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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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Phased read distributions of (A) miR-125b and (B) miR-191.
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gks247-F3: Phased read distributions of (A) miR-125b and (B) miR-191.

Mentions: Reads of moRs were very common for most of the miRNAs (Figure 3, Supplementary Tables S2, S3, S4, Supplementary Datasets S1, S2 and S3). Although more highly expressed miRNAs tended to have higher loop and moR reads, their levels were not strictly correlated with the expression level of mature miRNAs. A total of 77% of known miRNAs had >10 moR reads. Relatively fewer moR reads were sequenced in Ago-IP samples, compared to data from total small RNA profiling (Figure 1). Reads of 5′-moR reads exceeded 3′-moRs by > 3-fold in Group I and 5-fold in Group II samples. 5′-moRs were also reported to be more abundant than 3′-moRs in Drosophila (30), and therefore moR processing may be a highly conserved feature of the miRNA biogenesis pathway. The levels of 5′-moRs and 3′-moRs did not correlate (R2 = 0.025) suggesting some degree of independence in their generation. In Group II cells, miR-27b, miR-503, miR-21, miR-24 and miR-16 had the most abundant 5′-moRs, while miR-294 and miR-30e had the most 3′-moRs. In the hippocampus, miR-134 and miR-503 had abundant 5′-moRs (Supplementary Table S2, Supplementary Datasets S1, S2 and S3). Generally, the dominant moRs aligned perfectly with the dominant isomiRs (e.g. for a 3′-miR, the last base of the dominant isomiR was the base preceding the first base of the dominant moR), thereby suggesting that Drosha products without terminal modifications predominate among the phased fragments (Figure 3, Supplementary Datasets S1, S2 and S3). These findings also suggest that Drosha generates the ends of the 5′-and 3′-moRs that are adjacent to the pre-miR stem.Figure 3.


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)

Phased read distributions of (A) miR-125b and (B) miR-191.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks247-F3: Phased read distributions of (A) miR-125b and (B) miR-191.
Mentions: Reads of moRs were very common for most of the miRNAs (Figure 3, Supplementary Tables S2, S3, S4, Supplementary Datasets S1, S2 and S3). Although more highly expressed miRNAs tended to have higher loop and moR reads, their levels were not strictly correlated with the expression level of mature miRNAs. A total of 77% of known miRNAs had >10 moR reads. Relatively fewer moR reads were sequenced in Ago-IP samples, compared to data from total small RNA profiling (Figure 1). Reads of 5′-moR reads exceeded 3′-moRs by > 3-fold in Group I and 5-fold in Group II samples. 5′-moRs were also reported to be more abundant than 3′-moRs in Drosophila (30), and therefore moR processing may be a highly conserved feature of the miRNA biogenesis pathway. The levels of 5′-moRs and 3′-moRs did not correlate (R2 = 0.025) suggesting some degree of independence in their generation. In Group II cells, miR-27b, miR-503, miR-21, miR-24 and miR-16 had the most abundant 5′-moRs, while miR-294 and miR-30e had the most 3′-moRs. In the hippocampus, miR-134 and miR-503 had abundant 5′-moRs (Supplementary Table S2, Supplementary Datasets S1, S2 and S3). Generally, the dominant moRs aligned perfectly with the dominant isomiRs (e.g. for a 3′-miR, the last base of the dominant isomiR was the base preceding the first base of the dominant moR), thereby suggesting that Drosha products without terminal modifications predominate among the phased fragments (Figure 3, Supplementary Datasets S1, S2 and S3). These findings also suggest that Drosha generates the ends of the 5′-and 3′-moRs that are adjacent to the pre-miR stem.Figure 3.

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