|
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
|
- 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.
- 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.
- 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.
- 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 '-').
