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Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.

Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J - Open Biol (2012)

Bottom Line: The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species.We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes.We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACT
We present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nucleosome map based on sequencing mono- and dinucleosomal DNA fragments. The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species. We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes. We also describe a unique pattern found in the nucleosome-depleted region upstream of the TSS observed in the dinucleosome map and the precursor status of dinucleosomes prior to the digestion into mononucleosomes by comparing the mono- and dinucleosome maps. We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

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Histograms of (a) mononucleosomal and (b) dinucleosomal DNA fragment lengths of Mixia osmundae. The 30 386 916 mononucleosomal and 27 740 353 dinucleosomal DNA fragments were mapped to the genome. The distribution of the mononucleosomal DNA fragment lengths showed two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragment lengths showed only a single peak at 300 nt.
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RSOB120043F2: Histograms of (a) mononucleosomal and (b) dinucleosomal DNA fragment lengths of Mixia osmundae. The 30 386 916 mononucleosomal and 27 740 353 dinucleosomal DNA fragments were mapped to the genome. The distribution of the mononucleosomal DNA fragment lengths showed two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragment lengths showed only a single peak at 300 nt.

Mentions: We determined the positions of the 30 381 113 mono- (range 80–230 nt) and 27 443 027 dinucleosomes (range 200–400 nt) on the genome of M. osmundae by mapping the mono- and dinucleosomal DNA fragments sequenced by the Illumina GAIIx. The nucleosome position data can be downloaded at http://www.iu.a.u-tokyo.ac.jp/~hnishida/data_Mixia.zip. The size distribution of the mononucleosomal DNA fragments had two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragments had only a single peak at 300 nt (figure 2).Figure 2.


Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping.

Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J - Open Biol (2012)

Histograms of (a) mononucleosomal and (b) dinucleosomal DNA fragment lengths of Mixia osmundae. The 30 386 916 mononucleosomal and 27 740 353 dinucleosomal DNA fragments were mapped to the genome. The distribution of the mononucleosomal DNA fragment lengths showed two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragment lengths showed only a single peak at 300 nt.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3376729&req=5

RSOB120043F2: Histograms of (a) mononucleosomal and (b) dinucleosomal DNA fragment lengths of Mixia osmundae. The 30 386 916 mononucleosomal and 27 740 353 dinucleosomal DNA fragments were mapped to the genome. The distribution of the mononucleosomal DNA fragment lengths showed two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragment lengths showed only a single peak at 300 nt.
Mentions: We determined the positions of the 30 381 113 mono- (range 80–230 nt) and 27 443 027 dinucleosomes (range 200–400 nt) on the genome of M. osmundae by mapping the mono- and dinucleosomal DNA fragments sequenced by the Illumina GAIIx. The nucleosome position data can be downloaded at http://www.iu.a.u-tokyo.ac.jp/~hnishida/data_Mixia.zip. The size distribution of the mononucleosomal DNA fragments had two peaks at 132 and 150 nt, whereas that of the dinucleosomal DNA fragments had only a single peak at 300 nt (figure 2).Figure 2.

Bottom Line: The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species.We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes.We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

View Article: PubMed Central - PubMed

Affiliation: Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. hnishida@iu.a.u-tokyo.ac.jp

ABSTRACT
We present findings on the nucleosomal arrangement in the genome of the basidiomycete Mixia osmundae, focusing on nucleosomal linker DNA regions. We have assembled the genomic sequences of M. osmundae, annotated genes and transcription start sites (TSSs) on the genome, and created a detailed nucleosome map based on sequencing mono- and dinucleosomal DNA fragments. The nucleosomal DNA length distribution of M. osmundae is similar to that of the filamentous ascomycete Aspergillus fumigatus, but differs from that of ascomycetous yeasts, strongly suggesting that nucleosome positioning has evolved primarily through neutral drift in fungal species. We found clear association between dinucleotide frequencies and linker DNA regions mapped as the midpoints of dinucleosomes. We also describe a unique pattern found in the nucleosome-depleted region upstream of the TSS observed in the dinucleosome map and the precursor status of dinucleosomes prior to the digestion into mononucleosomes by comparing the mono- and dinucleosome maps. We demonstrate that observation of dinucleosomes as well as of mononucleosomes is valuable in investigating nucleosomal organization of the genome.

Show MeSH