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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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Enriched and depleted dinucleotides around the midpoints of highly positioned dinucleosomes of Mixia osmundae. Composite profiles of the distances between midpoints of highly positioned (five or more piles) dinucleosomes and their closest dinucleotides are shown. The x- and y-axes represent, respectively, the position relative to the TSS and the normalized frequencies of the distances from the midpoints of dinucleosomes to the closest dinucleotides. The frequencies of the distances were normalized to the average frequencies at all the genome positions and each of the 16 profiles was normalized to 100.
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RSOB120043F8: Enriched and depleted dinucleotides around the midpoints of highly positioned dinucleosomes of Mixia osmundae. Composite profiles of the distances between midpoints of highly positioned (five or more piles) dinucleosomes and their closest dinucleotides are shown. The x- and y-axes represent, respectively, the position relative to the TSS and the normalized frequencies of the distances from the midpoints of dinucleosomes to the closest dinucleotides. The frequencies of the distances were normalized to the average frequencies at all the genome positions and each of the 16 profiles was normalized to 100.

Mentions: Previous studies reported that sequences rich in guanine (G) and cytosine (C) favour core nucleosomes, while sequences rich in adenine (A) and thymine (T) disfavour them, although some variations of preferred sequences exist between species [25]. We examined the biases of all 16 dinucleotide sequences in and around the midpoints of the mono- and dinucleosome positions by comparing the profiles of distances to the closest dinucleotides (see electronic supplementary material, figure S5, for definition of the closest dinucleotide). The enriched and depleted dinucleotides in and around the midpoints of the mononucleosome of M. osmundae showed features common to those of humans [22] (i.e. G/C-rich and A/T-rich sequences tend to be enriched, respectively, at the centres and edges of the mononucleosomes). We also examined dinucleotide enrichment in and around the dinucleosomes. Interestingly, there were clear preferences of dinucleotides associated with dinucleosomes, and the dinucleotides enriched or depleted at the midpoints of dinucleosomes differed from those found in and around the midpoints of mononucleosomes (figures 7 and 8). We believe this is the first report of DNA sequence preference of the nucleosomal linker DNA regions, inferred from the direct DNA sequence data. The dinucleotide sequence distributions are very different between the nucleosome-bound region and the nucleosomal linker region (figures 7 and 8). For example, the dinucleotide sequences CC, CG, GC and GG are enriched in the nucleosomal linker regions (figure 8), while AT and TA are depleted in the nucleosomal linker regions (figure 8). These dinucleotide sequences, AT and TA, are enriched in the nucleosome core regions (figure 7), while they become enriched in regions away from the midpoints of dinucleosomes towards their edges (figure 8; see electronic supplementary material, figure S6, for the profile in extended regions from the midpoints).FigureĀ 7.


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)

Enriched and depleted dinucleotides around the midpoints of highly positioned dinucleosomes of Mixia osmundae. Composite profiles of the distances between midpoints of highly positioned (five or more piles) dinucleosomes and their closest dinucleotides are shown. The x- and y-axes represent, respectively, the position relative to the TSS and the normalized frequencies of the distances from the midpoints of dinucleosomes to the closest dinucleotides. The frequencies of the distances were normalized to the average frequencies at all the genome positions and each of the 16 profiles was normalized to 100.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120043F8: Enriched and depleted dinucleotides around the midpoints of highly positioned dinucleosomes of Mixia osmundae. Composite profiles of the distances between midpoints of highly positioned (five or more piles) dinucleosomes and their closest dinucleotides are shown. The x- and y-axes represent, respectively, the position relative to the TSS and the normalized frequencies of the distances from the midpoints of dinucleosomes to the closest dinucleotides. The frequencies of the distances were normalized to the average frequencies at all the genome positions and each of the 16 profiles was normalized to 100.
Mentions: Previous studies reported that sequences rich in guanine (G) and cytosine (C) favour core nucleosomes, while sequences rich in adenine (A) and thymine (T) disfavour them, although some variations of preferred sequences exist between species [25]. We examined the biases of all 16 dinucleotide sequences in and around the midpoints of the mono- and dinucleosome positions by comparing the profiles of distances to the closest dinucleotides (see electronic supplementary material, figure S5, for definition of the closest dinucleotide). The enriched and depleted dinucleotides in and around the midpoints of the mononucleosome of M. osmundae showed features common to those of humans [22] (i.e. G/C-rich and A/T-rich sequences tend to be enriched, respectively, at the centres and edges of the mononucleosomes). We also examined dinucleotide enrichment in and around the dinucleosomes. Interestingly, there were clear preferences of dinucleotides associated with dinucleosomes, and the dinucleotides enriched or depleted at the midpoints of dinucleosomes differed from those found in and around the midpoints of mononucleosomes (figures 7 and 8). We believe this is the first report of DNA sequence preference of the nucleosomal linker DNA regions, inferred from the direct DNA sequence data. The dinucleotide sequence distributions are very different between the nucleosome-bound region and the nucleosomal linker region (figures 7 and 8). For example, the dinucleotide sequences CC, CG, GC and GG are enriched in the nucleosomal linker regions (figure 8), while AT and TA are depleted in the nucleosomal linker regions (figure 8). These dinucleotide sequences, AT and TA, are enriched in the nucleosome core regions (figure 7), while they become enriched in regions away from the midpoints of dinucleosomes towards their edges (figure 8; see electronic supplementary material, figure S6, for the profile in extended regions from the midpoints).FigureĀ 7.

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