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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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Pie chart of the genera with which each CDS of Mixia osmundae showed the highest similarity. The BLASTP program at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for the protein sequence similarity search. A total of 5399 CDSs (E-value < 10−5) were analysed.
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RSOB120043F1: Pie chart of the genera with which each CDS of Mixia osmundae showed the highest similarity. The BLASTP program at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for the protein sequence similarity search. A total of 5399 CDSs (E-value < 10−5) were analysed.

Mentions: The 6726 protein-coding sequences were aligned to the protein sequences of 80 fungal organisms using the BLASTP program in Fungal Genomes Central at NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/guide/fungi/; electronic supplementary material, table S2). The BLASTP search revealed that 5399 (80.3%) of the 6726 CDSs had similar amino acid sequences with E-value < 10−5 among the fungal genes. Among the 5399 sequences, 4908 (90.9%), 402 (7.4%), 55 (1.0%) and 34 (0.6%) showed the highest similarity with proteins of Basidiomycota, Pezizomycotina (Ascomycota), Saccharomycotina (Ascomycota) and Taphrinomycotina (Ascomycota), respectively (figure 1). At the genus level, 1213 (22.5%), 753 (13.9%) and 665 (12.3%) showed the highest similarity with proteins of genera Melampsora, Rhodotorula and Puccinia, respectively (figure 1). As these three genera belong to Pucciniomycotina in Basidiomycota, M. osmundae is probably a member of Pucciniomycotina.Figure 1.


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)

Pie chart of the genera with which each CDS of Mixia osmundae showed the highest similarity. The BLASTP program at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for the protein sequence similarity search. A total of 5399 CDSs (E-value < 10−5) were analysed.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

RSOB120043F1: Pie chart of the genera with which each CDS of Mixia osmundae showed the highest similarity. The BLASTP program at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for the protein sequence similarity search. A total of 5399 CDSs (E-value < 10−5) were analysed.
Mentions: The 6726 protein-coding sequences were aligned to the protein sequences of 80 fungal organisms using the BLASTP program in Fungal Genomes Central at NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/guide/fungi/; electronic supplementary material, table S2). The BLASTP search revealed that 5399 (80.3%) of the 6726 CDSs had similar amino acid sequences with E-value < 10−5 among the fungal genes. Among the 5399 sequences, 4908 (90.9%), 402 (7.4%), 55 (1.0%) and 34 (0.6%) showed the highest similarity with proteins of Basidiomycota, Pezizomycotina (Ascomycota), Saccharomycotina (Ascomycota) and Taphrinomycotina (Ascomycota), respectively (figure 1). At the genus level, 1213 (22.5%), 753 (13.9%) and 665 (12.3%) showed the highest similarity with proteins of genera Melampsora, Rhodotorula and Puccinia, respectively (figure 1). As these three genera belong to Pucciniomycotina in Basidiomycota, M. osmundae is probably a member of Pucciniomycotina.Figure 1.

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