosomal assignment. By screening a cDNA-library constructed from human lung, 5.7 kb of cDNA were identified. The longest open reading frame predicts a type II integral membrane protein of 117 kDa. The extracellular domain contains the HEXXH + E motif that is characteristic of a certain family of Zn-dependent aminopeptidases. Within this family, the sequences of human and rat TRH-DE reveal an unusual high degree of conservation (96% identical residues). Specific enzymatic activity was observed after transfecting COS-7 cells with human TRH-DE cDNA yielding a Km for TRH hydrolysis of 29.7 microM. Northern blot analysis demonstrated a restricted tissue distribution with highest transcript levels in the brain. Using fluorescent in situ hybridization with the cDNA and a genomic lambda clone, respectively, we localized the TRH-DE gene to the long arm of human chromosome 12. Five independent P1 artificial chromosome clones were required to span the complete cDNA sequence and revealed that it is distributed on 19 exons. Interspecies Southern analysis suggests that the gene is present as a single copy in human, monkey, rat, mouse, dog, bovine, rabbit and chicken DNA. All of these data further the notion that the TRH-DE is not an ordinary enzyme but a specific neuropeptidase that has been highly conserved among species.

Amino Acid Sequence↗

PubMed1996

Genomic structure of the human D-site binding protein (DBP) gene.

The human gene for the D-Site Binding Protein (DBP) has been sequenced and characterized. This gene is a member of the b/ZIP family of transcription factors and is one of three genes forming the PAR subfamily. DBP has been implicated in the diurnal regulation of a variety of liver-specific genes. Examination of the genomic structure of DBP reveals that the gene is divided into four exons and is contained within a relatively compact region of approximately 6 kb. These exons appear to correspond to functional divisions of the DBP protein. Exon 1 contains a long 5' UTR, and conservation between the rat and the human genes of the presence of small open reading frames within this region suggests that it may play a role in translational control. Exon 2 contains a limited region of similarity to the other PAR domain genes, which may be part of a potential activation domain. Exon 3 contains the PAR domain and differs by only 1 of 71 amino acids between rat and human. Exon 4, containing both the basic and the leucine zipper domains, is likewise highly conserved. The overall degree of homology between the rat and the human cDNA sequences is 82% for the nucleic acid sequence and 92% for the protein sequence. Comparison of the rat and human proximal promoters reveals extensive sequence conservation, with two previously characterized DNA binding sites being conserved at the functional and sequence levels.

Amino Acid Sequence↗

PubMed1998

Genomic structure of the human Smad3 gene and its infrequent alterations in colorectal cancers.

The Smad3 gene is a member of the Smad family, vertebrate homologues of Drosophila Mad, and its gene product is a cytoplasmic element in the TGF-beta signaling pathway. Smad2 and Smad4/DPC4, other members of the Smad family, are possibly tumor suppressor genes because alterations of these genes occurred in various carcinomas. We determined the genomic structure of human Smad3 which consists of nine exons. Then we examined whether or not Smad3 gene mutations exist in sporadic and hereditary non-polyposis colorectal cancers and found no mutations in the entire coding region in 50 cancers. Loss of heterozygosity of Smad3 was observed in two of the 17 (11.8%) informative cases using a polymorphism found in intron 2. These findings suggest that the Smad3 gene may not play an important role in the tumorigenesis of colorectal cancers.

Base Sequence↗

PubMed1993

Genomic structure of the POU-related hepatic transcription factor HNF-1 alpha.

Hepatocyte Nuclear Factor-1 alpha (HNF-1 alpha) is a vertebrate transcriptional regulatory protein which plays a prominent role in the activation of a large family of hepatocyte-specific genes. It is the prototype of a new subfamily of POU-related proteins important in embryogenesis and cell-type specification. Here we report on the genomic structure and DNA sequence of HNF-1 alpha of the hen. Functional domains are non-uniformly conserved between hen and mammals consistent with the notion of functions in the hen oviduct that were lost in mammals after avian mammalian separation. The unusual homeo-related DNA-binding domain is well preserved between birds and mammals. The exon/intron pattern of the gene changed during evolution. The rat gene consists of 9 exons, the chicken gene of 10. In mammals one intron was eliminated that in hens subdivides the serine-rich transactivation domain. Comparison of the sequences at this junction indicates the involvement of elements of the V(D)J recombination system in the process of intron elimination.

