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At least 235 records · Page 13Linked to original sources
PubMed2001

Molecular and genomic characterization of human DLEC, a novel member of the C-type lectin receptor gene family preferentially expressed on monocyte-derived dendritic cells.

We have identified a novel gene encoding a protein designated DLEC (dendritic cell lectin), which is a type II membrane glycoprotein of 213 amino acids and belongs to the human calcium-dependent (C-type) lectin family. The cytoplasmic tail of DLEC lacks consensus signaling motifs and its extracellular region shows a single carbohydrate recognition domain (CRD), closest in homology to the dendritic cell immunoreceptor (DCIR) CRD. The DLEC gene has been localized linked to DCIR on the telomeric region of the NK gene complex. RT-PCR and Northern blot analyses show that DLEC mRNA is preferentially expressed in monocyte-derived dendritic cells.

Alternative Splicing↗
PubMed2026

Genomic Characterization of ETV6::RUNX1-Positive Childhood B-ALL in a Chinese Cohort: Novel Fusion Partners, Co-Occurring Mutations, and Risk-Stratifying Biomarkers.

BACKGROUND: ETV6::RUNX1 is the most common genetic abnormality in pediatric B-cell acute lymphoblastic leukemia (ALL; ∼25%), yet the comprehensive genetic architecture and molecular predictors of intermediate-risk (IR) stratification remain incompletely characterized. METHODS: We performed whole-transcriptome sequencing (Illumina NovaSeq 6000, rRNA depletion, 41.70 Gb/sample) on bone marrow samples from 93 pediatric ETV6::RUNX1-positive B-ALL patients. Bioinformatics analysis included STAR alignment, MuTect2 variant calling, FusionCatcher fusion detection, and VEP annotation. The Jaccard index with permutation testing assessed mutation co-occurrence; logistic regression identified independent predictors of IR classification. RESULTS: Beyond ETV6::RUNX1, we identified 51 distinct fusion genes across the cohort, including the reciprocal RUNX1-ETV6 (73.1%), chr8::KLF1210 (38.7%), and KLF12-chr8 (34.4%). Somatic mutations in 249 genes were detected; the most frequent were KIAA1715 (17.2%), KRAS (11.8%), and NSD2 (10.8%). Network analysis revealed significant chromatin modifier co-occurrence (KIAA1715-KMT2C: J = 0.136, p = 0.015) and KRAS-NRAS mutual exclusivity (J = 0.000, p = 0.042). PTCH1 (OR = 3.50, 95% CI 0.21-58.49, p = 0.41) and GNB1 (OR = 6.5, 95% CI 1.2-34.8, p = 0.029) mutations independently predicted IR classification. chr8::KLF1210 fusion correlated with higher Day-19 MRD levels (p = 0.038). CONCLUSIONS: GNB1 mutation represents a novel independent predictor of IR stratification in ETV6::RUNX1-positive B-ALL. The chromatin modifier co-occurrence module and extensive fusion architecture reveal biological heterogeneity within this favorable-risk subtype, with potential implications for risk-adapted therapeutic strategies.

B‐ALL↗
PubMed2005

Rapid array-based genomic characterization of a subtle structural abnormality: a patient with psychosis and der(18)t(5;18)(p14.1;p11.23).

Array-based copy number analysis has recently emerged as a rapid means of mapping complex and/or subtle chromosomal abnormalities. We have compared two such techniques, using bacterial artificial chromosome (BAC) and single nucleotide polymorphism (SNP) arrays in the evaluation of a 45-year-old woman with dysmorphic features, mental retardation, psychosis, and an unbalanced derivative chromosome 18, (46,XX, der(18)t(18;?)(p12;?)). Both array-based methods demonstrated that the additional material on chromosome 18 was of 5p origin. The 5p duplication mapped telomeric to 25.320 Mb (BAC array) and 25.607 Mb (SNP array), corresponding to the band 5p14.1. Both BAC and SNP arrays also showed a deletion involving chromosome 18p extending telomeric from 8.437 Mb (BAC array) and 8.352 Mb (SNP array), corresponding to the band 18p11.23. Molecular cytogenetic mapping using fluorescence in situ hybridization (FISH) supported the array findings and further refined the breakpoint regions, confirming that the BAC and SNP chips were both useful in this regard. Both case reports and linkage analyses have implicated these chromosomal intervals in psychosis. The array-based experiments were completed over the course of several days. While these methods do not eliminate the requirement for traditional fine-mapping, they provide an efficient approach to identifying the origin and extent of deleted and duplicated material in chromosomal rearrangements.

Chromosome Banding↗
PubMed1994

Genomic characterization of rotavirus strains obtained from hospitalized children with diarrhoea in Bangladesh.

