The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2

摘要 : Long non-coding RNAs (lncRNAs) regulate diverse biological processes, including cell lineage specification. Here, we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations.

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 expression

Long non-coding RNAs (lncRNAs) regulate diverse BioLogical processes, including cell lineage specification. Here, we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allows us to identify hundreds of lncRNAs that exhibit differentiation-stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA, definitive endoderm-associated lncRNA1 (DEANR1), and

demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating expression of the endoderm factor FOXA2. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1

facilitates FOXA2 activation by facilitating SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation stage-specific lncRNAs but also characterizes a functional lncRNA that is important for endoderm differentiation.


Figure 6. DEANR1 Associates with SMAD2/3 and Helps to Target It to the FOXA2 Promoter

(A) RNA-FISH demonstrates nuclear localization of DEANR1 only in FOXA2-positive DE Cells. Scalebar represents 5 mm.

(B) Dual RNA-DNA-FISH demonstrates that DEANR1 transcripts (green signal) are localized to the FOXA2 GENE locus (red signal).

(C) SMAD2/3 antibodies immunoprecipitate DEANR1, but not U1 snRNA or lncRNA MALAT1.

(D) ChIP analysis demonstrates binding of SMAD2/3 to the promoter region of the FOXA2 gene locus. IgG serves as a control. The genomic location of the analyzed regions is indicated in the diagram at the top of the panel.

(E) Knockdown of DEANR1 reduces binding of SMAD2/3 to the FOXA2 promoter, but not to another SMAD2/3 target, EOMES. The mean values are shown and error bars represent the SD from the mean (n = 3). Significance was determined by two-tailed Student’s t test, and the p value is presented.

(F) Hypothetical model illustrating how DEANR1 might regulate FOXA2 transcription in cis. The genomic locations of DEANR1 and FOXA2 genes are shown on the top line and the arrows indicate the transcription direction. Upon DEANR1 activation, chromatin looping brings the DEANR1 locus spatially close to the FOXA2 promoter region (~20 kb between the DEANR1 gene body and the FOXA2 promoter). The transcribed DEANR1 interacts

with SMAD2/3 protein and brings SMAD2/3 to the FOXA2 promoter by forming DNA-RNA hydride for specific targeting of SMAD2/3 to the FOXA2 promoter. Together with other transcription machinery, binding of SMAD2/3 to the FOXA2 promoter initiates transcription.

原文链接：http://www.cell.com/cell-reports/abstract/S2211-1247(15)00261-2

作者：赛诚生物

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