Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

Zakrzewski, Falk; Wenke, Torsten; Holtgräwe, Daniela; Weißhaar, Bernd; Schmidt, Thomas

doi:10.1186/1471-2229-10-8

Cited by 29 publications

(50 citation statements)

References 70 publications

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“…The satellites pBV and pEV were shown to be the most abundant repeat families in the sugar beet genome (Zakrzewski et al 2010). So far, only a subset of both satellites was analyzed and characterized Menzel et al 2008;Dechyeva et al 2003;.…”

Section: Heterochromatic Blocks Of Sugar Beet Chromosomes Are Enrichementioning

confidence: 98%

Epigenetic profiling of heterochromatic satellite DNA

Zakrzewski¹,

Weißhaar

Fuchs

et al. 2011

Chromosoma

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Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.

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Section: Heterochromatic Blocks Of Sugar Beet Chromosomes Are Enrichementioning

confidence: 98%

Epigenetic profiling of heterochromatic satellite DNA

Zakrzewski¹,

Weißhaar

Fuchs

et al. 2011

Chromosoma

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“…Satellite DNAs (repeat unit [100 bp) are predominantly located in subterminal, intercalary and centromeric regions of plant chromosomes. Minisatellites (repeat unit 7-100 bp) are often G/C rich and fast evolving and thought to originate from slippage replication or recombination between short direct repeats or slipped-strand mispairing replication at non-contiguous repeats (Zakrzewski et al 2010). Although the examined FESs represent only a small fraction of the Taxus gDNA, the identification of minisatellites and satellites is important as this is the first report of these elements in a gymnosperm.…”

Section: Transposable Elements Tandem Repeats and Ssrsmentioning

confidence: 99%

The first insight into the Taxus genome via fosmid library construction and end sequencing

2011

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Taxus mairei is a critically endangered and commercially important cultured medicinal gymnosperm in China and forms an important medicinal resource, but the research of its genome is absent. In this study, we constructed a T. mairei fosmid library and analyzed the fosmid end sequences to provide a preliminary assessment of the genome. The library consists of one million clones with an average insert size of about 39 kb, amounting to 3.9 genome equivalents. Fosmid stability assays indicate that T. mairei DNA was stable during propagation in the fosmid system. End sequencing of both 5 0 and 3 0 ends of 968 individual clones generated 1,923 sequences after trimming, with an average sequence length of 839 bp. BLASTN searches of the nr and EST databases of GenBank and BLASTX searches of the nr database resulted in 560 (29.1%) significant hits (E \ e -5 ). Repetitive sequences analysis revealed that 20.8% of end sequences are repetitive elements, which were composed of retroelements, DNA transposons, satellites, simple repeats, and low complexity sequences. The distribution pattern of various repeat types was found to be more similar to the gymnosperm Pinus and Picea than to the monocot and dicot. The satellites of T. mairei were significantly longer than those of P. taeda and P. glauca. The tetra-nucleotide repeats of T. mairei were much longer than those of P. glauca and P. taeda. The fosmid library and the fosmid end sequences, for the first time, will serve as a useful resource for large-scale genome sequencing, physical mapping, SSR marker development and positional cloning, and provide a better understanding of the Taxus genome.

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“…A prominent satellite is pEV which was first described in sugar beet [Schmidt and Metzlaff, 1991]. pEV is widespread in the genus and highly abundant in sugar beet and B. procumbens [Schmidt and Metzlaff, 1991;Zakrzewski et al, 2010] making it a suitable object for comparative investigation of satellite DNA diversity across species.…”

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Cytosine Methylation of an Ancient Satellite Family in the Wild Beet <b><i>Beta procumbens</i></b>

Schmidt

Hense

Minoche³

et al. 2014

Cytogenet Genome Res

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DNA methylation is an essential epigenetic feature for the regulation and maintenance of heterochromatin. Satellite DNA is a repetitive sequence component that often occurs in large arrays in heterochromatin of subtelomeric, intercalary and centromeric regions. Knowledge about the methylation status of satellite DNA is important for understanding the role of repetitive DNA in heterochromatization. In this study, we investigated the cytosine methylation of the ancient satellite family pEV in the wild beet Beta procumbens. The pEV satellite is widespread in species-specific pEV subfamilies in the genus Beta and most likely originated before the radiation of the Betoideae and Chenopodioideae. In B. procumbens, the pEV subfamily occurs abundantly and spans intercalary and centromeric regions. To uncover its cytosine methylation, we performed chromosome-wide immunostaining and bisulfite sequencing of pEV satellite repeats. We found that CG and CHG sites are highly methylated while CHH sites show only low levels of methylation. As a consequence of the low frequency of CG and CHG sites and the preferential occurrence of most cytosines in the CHH motif in pEV monomers, this satellite family displays only low levels of total cytosine methylation.

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Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

Cited by 29 publications

References 70 publications

Epigenetic profiling of heterochromatic satellite DNA

Epigenetic profiling of heterochromatic satellite DNA

The first insight into the Taxus genome via fosmid library construction and end sequencing

Cytosine Methylation of an Ancient Satellite Family in the Wild Beet <b><i>Beta procumbens</i></b>

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