Faecal samples were obtained from 111 children hospitalized with acute watery gastroenteritis in a children's hospital in Bangladesh from January to December, 1989. Rotavirus was detected as the aetiologic agent in 35 (32%) of these patients. The electrophoretic pattern of ds-RNA extracted from the rotaviruses showed 11 different migration patterns (six short and five long), as well as some short and long mixed profiles. All four major G serotypes were identified by amplification of a segment of the gene for VP7 using the polymerase chain reaction. A specific serotype could be assigned in 32 (91%) cases. Serotypes G1-G4 accounted for 11%, 37%, 11%, and 23% of isolates respectively. Three (9%) mixed serotypes were identified by this method and were found to be mixtures of serotypes G1 and G4, G2 and G4, and G3 and G4.

Adolescent↗
PubMed1994

Serological and genomic characterization of equine rotavirus VP4 proteins identifies three different P serotypes.

A series of viral reassortants was prepared between equine rotaviruses H1 (G5), H2 (G3), and L338 (G13) and human rotavirus ST3 (G4). All contained the VP4 cognate gene segment 4 from the equine parental virus and the VP7 cognate gene segment 9 from ST3. Using these viruses and antisera prepared to them, it was shown that each of the three equine viruses possessed a serologically distinct VP4 or P serotype with a > or = 16-fold difference in reciprocal cross-neutralization titers. H1 VP4 was closely related to that of porcine virus OSU, i.e., P7. L338 gene 4 was sequenced, and the sequence and serological data indicated that it constituted a novel P serotype L338. P serotype H2 was predominant among our cell culture-adapted equine rotavirus strains, but showed some serological cross-reactivity.

Amino Acid Sequence↗
PubMed1997

Genomic characterization of the region between HLA-B and TNF: implications for the evolution of multicopy gene families.

The major histocompatibility complex (MHC) contains genes which confer susceptibility to numerous diseases and must be important in primate evolution. In some instances, genes have been mapped to the region between human histocompatibility leukocyte antigen (HLA)-B and tumor necrosis factor (TNF) but precise localization has proven difficult especially since this region is subject to insertions, deletions, and duplications. Utilizing computer similarity searches and coding prediction programs, we have identified several potential coding sequences between HLA-B and TNF. Three of these sequences, PERB11.2, PERB15, and PERB 18, are similar to members of multicopy gene families that are located in other regions of the MHC. The identification of numerous fragmented and intact retroelements (L1, Alu, LTR, and THE sequences) flanking the PERB11 and PERB15 genes suggests that these retroelements are involved in the duplication process. The evaluation of candidate genes for disease susceptibility within the MHC is complicated by their similarity to other members of multicopy gene families. The determination of sequence differences within and between species provides a strategy with which to investigate the candidate genes between HLA-B and TNF.

Amino Acid Sequence↗
PubMed2001

Genomic characterization of human SEC14L1 splice variants within a 17q25 candidate tumor suppressor gene region and identification of an unrelated embedded expressed sequence tag.

Human SEC14L1 shows partial sequence homology to the budding yeast SEC14 protein and the Japanese flying squid retinal-binding protein and was previously generally localized to 17q25. We more precisely mapped SEC14L1 within a discrete region of 17q25 that likely harbors at least one putative breast and ovarian tumor suppressor gene. We determined that this gene consists of 18 exons ranging in size from 70 bp (exon 11) to 3088 bp (exon 17) and spanning at least 58 kb of DNA. Exon 17 contained a highly polymorphic variable number of tandem repeats (VNTR) and was present only in the larger ubiquitously expressed 5.5-kb transcript. The 3.0-kb ubiquitously expressed transcript included sequences at the beginning of exon 17 (designated exon 17a) and the end of exon 17 (designated exon 18), but lacked the internal 2439 bp of exon 17, including the VNTR. This alternative splicing resulted in a predicted protein of 719 residues from the smaller transcript with four more terminal amino acids than the 715 residue protein predicted from the larger transcript. EST H49244 spanned exon 11 of SEC14L1 and was specifically expressed in human peripheral blood leukocytes. One intragenic single nucleotide polymorphism (SNP) was confirmed. SEC14L1 contained the CRAL/TRIO domain also found in alpha-tocopherol transfer protein (TTPA) and cellular retinaldehyde-binding protein (CRALBP). As retinoids have been shown to inhibit the growth of breast cancer cells, loss of the proposed SEC14L1 retinal-binding function may contribute to breast tumorigenesis. As TTPA and CRALBP have been implicated in retinitis pigmentosa (RP), altered SEC14L1 expression may contribute to RP in previously unlinked families. Coding exon-specific PCR primers were designed to aid in future expression and mutational analyses.

