ABSTRACT
The human TCF12 gene, mapping to 15q21, encodes the helix-loop-helix transcription factor 4 (HTF4). A detailed analysis of this genomic region established the organization of the TCF12 gene. The gene includes 21 exons and is significantly larger than an average human gene. Preceding the second exon, two alternative acceptor sites for mRNA splicing yield two distinguishable transcripts (HTF4a and HTF4b) which differ in their 5' untranslated region but share identical coding sequences. Differential utilization of exon 15 in the TCF12 gene may reflect a mechanism producing a cell-type-specific protein (HTF4c). In addition, intron 5 in the TCF12 gene corresponds to the region involved in a translocation, t(9;15)(q22;q21), that results in a form of extraskeletal myxoid chondrosarcoma.
Subject(s)
DNA-Binding Proteins/genetics , RNA Splicing/genetics , Transcription Factors/genetics , 5' Flanking Region/genetics , Amino Acid Sequence , Base Sequence , Basic Helix-Loop-Helix Transcription Factors , Bone Neoplasms/genetics , Chondrosarcoma/genetics , Chromosomes, Human, Pair 15 , DNA-Binding Proteins/chemistry , Exons/genetics , Humans , Isomerism , Molecular Sequence Data , RNA, Messenger/genetics , Transcription Factors/chemistry , Translocation, GeneticABSTRACT
The availability of the complete genomic sequences of the human and mouse T cell receptor loci opens up new opportunities for understanding T cell receptors (TCRs) and their genes. The full complement of TCR gene segments is finally known and should prove a valuable resource for supporting functional studies. A rational nomenclature system has been implemented and is widely available through IMGT and other public databases. Systematic comparisons of the genomic sequences within each locus, between loci, and across species enable precise analyses of the various diversification mechanisms and some regulatory signals. The genomic landscape of the TCR loci provides fundamental insights into TCR evolution as highly localized and tightly regulated gene families.
Subject(s)
Chromosome Mapping , Genomics , Receptors, Antigen, T-Cell/genetics , Animals , Gene Conversion , Humans , Mice , Phylogeny , Promoter Regions, Genetic , Repetitive Sequences, Nucleic Acid , Terminology as TopicABSTRACT
Olfactory receptor (OR) genes represent approximately 1% of genomic coding sequence in mammals, and these genes are clustered on multiple chromosomes in both the mouse and human genomes. We have taken a comparative genomics approach to identify features that may be involved in the dynamic evolution of this gene family and in the transcriptional control that results in a single OR gene expressed per olfactory neuron. We sequenced approximately 350 kb of the murine P2 OR cluster and used synteny, gene linkage, and phylogenetic analysis to identify and sequence approximately 111 kb of an orthologous cluster in the human genome. In total, 18 mouse and 8 human OR genes were identified, including 7 orthologs that appear to be functional in both species. Noncoding homology is evident between orthologs and generally is confined within the transcriptional unit. We find no evidence for common regulatory features shared among paralogs, and promoter regions generally do not contain strong promoter motifs. We discuss these observations, as well as OR clustering, in the context of evolutionary expansion and transcriptional regulation of OR repertoires.
Subject(s)
Evolution, Molecular , Phylogeny , Receptors, Odorant/genetics , 5' Untranslated Regions/genetics , Animals , Chromosome Mapping , Exons/genetics , Humans , Mice , Mice, Inbred Strains , Molecular Sequence Data , Multigene Family , Open Reading Frames , Polymerase Chain ReactionABSTRACT
The human genome is by far the largest genome to be sequenced, and its size and complexity present many challenges for sequence assembly. The International Human Genome Sequencing Consortium constructed a map of the whole genome to enable the selection of clones for sequencing and for the accurate assembly of the genome sequence. Here we report the construction of the whole-genome bacterial artificial chromosome (BAC) map and its integration with previous landmark maps and information from mapping efforts focused on specific chromosomal regions. We also describe the integration of sequence data with the map.