Amino Acid Sequence↗

PubMed2000

Genomic structure and characterisation of the promoter region of the human IL-18 gene.

Interleukin (IL)-18 is a cytokine that plays an important role in the T helper (Th) 1 response, primarily by its ability to induce gamma interferon (IFN-gamma) production by T cells and Natural Killer (NK) cells. It also plays a role in host resistance to infection and in Lipopolysaccharides (LPS)-induced histopathology. By a direct sequencing on P1 Artificial Chromosomes (PAC) clones, we have determined the genomic structure and the promoter region of the human IL-18 gene. The IL-18 gene spans approximately 20 Kb and consists of 6 exous. The 5'-flanking regions of human IL-18 and mouse IL-18 show 75% homology suggesting conserved promoter regulatory factors.

Animals↗

PubMed1994

Genomic structure of the candidate proto-oncogene BCL3.

We previously reported the identification of a novel candidate proto-oncogene involved in the translocation t(14;19)(q32;q13) found in some cases of human B-cell chronic lymphocytic leukemia. This gene, BCL3, is a member of the I kappa B family, whose encoded proteins regulate the NF-kappa B family of transcription factors. Here we describe the genomic structure of BCL3. The gene contains nine exons, spanning 11.5 kb. In comparison to other members of the I kappa B family, there is a remarkable conservation of the exon-intron boundaries in relation to the coding sequences, consistent with an origin from a common ancestral gene. BCL3 is unusual in containing two CpG islands, a 5' island encompassing the first exon, the other lying within the gene. Southern blot analysis using methylation-sensitive restriction enzymes revealed that while the 5' CpG is unmethylated in all tissues tested, the degree of methylation of the internal CpG island varies.

Amino Acid Sequence↗

PubMed2002

Genomic structure of newly identified paralogue of RNA helicase II/Gu: detection of pseudogenes and multiple alternatively spliced mRNAs.

RNA helicase II/Gu (RH-II/Gu or DDX21) is a DEAD-box enzyme that localizes to the nucleoli and may be involved in ribosomal RNA synthesis or processing. It has two paralogues, RH-II/Gualpha and RH-II/Gubeta, both genes of which are on chromosome 10. Their similar genomic structures suggest the two genes arose by gene duplication. Both genes are expressed at higher levels in some normal human tissues compared to matching tumor tissues. Pseudogenes for RH-II/Gubeta exist on chromosomes 2, 3 and 4. No pseudogene was identified for RH-II/Gualpha. Both exon inclusion and exon skipping were found to post-transcriptionally regulate RH-II/Gubeta gene expression. No alternative splicing was identified for RH-II/Gualpha. Overall, the results suggest that the two paralogues of RH-II/Gu arose by gene duplication but the resulting genes are differentially regulated.

3T3 Cells↗

PubMed1996

Characterization of the genomic structure of the mouse APLP1 gene.

Amyloid beta protein (beta A4), the major component of the core of amyloid plaques in Alzheimer disease, is derived from the transmembrane amyloid precursor proteins (APPs). Our recent studies showed that a murine member of the evolutionarily conserved APP family, amyloid precursor-like protein 1 (APLP1), is specifically localized to the cerebral cortex postsynaptic density and may thus participate in brain synaptic function. To investigate regulatory mechanisms of APLP1 synthesis at the genomic level, we isolated and characterized genomic clones containing the mouse APLP1 gene. Sequence analysis revealed a genomic structure consisting of 17 exons and a promoter region that is devoid of apparent TATA and CCAAT boxes. The 5' region contains putative binding sites for AP-1, heat-shock protein, and Sp1, suggesting that multiple elements are potentially involved in regulating transcription of the APLP1 gene.

