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

Komissarov, Aleksey; Galkina, Svetlana; Koshel, Elena I.; Kulak, Maria; Dyomin, Aleksander G.; O’Brien, Stephen J.; Gaginskaya, Elena; Saifitdinova, Alsu

doi:10.1007/s00412-017-0646-5

Cited by 15 publications

(19 citation statements)

References 94 publications

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“…Lampbrush chromosome W consists of seven compact chromomeres associated with the clusters of certain tandem repeats [ 14 , 24 – 26 ]. All chromomeres of GGAW demonstrated enrichment with H3K9me3 and 5mC (Fig.…”

Section: Resultsmentioning

confidence: 99%

Mapping epigenetic modifications on chicken lampbrush chromosomes

et al. 2020

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Background The epigenetic regulation of genome is crucial for implementation of the genetic program of ontogenesis through establishing and maintaining differential gene expression. Thus mapping of various epigenetic modifications to the genome is relevant for studying the regulation of gene expression. Giant transcriptionally active lampbrush chromosomes are an established tool for high resolution physical mapping of the genome and its epigenetic modifications. This study is aimed at characterizing the epigenetic status of compact chromatin domains (chromomeres) of chicken lampbrush macrochromosomes. Results Distribution of three epigenetic modifications – 5-methylcytosine, histone H3 trimethylated at lysine 9 and hyperacetylated histone H4 – along the axes of chicken lampbrush chromosomes 1–4, Z and W was analyzed in details. Enrichment of chromatin domains with the investigated epigenetic modifications was indicated on the cytological chromomere-loop maps for corresponding chicken lampbrush chromosomes. Heterogeneity in the distribution of 5-methylcytosine and histone H3 trimethylated at lysine 9 along the chromosome axes was revealed. Conclusions On examples of certain chromomeres of chicken lampbrush chromosomes 1, 3, 4 and W we demonstrated that a combination of immunofluorescent staining and fluorescence in situ hybridization allows to relate the epigenetic status and a DNA sequence context of individual chromomeres.

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Section: Resultsmentioning

confidence: 99%

Mapping epigenetic modifications on chicken lampbrush chromosomes

et al. 2020

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“…In particular, some data were obtained for a small number of chromomeres consisting of massive arrays of tandemly repeated sequences. For instance, it was found that the majority of chromomeres on the chicken LBC W are occupied by specific families of DNA repeats (Solovei et al, 1998;Komissarov et al, 2018). Another example includes prominent dense chromomeres in the centromere regions of lampbrush chromosomes that were demonstrated to contain (peri) centromeric DNA repeats (Solovei et al, 1996;Saifitdinova et al, 2001;Krasikova et al, 2006;Krasikova et al, 2012;Zlotina et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing

et al. 2020

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Giant lampbrush chromosomes (LBCs) typical for growing oocytes of various animal species are characterized by a specific chromomere-loop appearance and massive transcription. Chromomeres represent universal units of chromatin packaging at LBC stage. While quite good progress has been made in investigation of LBCs structure and function, chromomere organization still remains poorly understood. To extend our knowledge on chromomere organization, we applied microdissection to chicken LBCs. In particular, 31 and 5 individual chromomeres were dissected one by one along the macrochromosome 4 and one microchromosome, respectively. The data on genomic context of individual chromomeres was obtained by high-throughput sequencing of the corresponding chromomere DNA. Alignment of adjacent chromomeres to chicken genome assembly provided information on chromomeres size and genomic boarders, indicating that prominent marker chromomeres are about 4-5 Mb in size, while common chromomeres of 1.5-3.5 Mb. Analysis of genomic features showed that the majority of chromomere-loop complexes combine gene-dense and gene-poor regions, while massive loopless DAPI-positive chromomeres lack genes and are remarkably enriched with different repetitive elements. Finally, dissected LBC chromomeres were compared with chromatin domains (topologically associated domains [TADs] and A/Bcompartments), earlier identified by Hi-C technique in interphase nucleus of chicken embryonic fibroblasts. Generally, the results obtained suggest that chromomeres of LBCs do not correspond unambiguously to any type of well-established spatial domains of interphase nucleus in chicken somatic cells.

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“…There are no genes on the W chromosome that determine sex. In the evolution of bird karyotypes, the W chromosome has undergone extensive degradation and accumulation of repetitive DNA [22,23]. Notably, the most common W chromosome-specific repeats XhoI, EcoRI, SspI, and newly described (GGAAA) n are compacted in densely packed chromomeres and do not transcribe at the lampbrush stage.…”

Section: W Chromosome and Its Rolementioning

confidence: 99%

“…The determination of the function of repeating sequences on Y or W chromosomes is in its infancy, but it is clear that these sequences play a functional role in gene regulation and chromatin structure [23]. Banded krait minor (Bkm) satellite repeat in the W chromosome consists of tandem arrays of GATA nucleotides.…”

Section: W Chromosome and Its Rolementioning

confidence: 99%

Specific Features of Sex Determination in Birds on the Example ofGallus gallusdomesticus

Smirnov¹,

Trukhina²

2020

Gene Expression and Phenotypic Traits

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The chapter is devoted to the consideration of sex determination in birds. The appearance of heteromorphic sex chromosomes (birds) has led to the emergence of some specific W chromosomal signal, which provides estrogen control of the development of a heterogametic sex. At present, two hypotheses about sex determination in birds compete. One of these hypotheses considers the number of Z chromosomes as a key sex-determining factor, while the other hypothesis supposes the presence in W chromosome of the key gene controlling ovarian development or suppressing the appearance of testes. Into the modern scheme of the genetic control of sex determination in birds (practically within the hypothesis of dose compensation), an epigenetic mechanism was added. The appearance of gonads in birds is most likely determined by sex hormones and to the greatest extent by estrogen under the control of W chromosome. It is desirable to pay attention to noncoding RNAs, their connection with the W chromosome and their role in bird sex determination.

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

Cited by 15 publications

References 94 publications

Mapping epigenetic modifications on chicken lampbrush chromosomes

Mapping epigenetic modifications on chicken lampbrush chromosomes

New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing

Specific Features of Sex Determination in Birds on the Example ofGallus gallusdomesticus

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