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Deep annotation of mouse iso-miR and iso-moR variation.

Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM, Kosik KS - Nucleic Acids Res. (2012)

Bottom Line: Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading.Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer.These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.

View Article: PubMed Central - PubMed

Affiliation: Neuroscience Research Institute and Department of Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.

ABSTRACT
With a dataset of more than 600 million small RNAs deeply sequenced from mouse hippocampal and staged sets of mouse cells that underwent reprogramming to induced pluripotent stem cells, we annotated the stem-loop precursors of the known miRNAs to identify isomoRs (miRNA-offset RNAs), loops, non-preferred strands, and guide strands. Products from both strands were readily detectable for most miRNAs. Changes in the dominant isomiR occurred among the cell types, as did switches of the preferred strand. The terminal nucleotide of the dominant isomiR aligned well with the dominant off-set sequence suggesting that Drosha cleavage generates most miRNA reads without terminal modification. Among the terminal modifications detected, most were non-templated mono- or di-nucleotide additions to the 3'-end. Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading. Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer. These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.

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Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.
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gks247-F8: Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.

Mentions: Sequence alterations of miRNAs can occur by addition of non-templated nucleotides to miRNA termini (38,40,49). Most miRNAs in our data set did not have non-templated nucleotide modifications. Of the total reads, 16.00%, 14.10% and 12.67% were extended by 1 nt in the Ago-IP, Group I, and Group II samples, respectively. Of the total reads, 7.81%, 6.85% and 3.18% were extended by 2 nt in the Ago-IP, Group I and Group II samples, respectively. The nucleotides most frequently added to murine miRNAs were U and A (Figure 8 and Table 3). However, in the Ago-IP sample from hippocampus the addition of C was most common; C also showed a small increase in the Group I samples compared to the Group II samples. Di-nucleotide extensions not infrequently consisted of two different nucleotides (Supplementary Table S5). Half of the miR-143-3p reads in our samples were extended similarly to the very high proportion of extended reads previously described for this miRNA (36). Among highly expressed miRNAs, 32% of the miR-124 reads were extended and 33% of the miR-24 reads were extended (Supplementary Table S6).Figure 8.


Deep annotation of mouse iso-miR and iso-moR variation.

Zhou H, Arcila ML, Li Z, Lee EJ, Henzler C, Liu J, Rana TM, Kosik KS - Nucleic Acids Res. (2012)

Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3401436&req=5

gks247-F8: Untemplated nucleotide addition rate at the 3′-ends of miRNA/miRNA*.
Mentions: Sequence alterations of miRNAs can occur by addition of non-templated nucleotides to miRNA termini (38,40,49). Most miRNAs in our data set did not have non-templated nucleotide modifications. Of the total reads, 16.00%, 14.10% and 12.67% were extended by 1 nt in the Ago-IP, Group I, and Group II samples, respectively. Of the total reads, 7.81%, 6.85% and 3.18% were extended by 2 nt in the Ago-IP, Group I and Group II samples, respectively. The nucleotides most frequently added to murine miRNAs were U and A (Figure 8 and Table 3). However, in the Ago-IP sample from hippocampus the addition of C was most common; C also showed a small increase in the Group I samples compared to the Group II samples. Di-nucleotide extensions not infrequently consisted of two different nucleotides (Supplementary Table S5). Half of the miR-143-3p reads in our samples were extended similarly to the very high proportion of extended reads previously described for this miRNA (36). Among highly expressed miRNAs, 32% of the miR-124 reads were extended and 33% of the miR-24 reads were extended (Supplementary Table S6).Figure 8.

Bottom Line: Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading.Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer.These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.

View Article: PubMed Central - PubMed

Affiliation: Neuroscience Research Institute and Department of Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.

ABSTRACT
With a dataset of more than 600 million small RNAs deeply sequenced from mouse hippocampal and staged sets of mouse cells that underwent reprogramming to induced pluripotent stem cells, we annotated the stem-loop precursors of the known miRNAs to identify isomoRs (miRNA-offset RNAs), loops, non-preferred strands, and guide strands. Products from both strands were readily detectable for most miRNAs. Changes in the dominant isomiR occurred among the cell types, as did switches of the preferred strand. The terminal nucleotide of the dominant isomiR aligned well with the dominant off-set sequence suggesting that Drosha cleavage generates most miRNA reads without terminal modification. Among the terminal modifications detected, most were non-templated mono- or di-nucleotide additions to the 3'-end. Based on the relative enrichment or depletion of specific nucleotide additions in an Ago-IP fraction there may be differential effects of these modifications on RISC loading. Sequence variation of the two strands at their cleavage sites suggested higher fidelity of Drosha than Dicer. These studies demonstrated multiple patterns of miRNA processing and considerable versatility in miRNA target selection.

Show MeSH