Alzheimer Disease↗

PubMed2002

Refinement of the genomic structure of STX1A and mutation analysis in nondeletion Williams syndrome patients.

Williams syndrome (WS) is a contiguous gene deletion disorder in which the commonly deleted region contains at least 17 genes. One of these genes, Syntaxin 1A (STX1A), codes for a protein that is highly expressed in the nervous system and is essential for the docking of synaptic vesicles with the presynaptic plasma membrane. In this study, we refine the complete genomic structure of the human STX1A gene by direct sequencing and primer walking of bacterial artificial chromosome (BAC) clones and show that STX1A contains at least 10 exons and 9 introns. The length of exons range from 27 bp to 138 bp and all splice sites conform to the GT-AG rule. Investigation of the STX1A gene sequence in five WS patients without detectable deletions did not identify any point mutations. Although the regulatory elements that control STX1A transcription were not examined, these results do not support a role for STX1A in the WS phenotype.

Adolescent↗

PubMed2001

Genomic structure and insulin-mediated repression of the aquaporin adipose (AQPap), adipose-specific glycerol channel.

Aquaporin adipose (AQPap) is a putative glycerol channel in adipocytes (Kishida, K., Kuriyama, H., Funahashi, T., Shimomura, I., Kihara, S., Ouchi, N., Nishida, M., Nishizawa, H., Matsuda, M., Takahashi, M., Hotta, K., Nakamura, T., Yamashita, S., Tochino, Y., and Matsuzawa, Y. (2000) J. Biol. Chem. 275, 20896-20902). In the current study, we examined the genomic structure of the mouse AQPap gene and its regulation by insulin. The mouse AQPap gene spanned 12 kilobase pairs in chromosome 4 and consisted of 8 exons and 7 introns. The first two exons, designated exon 1 and exon 1', are alternatively spliced to common exon 2, and thus the AQPap gene possessed two potential promoters. The exon 1-derived transcript is dominant in both adipose tissues and adipocytes on the basis of RNase protection assay and promoter analysis. The mRNA increased after fasting and decreased with refeeding. Insulin deficiency generated by streptozotocin enhanced the mRNA in adipose tissue. Insulin down-regulated AQPap mRNA in 3T3-L1 adipocytes. The AQPap promoter contained heptanucleotide sequences, TGTTTTT at -443/-437, similar to the insulin-response element identified previously in the promoters of insulin-repressed genes. Deletion and single base pair substitution analysis of the promoter revealed that these sequences were required for insulin-mediated repression of AQPap gene transcription. The phosphatidylinositol 3-kinase pathway was involved in this inhibition. We conclude that insulin represses the transcription of AQPap gene via insulin response element in its promoter. Sustained up-regulation of AQPap mRNA in adipose tissue in the insulin-resistant condition may disturb glucose homeostasis by increasing plasma glycerol.

3T3 Cells↗

PubMed2006

Genomic structure, promoter analysis, and expression of the porcine (Sus scrofa) Mx1 gene.

Allelic polymorphisms at the mouse Mx1 locus affect the probability of survival after experimental influenzal disease, raising the possibility that marker-assisted selection using the homologous locus could improve the innate resistance of pigs to natural influenza infections. Several issues need to be resolved before efficient large scale screening of the allelic polymorphism at the porcine (Sus scrofa) Mx1 locus can be implemented. First, the Mx1 genomic structure has to be established and sufficient flanking intronic sequences have to be gathered to enable simple PCR amplification of the coding portions of the gene. Then, a basic knowledge of the promoter region needs to be obtained as an allelic variation there can significantly alter absolute levels and/or tissue-specificity of MX protein expression. The results gathered here show that the porcine Mx1 gene and promoter share the major structural and functional characteristics displayed by their homologs described in cattle, mouse, chicken, and man. The crucial function of the proximal interferon-sensitive response elements motif for gene expression is also demonstrated. The sequence data compiled here will allow an extensive analysis of the polymorphisms present among the widest spectrum possible of porcine breeds with the aim to identify an Mx1 allele providing antiviral resistance.

Amino Acid Sequence↗