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Results for “Functional Genomics”

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At least 1,279 records · Page 71Linked to original sources
PubMed2001

Genomic and functional characteristics of novel human pancreatic 2P domain K(+) channels.

We isolated three novel 2P domain K(+) channel subunits from human. The first two subunits, TALK-1 and TALK-2, are distantly related to TASK-2. Their genes form a tight cluster of 25 kb on chromosome 6p21.1-p21.2. The corresponding channels produce quasi-instantaneous and non-inactivating currents that are activated at alkaline pHs. These currents are sensitive to Ba(2+), quinine, quinidine, chloroform, halothane, and isoflurane but are not affected by TEA, 4-AP, Cs(+), arachidonic acid, hypertonic solutions, agents activating protein kinases C and A, changes of internal Ca(2+) concentrations, and by activation of G(i) and G(q) proteins. TALK-1 is exclusively expressed in the pancreas. TALK-2 is mainly expressed in the pancreas, but is also expressed at a lower level in liver, placenta, heart, and lung. We also cloned a third subunit, named hTHIK-2 which is present in many tissues with high levels again in the pancreas but which could not be functionally expressed.

Amino Acid Sequence↗
PubMed2001

High-throughput yeast two-hybrid assays for large-scale protein interaction mapping.

Protein-protein interactions play fundamental roles in many biological processes. Hence, protein interaction mapping is becoming a well-established functional genomics approach to generate functional annotations for predicted proteins that so far have remained uncharacterized. The yeast two-hybrid system is currently one of the most standardized protein interaction mapping techniques. Here, we describe the protocols for a semiautomated, high-throughput, Gal4-based yeast two-hybrid system.

Culture Media↗
PubMed1996

Molecular cloning and structural analysis of the functional mouse genomic XPG gene.

The mouse XPG gene is a homolog of the human DNA excision repair gene known to be defective in the hereditary sun-sensitive disorder xeroderma pigmentosum (group-G). Defects in mouse XPG have been shown to directly affect the sensitivity of cultured cells to chemotherapy agents and may play a role in tumor cell drug resistance in vivo. A full-length cosmid clone of mouse XPG was isolated by complementation of the UV sensitivity and repair defect in CHO-UV135 cells. Exon mapping determined that the gene consisted of 15 exons within 32 kb of genomic DNA. Sequencing of intron-exon boundaries revealed that mouse XPG possesses a rare class of intron previously identified in only four other eukaryotic genes; it utilizes AT and AC dinucleotides instead of the expected GT and AG within the splice junctions. Promoter analysis determined that mouse XPG is expressed constitutively and probably initiates transcription from multiple start sites, yet, unlike the yeast homolog RAD2, we found no evidence that it is UVC inducible in cultured cells. Amino acid comparison with human XPG identified a highly conserved acidic region of homology not previously described.

Amino Acid Sequence↗
PubMed2005

Study of tissue-specific CpG methylation of DNA in extended genomic loci.

Modern approaches for studies on genome functioning include investigation of its epigenetic regulation. Methylation of cytosines in CpG dinucleotides is an inherited epigenetic modification that is responsible for both functional activity of certain genomic loci and total chromosomal stability. This review describes the main approaches for studies on DNA methylation. Under consideration are site-specific approaches based on bisulfite sequencing and methyl-sensitive PCR, whole-genome approaches aimed at searching for new methylation hot spots, and also mapping of unmethylated CpG sites in extended genomic loci.

Animals↗
PubMed1991

Vitamin D binding protein: genomic structure, functional domains, and mRNA expression in tissues.

The vitamin D binding protein (DBP), alternatively known as Gc-globulin, is a member of the albumin (ALB) and alpha-fetoprotein (AFP) gene family. The rat DBP gene is expressed at high levels in liver and at moderate levels in kidney, testis, abdominal fat, and yolk sac. Very low levels of DBP as well as ALB and AFP transcripts can be detected in all other tissues studied by the reverse transcriptase/polymerase chain reaction technique. During development, liver DBP gene transcripts are detectable at 14 days of gestation and levels rise gradually until adulthood in parallel with ALB. DBP present on the surface of U937 monocyte-derived cells is acquired from serum, suggesting cell surface binding sites for DBP. The rat DBP gene has been cloned and characterized. It spans 35 kb and contains 13 exons and 12 introns. The DBP gene contains two fewer exons than the ALB or AFP genes, accounting for the shortest size of its mRNA and protein product. Its 5'-flanking region contains a high degree of structural similarity to both ALB and AFP promoters.

