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Uracils at nucleotide position 9-11 are required for the rapid turnover of miR-29 family.

Zhang Z, Zou J, Wang GK, Zhang JT, Huang S, Qin YW, Jing Q - Nucleic Acids Res. (2011)

Bottom Line: Moreover, analysis of published data on microRNA expression profile during development reveals that a substantial subset of microRNAs with the uracil-rich sequence tends to be down-regulated compared to those without the sequence.The effect of uracil-rich sequence on microRNA turnover depends on the sequence context.The present work indicates that microRNAs contain sequence information in the middle region besides the sequence element at both ends.

View Article: PubMed Central - PubMed

Affiliation: Department of Cardiology, Changhai Hospital, Shanghai, China.

ABSTRACT
MicroRNAs are endogenous small RNA molecules that regulate gene expression. Although the biogenesis of microRNAs and their regulation have been thoroughly elucidated, the degradation of microRNAs has not been fully understood. Here by using the pulse-chase approach, we performed the direct measurement of microRNA lifespan. Five representative microRNAs demonstrated a general feature of relatively long lifespan. However, the decay dynamic varies considerably between these individual microRNAs. Mutation analysis of miR-29b sequence revealed that uracils at nucleotide position 9-11 are required for its rapid decay, in that both specific nucleotides and their position are critical. The effect of uracil-rich element on miR-29b decay dynamic occurs in duplex but not in single strand RNA. Moreover, analysis of published data on microRNA expression profile during development reveals that a substantial subset of microRNAs with the uracil-rich sequence tends to be down-regulated compared to those without the sequence. Among them, Northern blotting shows that miR-29c and fruit fly bantam possess a relatively rapid turnover rate. The effect of uracil-rich sequence on microRNA turnover depends on the sequence context. The present work indicates that microRNAs contain sequence information in the middle region besides the sequence element at both ends.

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(A) Sequence of miRNAs with uracil-rich element and their mutants. Nucleotides under investigation are underlined and centric uracils are marked as lowercase. (B) A subset of miRNAs containing U-rich sequences has an accelerated turnover rate. MiR-29c and fly miRNA bantam show a relatively short lifespan, and replacement of bantam 3′-end sequence with that of miR-29b does not alter the decay dynamics. For two miR-126 mutants, both are long-lived although the one with CAG in positions 9–11 is more stable than one with UUU.
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Figure 4: (A) Sequence of miRNAs with uracil-rich element and their mutants. Nucleotides under investigation are underlined and centric uracils are marked as lowercase. (B) A subset of miRNAs containing U-rich sequences has an accelerated turnover rate. MiR-29c and fly miRNA bantam show a relatively short lifespan, and replacement of bantam 3′-end sequence with that of miR-29b does not alter the decay dynamics. For two miR-126 mutants, both are long-lived although the one with CAG in positions 9–11 is more stable than one with UUU.

Mentions: The decrease in expression level of miRNA does not necessarily attribute to miRNA degradation, thus we examined the stability of miRNAs in the above list. MiR-29c is another member of miR-29 family, and our assay showed it was much more unstable than miR-29a, with a half life of 10.6 h (Figure 4). The fruit fly miRNA bantam was sharply down-regulated during the development (34). The abundance of bantam decreased with a relative rapid rate in HeLa cell (Figure 4B).Figure 4.


Uracils at nucleotide position 9-11 are required for the rapid turnover of miR-29 family.

Zhang Z, Zou J, Wang GK, Zhang JT, Huang S, Qin YW, Jing Q - Nucleic Acids Res. (2011)

(A) Sequence of miRNAs with uracil-rich element and their mutants. Nucleotides under investigation are underlined and centric uracils are marked as lowercase. (B) A subset of miRNAs containing U-rich sequences has an accelerated turnover rate. MiR-29c and fly miRNA bantam show a relatively short lifespan, and replacement of bantam 3′-end sequence with that of miR-29b does not alter the decay dynamics. For two miR-126 mutants, both are long-lived although the one with CAG in positions 9–11 is more stable than one with UUU.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3105410&req=5

Figure 4: (A) Sequence of miRNAs with uracil-rich element and their mutants. Nucleotides under investigation are underlined and centric uracils are marked as lowercase. (B) A subset of miRNAs containing U-rich sequences has an accelerated turnover rate. MiR-29c and fly miRNA bantam show a relatively short lifespan, and replacement of bantam 3′-end sequence with that of miR-29b does not alter the decay dynamics. For two miR-126 mutants, both are long-lived although the one with CAG in positions 9–11 is more stable than one with UUU.
Mentions: The decrease in expression level of miRNA does not necessarily attribute to miRNA degradation, thus we examined the stability of miRNAs in the above list. MiR-29c is another member of miR-29 family, and our assay showed it was much more unstable than miR-29a, with a half life of 10.6 h (Figure 4). The fruit fly miRNA bantam was sharply down-regulated during the development (34). The abundance of bantam decreased with a relative rapid rate in HeLa cell (Figure 4B).Figure 4.

Bottom Line: Moreover, analysis of published data on microRNA expression profile during development reveals that a substantial subset of microRNAs with the uracil-rich sequence tends to be down-regulated compared to those without the sequence.The effect of uracil-rich sequence on microRNA turnover depends on the sequence context.The present work indicates that microRNAs contain sequence information in the middle region besides the sequence element at both ends.

View Article: PubMed Central - PubMed

Affiliation: Department of Cardiology, Changhai Hospital, Shanghai, China.

ABSTRACT
MicroRNAs are endogenous small RNA molecules that regulate gene expression. Although the biogenesis of microRNAs and their regulation have been thoroughly elucidated, the degradation of microRNAs has not been fully understood. Here by using the pulse-chase approach, we performed the direct measurement of microRNA lifespan. Five representative microRNAs demonstrated a general feature of relatively long lifespan. However, the decay dynamic varies considerably between these individual microRNAs. Mutation analysis of miR-29b sequence revealed that uracils at nucleotide position 9-11 are required for its rapid decay, in that both specific nucleotides and their position are critical. The effect of uracil-rich element on miR-29b decay dynamic occurs in duplex but not in single strand RNA. Moreover, analysis of published data on microRNA expression profile during development reveals that a substantial subset of microRNAs with the uracil-rich sequence tends to be down-regulated compared to those without the sequence. Among them, Northern blotting shows that miR-29c and fruit fly bantam possess a relatively rapid turnover rate. The effect of uracil-rich sequence on microRNA turnover depends on the sequence context. The present work indicates that microRNAs contain sequence information in the middle region besides the sequence element at both ends.

Show MeSH
Related in: MedlinePlus