Subject(s)
Contig Mapping , Genome, Human , Chromosomes, Artificial, Bacterial , Cloning, Molecular , DNA Fingerprinting , Gene Duplication , Humans , In Situ Hybridization, Fluorescence , Repetitive Sequences, Nucleic AcidABSTRACT
We report the construction of a tiling path of around 650 clones covering more than 99% of human chromosome 14. Clone overlap information to assemble the map was derived by comparing fully sequenced clones with a database of clone end sequences (sequence tag connector strategy). We selected homogeneously distributed seed points using an auxiliary high-resolution radiation hybrid map comprising 1,895 distinct positions. The high long-range continuity and low redundancy of the tiling path indicates that the sequence tag connector approach compares favourably with alternative mapping strategies.
Subject(s)
Chromosomes, Human, Pair 14 , Chromosomes, Artificial, Bacterial , Cloning, Molecular , Escherichia coli , Humans , Physical Chromosome Mapping , Radiation Hybrid Mapping , Sequence Tagged SitesABSTRACT
We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.
Subject(s)
Chromosome Aberrations , Genetic Markers , Genome, Human , Chromosome Mapping , Chromosomes, Artificial, Bacterial , Cytogenetic Analysis , Human Genome Project , Humans , In Situ Hybridization, Fluorescence , Radiation Hybrid Mapping , Sequence Tagged SitesABSTRACT
The promoter sequences of individual murine TCR Vbeta segments are dissimilar, but any functional differences between them are masked after productive gene rearrangement by the dominance of the TCRbeta 3' enhancer. However, thymocytes of recombination-activating gene-2 (Rag2)-deficient mice allow the transcriptional activity of Vbeta promoters to be studied before rearrangement. Here we report that many Vbeta segments are detectably transcribed in Rag2(-/-) thymocytes and that there are significant differences in expression among different Vbeta segments. Primer extension and characterization of cDNA clones from SCID thymocytes suggest that these germline Vbeta transcripts generally use the same start sites as those previously determined in mature T cells. The strength of expression before rearrangement does not correlate with proximity to the known enhancer, because members of the most distal Vbeta cluster (Vbeta2.1, Vbeta1.1, Vbeta4.1) are relatively strongly expressed and more proximal Vbeta segments (Vbeta14.1, Vbeta3.1, Vbeta7.1, Vbeta6.1) are only weakly expressed. Different Vbeta segments also show different developmental programs of activation in different thymocyte subsets, with the Vbeta5.1(L)-8.2(V) spliced transcript expressed earliest as well as most strongly overall. Comparison with Rag(+) MHC class I(-/-) and class II(-/-) thymocytes confirms that many of these expression differences are leveled by rearrangement and/or by beta selection, before MHC-dependent selection. However, the expression pattern of Vbeta2.1 is highly distinctive and includes cell types apparently outside the T lineage, suggesting potential acquisition of specialized roles.
Subject(s)
Gene Expression Regulation, Developmental/immunology , Gene Rearrangement, beta-Chain T-Cell Antigen Receptor/immunology , Genes, T-Cell Receptor beta/immunology , Regulatory Sequences, Nucleic Acid/immunology , Transcription, Genetic/immunology , Animals , Cell Differentiation/genetics , Cell Differentiation/immunology , Cloning, Molecular , Enhancer Elements, Genetic/immunology , Mice , Mice, Inbred C57BL , Mice, Knockout , Mice, SCID , Molecular Sequence Data , Promoter Regions, Genetic/immunology , T-Lymphocyte Subsets/cytology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolismABSTRACT
Within the ARVD1 (arrhythmogenic right ventricular dysplasia/cardiomyopathy, type 1) critical region, mapped to 14q24.3, we detected an intronless gene of 4859 bp, predominantly expressed in the heart tissue. This gene encodes a 796-amino-acid, proline-rich protein showing polyglutamine and polyalanine tracks with variable length at the N-terminus and a C3HC4 RING finger domain at the C-terminus. CREB and AP-2 binding sites are present in the promoter region. The 5' flanking region contains neither a TATA box nor a CAAT box, but it is high in GC content and includes several Sp1 binding sites. Protein similarity searches revealed a significant match between the C-terminus and a human hypothetical protein, whose gene is located on the chromosome 19 long arm. The predicted protein shows PEST sequences, suggesting its rapid degradation. The novel intronless gene, provisionally named C14orf4 and probably encoding a nuclear protein, was excluded from being the ARVD1 gene.
