Transcription of dispersed repeated sequences during Pleurodeles waltl oogenesis

New high copy tandem repeat in the content of the chicken W chromosome

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA)_n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA)_n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

Asymmetrical DNA and AT/GC base content of differential sector of Pleurodeles waltl sexual bivalent: a quantitative fluorescence imaging analysis in lampbrush chromosomes

The mitotic Z and W sex chromosomes in Pleurodeles seem to be identical. Earlier morphological and molecular analyses of lampbrush paired chromosomes in the female meiosis showed clearly that 20% of the chromosomal length located in the middle part of the sex bivalent (bivalent IV) is heteromorphic. We investigated here the base content and composition of the DNA axes in the heteromorphic region by quantitative fluorescence imaging using various base-specific (DAPI, Hoechst 33342 and chromo-mycin A3) or base-nonspecific (ethidium bromide) fluorescent DNA probes. Our results show a significantly higher percentage of AT bases in Z than in W differential sectors. In addition the entire base content of Z appears slightly higher than that of W.

Microdissection and cloning of DNA from landmark loops of amphibian lampbrush chromosomes

Microdissection of the "globular" and "granular" landmark loops of Pleurodeles lampbrush chromosomes and subsequent cloning of their DNA yielded several recombinant clones. The 6.6-kb insert of one of them was subcloned and the 600 bp of one subclone was characterized by Southern and slot hybridizations as well as by sequencing. This sequence, designated p130B, was shown to belong to a class of moderately repetitive DNA. RNA expression of this sequence was investigated by in situ hybridization of p130B to the nascent transcripts of lateral loops. Results showed that: (1) the same transcripts were not always found in matrices of landmarks exhibiting the same morphological features; (2) the same transcripts were expressed in loops of different morphological types. Based on these results we suggest that even if there is a morphological similarity of landmark loops, this does not reflect total similarity of their transcripts.

Lampbrush W and Z heterochromosome characterization with a monoclonal antibody and heat-induced chromosomal markers in the newt Pleurodeles waltl: W chromosome plays a role in female sex determination

Two subsets of lateral loops scattered on lampbrush chromosomes of the newt Pleurodeles waltl were characterized. One group was identified by labelling with a monoclonal antibody (A1). The second group was identified by the ability of the loops to be induced by heat treatment. Three loops of each subset were mapped on a short region of the two homologues of lampbrush bivalent IV. These regions appear to be heteromorphic because the six loops are always heterozygous. Five loops are found on one homologue and the sixth on the partner. The distribution of these markers in phenotypic females corresponding to the three sexual genotypes ZW, WW and ZZ shows an absolute correlation of the five loop group with the W chromosome and of the other loop with the Z chromosome. Therefore the heteromorphic regions of the homologues correspond to the differential segments of the heterochromosomes. The identification of a trisomic ZZW female suggests that the W chromosome bears female sex determinants. Furthermore the results show that heat induces loop development and that under normal conditions giant loop development is influenced by the sexual genotype.