Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982 Supplementary Figure 1 Distribution of miRNAs between lncRNA and protein-coding genes. Pie chart showing distribution of human miRNA between protein coding and lncRNA genes. To the right, lncRNA miRNA genes are further subdivided into intergenic (lincRNA) or other less well-characterized subdivisions such as pseudogene or antisense.
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Nature Structural and Molecular Biology: doi:10.1038/nsmb · Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982 Supplementary Figure 2 Mapped 3 ends of lnc-pri-miR-122.
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Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 1
Distribution of miRNAs between lncRNA and protein-coding genes.
Pie chart showing distribution of human miRNA between protein coding and lncRNA genes. To the right, lncRNA miRNA genes are
further subdivided into intergenic (lincRNA) or other less well-characterized subdivisions such as pseudogene or antisense.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 2
Mapped 3 ends of lnc-pri-miR-122.
Sequencing results of lnc-pri-miR-122 3’RACE products amplified by poly(A) polymerase dependent method. Red arrow head marks the 3’ end cleavage sites based on sequence analysis.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 3
Microprocessor but not Dicer is required for lnc-pri-miRNA-122 transcription termination.
a. Chromatin-associated Huh7 RNA was analyzed by RT-qPCR as in Fig. 3a. b. Pol II ChIP and qPCR analysis of lnc-pri-miR-122
following DGCR8 depletion in Huh7 cells. Positions of the primers are indicated on the gene map above. Error bars represent s.d. of an
average (n=3 independent experiments).
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 4
Microprocessor depletion leads to transcriptional readthrough on MIR17HG but not MIRLET7BHG.
a. Chromatin RNA-seq profile for the MIR17HG locus following Drosha or DGCR8 depletion in HeLa cells. b. Chromatin RNA-seq
profile for the MIRLET7BHG locus following Drosha or DGCR8 depletion.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 5
Dicer depletion does not lead to transcriptional readthrough on lnc-pri-miRNA.
a. Western blot showing effective Dicer depletion by siRNA transfection in HeLa cells. b. Chromatin RNA-seq profiles for MIR181A1HGand LINC00472 following DGCR8 or Dicer depletion in HeLa cells.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 6
Effect of Microprocessor knockdown on levels of TSS transcripts in genes containing miRNAs in HeLa cells.
a. and b. TSS metagene plot of chromatin RNA-seq of lnc-pri-miRNA versus protein coding genes harboring miRNA showing region
1 kb before and after TSS. TSS denotes transcription start site.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 7
Scatter plots showing reproducibility of replicate chromatin RNA–seq in HeLa cells.
a. Replicate of control siRNA treated samples. b. Replicate of DGCR8 siRNA treated samples.
Nature Structural and Molecular Biology: doi:10.1038/nsmb.2982
Supplementary Figure 8
Additional views of GPC5 chromatin RNA–seq profiles.
a. Compressed view showing full extent of MIR17HG-GPC5 transcription unit. b. Magnified view of GPC5 exon 1 following
Microprocessor knockdown in HeLa cells. Coding sequence (CDS) that translates first 55 amino acids of the GPC5 protein is located in
exon 1 and is denoted by bracket. HeLa cell RNA employed. Direction of transcription indicated by green arrows.
Supplementary Table 1: List of miRNA harbouring lncRNA host genes showing
termination defect following Drosha or DGCR8 depletion in HeLa cell line.