Subject(s)
Cardiomyopathies/genetics , Carrier Proteins/genetics , Chromosomes, Human, Pair 14 , Nuclear Proteins/genetics , Open Reading Frames , Peptides/genetics , Ventricular Dysfunction, Right/genetics , Amino Acid Sequence , Animals , Base Sequence , Caenorhabditis elegans/genetics , Carrier Proteins/chemistry , Chromosome Mapping , DNA/genetics , DNA, Complementary , Drosophila melanogaster/genetics , Humans , Molecular Sequence Data , Nuclear Proteins/chemistry , Polymerase Chain Reaction , Repetitive Sequences, Nucleic Acid , Reverse Transcriptase Polymerase Chain Reaction , Sequence Alignment , Sequence Homology, Amino AcidABSTRACT
Lymphocyte antigen receptors are not encoded by germline genes, but rather are produced by combinatorial joining between clusters of gene segments in somatic cells. Within a given cluster, gene segment usage during recombination is thought to be largely random, with biased representation in mature T lymphocytes resulting from protein-mediated selection of a subset of the total repertoire. Here we show that T cell receptor D beta and J beta gene segment usage is not random, but is patterned at the time of recombination. The hierarchy of gene segment usage is independent of gene segment proximity, but rather is influenced by the ability of the flanking recombination signal sequences (RSS) to bind the recombinase and/or to form a paired synaptic complex. Importantly, the relative frequency of gene segment usage established during recombination is very similar to that found after protein-mediated selection, suggesting that in addition to targeting recombinase activity, the RSS may have evolved to bias the naive repertoire in favor of useful gene products.
Subject(s)
Genes, T-Cell Receptor beta , Genes, T-Cell Receptor , Recombination, Genetic , T-Lymphocytes/immunology , Animals , Base Sequence , Consensus Sequence , DNA Primers , DNA, Ribosomal/genetics , Kidney/immunology , Mice , Mice, Inbred C57BL , Polymerase Chain ReactionABSTRACT
The open data release policy adopted by the large-scale DNA sequencing centers has made accessible valuable information that facilitates research. Herein, we argue that the data producers' rights to receive credit for at least some portion of the analyses of the data must be protected. We suggest that this protection take the form of a specification of the probable content of the primary paper the data producers intend to publish when the data gathering is complete. Rights to publish that paper ought then be restricted to the producers unless they give permission otherwise.
Subject(s)
Human Genome Project , Intellectual Property , Publishing , Animals , Databases, Factual , Humans , Information Services , MiceABSTRACT
Comparison of human and mouse genomic sequence at the border of the major histocompatibility complex (MHC) class II and class III regions revealed a locus encoding six exons with homology to the butyrophilin gene family and the location of a previously described gene, testis-specific basic protein (TSBP). We named the new locus BTL-II, for butyrophilin-like MHC class II associated. The six discernable exons of the BTL-II locus encode a small hydrophobic amino acid sequence (which may be a signal peptide), two immunoglobulin domains, a small 7-amino acid, heptad repeat-like exon, and a further two immunoglobulin domains. In mouse, an additional butyrophilin-like gene (NG10) is situated adjacent to BTL-II. Expression studies of the BTL-II locus in mouse showed that it is expressed in a range of gut tissues. We demonstrate that like many other genes from the MHC, BTL-II is polymorphic in a selection of diverse HLA haplotypes. In the light of the newly discovered locus, we revisit and discuss the possible origin of the butyrophilin gene family.
Subject(s)
Genes, MHC Class II/genetics , Major Histocompatibility Complex/genetics , Membrane Glycoproteins/genetics , Polymorphism, Genetic , Amino Acid Sequence , Animals , Butyrophilins , Cloning, Molecular , Exons , Humans , Inflammatory Bowel Diseases/etiology , Intestines , Mice , Molecular Sequence Data , Multigene Family , Phylogeny , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Tissue DistributionABSTRACT
We have mapped and sequenced the region immediately centromeric of the human major histocompatibility complex (MHC). A cluster of 13 genes/pseudogenes was identified in a 175 kb PAC linking the TAPASIN locus with the class II region. It includes two novel human genes (BING4 and SACM2L) and a thus far unnoticed human leucocyte antigen (HLA) class II pseudogene, termed HLA-DPA3. Analysis of the G+C content revealed an isochore boundary which, together with the previously reported telomeric boundary, defines the MHC class II region as one of the first completely sequenced isochores in the human genome. Comparison of the sequence with limited sequence from other cell lines shows that the high sequence variation found within the classical class II region extends beyond the identified isochore boundary leading us to propose the concept of an "extended MHC". By comparative analysis, we have precisely identified the mouse/human synteny breakpoint at the centromeric end of the extended MHC class II region between the genes HSET and PHF1.
