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T Haaf

Publications and source records attributed to T Haaf.

At least 19 recordsLinked to original sources
PubMed2006

Methylation dynamics in the early mammalian embryo: implications of genome reprogramming defects for development.

In mouse and most other mammalian species, the paternal and maternal genomes undergo parent-specific epigenetic reprogramming during preimplantation development. The paternal genome is actively demethylated within a few hours after fertilization in the mouse, rat, pig, bovine, and human zygote, whereas the maternal genome is passively demethylated by a replication-dependent mechanism after the two-cell embryo stage. These genome-wide demethylation waves may have a role in reprogramming of the genetically inactive sperm and egg chromatin for somatic development. Disturbances in this highly coordinated process may contribute to developmental failures and defects in mammals. The frequency and severity of abnormal phenotypes increase after interfering with or bypassing essential steps of gametogenesis, early embryogenesis, or both. Nevertheless, it is plausible that normal fertilization, assisted reproduction, and embryo cloning are all susceptible to similar dysregulation of epigenetic components. Although the mouse maybe an excellent model for early human development, species and strain differences in the molecular and cellular events shortly after fertilization may have important implications for the efficiency of epigenetic reprogramming and the incidence of reprogramming defects. Some species, i.e., rabbit and sheep, do not require drastic genome-wide demethylation for early development, most likely because the transition from maternal to embryonic control occurs relatively late during preimplantation development. A better understanding of key reprogramming factors--in particular the demethylase activity in the fertilized egg--is crucial for improving human infertility treatment and the efficiency of mammalian embryo cloning.

Animals↗
PubMed2006

7E olfactory receptor gene clusters and evolutionary chromosome rearrangements.

Olfactory receptor (OR) genes of the 7E subfamily have been duplicated to multiple regions throughout the human genome. Segmental duplications containing 7E OR genes have been associated with both pathological and evolutionary chromosome rearrangements. Many of these breakpoint regions coincide with breaks of chromosomal synteny in the mouse, rat and/or chicken genomes. Collectively, these data suggest that 7E OR-containing regions represent hot spots of genomic instability.

Animals↗
PubMed2006

Segmental duplication associated with evolutionary instability of human chromosome 3p25.1.

Fluorescence in situ hybridization (FISH) of human bacterial artificial chromosome (BAC) clones to orangutan metaphase spreads localized a breakpoint between human chromosome 3p25.1 and orangutan chromosome 2 to a <30-kb interval. The inversion occurred in a relatively gene-rich region with seven genes within 500 kb. The underlying breakpoint is closely juxtaposed to validated genes, however no functional gene has been disrupted by the evolutionary rearrangement. An approximately 21-kb DNA segment at the 3p25.1 breakpoint region has been duplicated intrachromosomally and interchromosomally to multiple regions in the orangutan and human genomes, providing additional evidence for the role of segmental duplications in hominoid chromosome evolution.

Animals↗
PubMed2005

Disruption of TCBA1 associated with a de novo t(1;6)(q32.2;q22.3) presenting in a child with developmental delay and recurrent infections.

A boy with developmental delay, particularly of speech, a distinct face, antineutrophil cytoplasmic antibodies, and recurrent infections was found to have an apparently balanced de novo t(1;6)(q32.3;q22.3) translocation. Fluorescent in situ hybridisation with BAC/PAC clones and long range polymerase chain reaction products assessed in the human genome sequence localised the chromosome 1 breakpoint to a 9.8 kb segment within a hypothetical gene, LOC388735, and the chromosome 6 breakpoint to a 12.8 kb segment in intron 4 of the T-cell lymphoma breakpoint-associated target 1 (TCBA1) gene. Disruption and/or formation of TCBA1 fusion genes in T cell lymphoma and leukaemia cell lines suggests a role for this gene in tumorigenesis. The isolated mouse Tcba1 gene shows 91% amino acid sequence similarity with human TCBA1. It is expressed in fetal and adult brain and with lower levels in liver and testis. The human gene has been reported to be expressed exclusively in brain and thymus. Reduced TCBA1 expression in brain and thymus may explain at least some of the symptoms in this patient. It is concluded that germline alterations of the TCBA1 gene are associated with developmental delay and typical physical features.

Amino Acid Sequence↗
PubMed2005

Genomic structure and paralogous regions of the inversion breakpoint occurring between human chromosome 3p12.3 and orangutan chromosome 2.

