Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “ENCODE”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources
PubMed2001

Role of exon 2-encoded beta -domain of the von Hippel-Lindau tumor suppressor protein.

Sporadic clear cell renal carcinomas frequently harbor inactivating mutations in exon 2 of the von Hippel-Lindau (VHL) tumor suppressor gene. Here, we examine the effect of the loss of exon 2-encoded beta-domain function on VHL biochemical properties. Exon 2-encoded residues are required for VHL-mediated NEDD8 conjugation on cullin-2 and assembly with hypoxia-inducible factor alpha (HIFalpha) and fibronectin. These residues are not essential for VHL ability to assemble with elongin BC/cullin-2, to display E3 ubiquitin ligase activity in vitro and to confer energy-dependent nuclear import properties to a reporter protein. Localization studies in HIF-1alpha-null embryonic cells suggest that exon 2-encoded beta-domain mediates transcription-dependent nuclear/cytoplasmic shuttling of VHL independently of assembly with HIF-1alpha and oxygen concentration. Exon 3-encoded alpha-helical domain is required for VHL complex formation with BC/cullin-2 and E3 ubiquitin ligase activity, for binding to HIFalpha/fibronectin, but this domain is not essential for transcription-dependent nuclear/cytoplasmic trafficking. VHL(-/-) renal carcinoma cells expressing beta-domain mutants failed to produce an extracellular fibronectin matrix and to degrade HIFalpha, which accumulated exclusively in the nucleus of normoxic cells. These results demonstrate that exon 2-encoded residues are involved in two independent functions: substrate protein recognition and transcription-dependent nuclear/cytoplasmic trafficking. They also suggest that beta-domain mutations inactivate VHL function differently than alpha-domain mutations, potentially providing an explanation for the relationship between different mutations of the VHL gene and clinical outcome.

Adenoviridae↗
PubMed2000

Subunit II of cytochrome c oxidase in Chlamydomonad algae is a heterodimer encoded by two independent nuclear genes.

The mitochondrial genomes of Chlamydomonad algae lack the cox2 gene that encodes the essential subunit COX II of cytochrome c oxidase. COX II is normally a single polypeptide encoded by a single mitochondrial gene. In this work we cloned two nuclear genes encoding COX II from both Chlamydomonas reinhardtii and Polytomella sp. The cox2a gene encodes a protein, COX IIA, corresponding to the N-terminal portion of subunit II of cytochrome c oxidase, and the cox2b gene encodes COX IIB, corresponding to the C-terminal region. The cox2a and cox2b genes are located in the nucleus and are independently transcribed into mRNAs that are translated into separate polypeptides. These two proteins assemble with other cytochrome c oxidase subunits in the inner mitochondrial membrane to form the mature multi-subunit complex. We propose that during the evolution of the Chlorophyte algae, the cox2 gene was divided into two mitochondrial genes that were subsequently transferred to the nucleus. This event was evolutionarily distinct from the transfer of an intact cox2 gene to the nucleus in some members the Leguminosae plant family.

Amino Acid Sequence↗
PubMed2003

Paramecium bursaria Chlorella virus 1 encodes two enzymes involved in the biosynthesis of GDP-L-fucose and GDP-D-rhamnose.

At least three structural proteins in Paramecium bursaria Chlorella virus (PBCV-1) are glycosylated, including the major capsid protein Vp54. However, unlike other glycoprotein-containing viruses that use host-encoded enzymes in the endoplasmic reticulum-Golgi to glycosylate their proteins, PBCV-1 encodes at least many, if not all, of the glycosyltransferases used to glycosylate its structural proteins. As described here, PBCV-1 also encodes two open reading frames that resemble bacterial and mammalian enzymes involved in de novo GDP-L-fucose biosynthesis. This pathway, starting from GDP-D-mannose, consists of two sequential steps catalyzed by GDP-D-mannose 4,6 dehydratase (GMD) and GDP-4-keto-6-deoxy-D-mannose epimerase/reductase, respectively. The two PBCV-1-encoded genes were expressed in Escherichia coli, and the recombinant proteins had the predicted enzyme activity. However, in addition to the dehydratase activity, PBCV-1 GMD also had a reductase activity, producing GDP-D-rhamnose. In vivo studies established that PBCV-1 GMD and GDP-4-keto-6-deoxy-D-mannose epimerase/reductase are expressed after virus infection and that both GDP-L-fucose and GDP-D-rhamnose are produced in virus-infected cells. Thus, PBCV-1 is the first virus known to encode enzymes involved in nucleotide sugar metabolism. Because fucose and rhamnose are components of the glycans attached to Vp54, the pathway could circumvent a limited supply of GDP sugars by the algal host.

