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. 2010 Jan;38(Database issue):D98-104.
doi: 10.1093/nar/gkp1017. Epub 2009 Nov 12.

DBTSS Provides a Tissue Specific Dynamic View of Transcription Start Sites

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Free PMC article

DBTSS Provides a Tissue Specific Dynamic View of Transcription Start Sites

Riu Yamashita et al. Nucleic Acids Res. .
Free PMC article

Abstract

DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. In this update, we included 330 million new tags generated by massively sequencing the 5'-end of oligo-cap selected cDNAs in humans and mice. The tags were collected from normal fetal or adult human tissues, including brain, thymus, liver, kidney and heart, from 6 human cell lines in 21 diverse growth conditions as well as from mouse NIH3T3 cell line: altogether 31 different cell types or culture conditions are represented. This unprecedented increase in depth of data now allows DBTSS to faithfully represent the dynamically changing landscape of TSSs in different cell types and conditions, during development and in the course of evolution. Differential usage of alternative 5'-ends across cell types and conditions can be viewed in a series of new interfaces. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/.

Figures

Figure 1.
Figure 1.
Interfaces of the newly implemented ‘TSS tag viewer’. TSS sequence tag information can be retrieved from the top page (A) by following either of the links. The viewers corresponding to each link are represented in the indicated figures. (B) In the ‘Database Search’ form, users can directly specify the 5′-end tags of a gene or a cell type they want to view. (C) In the ‘TSS tag search’ form, users can search TSS tags by specifying cell types, fold induction and/or tag counts. They can also choose which category of tags should be considered (e.g. whether tags of different alternative promoters should be counted separately or not). (D) An example of developmental stage-specific alternative promoters. In the zinc finger protein 622 gene (NM_033414), the promoter indicated in moss green (second panel) is selectively used in fetal heart. The upper and lower panels represent the TSS tag usages in adult and fetal tissues, respectively. Height of the vertical bars represents the number of TSS Seq tags located in the corresponding genomic regions. Different alternative promoters are represented by different colors. Each horizontal line represents the experimental condition from which TSS tags were derived. Legends for the tissues and sum of the TSS tag counts are shown at the right margin. (E) Example of the case in which alternative promoter-specific induction was observed in response to IL-4 stimulation in Ramos cells. In the hypothetical protein LOC746 gene (NM_ 014206), the alternative promoter indicated in red (first panel) is selectively induced while the other alternative promoter indicated in blue (second panel) remained unchanged. The indicated TSS regions are magnified to the nucleotide level in the bottom lower panels.
Figure 1.
Figure 1.
Interfaces of the newly implemented ‘TSS tag viewer’. TSS sequence tag information can be retrieved from the top page (A) by following either of the links. The viewers corresponding to each link are represented in the indicated figures. (B) In the ‘Database Search’ form, users can directly specify the 5′-end tags of a gene or a cell type they want to view. (C) In the ‘TSS tag search’ form, users can search TSS tags by specifying cell types, fold induction and/or tag counts. They can also choose which category of tags should be considered (e.g. whether tags of different alternative promoters should be counted separately or not). (D) An example of developmental stage-specific alternative promoters. In the zinc finger protein 622 gene (NM_033414), the promoter indicated in moss green (second panel) is selectively used in fetal heart. The upper and lower panels represent the TSS tag usages in adult and fetal tissues, respectively. Height of the vertical bars represents the number of TSS Seq tags located in the corresponding genomic regions. Different alternative promoters are represented by different colors. Each horizontal line represents the experimental condition from which TSS tags were derived. Legends for the tissues and sum of the TSS tag counts are shown at the right margin. (E) Example of the case in which alternative promoter-specific induction was observed in response to IL-4 stimulation in Ramos cells. In the hypothetical protein LOC746 gene (NM_ 014206), the alternative promoter indicated in red (first panel) is selectively induced while the other alternative promoter indicated in blue (second panel) remained unchanged. The indicated TSS regions are magnified to the nucleotide level in the bottom lower panels.
Figure 2.
Figure 2.
Interface of the updated ‘ncRNA viewer’ and ‘Comparative Genomic viewer’. (A) Example of the TSS tags identified from the surrounding regions of reported small RNAs. The result of the search for a small ncRNA, miR9-2, is shown. Complete cDNA (AK091356) identified in the same region is also represented by orange boxes. (B) Evolutional conservation of the alternative promoters of the protein kinase C zeta (PRKCZ) genes (NM_002744). Different alternative promoters are marked by different colors. Upper and lower panels represent the TSS information in humans and mice, respectively. Corresponding genomic sequences were aligned according to the UCSC Genome Browser information.

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