BMC Genomics
Volume 9

Viewing options:

Abstract
Full text
PDF (811KB)
Additional files

Associated material:

Related literature:

Articles citing this article
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Kawaji H
Nakamura M
Takahashi Y
Sandelin A
Katayama S
Fukuda S
Daub CO
Kai C
Kawai J
Yasuda J
Carninci P
Hayashizaki Y

on PubMed

Kawaji H
Nakamura M
Takahashi Y
Sandelin A
Katayama S
Fukuda S
Daub CO
Kai C
Kawai J
Yasuda J
Carninci P
Hayashizaki Y
Related articles/pages
on Google

on Google Scholar

on PubMed
Evaluation of this article
in F1000 Biology

Tools:

Post to:

Research article

Hidden layers of human small RNAs

Hideya Kawaji¹^,2^,3 , Mari Nakamura² , Yukari Takahashi¹^,2 , Albin Sandelin⁴ , Shintaro Katayama² , Shiro Fukuda² , Carsten O Daub² , Chikatoshi Kai² , Jun Kawai² , Jun Yasuda¹^,2 , Piero Carninci⁵ and Yoshihide Hayashizaki¹^,2^,5

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

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

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

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

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

author email corresponding author email

BMC Genomics 2008, 9:157doi: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.

Format: PDF Size: 55KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 41KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 25KB Download file

This file can be viewed with: Adobe Acrobat Reader

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)

Format: PDF Size: 72KB Download file

This file can be viewed with: Adobe Acrobat Reader

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).

Format: PDF Size: 23KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 6:

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

Format: PDF Size: 13KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 19KB Download file

This file can be viewed with: Adobe Acrobat Reader

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

Format: PDF Size: 11KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 9:

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

Format: PDF Size: 20KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 456KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: ZIP Size: 10KB Download file

Additional file 12:

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

Format: FA Size: 1KB Download file

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.

Format: PDF Size: 29KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 14:

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

Format: PDF Size: 133KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 269KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: PDF Size: 36KB Download file

This file can be viewed with: Adobe Acrobat Reader

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)

Format: PDF Size: 111KB Download file

This file can be viewed with: Adobe Acrobat Reader

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.

Format: ZIP Size: 321KB Download file

Additional file 19:

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

Format: ZIP Size: 163KB Download file

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).

Format: PDF Size: 88KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional file 21:

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

Format: PDF Size: 19KB Download file

This file can be viewed with: Adobe Acrobat Reader