Amino Acid Sequence↗
PubMed2005

New paradigms in cardiovascular medicine: emerging technologies and practices: perioperative genomics.

Considerable progress has been made in understanding the pathophysiology of perioperative stress responses and their impact on the cardiovascular system; however, researchers are just beginning to unravel genetic and molecular determinants that predispose to increased risk for postoperative cardiovascular adverse events. A new field, coined perioperative genomics, aims to apply functional genomic approaches to uncover the biological reasons why similar patients can have dramatically different clinical outcomes after surgery. For the perioperative physician, such findings may soon translate into prospective risk assessment incorporating genomic profiling of markers important in inflammatory, thrombotic, vascular, and neurologic responses to perioperative stress, with implications ranging from individualized additional pre-operative testing and physiological optimization, to perioperative decision-making, choice of monitoring strategies, and critical care resource utilization. We review current knowledge regarding genomic technologies in perioperative cardiovascular disease characterization and outcome prediction, as well as discuss future trends/challenges for translating integrated "omic" information into daily clinical management of the surgical patient.

Animals↗
PubMed2006

Structure meets function--centrosomes, genome maintenance and the DNA damage response.

Centrosomes are cytoplasmic organelles playing a fundamental role in organizing both the interphase cytoskeleton and the bipolar mitotic spindle. In addition, the centrosome has recently come into focus as part of the network that integrates cell cycle arrest and repair signals in response to genotoxic stress--the DNA damage response. One important mediator of this response, the checkpoint kinase Chk1, has been shown to negatively regulate the G(2)/M transition via its centrosomal localization. Moreover, there is growing evidence that a centrosome inactivation checkpoint exists, which utilizes DNA damage-induced centrosome fragmentation or amplification to provoke a "mitotic catastrophe" and eliminate damaged cells. Candidate regulators of this centrosomal checkpoint include the checkpoint kinase Chk2 and its upstream regulators ATM and ATR. In addition, a growing number of other proteins have been implicated in centrosomal regulation of the DNA damage response, e.g. the tumor suppressor p53, the breast cancer susceptibility gene product BRCA1 and mitotic regulators such as Aurora A, Nek2 and the Polo-like kinases Plk1 and Plk3. However, many missing links and discrepancies between different model systems remain.

Animals↗
PubMed1999

Murine 12(R)-lipoxygenase: functional expression, genomic structure and chromosomal localization.

A cDNA, recently cloned (by Krieg et al. (1998)) from mouse skin, was shown to encode a 12(R)-lipoxygenase. When expressed in HEK cells, the recombinant protein converted methyl arachidonate into the corresponding 12-HETE ester which was shown to be the R-enantiomer by chiral phase chromatography. Neither arachidonic acid nor linoleic acid were substrates for the recombinant protein. The structure of the 12(R)-lipoxygenase gene is unique among all animal lipoxygenases in that it is divided into 15 exons and 14 introns spanning approximately 12.5 kb. By interspecific backcross analysis, the 12(R)-lipoxygenase gene was localized to the central region of mouse chromosome 11.

Animals↗
PubMed2000

Natural selection and the function of genome imprinting: beyond the silenced minority.

Most hypotheses of the evolutionary origin of genome imprinting assume that the biochemical character on which natural selection has operated is the expression of the allele from only one parent at an affected locus. We propose an alternative - that natural selection has operated on differences in the chromatin structure of maternal and paternal chromosomes to facilitate pairing during meiosis and to maintain the distinction between homologues during DNA repair and recombination in both meiotic and mitotic cells. Maintenance of differences in chromatin structure in somatic cells can sometimes result in the transcription of only one allele at a locus. This pattern of transcription might be selected, in some instances, for reasons that are unrelated to the original establishment of the imprint. Differences in the chromatin structure of homologous chromosomes might facilitate pairing and recombination during meiosis, but some such differences could also result in non-random segregation of chromosomes, leading to parental-origin-dependent transmission ratio distortion. This hypothesis unites two broad classes of parental origin effects under a single selective force and identifies a single substrate through which Mendel's first and second laws might be violated.

Animals↗
PubMed2002

Molecular, functional, and genomic characterization of human KCC2, the neuronal K-Cl cotransporter.