Animals↗
PubMed2003

Four inteins and three group II introns encoded in a bacterial ribonucleotide reductase gene.

A bacterial ribonucleotide reductase gene was found to encode four inteins and three group II introns in the oceanic N2-fixing cyanobacterium Trichodesmium erythraeum. The 13,650-bp ribonucleotide reductase gene is divided into eight extein- or exon-coding sequences that together encode a 768-amino acid mature ribonucleotide reductase protein, with 83% of the gene sequence encoding introns and inteins. The four inteins are encoded on the second half of the gene, and each has conserved sequence motifs for a protein-splicing domain and an endonuclease domain. These four inteins, together with known inteins, define five intein insertion sites in ribonucleotide reductase homologues. Two of the insertion sites are 10 amino acids apart and next to key catalytic residues of the enzyme. Protein-splicing activities of all four inteins were demonstrated in Escherichia coli. The four inteins coexist with three group II introns encoded on the first half of the same gene, which suggests a breakdown of the presumed barrier against intron insertion in this bacterial conserved protein-coding gene.

Amino Acid Motifs↗
PubMed2004

The Human hydroxyacylglutathione hydrolase (HAGH) gene encodes both cytosolic and mitochondrial forms of glyoxalase II.

In yeast and higher plants, separate genes encode the cytosolic and mitochondrial forms of glyoxalase II. In contrast, although glyoxalase II activity has been detected both in the cytosol and mitochondria of mammals, only a single gene encoding glyoxalase II has been identified. Previously it was thought that this gene (the hydroxyacylglutathione hydrolase gene), comprised 8 exons that are transcribed into mRNA and that the resulting mRNA species encoded a single cytosolic form of glyoxalase II. Here we show that this gene gives rise to two distinct mRNA species transcribed from 9 and 10 exons, respectively. The 9-exon-derived transcript encodes two protein species: mitochondrially targeted glyoxylase II, which is initiated from an AUG codon in a previously uncharacterized part of the mRNA sequence, and cytosolic glyoxalase II, which is initiated by internal ribosome entry at a downstream AUG codon. The transcript deriving from 10 exons has an in-frame termination codon between the two initiating AUG codons and hence only encodes the cytosolic form of the protein. Confocal fluorescence microscopy indicates that the mitochondrially targeted form of glyoxalase II is directed to the mitochondrial matrix. Analysis of glyoxalase II mRNA sequences from a number of species indicates that dual initiation from alternative AUG codons is conserved throughout vertebrates.

Alternative Splicing↗
PubMed2001

Verbal encoding deficits in a patient with a left retrosplenial lesion.

Over the past decade, memory impairments associated with retrosplenial damage have received increased attention among neuroscientists, although the exact role of the retrosplenial region in memory has not been clearly defined. Evidence from lesion studies and functional neuroimaging has implicated the retrosplenial region in verbal episodic memory, temporal ordering of information, and topographical memory. In addition, recent positron emission tomography studies have shown increased activation of the retrosplenial cortex during tasks involving both the encoding and retrieval of episodic information. The objective of this study was to define more clearly the nature of memory impairments observed in retrosplenial amnesia. A 47-year-old amnesic male with a left retrosplenial arteriovenous malformation was examined on neurocognitive tasks of automatic and directed encoding, temporal ordering of information, and remote memory. Despite normal performance on frontal cognitive tasks, intact memory for remote information, and a superior IQ, this individual exhibited a profound deficit in the encoding of information, evidenced by poor release from proactive interference, poor category clustering on word list recall, poor semantic encoding on a levels of processing task, and mild impairments in temporal ordering. These results imply that the retrosplenial region plays a role in the verbal encoding of information, which contributes to the profound verbal memory impairment reported in previous case studies of patients with retrosplenial damage.

Adult↗
PubMedDate not supplied

The effects of attention switching on encoding and retrieval of words in younger and older adults.

Two experiments examined the interaction between aging, attention switching, encoding process, and recognition memory using different versions of a cued attention switching paradigm. In Experiment 1, 30 younger and 35 older adults encoded words based on font color, meaning, or by explicit learning with a color response during performance of a choice-reaction time (RT) task. Attention switches were cued by means of stimulus location, and occurred on average every seven trials. In Experiment 2, attention switching was precued from a central fixation point and the number of critical switch trials was increased, occurring on average every four trials. Memory was assessed in both experiments by means of a forced-choice recognition task. Results indicated that, relative to color encoding, older adults benefited more than younger adults from semantic encoding, but less from explicit learning instructions. Attention switching disrupted encoding task performance of older adults more than that of younger adults, but recognition memory was generally unaffected. Results are discussed in light of theoretical models of aging memory that posit a role for executive control processing.

