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Identification of aberrant tRNA-halves expression patterns in clear cell renal cell carcinoma

View Article: PubMed Central - PubMed

ABSTRACT

Small non-coding RNAs (sncRNA; <200 nt) regulate various cellular processes and modify gene expression. Under nutritional, biological or physiochemical stress some mature sncRNAs (e.g. tRNAs) are cleaved into halves (30–50 nt) and smaller fragments (18–22 nt); the significance and functional role of these tRNA fragments is unknown, but their existence has been linked to carcinogenesis. We used small RNA sequencing to determine the expression of sncRNAs. Subsequently the findings were validated for miR-122-5p, miR-142-3p and 5'tRNA4-Val-AAC using qPCR. We identified differential expression of 132 miRNAs (upregulated: 61, downregulated: 71) and 32 tRNAs (upregulated: 13, downregulated: 19). Read length analysis showed that miRNAs mapped in the 20–24 nt fraction, whereas tRNA reads mapped in the 30–36 nt fraction instead the expected size of 73–95 nt thereby indicating cleavage of tRNAs. Overexpression of miR-122-5p and miR-142-3p as well as downregulation of 5'tRNA4-Val-AAC was validated in an independent cohort of 118 ccRCC and 74 normal renal tissues. Furthermore, staging and grading was inversely correlated with the 5'tRNA4-Val-AAC expression. Serum levels of miR-122-5p, miR-142-3p and 5'tRNA4-Val-AAC did not differ in ccRCC and control subjects. In conclusion, 5′ cleavage of tRNAs occurs in ccRCC, but the exact functional implication of tRNA-halve deregulation remains to be clarified.

No MeSH data available.


Read length distributions demonstrate the presence of tRNA cleavage.Read length distributions indicated the presence of two major peaks: a green peak indicates the enrichment of miRNA in the typical 20–24 nt fraction; a pink peak at 30–35 nt indicates the presence of 5′tRNA-halves. Exemplarily, the read length distribution of one corresponding pair of normal renal (A) and ccRCC (B) tissue is shown. It is important to note that the distribution of the read counts vary between the different corresponding samples. (C) the structure of tRNA4-Val-AAC is shown; it may be cleaved at the anticodon loop, resulting in 5′tRNA-halves of 30 to 35 nt, tRNA covariance model fold borrowed from Chan, P.P. & Lowe, T.M. (2009) GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucl. Acids Res. 37(Database issue):D93-D97.
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f2: Read length distributions demonstrate the presence of tRNA cleavage.Read length distributions indicated the presence of two major peaks: a green peak indicates the enrichment of miRNA in the typical 20–24 nt fraction; a pink peak at 30–35 nt indicates the presence of 5′tRNA-halves. Exemplarily, the read length distribution of one corresponding pair of normal renal (A) and ccRCC (B) tissue is shown. It is important to note that the distribution of the read counts vary between the different corresponding samples. (C) the structure of tRNA4-Val-AAC is shown; it may be cleaved at the anticodon loop, resulting in 5′tRNA-halves of 30 to 35 nt, tRNA covariance model fold borrowed from Chan, P.P. & Lowe, T.M. (2009) GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucl. Acids Res. 37(Database issue):D93-D97.

Mentions: Beside the enrichment of miRNA, read length distribution analysis showed a second peak of RNA in the 30–36 nt part. Annotation analysis revealed that these reads derived from tRNAs (see Fig. 2). Among the 345 analyzed tRNA transcripts, we found 32 differentially expressed tRNAs: among these, 13 tRNA were upregulated and 19 were downregulated in ccRCC. The 10 most up- and downregulated tRNAs in ccRCC tissue are listed in Table 2. The differential tRNA expression is shown in a volcano plot in Fig. 1C. A heatmap of tRNA expression in renal tissues is provided in Supplementary Figure S2.


Identification of aberrant tRNA-halves expression patterns in clear cell renal cell carcinoma
Read length distributions demonstrate the presence of tRNA cleavage.Read length distributions indicated the presence of two major peaks: a green peak indicates the enrichment of miRNA in the typical 20–24 nt fraction; a pink peak at 30–35 nt indicates the presence of 5′tRNA-halves. Exemplarily, the read length distribution of one corresponding pair of normal renal (A) and ccRCC (B) tissue is shown. It is important to note that the distribution of the read counts vary between the different corresponding samples. (C) the structure of tRNA4-Val-AAC is shown; it may be cleaved at the anticodon loop, resulting in 5′tRNA-halves of 30 to 35 nt, tRNA covariance model fold borrowed from Chan, P.P. & Lowe, T.M. (2009) GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucl. Acids Res. 37(Database issue):D93-D97.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121638&req=5

f2: Read length distributions demonstrate the presence of tRNA cleavage.Read length distributions indicated the presence of two major peaks: a green peak indicates the enrichment of miRNA in the typical 20–24 nt fraction; a pink peak at 30–35 nt indicates the presence of 5′tRNA-halves. Exemplarily, the read length distribution of one corresponding pair of normal renal (A) and ccRCC (B) tissue is shown. It is important to note that the distribution of the read counts vary between the different corresponding samples. (C) the structure of tRNA4-Val-AAC is shown; it may be cleaved at the anticodon loop, resulting in 5′tRNA-halves of 30 to 35 nt, tRNA covariance model fold borrowed from Chan, P.P. & Lowe, T.M. (2009) GtRNAdb: A database of transfer RNA genes detected in genomic sequence. Nucl. Acids Res. 37(Database issue):D93-D97.
Mentions: Beside the enrichment of miRNA, read length distribution analysis showed a second peak of RNA in the 30–36 nt part. Annotation analysis revealed that these reads derived from tRNAs (see Fig. 2). Among the 345 analyzed tRNA transcripts, we found 32 differentially expressed tRNAs: among these, 13 tRNA were upregulated and 19 were downregulated in ccRCC. The 10 most up- and downregulated tRNAs in ccRCC tissue are listed in Table 2. The differential tRNA expression is shown in a volcano plot in Fig. 1C. A heatmap of tRNA expression in renal tissues is provided in Supplementary Figure S2.

View Article: PubMed Central - PubMed

ABSTRACT

Small non-coding RNAs (sncRNA; <200 nt) regulate various cellular processes and modify gene expression. Under nutritional, biological or physiochemical stress some mature sncRNAs (e.g. tRNAs) are cleaved into halves (30–50 nt) and smaller fragments (18–22 nt); the significance and functional role of these tRNA fragments is unknown, but their existence has been linked to carcinogenesis. We used small RNA sequencing to determine the expression of sncRNAs. Subsequently the findings were validated for miR-122-5p, miR-142-3p and 5'tRNA4-Val-AAC using qPCR. We identified differential expression of 132 miRNAs (upregulated: 61, downregulated: 71) and 32 tRNAs (upregulated: 13, downregulated: 19). Read length analysis showed that miRNAs mapped in the 20–24 nt fraction, whereas tRNA reads mapped in the 30–36 nt fraction instead the expected size of 73–95 nt thereby indicating cleavage of tRNAs. Overexpression of miR-122-5p and miR-142-3p as well as downregulation of 5'tRNA4-Val-AAC was validated in an independent cohort of 118 ccRCC and 74 normal renal tissues. Furthermore, staging and grading was inversely correlated with the 5'tRNA4-Val-AAC expression. Serum levels of miR-122-5p, miR-142-3p and 5'tRNA4-Val-AAC did not differ in ccRCC and control subjects. In conclusion, 5′ cleavage of tRNAs occurs in ccRCC, but the exact functional implication of tRNA-halve deregulation remains to be clarified.

No MeSH data available.