Adult↗
PubMed2002

Genomic characterization of the human prion protein (PrP) gene locus.

Prion protein (PrP) is intimately linked with a class of neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs). Employing bioinformatics and direct molecular analysis, we demonstrated that the human PrP gene (PRNP) locus, which is situated at Chromosome (Chr) position 20p12-ter, contains three genes within a 55-kb interval: PRNP; DOPPEL or PRND, located 20 kb 3' of PRNP; and a novel gene, designated PRNT, that maps 3 kb 3' to PRND and is transcribed to generate at least three alternatively spliced mRNAs. All three genes of this locus demonstrate low sequence homology, implying that, although they may be evolutionarily related, they are functionally distinct. Analysis of both adult and fetal human tissues confirmed the ubiquitous but variable expression profile of PRNP, with the highest levels observed in the CNS and testis. Contrastingly, although PRND shows a wide tissue expression pattern in fetal tissues, it is expressed exclusively in adult testis, whereas all three PRNT isoforms were detected only in adult testis, implying that PRND is developmentally regulated. An investigation of the regulatory mechanisms underlying this complex gene expression pattern from the PRNP locus should provide insight into the function of these genes and the possible involvement of the non-PrP proteins in the development of TSEs.

Adult↗
PubMed1985

Mitochondrial DNA-like sequences in the human nuclear genome. Characterization and implications in the evolution of mitochondrial DNA.

Thirty-three phage clones carrying DNAs homologous to human mitochondrial DNA (mtDNA) were isolated from two independently constructed human gene libraries, and the region and extent of homology of mtDNA-like sequences carried by these clones were examined in hybridization experiments. Each phage clone contained DNA sequences homologous to various parts of the mtDNA and the extent of homology differed from clone to clone. From the efficiency of the library screening, it was estimated that human nuclear DNA contains at least several hundred copies of mtDNA-like fragments. Four clones carrying nuclear DNA sequences homologous to the mitochondrial Unidentified Reading Frame (URF) 4 and URF5 regions were chosen for further studies, and their structures were analyzed by DNA sequencing. Comparison of these mtDNA-like sequences with that of mtDNAs of several mammalian species revealed conservation of a part of the structures present in direct ancestral mtDNAs. The mtDNA fragments seem to have been continuously integrated into mammalian nuclear DNA during evolution.

Bacteriophage lambda↗
PubMed1986

Oncogenic retrovirus from spontaneous murine osteomas. II. Molecular cloning and genomic characterization.

An N-ecotropic murine leukemia virus (OA MuLV), originally isolated from spontaneous osteomas of strain 101 mice, was molecularly cloned. The virus induces osteomas, osteopetrosis, and malignant lymphomas in NMRI mice. The cloned virus was analyzed by heteroduplex analysis, restriction enzyme mapping, and oligonucleotide mapping. The data show a very close relationship to the endogenous Akv prototype virus with some differences in the gag and the env region. The nucleotide sequence of the U3 region of OA MuLV LTR revealed a structure within the presumable enhancer region very similar to the U3 sequences of the FBJ murine sarcoma virus and its associated helper virus. The significance of these specific structures for the oncogenicity of the virus and the development of the typical disease pattern is discussed.

Animals↗
PubMed1993

Genomic characterization of the human DNA excision repair-controlling gene XPAC.

We have characterized the human DNA excision repair gene, XPAC (xeroderma pigmentosum group A complementing). This gene of approximately 25 kb consists of six exons. The 5'-flanking region of the gene has a CAAT box, but no TATA box. The region upstream from the coding sequence of exon 1 is G + C rich (73%), and has a GC box. Transcriptional mapping analysis suggested that there is one major transcription start point (tsp). The presence of two polyadenylation signals suggests that the two XPAC mRNAs with different 3' untranslated regions in normal human cells are due to alternative polyadenylations. The promoter activity, measured by transient expression of the cat gene with the 5' flanking regions, indicated the presence of a functional promoter.

Amino Acid Sequence↗
PubMed2001

Variations and constant patterns in eukaryotic MDR enzymes. Conclusions from novel structures and characterized genomes.

Medium-chain dehydrogenases/reductases (MDR) alcohol dehydrogenases exhibit multiple forms through a number of gene duplications. A crucial duplication was the one leading from the glutathione-dependent formaldehyde dehydrogenase line to the liver alcohol dehydrogenase (ADH) lines of vertebrates, the first duplication of which can now be further positioned at early vertebrate times. Similarly, screening of MDR forms in recently completed eukaryotic genomes of Caenorhabditis elegans and Drosophila melanogaster suggest that the MDR family may constitute a moderately sized protein family centered around a limited number of enzyme activities of five different structural types.

Alcohol Dehydrogenase↗
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↗