Adolescent↗
PubMedDate not supplied

The myth of the encoding-retrieval match.

Modern memory researchers rely heavily on the encoding-retrieval match, defined as the similarity between coded retrieval cues and previously encoded engrams, to explain variability in retention. The encoding-retrieval match is assumed to be causally and monotonically related to retention, although other factors (such as cue overload) presumably operate in some circumstances. I argue here that the link between the encoding-retrieval match and retention, although generally positive, is essentially correlational rather than causal--much like the link between deep/elaborative processing and retention. Empirically, increasing the functional match between a cue and a target trace can improve, have no effect, or even decrease retention performance depending on the circumstance. We cannot make unequivocal predictions about retention by appealing to the encoding-retrieval match; instead, we should be focusing our attention on the extent to which retrieval cues provide diagnostic information about target occurrence.

Cues↗
PubMed2005

Memory for temporal context: effects of ageing, encoding instructions, and retrieval strategies.

Young and older adults were compared on a list discrimination task. In Experiment 1, performance declined with ageing after incidental and intentional encoding of the temporal context. Moreover, there was no benefit for intentional encoding in either group. In Experiment 2, each list was associated with a different encoding context. There were age differences in performance when participants tried to retrieve the encoding context of the items as a cue for their list of occurrence, but not when participants evaluated temporal distance from the strength of the memory trace. This suggests that the age-related decrease in list discrimination could be at least partly due to a difficulty in inferring strategically the temporal context of the items from information encoded in the same time.

Adult↗
PubMedDate not supplied

Direct comparison of episodic encoding and retrieval of words: an event-related fMRI study.

Functional magnetic resonance imaging (fMRI) was used to compare directly episodic encoding and retrieval. During encoding, subjects studied visually presented words and reported via keypress whether each word represented a pleasant or unpleasant concept (intentional, deep encoding). During the retrieval phase, subjects indicated (via keypress) whether visually presented words had previously been studied. No reliable differences were found during the recognition phase for words that had been previously studied and those that had not been studied. Areas preferentially active during encoding (relative to retrieval) included left superior frontal cortex, medial frontal cortex, left superior temporal cortex, posterior cingulate, left parahippocampal gyrus, and left inferior frontal gyrus. Regions more active in retrieval than encoding included bilateral inferior parietal cortex, bilateral precuneus, right frontal polar cortex, right dorsolateral prefrontal cortex, and right inferior frontal/insular cortex.

Adult↗
PubMed1999

Erythropoiesis: Splenic Immunoglobulin Variable Region Genes Encoding Red Blood Cell Binding Fab Fragments in Autoimmune Hemolytic Anemia.

An absolute requirement for the V(H(4-34) ) immunoglobulin (Ig) variable (V) region heavy chain (V(H) ) gene has been demonstrated in pathogenic cold agglutinin autoantibodies. Investigation of IgG binding anti-Rhesus (Rh) alloantibodies provides further evidence of V gene restriction in red blood cell (RBC) binding antibodies and demonstrates that the V(H(4-34) ) gene used to form cold agglutinins may also encode RBC antibodies of varied specificities. We reasoned that a similar V gene restriction may be evident in the gene segments encoding IgG anti-RBC autoantibodies mediating autoimmune hemolytic anemia (AIHA). To further examine this question IgG Fab fragment phage display libraries were constructed from the spleen of a patient with AIHA. The index autoantibody appeared to have incomplete anti-C specificity and bound all panel RBCs except Rh null. The Fab fragment phage display libraries were therefore panned twice on CDE/CDe RBCs and binding phage were eluted. Binding of the phage displayed Fab fragments to RBCs was confirmed by immunoflourescence and flow cytometry. Specificity was confirmed by the absence of binding to Rh null cells, murine RBCs and to human peripheral blood lymphocytes. Molecular analysis of Ig V genes encoding the pan RBC binding Fab fragments revealed a relative V(H) gene restriction and evidence of somatic mutation. The V(H(3) ) family member V(H(26) ) was prominent in RBC binding Fabs. The V(H(3) ) family member hV3005 and the V(H(4) ) family DP-65 gene segments also encoded RBC binding Fabs. The J(H(4) ) gene segment was present in all binding clones. Varied kappa and lambda light chain (V(L) ) genes were identified by sequencing and no single light chain was prevalent. Three of the ten V(L) and two of the three V(H) identified by sequencing appeared to derive from germline genes previously noted to have RBC binding specificity. We conclude that splenic Ig V genes can encode pan RBC binding antibodies with specificities similar to autoantibodies found in AIHA and that V(H) gene segment utilization by these antibodies is derived from a limited pool of somatically mutated V(H) gene segments.

