1,328 research outputs found

    Cloning and characterization of four murine homeobox genes.

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    The isolation and characterization of a P. Angulosus homeobox

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    Bibliography: pages 93-108.The aim of this thesis was to isolate and characterize a homeobox-containing gene of the South African sea urchin Parechinus angulosus. This was achieved by constructing a genomic library of several individuals and screening this library using a probe containing the Antennapedia homeobox. Eight clones were isolated and shown to represent different alleles of the same gene. One clone was sequenced, revealing a homeobox which was termed PaHboxl. This homeobox was compared to published homeobox sequences and shown to be a member of the Antp (Hoxl.l) subclass (table 1.1). A splice donor site was identified 23 bp upstream of the homeobox and the observation confirmed by RNAase mapping. PaHboxl is situated in a genomic area showing a significantly higher degree of restriction fragment polymorphism than expected. This was shown by a statistical analysis which should be of general value in the interpretation of such polymorphisms. The expression of PaHboxl was examined by RNAase protection assays and Northern blotting. Two distinct phases of expression were observed - during embryogenesis PaHboxl is expressed transiently at low levels in 11,5 hr mesenchyme blastula stage embryos (44 ± 8 transcripts per embryo) with levels 3-5 fold lower 2,5 hr before and after this stage. Expression is observed again at up to 160 fold higher levels in the adult with maximal expression in testis (11 transcripts per 10 pg total RNA), and increasingly lower levels in intestines, ovary and Aristotle's lantern. Two transcripts of size 5,2 and 5,7 kbp were observed. Expression in Aristotle's lantern and embryonic stages could not be detected by Northern analysis

    Identification and expression of a novel homeobox gene in a megakaryocytic leukemia cell line

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    Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

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    The onset of prezygotic and postzygotic barriers to gene flow between populations is a hallmark of speciation. One of the earliest postzygotic isolating barriers to arise between incipient species is the sterility of the heterogametic sex in interspecies' hybrids. Four genes that underlie hybrid sterility have been identified in animals: Odysseus, JYalpha, and Overdrive in Drosophila and Prdm9 (Meisetz) in mice. Mouse Prdm9 encodes a protein with a KRAB motif, a histone methyltransferase domain and several zinc fingers. The difference of a single zinc finger distinguishes Prdm9 alleles that cause hybrid sterility from those that do not. We find that concerted evolution and positive selection have rapidly altered the number and sequence of Prdm9 zinc fingers across 13 rodent genomes. The patterns of positive selection in Prdm9 zinc fingers imply that rapid evolution has acted on the interface between the Prdm9 protein and the DNA sequences to which it binds. Similar patterns are apparent for Prdm9 zinc fingers for diverse metazoans, including primates. Indeed, allelic variation at the DNA–binding positions of human PRDM9 zinc fingers show significant association with decreased risk of infertility. Prdm9 thus plays a role in determining male sterility both between species (mouse) and within species (human). The recurrent episodes of positive selection acting on Prdm9 suggest that the DNA sequences to which it binds must also be evolving rapidly. Our findings do not identify the nature of the underlying DNA sequences, but argue against the proposed role of Prdm9 as an essential transcription factor in mouse meiosis. We propose a hypothetical model in which incompatibilities between Prdm9-binding specificity and satellite DNAs provide the molecular basis for Prdm9-mediated hybrid sterility. We suggest that Prdm9 should be investigated as a candidate gene in other instances of hybrid sterility in metazoans

    Comparative and functional analysis of the Msx-1 proximal regulatory region

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    Classification and nomenclature of all human homeobox genes

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    <p>Abstract</p> <p>Background</p> <p>The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.</p> <p>Results</p> <p>We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive <it>DUX1 </it>to <it>DUX5 </it>homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.</p> <p>Conclusion</p> <p>We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.</p

    A novel non-coding DNA family in Caenorhabditis elegans

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    Many repetitive elements, for example, SINEs, LINEs, LTR-retrotransposons and other SSRs are dispersed throughout eukaryotic genomes. To understand the biological function of these repetitive elements is of great current research interest. previous termInnext term this study, we report on the identification of previous terma novel non-coding DNA family,next term designated CE1 previous termfamily, innext term the nematode C. previous termelegansnext term genome. Some CE1 elements constituted previous termanext term large palindrome sequence. The CE1 elements were interspersed at 95 sites previous terminnext term the C. previous termelegansnext term genome. Most of the CE1 elements were associated with, or were within, protein-coding genes. The sequence of the CE1 elements indicated that some could form previous termanext term hairpin structure. One of the CE1 previous termfamily,next term CE1(bs258), is located previous terminnext term the first intron of previous terma novelnext term gene, C46H11.6 which encodes previous termanext term PDZ/DHR/GLGF domain protein. previous termInnext term gfp and lacZ reporter gene assays the CE1(bs258) element appeared to behave as an enhancer element for the expression of C46H11.6 but no effect on the expression of the opposite direction gene, pat-10 which encodes the body-wall muscle troponin C. The CE1(bs258) RNA transcript was detected by RT-PCR even when CE1(bs258) was located previous terminnext term an intron. We conclude that CE1 elements are involved previous terminnext term the expression of adjacent genes and are therefore selectively retained previous terminnext term the C. previous termelegansnext term genome. We discussed previous termanext term biological function of the CE1(bs258) having many transcription factor-binding sites.</p

    Transcriptional Regulation: a Genomic Overview

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    The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic principles and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription

    The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes: evidence from the starlet sea anemone, Nematostella vectensis

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    BACKGROUND: Homeodomain transcription factors are key components in the developmental toolkits of animals. While this gene superclass predates the evolutionary split between animals, plants, and fungi, many homeobox genes appear unique to animals. The origin of particular homeobox genes may, therefore, be associated with the evolution of particular animal traits. Here we report the first near-complete set of homeodomains from a basal (diploblastic) animal. RESULTS: Phylogenetic analyses were performed on 130 homeodomains from the sequenced genome of the sea anemone Nematostella vectensis along with 228 homeodomains from human and 97 homeodomains from Drosophila. The Nematostella homeodomains appear to be distributed among established homeodomain classes in the following fashion: 72 ANTP class; one HNF class; four LIM class; five POU class; 33 PRD class; five SINE class; and six TALE class. For four of the Nematostella homeodomains, there is disagreement between neighbor-joining and Bayesian trees regarding their class membership. A putative Nematostella CUT class gene is also identified. CONCLUSION: The homeodomain superclass underwent extensive radiations prior to the evolutionary split between Cnidaria and Bilateria. Fifty-six homeodomain families found in human and/or fruit fly are also found in Nematostella, though seventeen families shared by human and fly appear absent in Nematostella. Homeodomain loss is also apparent in the bilaterian taxa: eight homeodomain families shared by Drosophila and Nematostella appear absent from human (CG13424, EMXLX, HOMEOBRAIN, MSXLX, NK7, REPO, ROUGH, and UNC4), and six homeodomain families shared by human and Nematostella appear absent from fruit fly (ALX, DMBX, DUX, HNF, POU1, and VAX)
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