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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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Total phased reads of miRNA/miRNA*, moRs and loops.
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gks247-F1: Total phased reads of miRNA/miRNA*, moRs and loops.

Mentions: A total of 34 datasets from 17 samples and more than 626 million (M) reads were analyzed (see Materials and Methods section and Supplementary Table S1). The 188M reads matched known mouse miRNA precursors from miRBase (Figure 1) and an additional 128 M matched exons, introns and intergenic regions in the mouse genome. Reads that matched multiple miRNAs were rejected and only perfect matches were kept for downstream analysis. miRBase version 16 contains 582 well-authenticated mouse miRNA species and we identified 526 miRNA species in our samples (416 for Group I and 489 for Group II) by requiring detection of both strands with at least ten reads on the non-preferred strand. Those miRNAs not validated in our samples may be expressed in tissues not used in our analysis. miRNA expression in Group I and Group II have distinct and overlapping patterns of miRNA expression (Supplementary Figure S2, Supplementary Tables S2 and S3). The miRNAs in AGO-IP data from the mouse hippocampus (Supplementary Table S4) correlated very well with total hippocampus small RNA profiling data, whereas groups I and II miRNAs were not significantly correlated. With a cutoff of >0.1% of miRNA percent in the sample, half of the expressed known miRNAs overlapped between Group I and II.Figure 1.


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)

Total phased reads of miRNA/miRNA*, moRs and loops.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks247-F1: Total phased reads of miRNA/miRNA*, moRs and loops.
Mentions: A total of 34 datasets from 17 samples and more than 626 million (M) reads were analyzed (see Materials and Methods section and Supplementary Table S1). The 188M reads matched known mouse miRNA precursors from miRBase (Figure 1) and an additional 128 M matched exons, introns and intergenic regions in the mouse genome. Reads that matched multiple miRNAs were rejected and only perfect matches were kept for downstream analysis. miRBase version 16 contains 582 well-authenticated mouse miRNA species and we identified 526 miRNA species in our samples (416 for Group I and 489 for Group II) by requiring detection of both strands with at least ten reads on the non-preferred strand. Those miRNAs not validated in our samples may be expressed in tissues not used in our analysis. miRNA expression in Group I and Group II have distinct and overlapping patterns of miRNA expression (Supplementary Figure S2, Supplementary Tables S2 and S3). The miRNAs in AGO-IP data from the mouse hippocampus (Supplementary Table S4) correlated very well with total hippocampus small RNA profiling data, whereas groups I and II miRNAs were not significantly correlated. With a cutoff of >0.1% of miRNA percent in the sample, half of the expressed known miRNAs overlapped between Group I and II.Figure 1.

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