Intrachromosomal duplications play a significant role in human genome pathology and evolution. To better understand the molecular basis of evolutionary chromosome rearrangements, we performed molecular cytogenetic and sequence analyses of the breakpoint region that distinguishes human chromosome 3p12.3 and orangutan chromosome 2. FISH with region-specific BAC clones demonstrated that the breakpoint-flanking sequences are duplicated intrachromosomally on orangutan 2 and human 3q21 as well as at many pericentromeric and subtelomeric sites throughout the genomes. Breakage and rearrangement of the human 3p12.3-homologous region in the orangutan lineage were associated with a partial loss of duplicated sequences in the breakpoint region. Consistent with our FISH mapping results, computational analysis of the human chromosome 3 genomic sequence revealed three 3p12.3-paralogous sequence blocks on human chromosome 3q21 and smaller blocks on the short arm end 3p26-->p25. This is consistent with the view that sequences from an ancestral site at 3q21 were duplicated at 3p12.3 in a common ancestor of orangutan and humans. Our results show that evolutionary chromosome rearrangements are associated with microduplications and microdeletions, contributing to the DNA differences between closely related species.

Animals↗
PubMed2004

Chromosome banding in Amphibia. XXX. Karyotype aberrations in cultured fibroblast cells.

The present study reports for the first time on the numerical and structural chromosome anomalies that spontaneously arise in aging cultured fibroblast cells of Amphibia. The analyses were conducted on kidney fibroblasts of three anuran species with extremely divergent genome sizes (Bufo rubropunctatus, Scaphiopus holbrooki, Gastrotheca riobambae), in the sixth up to the 14th culture passage. The chromosomal rearrangements were identified by means of the 5-bromodeoxyuridine/deoxythymidine (BrdU/dT) replication banding technique. The aberrations can be either confined to a single chromosome, or else involve all chromosomes of the karyotype. The most frequent structural aberrations in the cell cultures of S. holbrooki and G. riobambae are tandem fusions between two or more chromosomes. These tandem fusions originating in vitro in long-termed cell cultures reflect the chromosome mutations which also took place during amphibian phylogenesis.

Animals↗
PubMed2003

D4F104S1 deletion in facioscapulohumeral muscular dystrophy: phenotype, size, and detection.

BACKGROUND: The facioscapulohumeral muscular dystrophy (FSHD) locus maps to 4q35 where it is closely linked to D4F104S1 (p13E-11), a probe that recognizes the pathognomonic FSHD deletion involving the subtelomeric D4Z4 tandem repeat array. Extended deletions that include both the more proximal D4F104S1 region and the D4Z4 repeat array proper do, however, occur, albeit rarely, and such deletions can lead to difficulties of interpretation in the diagnostic setting. OBJECTIVE: To devise a means to determine the true frequency of proximally extended deletions in individuals with FSHD. METHODS: Three families selected for this study were originally identified during routine FSHD analysis on the basis that the affected individuals in each family had failed to exhibit a small (<38-kb) EcoRI fragment. High molecular weight DNA from these families was analyzed with both conventional and pulsed-field gel electrophoresis using DNA markers p13E-11, 9B6A, B31, 4qA, and 4qB. RESULTS: Large genomic deletions were identified involving both D4Z4 and D4F104S1. The precise number of D4Z4 repeat units borne by the p13E11 deletion allele was established by the use of an additional restriction enzyme (MseI) digest. All three cases carry different sizes of deletion proximal to the D4Z4 repeat units. With use of a recently described telomeric probe, 4qA, a method was developed that identifies large genomic deletions involving both D4Z4 and D4F104S1 using conventional gel electrophoresis. CONCLUSION: Proximally extended deletions can be found in patients with a normal spectrum of the disease. This assay promises to allow estimation of the true frequency of proximally extended deletions and should improve the accuracy and reliability of molecular diagnostic testing for FSHD.

Adult↗
PubMed2003

Chromosome banding in Amphibia. XXVII. DNA replication banding patterns in three anuran species with greatly differing genome sizes.

The mitotic chromosomes of three anuran species, Scaphiopus holbrooki, Litoria infrafrenata and Odontophrynus americanus, were analyzed by means of the 5-bromodeoxyuridine/deoxythymidine (BrdU/dT) replication banding technique. These species exhibit large differences in their genome sizes: S. holbrooki possesses one of the smallest genomes among vertebrates, L. infrafrenata has a genome size near the modal DNA value of most Amphibia, whereas O. americanus is a tetraploid species. BrdU/dT labeling induces reproducible and reliable R- and G-replication bands along the metaphase chromosomes of all three species. Irrespective of the genome size of the species considered, the number of early (R-) and late (G-) replicating bands per haploid karyotype is nearly the same. The chromosomes of the autotetraploid O. americanus can be arranged into sets of four homologous chromosomes (quartets). C-bands and BrdU/dT replication bands reveal heterogeneity within the quartets 1, 3 and 4 that are interpreted as the initiation of a diploidization process.

