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Elife. 2016 Jun 22;5. pii: e16030. doi: 10.7554/eLife.16030.

Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development.

Author information

Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan.
Department of Nephrology, Kyoto University Graduate School of Medicine, Kyoto, Japan.
Developmental Genetics Group, Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.
Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan.
Center for Medical Research and Education, Osaka University Graduate School of Medicine, Suita, Japan.
Department of Biology and Biochemistry, University of Houston, Houston, Unites States.
Genome Science Division, Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan.


Transcription factors organize gene expression profiles by regulating promoter activity. However, the role of transcription factors after transcription initiation is poorly understood. Here, we show that the homeoprotein Nkx2-5 and the 5'-3' exonuclease Xrn2 are involved in the regulation of alternative polyadenylation (APA) during mouse heart development. Nkx2-5 occupied not only the transcription start sites (TSSs) but also the downstream regions of genes, serving to connect these regions in primary embryonic cardiomyocytes (eCMs). Nkx2-5 deficiency affected Xrn2 binding to target loci and resulted in increases in RNA polymerase II (RNAPII) occupancy and in the expression of mRNAs with long 3'untranslated regions (3' UTRs) from genes related to heart development. siRNA-mediated suppression of Nkx2-5 and Xrn2 led to heart looping anomaly. Moreover, Nkx2-5 genetically interacts with Xrn2 because Nkx2-5(+/-)Xrn2(+/-), but neither Nkx2-5(+/-)nor Xrn2(+/-), newborns exhibited a defect in ventricular septum formation, suggesting that the association between Nkx2-5 and Xrn2 is essential for heart development. Our results indicate that Nkx2-5 regulates not only the initiation but also the usage of poly(A) sites during heart development. Our findings suggest that tissue-specific transcription factors is involved in the regulation of APA.


chromosomes; development; gene expression; genes; mouse; transcription factors

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