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tRFdb: a database for transfer RNA fragments.

Kumar P, Mudunuri SB, Anaya J, Dutta A - Nucleic Acids Res. (2014)

Bottom Line: The database can be searched by tRF ID or tRF sequence, and the results can be limited by organism.The search results show the genome coordinates and names of the tRNAs the sequence may derive from, and there are links for the sequence of the tRF and parental tRNA, and links for the read counts in all the corresponding small RNA libraries.As a case study for how this database may be used, we have shown that a certain class of tRFs, tRF-1s, is highly upregulated in B-cell malignancies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.

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Related in: MedlinePlus

Illustration of primary tRNA, mature tRNA and tRF-5, -3 and -1. tRF-1 (shown in green) is generated from primary tRNA. tRF-5 and -3 are produced from mature tRNA. The tRF-3s always have ‘CCA’ at their 3′ end.
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Figure 1: Illustration of primary tRNA, mature tRNA and tRF-5, -3 and -1. tRF-1 (shown in green) is generated from primary tRNA. tRF-5 and -3 are produced from mature tRNA. The tRF-3s always have ‘CCA’ at their 3′ end.

Mentions: tRNA-derived RNA fragments approaching the size of microRNAs were first appreciated as a class of small non-coding RNA in 2009 by three different laboratories (1–3). Sequences mapping to the 5′ ends of tRNAs (transfer RNA fragment (tRF)-5s), the 3′ ends of tRNAs (tRF-3s) and the trailer sequence (tRF-1s) were observed in LNCap and C4-2 cells, and a tRF-1 was shown to be involved in cell proliferation (Figure 1) (2). tRFs were also found to be present in HeLa nuclei and associated with Argonautes, and present in HEK 293 cells and involved in RNA silencing (1,3). Since then tRFs have been found in all domains of life, and there are now a few reviews cataloging the known functions of tRFs (4,5). Despite this work on tRFs, it is not known how tRF-5s or tRF-3s are generated, and the function of the majority of tRFs is unknown.


tRFdb: a database for transfer RNA fragments.

Kumar P, Mudunuri SB, Anaya J, Dutta A - Nucleic Acids Res. (2014)

Illustration of primary tRNA, mature tRNA and tRF-5, -3 and -1. tRF-1 (shown in green) is generated from primary tRNA. tRF-5 and -3 are produced from mature tRNA. The tRF-3s always have ‘CCA’ at their 3′ end.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383946&req=5

Figure 1: Illustration of primary tRNA, mature tRNA and tRF-5, -3 and -1. tRF-1 (shown in green) is generated from primary tRNA. tRF-5 and -3 are produced from mature tRNA. The tRF-3s always have ‘CCA’ at their 3′ end.
Mentions: tRNA-derived RNA fragments approaching the size of microRNAs were first appreciated as a class of small non-coding RNA in 2009 by three different laboratories (1–3). Sequences mapping to the 5′ ends of tRNAs (transfer RNA fragment (tRF)-5s), the 3′ ends of tRNAs (tRF-3s) and the trailer sequence (tRF-1s) were observed in LNCap and C4-2 cells, and a tRF-1 was shown to be involved in cell proliferation (Figure 1) (2). tRFs were also found to be present in HeLa nuclei and associated with Argonautes, and present in HEK 293 cells and involved in RNA silencing (1,3). Since then tRFs have been found in all domains of life, and there are now a few reviews cataloging the known functions of tRFs (4,5). Despite this work on tRFs, it is not known how tRF-5s or tRF-3s are generated, and the function of the majority of tRFs is unknown.

Bottom Line: The database can be searched by tRF ID or tRF sequence, and the results can be limited by organism.The search results show the genome coordinates and names of the tRNAs the sequence may derive from, and there are links for the sequence of the tRF and parental tRNA, and links for the read counts in all the corresponding small RNA libraries.As a case study for how this database may be used, we have shown that a certain class of tRFs, tRF-1s, is highly upregulated in B-cell malignancies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA.

Show MeSH
Related in: MedlinePlus