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Open Access Research article

Effects of Alu elements on global nucleosome positioning in the human genome

Yoshiaki Tanaka12, Riu Yamashita24, Yutaka Suzuki1 and Kenta Nakai123*

Author Affiliations

1 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

2 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

3 Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Agency, 5-3 Yonbancho, Chiyoda-ku, Tokyo 102-0081, Japan

4 Frontier Research Initiative, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

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BMC Genomics 2010, 11:309  doi:10.1186/1471-2164-11-309

Published: 17 May 2010

Additional files

Additional file 1:

List of genome sequences used in this study. Sources and versions of genome sequences are listed.

Format: XLS Size: 21KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 2:

Degree of the genome-wide nucleotide periodicity of mono- and di-nucleotide steps from 2 bp to 22 bp. For each mono-/di-nucleotide step, the degree of the nucleotide periodicity within the ranges of 2-22 bp is shown.

Format: PDF Size: 2.4MB Download file

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Open Data

Additional file 3:

Degree of the genome-wide nucleotide periodicity of mono- and di-nucleotide steps from 2 bp to 250 bp. For each mono-/di-nucleotide step, the degree of the nucleotide periodicity within the ranges of 2-250 bp is shown.

Format: PDF Size: 1.3MB Download file

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Open Data

Additional file 4:

Frequency of mononucleotides within and around Alu elements. Distribution of mononucleotides within and around Alu elements is shown. Red, green, blue and cyan lines represent the frequency of adenine, cytosine, guanine and thymine, respectively.

Format: PDF Size: 622KB Download file

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Open Data

Additional file 5:

Nucleosome distribution around Alu elements with multi-hit tags considered. Nucleosome distribution around dimeric Alu elements, FLAMs, and FRAMs are shown. In this data, multi-hit tags are included.

Format: PDF Size: 1.1MB Download file

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Open Data

Additional file 6:

Distributions of hybridization signals around (A) Alu elements and (B) other repetitive elements. In each cell type (A375, IMR90, MALME, MCF7, MEC, PM or T47D) or in all cells, average hybridization signals around repetitive elements are shown.

Format: PDF Size: 301KB Download file

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Open Data

Additional file 7:

List of "repName" used for the classification of Alu family. Correspondence between the names of repeats ("repName" in UCSC) and the three Alu types (dimeric Alu elements, FLAMs and FRAMs) are listed.

Format: XLS Size: 19KB Download file

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Open Data

Additional file 8:

Strategy of detection of sequence tags within ± 150 bp of TSSs. Green arrows represent DNA sequences used as reference sequences. The orientation of the arrow shows the strand.

Format: PDF Size: 31KB Download file

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Open Data