Journal Article↗
PubMed2004

Non-specific encoding of threat in social phobia and panic disorder.

This study employs a release of proactive interference technique to explore encoding-related processes in social phobia. Twenty-six individuals with social phobia and 24 individuals with panic disorder participated in the memory task. Significant release of proactive interference was found when neutral and threat dimensions were encoded, but not when social and physical threat dimensions, or when positive and threat dimensions were presented. Threat was therefore differently encoded depending on the active encoding context in which semantic processing occurred. Individuals with social phobia or panic disorder did not differ in the release of proactive interference. The present experiment consequently yields little support for the specificity hypothesis in memory of anxious individuals. Instead, the findings generally demonstrate that threat encoding is similar for people with social phobia and those with panic disorder.

Adult↗
PubMed2000

The effects of divided attention on encoding and retrieval processes: the resiliency of retrieval processes.

We have recently cast doubt (Craik, Govoni, Naveh-Benjamin, & Anderson, 1996; Naveh-Benjamin, Craik, Guez, & Dori, 1998) on the view that encoding and retrieval processes in human memory are similar. Divided attention at encoding was shown to reduce memory performance significantly, whereas divided attention at retrieval affected memory performance only minimally. In this article we examined this asymmetry further by using more difficult retrieval tasks, which require substantial effort. In one experiment, subjects had to encode and retrieve lists of unfamiliar name-nouns combinations attached to people's photographs, and in the other, subjects had to encode words that were either strong or weak associates of the cues presented with them and then to retrieve those words with either intra- or extra-list cues. The results of both experiments showed that unlike division of attention at encoding, which reduces memory performance markedly, division of attention at retrieval has almost no effect on memory performance, but was accompanied by an increase in secondary-task cost. Such findings again illustrated the resiliency of retrieval processes to manipulations involving the withdrawal of attention. We contend that retrieval processes are obligatory or protected, but that they require attentional resources for their execution.

Adult↗
PubMed1987

Cloning and sequence analysis of cDNA encoding p38, a major synaptic vesicle protein.

We have isolated from a lambda gt11 rat brain cDNA library cDNA clones encoding greater than 95% of the open reading frame and untranslated regions of the mRNA for p38, the most abundant of the integral membrane proteins of the synaptic vesicle. Phage containing cDNA that encoded vesicle proteins were identified by screening fusion proteins with a polyclonal serum to rat brain synaptic vesicles. To identify phage carrying p38 sequences, fusion proteins were used to affinity purify monospecific antibodies from the original heterogeneous serum; antibodies to a 38,000-D protein were then identified by Western blotting. Inserts carrying DNA-encoding p38 sequences were subcloned into plasmid vectors and used to generate cDNA probes for Northern blot analysis. A major transcript of 2.4 kb was expressed specifically in brain and endocrine tissue but not in liver, consistent with the tissue-specific expression of the protein detected by antibody techniques. Using three overlapping clones that encoded fusion proteins, we identified and sequenced approximately 85% of the cDNA. Two additional Eco RI fragments at the 5' end of the mRNA were obtained from a fourth clone identified by screening a second lambda gt11 library with a 5' cDNA probe. The cDNA encoded an open reading frame of 298 amino acids with a 3' untranslated region of 1.4 kb. The protein shares no sequence homology with other Ca2+-binding proteins. The availability of a cDNA clone for an integral synaptic vesicle protein should facilitate studies of its function in transmitter release, its intracellular targeting, and regulation of synaptic vesicle biogenesis during development and regeneration of nerve terminals.

Amino Acid Sequence↗
PubMed1993

Tenascin-X: a novel extracellular matrix protein encoded by the human XB gene overlapping P450c21B.

A human gene termed XB overlaps the P450c21B gene encoding steroid 21-hydroxylase and encodes a protein that closely resembles extracellular matrix proteins. Sequencing of phage and cosmid clones and of cDNA fragments shows that the XB gene spans 65 kb of DNA, consisting of 39 exons that encode a 12-kb mRNA. The predicted protein of over 400 kD consists of five distinct domains: a signal peptide, a hydrophobic domain containing three heptad repeats, a series of 18.5 EGF-like repeats, 29 fibronectin type III repeats, and a carboxy-terminal fibrinogen-like domain. Because the structure of the protein encoded by the XB gene closely resembles tenascin, we term this protein tenascin-X (TN-X), and propose a simplified nomenclature system for the family of tenascins. RNase protection experiments show that the TN-X transcript is expressed ubiquitously in human fetal tissues, with the greatest expression in the fetal testis and in fetal skeletal, cardiac, and smooth muscle. Two adrenal-specific transcripts, P450c21B (steroid 21-hydroxylase) and Y (an untranslated transcript) overlap the XB gene on the complementary strand of DNA, yielding a unique array of overlapping transcripts: a "polygene." In situ hybridization histochemistry experiments show that the TN-X transcript and the P450c21 and Y transcripts encoded on the complementary DNA strand are all expressed in the same cells of the human adrenal cortex. Genetic data suggest that TN-X may be essential for life.

