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

BMC Genomics

Table 3 Annotation of ST miRNA candidates under putative 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

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 '-').

ISSN: 1471-2164