We are analyzing https://link.springer.com/article/10.1186/s12915-014-0078-0.

Title:
Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets | BMC Biology
Description:
Background tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function. Results This is the first meta-analysis of tRFs. Analysis of more than 50 short RNA libraries has revealed that tRFs are precisely generated fragments present in all domains of life (bacteria to humans), and are not produced by the miRNA biogenesis pathway. Human PAR-CLIP data shows a striking preference for tRF-5s and tRF-3s to associate with AGO1, 3 and 4 rather than AGO2, and analysis of positional T to C mutational frequency indicates these tRFs associate with Argonautes in a manner similar to miRNAs. The reverse complements of canonical seed positions in these sequences match cross-link centered regions, suggesting these tRF-5s and tRF-3s interact with RNAs in the cell. Consistent with these results, human AGO1 CLASH data contains thousands of tRF-5 and tRF-3 reads chimeric with mRNAs. Conclusions tRFs are an abundant class of small RNA present in all domains of life whose biogenesis is distinct from miRNAs. In human HEK293 cells tRFs associate with Argonautes 1, 3 and 4 and not Argonaute 2 which is the main effector protein of miRNA function, but otherwise have very similar properties to miRNAs, indicating tRFs may play a major role in RNA silencing.
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Keywords {🔍}

trfs, trf, rna, trna, pubmed, small, data, article, figure, rnas, google, scholar, cas, reads, central, cell, mirnas, human, ago, analysis, mirna, abundant, sequence, cells, genes, fragments, parclip, shown, read, sequences, gene, size, bases, mouse, number, clash, mapped, file, trnas, database, end, specific, found, frequency, argonautes, positions, drosophila, observed, target, dicer,

Topics {✒️}

article download pdf n1-methyl-adenosine modification 4 photoactivatable-ribonucleoside-enhanced crosslinking photoactivatable-ribonucleoside-enhanced crosslinking human protein-coding genes open access license homologous cell-free extracts trf-1s versus trf-5s trf-3s versus trf-5s trf-1s versus trf-3s rna-induced silencing complex trna-derived rna fragments trna-derived fragments target dicer-dependent small rnas target rna-directed trimming established par-clip data drosophila endo-sirnas depends trf-3003a-hist2h2aa4 interaction trf-3034a-rpl35a interaction trna-related rna sequences small rna-mrna chimera ago1-mirna-target rna interactome human ref-seq rna human ref-seq database central cross-linked dgcr8-/-mouse es cells 319 crosslink-centered regions small rna-seq data stem-loop binding protein paper argues trf-5s par-clip data analysis primary transcription product ago1 par-clip data d'agostino dm privacy choices/manage cookies high-throughput sequencing reads trf-3-mrna clash chimeras trna related fragments full size image trna-derived fragments transcription termination signal inhibit protein translation regulatory rnas derived de hoon ml stress-induced cleavage article kumar small rnas derived abundant trf-mrna interactions related subjects blast search excluding

Questions {❓}

If DICER1 and DROSHA are not involved in tRF generation then which proteins are?
Pederson T: Regulatory RNAs derived from transfer RNA?

Schema {🗺️}

WebPage:
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         headline:Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets
         description:tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function. This is the first meta-analysis of tRFs. Analysis of more than 50 short RNA libraries has revealed that tRFs are precisely generated fragments present in all domains of life (bacteria to humans), and are not produced by the miRNA biogenesis pathway. Human PAR-CLIP data shows a striking preference for tRF-5s and tRF-3s to associate with AGO1, 3 and 4 rather than AGO2, and analysis of positional T to C mutational frequency indicates these tRFs associate with Argonautes in a manner similar to miRNAs. The reverse complements of canonical seed positions in these sequences match cross-link centered regions, suggesting these tRF-5s and tRF-3s interact with RNAs in the cell. Consistent with these results, human AGO1 CLASH data contains thousands of tRF-5 and tRF-3 reads chimeric with mRNAs. tRFs are an abundant class of small RNA present in all domains of life whose biogenesis is distinct from miRNAs. In human HEK293 cells tRFs associate with Argonautes 1, 3 and 4 and not Argonaute 2 which is the main effector protein of miRNA function, but otherwise have very similar properties to miRNAs, indicating tRFs may play a major role in RNA silencing.
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      description:tRFs, 14 to 32 nt long single-stranded RNA derived from mature or precursor tRNAs, are a recently discovered class of small RNA that have been found to be present in diverse organisms at read counts comparable to miRNAs. Currently, there is a debate about their biogenesis and function. This is the first meta-analysis of tRFs. Analysis of more than 50 short RNA libraries has revealed that tRFs are precisely generated fragments present in all domains of life (bacteria to humans), and are not produced by the miRNA biogenesis pathway. Human PAR-CLIP data shows a striking preference for tRF-5s and tRF-3s to associate with AGO1, 3 and 4 rather than AGO2, and analysis of positional T to C mutational frequency indicates these tRFs associate with Argonautes in a manner similar to miRNAs. The reverse complements of canonical seed positions in these sequences match cross-link centered regions, suggesting these tRF-5s and tRF-3s interact with RNAs in the cell. Consistent with these results, human AGO1 CLASH data contains thousands of tRF-5 and tRF-3 reads chimeric with mRNAs. tRFs are an abundant class of small RNA present in all domains of life whose biogenesis is distinct from miRNAs. In human HEK293 cells tRFs associate with Argonautes 1, 3 and 4 and not Argonaute 2 which is the main effector protein of miRNA function, but otherwise have very similar properties to miRNAs, indicating tRFs may play a major role in RNA silencing.
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