Adrenal Glands↗
PubMed1994

Mitochondrial heat shock protein 70, a molecular chaperone for proteins encoded by mitochondrial DNA.

Mitochondrial heat shock protein 70 (mt-Hsp70) has been shown to play an important role in facilitating import into, as well as folding and assembly of nuclear-encoded proteins in the mitochondrial matrix. Here, we describe a role for mt-Hsp70 in chaperoning proteins encoded by mitochondrial DNA and synthesized within mitochondria. The availability of mt-Hsp70 function influences the pattern of proteins synthesized in mitochondria of yeast both in vivo and in vitro. In particular, we show that mt-Hsp70 acts in maintaining the var1 protein, the only mitochondrially encoded subunit of mitochondrial ribosomes, in an assembly competent state, especially under heat stress conditions. Furthermore, mt-Hsp70 helps to facilitate assembly of mitochondrially encoded subunits of the ATP synthase complex. By interacting with the ATP-ase 9 oligomer, mt-Hsp70 promotes assembly of ATP-ase 6, and thereby protects the latter protein from proteolytic degradation. Thus mt-Hsp70 by acting as a chaperone for proteins encoded by the mitochondrial DNA, has a critical role in the assembly of supra-molecular complexes.

DNA, Mitochondrial↗
PubMed1986

A single germline VH gene segment of normal A/J mice encodes autoantibodies characteristic of systemic lupus erythematosus.

These experiments tested the hypothesis that unmutated germline genes from normal mice can encode autoantibodies. We found that the unmutated VHIdCR gene segment, which encodes a large proportion of antiarsonate antibodies in A/J mice, also encodes antibodies with the ability to bind to DNA and cytoskeletal proteins. After Ars immunization, at a time when the VHIdCR gene segment mutates and antibody affinity for the hapten increases, reactivity with the autoantigens was lost. Six antibodies obtained after immunization with Ars bound both the Ars and DNA. Results of competitive inhibition assays suggested that the same variable region site in the antibodies bound to both Ars and DNA. The properties of the individual germline-encoded antibodies, which include reactivity to both DNA and cytoskeletal proteins, suggest that autoantibodies characteristic of SLE might be a subset of antibodies encoded by unmutated germline V genes.

Animals↗
PubMed1992

Two unusual forms of human immunoglobulin E encoded by alternative RNA splicing of epsilon heavy chain membrane exons.

We present evidence for RNA transcripts encoding two forms of human epsilon immunoglobulin (Ig) heavy chain that differ significantly from those of other isotypes. We previously demonstrated three human epsilon mRNA species, instead of the two, corresponding to membrane and secreted proteins, seen with other heavy chain transcripts. In human genomic DNA downstream of the C epsilon gene, we identified sequences homologous to the two putative murine exons M1 (encoding a hydrophobic, presumably transmembrane region) and M2 (encoding hydrophilic residues). To determine the structures of epsilon transcripts containing these sequences, we amplified epsilon-related RNAs with the reverse transcriptase polymerase chain reaction. RNA was examined from fresh human B cells stimulated to IgE production by interleukin 4 plus anti-CD40, as well as from the human IgE-producing line AF10. Instead of the single CH4-M1-M2 splice product predicted for murine membrane IgE, we found two other RNA species. One form has the structure CH4-M1'-M2, in which M1' includes the human sequence homologous to the murine M1 as well as a unique segment of 52 codons further upstream in the genomic sequence; this RNA species apparently encodes the IgE expressed on the membrane of IgE-producing lymphocytes. The other RNA has the structure CH4-M2', in which M2' is spliced in an alternative reading frame that includes an additional 109 codons downstream of the termination codon of the CH4-M1'-M2 form. Because the CH4-M2' mRNA form does not encode a hydrophobic segment, its translated product should be secreted. A secreted epsilon protein of approximately the size predicted for this form was identified by Western blotting. This novel IgE protein could play a significant and distinctive role in allergic disorders.

Amino Acid Sequence↗