MicroRNAs control intestinal epithelial differentiation, architecture, and barrier function.
OBJECTIVE
Whereas the importance of microRNA (miRNA) for the development of several tissues is well established, its role in the intestine is unknown. We aimed to quantify the complete miRNA expression profile of the mammalian intestinal mucosa and to determine the contribution of miRNAs to intestinal homeostasis using genetic means.


METHODS
We determined the miRNA transcriptome of the mouse intestinal mucosa using ultrahigh throughput sequencing. Using high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP), we identified miRNA-messenger RNA target relationships in the jejunum. We employed gene ablation of the obligatory miRNA-processing enzyme Dicer1 to derive mice deficient for all miRNAs in intestinal epithelia.


RESULTS
miRNA abundance varies dramatically in the intestinal mucosa, from 1 read per million to 250,000. Of the 453 miRNA families identified, mmu-miR-192 is the most highly expressed in both the small and large intestinal mucosa, and there is a 53% overlap in the top 15 expressed miRNAs between the 2 tissues. The intestinal epithelium of Dicer1(loxP/loxP);Villin-Cre mutant mice is disorganized, with a decrease in goblet cells, a dramatic increase in apoptosis in crypts of both jejunum and colon, and accelerated jejunal cell migration. Furthermore, intestinal barrier function is impaired in Dicer1-deficient mice, resulting in intestinal inflammation with lymphocyte and neutrophil infiltration. Our list of miRNA-messenger RNA targeting relationships in the small intestinal mucosa provides insight into the molecular mechanisms behind the phenotype of Dicer1 mutant mice.


CONCLUSIONS
We have identified all intestinal miRNAs and shown using gene ablation of Dicer1 that miRNAs play a vital role in the differentiation and function of the intestinal epithelium.
McKenna
Lindsay B
LB
Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19103, USA.
Schug
Jonathan
J
Vourekas
Anastassios
A
McKenna
Jaime B
JB
Bramswig
Nuria C
NC
Friedman
Joshua R
JR
Kaestner
Klaus H
KH
D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D053487:DEAD-box RNA Helicases / Q000235:genetics* / Q000378:metabolism; D004195:Disease Models, Animal; D004722:Endoribonucleases / Q000235:genetics* / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D047468:Immunoprecipitation; D007413:Intestinal Mucosa / Q000378:metabolism / Q000473:pathology*; D007579:Jejunal Diseases / Q000201:enzymology / Q000235:genetics* / Q000473:pathology; D051379:Mice; D008817:Mice, Mutant Strains; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012333:RNA, Messenger / Q000235:genetics*; D043244:Ribonuclease III
D035683:MicroRNAs; D012333:RNA, Messenger; D004722:Endoribonucleases; C509781:Dicer1 protein, mouse; D043244:Ribonuclease III; D053487:DEAD-box RNA Helicases