The expression level of the neuronal-specific K-Cl cotransporter KCC2 (SLC12A5) is a major determinant of whether neurons will respond to GABA with a depolarizing, excitatory response or a hyperpolarizing, inhibitory response. In view of the potential role in human neuronal excitability we have characterized the hKCC2 cDNA and gene. The 5.9 kb hKCC2 transcript is specific to brain, and is induced during in vitro differentiation of NT2 teratocarcinoma cells into neuronal NT2-N cells. The 24-exon SLC12A5 gene is on human chromosome 20q13, and contains a polymorphic dinucleotide repeat within intron 1 near a potential binding site for neuron-restrictive silencing factor. Expression of hKCC2 cRNA in Xenopus laevis oocytes results in significant Cl(-)-dependent (86)Rb(+) uptake under isotonic conditions; cell swelling under hypotonic conditions causes a 20-fold activation, which is blocked by the protein phosphatase inhibitor calyculin-A. In contrast, oocytes expressing mouse KCC4 do not mediate isotonic K-Cl cotransport but express much higher absolute transport activity than KCC2 oocytes under hypotonic conditions. Initial and steady state kinetics of hKCC2-injected oocytes were performed in both isotonic and hypotonic conditions, revealing K(m)s for K(+) and Cl(-) of 9.3+/-1.8 mM and 6.8+/-0.9 mM, respectively; both affinities are significantly higher than KCC1 and KCC4. The K(m) for Cl(-) is close to the intracellular Cl(-) activity of mature neurons, as befits a neuronal efflux mechanism.

Amino Acid Sequence↗
PubMed2000

Characterization of the hCTR1 gene: genomic organization, functional expression, and identification of a highly homologous processed gene.

The human hCTR1 gene was originally identified by its ability to complement a yeast mutant deficient in high-affinity copper uptake (Zhou, B., Gitschier, J., 1997. A human gene for copper uptake identified by complementation in yeast. Proc. Natl. Acad. Sci. USA 94, 7481-7486). Here, we have determined the DNA sequence of the exon-intron borders of the hCTR1 structural gene and report that the coding sequence is disrupted by three introns, all of which comply with the GT/AG rule. Furthermore, human fibroblasts, transfected with hCTR1 cDNA, were shown to have a dramatically increased capacity for (64)Cu uptake, indicating that the hCtr1 protein is functional in copper uptake in human cells. In contrast, no evidence was found for involvement of the hCTR2 gene product in copper uptake. Finally, we have identified a highly homologous processed pseudogene, hCTR1psi, which was localized to chromosome 3q25/26. The processed gene was found to be transcribed, but due to a frame shift mutation, it only had the potential to encode a truncated protein of 95 amino acid residues, and cells transfected with hCTR1psi DNA showed no increase of (64)Cu uptake.

Amino Acid Sequence↗
PubMed2003

Histone and chromatin cross-talk.

Chromatin is the physiologically relevant substrate for all genetic processes inside the nuclei of eukaryotic cells. Dynamic changes in the local and global organization of chromatin are emerging as key regulators of genomic function. Indeed, a multitude of signals from outside and inside the cell converges on this gigantic signaling platform. Numerous post-translational modifications of histones, the main protein components of chromatin, have been documented and analyzed in detail. These 'marks' appear to crucially mediate the functional activity of the genome in response to upstream signaling pathways. Different layers of cross-talk between several components of this complex regulatory system are emerging, and these epigenetic circuits are the focus of this review.

Animals↗
PubMedDate not supplied

The X chromosome and the ovary.

X chromosome abnormalities are the leading identifiable cause of premature ovarian failure (POF). POF-related abnormalities range from the complete absence of one X chromosome to assorted deletions and translocations to mutations in specific genes. The diversity of X chromosome abnormalities associated with POF indicates that the disorder is genetically heterogeneous. Potential molecular mechanisms include both dominant and recessive mutations in X-linked genes as well as nonspecific chromosome effects that impair meiosis. A list of candidate X-linked POF genes is emerging from molecular studies of X chromosome abnormalities, data from the Human Genome Project and related functional genomics projects, and the results of gene targeting experiments in mice. Mutational analysis of candidate genes in a large number of women with idiopathic POF is needed to determine which of these genes contribute to the cause of this disorder.

Female↗