Animals↗
PubMed2002

Aberrant methylation patterns at the two-cell stage as an indicator of early developmental failure.

The fertilized mouse egg actively demethylates the paternal genome within a few hours after fertilization, whereas the maternal genome is only passively demethylated by a replication-dependent mechanism after the two-cell stage. This evolutionarily conserved assymetry in the early diploid mammalian embryo may have a role in methylation reprogramming of the two very different sets of sperm and egg chromatin for somatic development and formation of totipotent cells. Immunofluorescence staining with an antibody against 5-methylcytosine (MeC) showed that the incidence of abnormal methylation patterns differs between mouse two-cell embryos from superovulated females, nonsuperovulated matings, and in vitro fertilization (IVF). It also depends on embryo culture conditions and genetic background. In general, there was a good correlation with the number of embryos (from the same experiment) which did not develop in vitro up to the blastocyst stage. Thus, aberrant genome-wide DNA methylation in early embryos may be an important mechanism contributing to the high incidence of developmental failure in mammals. Similar to the situation in abnormally methylated embryos from nuclear transfer, it may cause a high incidence of pregnancy loss and abnormal phenotypes.

Acetaldehyde↗
PubMed2002

Chromosome banding in Amphibia. XXII. Atypical y chromosomes in Gastrotheca walkeri and Gastrotheca ovifera (Anura, Hylidae).

The chromosomes of the rare South American marsupial frogs Gastrotheca walkeri and G. ovifera were extensively reexamined with various banding techniques. The karyotypes of both species are distinguished by a new category of XY female symbol /XX male symbol female sex chromosomes. The unusual Y chromosomes are characterized by containing the least amount of constitutive heterochromatin in the karyotypes. This is in contrast to all previously known amphibian Y chromosomes and does not fit the evolutionary model of early XY differentiation in vertebrates. In male meiosis, the heteromorphic XY chromosomes of both species still exhibit the same pairing configurations as the autosomes. DNA flow cytometric measurements show the nuclear DNA amount of G. walkeri to be 10.90 pg. The significance of the XY/XX sex chromosomes of these marsupial frogs, the various classes of constitutive heterochromatin detected, and the data obtained from meiotic analyses are discussed in detail.

Animals↗
PubMed2002

Chromosome banding in amphibia. XXIII. Giant W sex chromosomes and extremely small genomes in Eleutherodactylus euphronides and Eleutherodactylus shrevei (Anura, Leptodactylidae).

Highly differentiated, heteromorphic ZZ female symbol /ZW male symbol sex chromosomes were found in the karyotypes of the neotropical leptodactylid frogs Eleutherodactylus euphronides and E. shrevei. The W chromosomes are the largest heterochromatic, female-specific chromosomes so far discovered in the class Amphibia. The analyses of the banding patterns with AT- and GC base-pair specific fluorochromes show that the constitutive heterochromatin in the giant W chromosomes consists of various categories of repetitive DNA sequences. The W chromosomes of both species are similar in size, morphology and banding patterns, whereas their Z chromosomes exhibit conspicuous differences. In the cell nuclei of female animals, the W chromosomes form very prominent chromatin bodies (W chromatin). DNA flow cytometric measurements demonstrate clear differences in the DNA content of male and female erythrocytes caused by the giant W chromosome, and also shows that these Eleutherodactylus genomes are among the smallest of all amphibian genomes. The importance of the heteromorphic ZW sex chromosomes for the study of Z-linked genes, the similarities and differences of the two karyotypes, and the significance of the exceptionally small genomes are discussed.

Animals↗
PubMed2002

Chromosome banding in Amphibia. XXV. Karyotype evolution and heterochromatin characterization in Australian Mixophyes (Anura, Myobatrachidae).

The mitotic chromosomes of the Australian ground frogs Mixophyes fasciolatus and M. schevilli were analyzed by means of banding techniques and restriction endonuclease digestions. Chromosomal differentiation in these two species occurred exclusively by considerable changes in the amount of telomeric and centromeric heterochromatin, whereas the sizes and locations of interstitial heterochromatic regions, the sizes of all euchromatic segments as well as the positions of centromeres remained nearly identical during karyotype evolution. The major heterochromatic regions in the karyotypes of M. fasciolatus and M. schevilli amount to 30.2% and 20.7%, respectively. They consist of AT base pair-rich repetitive DNA sequences that are brightly labeled by AT-specific fluorochromes and display quenched fluorescence after staining with GC-specific fluorochromes. The heterochromatic regions can be differentiated by treatment of metaphase chromosomes and interphase cell nuclei with various restriction enzymes which either disclose the complete set of C-band patterns in the karyotypes of both species, or else reveal several subsets of these C-bands.

