title: Genome-wide analysis of miRNA-mRNA interactions in marrow stromal cells.
abstract: 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.
authors.affiliation: Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA.
authors.forename: Ilango
authors.initials: I
authors.lastname: Balakrishnan
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Yang
authors.forename: Joseph
authors.initials: J
authors.lastname: Brown
authors.forename: Aravind
authors.initials: A
authors.lastname: Ramakrishnan
authors.forename: Beverly
authors.initials: B
authors.lastname: Torok-Storb
authors.forename: Peter
authors.initials: P
authors.lastname: Kabos
authors.forename: Jay R
authors.initials: JR
authors.lastname: Hesselberth
authors.forename: Manoj M
authors.initials: MM
authors.lastname: Pillai
mesh_terms: D060565:Argonaute Proteins / Q000378:metabolism; D001483:Base Sequence; D001854:Bone Marrow Cells / Q000166:cytology* / Q000378:metabolism*; D002135:Calcium-Binding Proteins / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D060833:Cellular Microenvironment; D015536:Down-Regulation / Q000235:genetics; D042783:Endothelial Cells / Q000166:cytology / Q000378:metabolism; D015894:Genome, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D047468:Immunoprecipitation; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D000072100:Jagged-1 Protein; D020778:Matrix Metalloproteinase 2 / Q000378:metabolism; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D000072099:Serrate-Jagged Proteins; D017154:Stromal Cells / Q000378:metabolism; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics / Q000378:metabolism; D051153:Wnt Proteins / Q000235:genetics / Q000378:metabolism; D000071818:Wnt-5a Protein
chemical_list: D060565:Argonaute Proteins; D002135:Calcium-Binding Proteins; D036341:Intercellular Signaling Peptides and Proteins; C000606273:JAG1 protein, human; D000072100:Jagged-1 Protein; D008565:Membrane Proteins; D035683:MicroRNAs; D011518:Proto-Oncogene Proteins; D012333:RNA, Messenger; D000072099:Serrate-Jagged Proteins; D042461:Vascular Endothelial Growth Factor A; C085389:WNT5A protein, human; D051153:Wnt Proteins; D000071818:Wnt-5a Protein; D020778:Matrix Metalloproteinase 2
keywords: Bone marrow stromal cells; Endothelium; JAG1; MMP2; Mesenchymal stromal cells; Stem cell microenvironment; VEGFA; WNT5A; miRNA
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