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Table 3 Annotation of ST miRNA candidates under putative long-range developmental regulation

From: Genomic features and computational identification of human microRNAs under long-range developmental regulation

Name Intergenic/Intragenic Cell type of bivalent promoter1 Potential alternative GRB target gene2 CGIs3
hsa-mir-196b Intergenic mES, MEF HOXA cluster 0
hsa-mir-132~212 Intergenic hES, mES - 1
hsa-mir-196a-2 Intergenic MEF HOXC cluster 2
hsa-mir-9-1 Intron of C1orf61 mES, MEF - -
hsa-mir-9-3 Intergenic hES, mES - 6
hsa-mir-9-2 Intergenic hES MEF2C 8
hsa-mir-10a Intergenic hES, mES, MEF HOXB cluster 1
hsa-mir-196a-1 Intergenic hES HOXB cluster 6
hsa-mir-137 Intergenic hES - 2
hsa-mir-375 Intergenic hES, mES FEV, INN 2
hsa-mir-124-2 Intergenic hES, mES - 3
hsa-mir-542~450b Intergenic hES, mES - 3
hsa-mir-219-2 intergenic hES, mES - 1
hsa-mir-708 Intergenic hES - 1
hsa-mir-365-2 Intergenic hES, mES - 3
hsa-mir-193a Intergenic hES, mES - 3
hsa-mir-129-1 Intergenic hES, mES, MEF - 2
hsa-mir-129-2 intergenic hES, mES, MEF - 3
hsa-mir-124-1 Intergenic hES, mES, MEF - 3
hsa-mir-146b Intergenic hES NFKB2 0
hsa-mir-370 Intergenic hES - 0
hsa-mir-124-3 Intergenic mES, MEF - 3
hsa-mir-17~92a-1 Intergenic MEF - 1
hsa-mir-182~183 Intergenic hES, MEF - 4
hsa-mir-1-1 Intron of C20orf166 mES GATA5 -
hsa-mir-133a-2 Intron of C20orf166 mES GATA5 -
hsa-mir-203 Intergenic mES, MEF - 4
hsa-mir-16-1~15a Intron of DLEU2 mES - -
hsa-let-7a-3~let-7b Intergenic mES WNT7B 3
  1. List of conserved human ST miRNAs that have been annotated as targets of putative long-range regulation during development and differentiation. The mir-9 family of miRNAs is highlighted since it contains know examples of GRB target miRNAs that were captured using our two prediction features: 1) localization in regions of high HCNE density and 2) association with a bivalent promoter.
  2. 1The cell type in which the promoter of the miRNA is predicted to be a bivalent promoter. hES and mES represent embryonic stem cells of human and mouse, respectively. MEFs are mouse embryonic fibroblasts and NPCs are mouse neural progenitor cells.
  3. 2Further annotated GRB target genes within the 300kb region that was analyzed. The annotation of the GRB target genes was performed as described in the Methods section.
  4. 3Number of CpG islands overlapping with pri-miRNAs. The pri-miRNA is defined as the region 50 kb upstream to 20 kb downstream of the pre-miRNAs. If the defined pri-miRNA overlapped known protein-coding genes (the gene itself plus 1 kb up- and downstream of it), it was truncated to exclude the overlapping gene (see Methods). We did not count CGIs for intragenic miRNAs (denoted as '-').