MicroRNA-125b Promotes Neuronal Differentiation in Human Cells by Repressing Multiple Targets

Abstract

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the posttranscriptional level. Research on miRNAs has highlighted their importance in neural development, but the specific functions of neurally enriched miRNAs remain poorly understood. We report here the expression profile of miRNAs during neuronal differentiation in the human neuroblastoma cell line SH-SY5Y. Six miRNAs were significantly upregulated during differentiation induced by all-trans-retinoic acid and brain-derived neurotrophic factor. We demonstrated that the ectopic expression of either miR-124a or miR-125b increases the percentage of differentiated SH-SY5Y cells with neurite outgrowth. Subsequently, we focused our functional analysis on miR-125b and demonstrated the important role of this miRNA in both the spontaneous and induced differentiations of SH-SH5Y cells. miR-125b is also upregulated during the differentiation of human neural progenitor ReNcell VM cells, and miR-125b ectopic expression significantly promotes the neurite outgrowth of these cells. To identify the targets of miR-125b regulation, we profiled the global changes in gene expression following miR-125b ectopic expression in SH-SY5Y cells. miR-125b represses 164 genes that contain the seed match sequence of the miRNA and/or that are predicted to be direct targets of miR-125b by conventional methods. Pathway analysis suggests that a subset of miR-125b-repressed targets antagonizes neuronal genes in several neurogenic pathways, thereby mediating the positive effect of miR-125b on neuronal differentiation. We have further validated the binding of miR-125b to the miRNA response elements of 10 selected mRNA targets. Together, we report here for the first time the important role of miR-125b in human neuronal differentiation.

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at http://mcb.asm.org/ .

ACKNOWLEDGMENTS

We thank all our colleagues in Biopolis and the Whitehead Institute, especially Philip Gaughwin, Boon Seng Soh, Wai Leong Tam, Yen Sin Ang, Yvonne Tay, Yin Loon Lee, Andrew Thomson, Prakash Rao, Shilpa Hattangadi, and Cheng Cheng Zhang for fruitful discussions and Ng Shyh-Chang and Senthil Raja Jayapal for proofreading the paper. We thank David Bartel and his laboratory for providing the miRNA microarray and other reagents. We also thank the staffs at the Biopolis High Content Screening Facility for providing the HCS service and advices.

M.T.N.L. and H.X. were supported by an SMA graduate fellowship. P.H.C., P.R., G.U., and H.Y. were supported by A*STAR, Singapore. B.L. and H.F.L. were partially supported by SMA grant C-382-641-001-091. B.L. was also supported by NIH grants DK047636 and AI54973. H.F.L. and B.Z. were supported by NIH grant R01 DK068348.