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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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The sizes of both short and long mononucleosome groups converged to their respective mean sizes as the number of piles increased. Normalized distributions of mononucleosomal DNA fragments were compared between distinct pile levels. The same number (27 801) of mononucleosomal DNA fragments was used to compute the frequency distribution of each pile subset. The Mann–Whitney U-test yielded p-values of 0.005 or less in all the pairwise size comparisons. Red line, 10 piles; yellow line, 5 piles; green line, 3 piles; blue line, 2 piles; black line, 1 pile.
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RSOB120043F3: The sizes of both short and long mononucleosome groups converged to their respective mean sizes as the number of piles increased. Normalized distributions of mononucleosomal DNA fragments were compared between distinct pile levels. The same number (27 801) of mononucleosomal DNA fragments was used to compute the frequency distribution of each pile subset. The Mann–Whitney U-test yielded p-values of 0.005 or less in all the pairwise size comparisons. Red line, 10 piles; yellow line, 5 piles; green line, 3 piles; blue line, 2 piles; black line, 1 pile.

Mentions: To investigate potential differences in the nucleosome sizes between loosely and well-positioned nucleosomes, we examined how the double-peak distribution of mononucleosome lengths changes with increasing pile level (see §5). Interestingly, the sizes of both short- and long-mononucleosome groups converged to their respective mean sizes as the piles increased (figure 3). This convergence to the mean size was also observed in highly positioned dinucleosomes (figure 4). These sizes to which highly positioned mono- and dinucleosomes converge may be their canonical sizes taken to optimize functionality related to transcription, and the increase of the canonical portion may be required to optimize the nucleosome organization for the processes.Figure 3.


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)

The sizes of both short and long mononucleosome groups converged to their respective mean sizes as the number of piles increased. Normalized distributions of mononucleosomal DNA fragments were compared between distinct pile levels. The same number (27 801) of mononucleosomal DNA fragments was used to compute the frequency distribution of each pile subset. The Mann–Whitney U-test yielded p-values of 0.005 or less in all the pairwise size comparisons. Red line, 10 piles; yellow line, 5 piles; green line, 3 piles; blue line, 2 piles; black line, 1 pile.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120043F3: The sizes of both short and long mononucleosome groups converged to their respective mean sizes as the number of piles increased. Normalized distributions of mononucleosomal DNA fragments were compared between distinct pile levels. The same number (27 801) of mononucleosomal DNA fragments was used to compute the frequency distribution of each pile subset. The Mann–Whitney U-test yielded p-values of 0.005 or less in all the pairwise size comparisons. Red line, 10 piles; yellow line, 5 piles; green line, 3 piles; blue line, 2 piles; black line, 1 pile.
Mentions: To investigate potential differences in the nucleosome sizes between loosely and well-positioned nucleosomes, we examined how the double-peak distribution of mononucleosome lengths changes with increasing pile level (see §5). Interestingly, the sizes of both short- and long-mononucleosome groups converged to their respective mean sizes as the piles increased (figure 3). This convergence to the mean size was also observed in highly positioned dinucleosomes (figure 4). These sizes to which highly positioned mono- and dinucleosomes converge may be their canonical sizes taken to optimize functionality related to transcription, and the increase of the canonical portion may be required to optimize the nucleosome organization for the processes.Figure 3.

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
Related in: MedlinePlus