Subject(s)
Major Histocompatibility Complex , Amino Acid Sequence , Animals , Base Composition , Base Sequence , Centromere/genetics , Chromosome Mapping , DNA, Complementary/chemistry , DNA, Complementary/genetics , Genes, MHC Class II , Genetic Variation , Genome, Human , HLA-DP Antigens/genetics , Humans , Mice , Molecular Sequence Data , Phylogeny , Pseudogenes , Sequence Homology, Amino AcidABSTRACT
The first complete mammalian genomic sequence reported thus far in the Notch gene family, including a putative promoter region and 30 exons of the human NOTCH4 gene spanning 56.8 kb of DNA, were sequenced. The NOTCH4 locus contains a TATA-less promoter with two putative transcription initiation sites (Inr), three RBP-Jkappa sites, and two GATA recognition sites. Two cDNA isoforms, NOTCH4(L) and NOTCH4(S),were identified. Whereas the NOTCH4(S) isoform contains the entire coding sequence, the NOTCH4(L) isoform has two unspliced intronic sequences between exons 11 and 12 and exons 20 and 21 and a misspliced exon 6. Consistent with these results, two alternatively spliced isoforms of transcripts of approximately 9.3 and 6.7 kb were detected by Northern blot analysis. The predicted amino acid sequence of the NOTCH4 protein based on the NOTCH4(S) cDNA sequence contains 2003 amino acids and includes the predominant motifs of the Notch family: 29 epidermal growth factor (EGF)-like repeats, 3 Notch/lin-12 repeats, a transmembrane region, 6 cdc10/Ankyrin repeats, and a PEST domain.
Subject(s)
Chromosomes, Human, Pair 6/genetics , Major Histocompatibility Complex/genetics , Proto-Oncogene Proteins/genetics , Receptors, Cell Surface , Adult , Alternative Splicing , Amino Acid Sequence , Base Sequence , Chromosome Mapping , Cloning, Molecular , DNA, Complementary/genetics , Exons , Gene Expression , Genome, Human , Humans , Molecular Sequence Data , Polymorphism, Genetic , Promoter Regions, Genetic , Receptor, Notch4 , Receptors, Notch , Sequence Alignment , Sequence Analysis, DNA , Tissue DistributionABSTRACT
We have identified three new members of the olfactory receptor (OR) gene family within a large segment of DNA that is duplicated with high similarity near many human telomeres. This segment is present at 3q, 15q, and 19p in each of 45 unrelated humans sampled from various populations. Additional copies are present polymorphically at 11 other subtelomeric locations. The frequency with which the block is present at some locations varies among populations. While humans carry seven to 11 copies of the OR-containing block, it is located in chimpanzee and gorilla predominantly at a single site, which is not orthologous to any of the locations in the human genome. The observation that sequences flanking the OR-containing segment are duplicated on larger and different sets of chromosomes than the OR block itself demonstrates that the segment is part of a much larger, complex patchwork of subtelomeric duplications. The population analyses and structural results suggest the types of processes that have shaped these regions during evolution. From its sequence, one of the OR genes in this duplicated block appears to be potentially functional. Our findings raise the possibility that functional diversity in the OR family is generated in part through duplications and inter-chromosomal rearrangements of the DNA near human telomeres.