Animals↗
PubMed2002

Chromosome banding in Amphibia. XXIV. The B chromosomes of Gastrotheca espeletia (Anura, Hylidae).

The mitotic chromosomes of an Ecuadorian population of the marsupial frog Gastrotheca espeletia were analyzed by means of banding techniques and fluorescence in situ hybridization. This species is characterized by unusual supernumerary (B) chromosomes. The maximum number of B chromosomes is 9 and they occur in three different morphological types. Banding analyses show that the B chromosomes are completely heterochromatic, consist of AT base pair-rich repeated DNA sequences, replicate their DNA in very late S-phase of the cell cycle, and are probably derived from a centromeric or paracentromeric region of a standard (A) chromosome. Exceptionally, the B chromosomes carry 18S + 28S ribosomal RNA genes and the conserved vertebrate telomeric DNA sequence appears to be underrepresented. Flow cytometric measurements of the nuclear DNA content differentiate between individuals with different numbers of B chromosomes. Significantly more B chromosomes are present in female than in male animals.

Animals↗
PubMed2002

Effects of higher-order nuclear structure and Rad51 overexpression on radiation-induced chromosome rearrangements.

The microchromosomes (MICs) in chicken DT40 lymphocytes are usually clustered in the center of the nucleus, whereas the macrochromosomes (MACs) are preferentially located toward the nuclear periphery. This compartmentalized architecture of the nucleus is associated with a low frequency of translocations between MICs and MACs after induction of DNA breaks by a radiation track(s). In contrast, the MICs in chick embryo fibroblasts (CEFs) tend to be located throughout the entire nuclear volume. The resulting side-to-side arrangement of MIC and MAC territories favors radiation-induced MIC/MAC translocations, which occur more frequently in CEF cells than MIC/MIC or MAC/MAC rearrangements. Collectively, our results suggest that preformed physical contacts are a prerequisite for the generation of chromosome rearrangements through recombinational repair of DNA damage. Cell type-specific higher-order nuclear organization may prevent or stimulate the formation of particular chromosome aberrations in pathology and evolution. Ectopic expression of the recombination protein Rad51 can protect cells from radiation-induced translocations. The repair activity of overexpressed Rad51 is more important for cells that are irradiated in S/G(2) phase than for cells in G(1) phase. Evidently, homologous recombination between sister chromatids of a replicated chromosome is more frequent than that between homologous or heterologous chromosomes during G(1) phase.

Animals↗
PubMed2002

Comparative mapping of Z-orthologous genes in vertebrates: implications for the evolution of avian sex chromosomes.

Sex chromosomes of birds and mammals are highly differentiated and share several cytological features. However, comparative gene mapping reveals extensive conserved synteny between the chicken Z sex chromosome and human chromosome 9 but not the human X sex chromosome, implying an independent origin of avian and mammalian sex chromosomes. To better understand the evolution of the avian Z chromosome we analysed the synteny of chicken Z-linked genes in zebrafish, which is the best-mapped teleost genome so far. Existing zebrafish maps do not support the existence of an ancestral Z linkage group in the zebrafish genome, whereas mammalian X-linked genes show at least some degree of synteny conservation. This is consistent with in situ hybridisation mapping data in the freshwater pufferfish, Tetraodon nigroviridis where mammalian X-linked genes show a much higher degree of conserved synteny than human chromosome 9 or the avian Z chromosome. Collectively, these data argue in favour of a more recent evolution of the avian Z chromosome, compared with the mammalian X.

Animals↗
PubMed2002

X chromosomes of American marsupials contain minimal amounts of euchromatin.

The karyotypes of four South American didelphid marsupials, representing diploid numbers of 2n = 14 and 18, have been analyzed by a variety of banding techniques. The 2n = 14 karyotypes display a high degree of homoeology, but there also exist distinct similarities between the 2n = 14 and 2n = 18 karyotypes. The interspecific differences found are due to centric fissions, pericentric inversions, and variations in the amount and composition of the constitutive heterochromatin. Contrary to the evolutionary conservation of the banding patterns in all autosomal arms, there are multiple differences in the number and chromosomal location of the nucleolus organizer regions. In species with X-linked nucleolus organizers, the 18S + 28S ribosomal RNA genes escape inactivation in female cells. Measurements on the X chromosomes of Marmosa fuscata and Micoureus demerarae unexpectedly reveal the lowest quantities of euchromatin so far determined in the X chromosomes of mammals: 1.5% and 1.8%, respectively, of their haploid female genomes. This is significantly less than the amount of euchromatin in the basic X chromosomes of other marsupials (3%) or eutherians (5%).

Animals↗