Open Access Highly Accessed Research article

Hidden layers of human small RNAs

Hideya Kawaji123, Mari Nakamura2, Yukari Takahashi12, Albin Sandelin4, Shintaro Katayama2, Shiro Fukuda2, Carsten O Daub2, Chikatoshi Kai2, Jun Kawai2, Jun Yasuda12, Piero Carninci5* and Yoshihide Hayashizaki125

Author Affiliations

1 Functional RNA Research Program, RIKEN Frontier Research System, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

2 Genome Exploration Research Group, RIKEN Genomic Sciences Center(GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan

3 NTT Software Corporation, Teisan Kannai Bldg. 209, Yamashita-cho Naka-ku, Yokohama, Kanagawa, 231-8551, Japan

4 The Bioinformatics Centre, Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK-2100 København ∅, Denmark

5 Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan

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BMC Genomics 2008, 9:157  doi:10.1186/1471-2164-9-157

Published: 10 April 2008

Additional files

Additional file 1:

Schematic representation of the experimental protocols of small RNA library preparation. Ten steps in the protocols are shown.

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Additional file 2:

Length distributions of tRNA derived smallRNAs per isoacceptor. The distributions are shown as histograms, where X and Y axes mean the length of the small RNAs and their frequencies, respectively.

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Additional file 3:

Length distributions of repeat derived small RNAs per repeat classes and strands. Histograms are shown in the same way to the additional file 2.

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Additional file 4:

Relationship between tRNA and LTR. Schematic structure of tRNA priming of LTR reverse transcription (A), and alignment of LTR's primer binding site (PBS), tRNA 3'-end, and the small RNA matching them (B, C, D)

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Additional file 5:

snoRNA derived small RNA. Predicted secondary structure of snoRNA, mgU6-77, and the small RNAs derived from this (indicated with a dashed box).

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Additional file 6:

snRNA derived small RNA. Alignments of snRNA sequences and their derived small RNAs

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Additional file 7:

Length distributions of small RNAs derived from protein coding genes. Histograms are shown in the same way to the additional file 2.

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Additional file 8:

Predicted secondary structure of CEND1 proximal region. Predicted secondary structure of the proximal region (chr11:777439,777638) of the small RNAs located at the antisense of CEND1 gene. The region corresponding to the small RNA is indicated with red

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Additional file 9:

Small RNA clusters overlapping bidirectional promoters. Small RNA clusters overlapping bidirectional promoters are listed with their genomic coordinates and associated rRNAs

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Additional file 10:

Bidirectional promoters, small RNAs, and interstitial rRNA loci. Genomic view of small RNA generating loci, which are associated with small RNA, bidirectional promoters, and interstitial rRNAs.

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Additional file 11:

Interstitial rRNA. "rrna.psl" is the raw result of blat query for the genome with rRNA sequences. "rrna_overlapping_smallRNA.txt" and "rrna_overlapping_cage.txt" list the rrna aligned regions overlapping with the small RNA and the CAGE, respectively.

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Additional file 12:

Novel miRNA sequences. Hairpin sequences are described, where lower-case letters show the mature sequences.

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Additional file 13:

Predicted secondary structures of the novel miRNA precursors. Predicted hairpin structures of the novel miRNAs are shown. The region corresponding to the mature miRNAs are indicated with red.

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Additional file 14:

miRNAs derived from H19. Predicted hairpin structure of the miRNA (A), and genomic view of the loci.

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Additional file 15:

5'- and 3'-end nucleotide frequencies of the tRNA derived small RNAs. The frequencies are plotted as bar plot. The left shows the frequencies computed based on for all reads, and the right shows one based on only the unique sequences.

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Additional file 16:

Relationship between tRNAs originating the cleaved products and ones used as primers in LTR's reverse transcription. The Venn diagram shows if each of tRNA produces shorter or longer forms of the fragment, and involves in LTR reverse-transcription or not.

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Additional file 17:

Counts of the tRNA derived small RNAs depending on the 3'-ends. Counts of the tRNA derived small RNAs per their length, with distinction of the 3'-ends (harboring CCA or not)

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Additional file 18:

Small RNA sequences and their annotations. All of the unique sequences from our libraries are listed. DDBJ accession, internal id, count (or frequencies) of the sequence, length, annotations, RNA sequence, and clusters on the genome are described.

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Additional file 19:

Genomic coordinates of the small RNA clusters. Genomic coordinates of the clusters are described in GFF format.

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Additional file 20:

Counts of the small RNAs with alignment status. The number of small RNAs in each class is shown depending on the mapping methods: the mapping strategy adopted in this paper (A), and only the exact matches (B).

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Additional file 21:

Northern probes. List of the probes used in the Northern blotting experiments.

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