Subject(s)
Chromosomes, Human, Pair 19 , Polymorphism, Genetic , Receptors, Odorant/genetics , Telomere/genetics , Amino Acid Sequence , Chromosome Mapping , DNA/analysis , Humans , Molecular Sequence Data , Repetitive Sequences, Nucleic Acid , Sequence AlignmentSubject(s)
Academic Medical Centers/organization & administration , Hospital Restructuring/organization & administration , Nursing Staff, Hospital/organization & administration , Nursing, Team/organization & administration , Patient-Centered Care/organization & administration , Personnel Staffing and Scheduling/organization & administration , Critical Pathways , Focus Groups , Humans , Licensure, Nursing , Nursing Staff, Hospital/educationSubject(s)
Human Genome Project , Sequence Analysis, DNA , Animals , Chromosome Mapping , Chromosomes, Human , Cloning, Molecular , Computer Communication Networks , Databases, Factual , Diffusion of Innovation , Gene Library , Genetic Techniques , Genome , Genome, Human , Humans , Sequence Analysis, DNA/methods , Sequence Analysis, DNA/standards , Sequence Tagged SitesABSTRACT
The human beta T cell receptor (TCR) locus, comprising a complex family of genes, has been sequenced. The locus contains two types of coding elements--TCR elements (65 variable gene segments and two clusters of diversity, joining, and constant segments) and eight trypsinogen genes --that constitute 4.6 percent of the DNA. Genome-wide interspersed repeats and locus-specific repeats span 30 and 47 percent, respectively, of the 685-kilobase sequence. A comparison of the germline variable elements with their approximately 300 complementary DNA counterparts reveals marked differential patterns of variable gene expression, the importance of exonuclease activity in generating TCR diversity, and the predominant tendency for only functional variable elements to be present in complementary DNA libraries.
Subject(s)
Multigene Family , Receptors, Antigen, T-Cell, alpha-beta/genetics , Amino Acid Sequence , Base Sequence , Biological Evolution , Chromosomes, Human, Pair 7 , Chromosomes, Human, Pair 9 , DNA, Complementary/genetics , Exons , Genetic Variation , Humans , Introns , Molecular Sequence Data , Polymorphism, Genetic , Promoter Regions, Genetic , Pseudogenes , RNA Splicing , Repetitive Sequences, Nucleic Acid , Translocation, Genetic , Trypsinogen/geneticsABSTRACT
With efforts underway to develop a preventive human immunodeficiency virus type 1 (HIV-1) vaccine, it remains unclear which immune responses are sufficient to protect against infection and whether prior HIV-1 immunity can alter the subsequent course of HIV-1 infection. We investigated these issues in the context of a volunteer who received six HIV-1LAI envelope immunizations and 10 weeks thereafter acquired HIV-1 infection through a high-risk sexual exposure. In contrast to nonvaccinated acutely infected individuals, anamnestic HIV-1-specific B- and T-cell responses appeared within 3 weeks in this individual, and neutralizing antibody preceded CD8+ cytotoxic responses. Despite an asymptomatic course and an initial low level of detectable infectious virus, a progressive CD4+ cell decline and dysfunction occurred within 2 years. Although vaccination elicited immunity to HIV-1 envelope, which was recalled upon HIV-1 exposure, it was insufficient to prevent infection and subsequent immunodeficiency.
Subject(s)
AIDS Vaccines , Gene Products, env/immunology , HIV Antibodies/blood , HIV Infections/immunology , HIV Seropositivity , HIV-1 , Vaccines, Synthetic , Adult , Amino Acid Sequence , B-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Gene Products, env/biosynthesis , Gene Products, env/chemistry , HIV Envelope Protein gp160 , Homosexuality, Male , Humans , Male , Molecular Sequence Data , Protein Precursors/immunology , Risk-Taking , Smallpox Vaccine , T-Lymphocytes/immunology , Time FactorsABSTRACT
The human T-cell receptor beta-chain (TCRB) gene complex spans 575 kb in chromosome region 7q35 and has been the subject of a large-scale DNA sequencing effort. A contiguous 685-kb DNA sequence from this region was searched by computer analysis for the occurrence of simple sequence repeats (microsatellites) with core sequence lengths of 2-5 nucleotides. Twenty-nine such microsatellites of repeat number n > or = 9 were found, with the majority being dinucleotide repeats. By PCR analysis, 19 were found to be polymorphic in repeat number, thus averaging one per 36 kb. These polymorphic di-, tri-, and tetranucleotide repeats had between 3 and 15 differently sized alleles each. The potential usefulness of these TCRB microsatellites for detecting disease susceptibility alleles was examined by measuring the linkage disequilibrium between these markers and flanking biallelic mutations. All but 4 microsatellites (79%) demonstrated significant linkage disequilibrium (P < 0.0001). This present study highlights the utility and potential outcomes of large-scale DNA sequencing for the identification of polymorphic simple sequence repeats.