Basic—Alimentary TractMicroRNAs Control Intestinal Epithelial Differentiation, Architecture, and Barrier Function
Section snippets
Identification and Quantification of miRNAs
Jejunal mucosa was scraped from the longitudinally sliced intestine of CD1 mice (n = 4), and small RNAs were isolated using the mirVana miRNA kit (Ambion catalogue No. AM1560). Libraries were prepared using the Digital Gene Expression-Small RNA sample prep kit (Illumina, San Diego, CA, FC-102-1009) and sequenced on a Genome Analyzer II (Illumina). Trimmed reads were aligned to precursor miRNA sequence from miRBase (release 13.0), reference sequence (RefSeq) sequence (National Center for
Results
We quantified small RNAs from jejunal and colonic mucosa of adult wild-type mice using ultrahigh throughput sequencing. We aligned the resulting sequence reads to known miRNA precursor genes obtained from miRBase.16 Next, we verified that these sequence reads represented miRNAs and not degraded mRNAs by aligning them to the RefSeq database. As shown in Figure 1A, less than 20% of reads in the miRNA size range aligned to mRNAs, whereas more than 90% matched precursor miRNAs, indicating that our
Discussion
By combining the mRNA microarray data with HITS-CLIP-derived targeting information, we can identify a set of miRNA targets whose expression levels are affected in the small intestine by deletion of Dicer1, among them the aforementioned Cadherin 1 and Cathepsin B genes (see Supplementary Table 4 for summary). We analyzed transcription factors as potentially important targets because they control transcriptional networks and often play fundamental well-studied roles in processes such as
Acknowledgments
The authors thank Drs Merkenschlager, Gumucio, Rustgi, and Mourelatos for reagents; Elizabeth Helmbrecht and Karrie Brondell for maintenance of the mouse colony; Amber Horner for technical assistance; Dr Gary Swain, Jaclyn Twaddle, and the entire morphology core of the Penn Center for Molecular Studies in Digestive and Kidney Disease (DK-050306) for reagents and technical assistance; Dr Marie Hildebrandt, Markiyan Doliba, and Christopher Morgan for technical assistance; and Dr John Le Lay for
References (33)
MicroRNAs: target recognition and regulatory functions
Cell
(2009)- et al.
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
Cell
(2005) MicroRNAs: genomics, biogenesis, mechanism, and function
Cell
(2004)- et al.
A mammalian microRNA expression atlas based on small RNA library sequencing
Cell
(2007) - et al.
Cis elements of the villin gene control expression in restricted domains of the vertical (crypt) and horizontal (duodenum, cecum) axes of the intestine
J Biol Chem
(2002) - et al.
Resistin-like molecule β regulates innate colonic function: barrier integrity and inflammation susceptibility
J Allergy Clin Immunol
(2006) - et al.
WNT/TCF signaling through LEF1 and HOXB9 mediates lung adenocarcinoma metastasis
Cell
(2009) - et al.
Role of the Onecut transcription factors in pancreas morphogenesis and in pancreatic and enteric endocrine differentiation
Dev Biol
(2007) - et al.
miR-495 and miR-218 regulate the expression of the Onecut transcription factors HNF-6 and OC-2
Biochem Biophys Res Commun
(2010) - et al.
T-cell lineage choice and differentiation in the absence of the RNase III enzyme Dicer
J Exp Med
(2005)
Hepatic function is preserved in the absence of mature microRNAs
Hepatology
Disruption of Dicer1 induces dysregulated fetal gene expression and promotes hepatocarcinogenesis
Gastroenterology
let-7 microRNA functions as a potential growth supressor in human colon cancer cells
Biol Pharm Bull
MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2a
Gastroenterology
The colorectal microRNAome
Proc Natl Acad Sci U S A
Expansion of adult β-cell mass in response to increased metabolic demand is dependent on HNF-4α
Genes Dev
Cited by (285)
MicroRNAs in Gut Health: Modulation of Host-Microbial Interactions in the Gastrointestinal Tract
2023, MicroRNA in Regenerative Medicine, Second EditionInflammatory auto-immune diseases of the intestine and their management by natural bioactive compounds
2022, Biomedicine and Pharmacotherapy
Conflicts of interest The authors disclose no conflicts.
Funding Supported by T32-HD007516 (to L.B.M.) and NIDDK grant R01-DK053839 (to K.H.K.).