>Wars|NM_001164314|3'UTR
   1 TGTCTCTTTTCTGTGGCAAGCCTGTCTGTAACCCACCCTGTCAAATCAAGTCACACTCCCAATAGGCTTCTCACGTGGTA
  81 ATTCCTGGACCTGGGTCTCTGTGCACGTGTGCATCCTGGATGCTGTTTCTTCTCTGATGTCTCCCCGTCTGTTGTCTGCT
 161 ACGGGTGATCAAGCGATGCTAATGTTGTGTGGTCAGATAGAACCCCAGCCCGCAGTCTCTCCCACAAAGAGCCCAGAGGT
 241 AGTGCTTCCCTGGCCCACAGAAGACTGTCCAGCTAGCAGCCTGGGGTTCCAGAACAAATTCTGAAATGTATTCCAGTTTT
 321 TCTTTAAAGTGCGTGTGCCCGGTTGGCCACGGTGGGGTGCACTGTATCATCTCTGTTCTCAGGAGGCTGAGACACGAGGT
 401 CTGAGCCAGCCTGGTAGTAATCTGCCTTTGATTCTGCTGCTGTGGAGTCACAATGTCATTACTGTAAAACTGAACACTGC
 481 TGTGAGGAACTGACAAGGAGACATGTAGTGGGACATGCCGCTGCTCCAGCCCACGCCCCCCCCCACACACGCACACACAC
 561 TTACATGTAATGTGTGCAAACTTTGCTTTATACTTGGCTAAGAAGCCATCAGCTTTGTTCTGAAGGTGTAGCTCAGTAGT
 641 AGAGCACTCGCCTAGCACGCCTGCTGGCCCGGGTTCAGTCTCCTGCCCCACGAAGCCGGGCGGATAACTGAGCTCTCTGC
 721 TTTTAACCCTGATTATGGACCAGGCTGGGTCTTTCCACTAACCTGAGGCTGAGGTAGCTAACCTCCAGCTCCCGTGTGCC
 801 GTCCACTCCAAAATCATGCTTGCGCCCTTGGTGTACTAACTTCCCCACAGATGGCCCAGACTCCACCCTGTGACGTGCAG
 881 GGCTGCAGCTCCTGACCCCCGGGTCCTGAGGACGGCTTGTTCCCTTTGCAGGTGCTTCTGCTTTGACACTTGACTGACGG
 961 GGAGGGCAGGCCAGAGCAGTGTGCTGGCCATGCCTCAGGCCGTTGACCATAGCTAGACAGAAAAGAACAGCAGCCGTCCA
1041 GGCCGCAGCGTTCTCCCTCTGGGCGGGCTGCATGGAATGAGCCTCCACTCAGAGTCTTGGAAAAGCAGAAGCCGTACCTC
1121 AGGGAAAGCCCCTGGTTGAAGTGTCTGTCCTCTCTGAAGGCACAAGGGCCACTCTGAGTGTTCTGTCCTTGCATCATTTT
1201 TAGGAAAAAACAATAAACTTTGTTGAGCTCCTGTC

ID	Duplex structure	Position	Score	MFE
1	miRNA 3' cgaaagagCCUCGAGUCUCGUu 5' | || ||||||| Target 5' cggggaggGCAGGCCAGAGCAg 3'	958 - 979	146.00	-15.70
2	miRNA 3' cgaAAGA-----GCCUCGA------GUCUCGUu 5' |||| :| |||| :|||||| Target 5' ttgTTCTGAAGGTGTAGCTCAGTAGTAGAGCAc 3'	615 - 647	133.00	-16.00
3	miRNA 3' cgaaaGAGCCUCGA-GUCUCGUu 5' | :||:|:| |||| || Target 5' agcagCCTGGGGTTCCAGAACAa 3'	275 - 297	125.00	-15.70

- Stem cells (Dayton, Ohio), 2014

Regulation of hematopoietic stem cell proliferation, lineage commitment, and differentiation in adult vertebrates requires extrinsic signals provided by cells in the marrow microenvironment (ME) located within the bone marrow. Both secreted and cell-surface bound factors critical to this regulation have been identified, yet control of their expression by cells within the ME has not been addressed. Herein we hypothesize that microRNAs (miRNAs) contribute to their controlled expression. MiRNAs are small noncoding RNAs that bind to target mRNAs and downregulate gene expression by either initiating mRNA degradation or preventing peptide translation. Testing the role of miRNAs in downregulating gene expression has been difficult since conventional techniques used to define miRNA-mRNA interactions are indirect and have high false-positive and negative rates. In this report, a genome-wide biochemical technique (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation or HITS-CLIP) was used to generate unbiased genome-wide maps of miRNA-mRNA interactions in two critical cellular components of the marrow ME: marrow stromal cells and bone marrow endothelial cells. Analysis of these datasets identified miRNAs as direct regulators of JAG1, WNT5A, MMP2, and VEGFA; four factors that are important to ME function. Our results show the feasibility and utility of unbiased genome-wide biochemical techniques in dissecting the role of miRNAs in regulation of complex tissues such as the marrow ME.