Imprinted lncRNA KCNQ1OT1 regulates CDKN1C expression through promoter binding and chromatin folding in pigs

Yongfeng Zhou; Hao Yu; Daoyu Zhang; Zhengzhu Wang; Qi Li; Xinglan An; Sheng Zhang; Ziyi Li

doi:10.1016/j.gene.2024.148590

Imprinted lncRNA KCNQ1OT1 regulates CDKN1C expression through promoter binding and chromatin folding in pigs

Gene. 2024 May 19:923:148590. doi: 10.1016/j.gene.2024.148590. Online ahead of print.

Authors

Yongfeng Zhou¹, Hao Yu², Daoyu Zhang³, Zhengzhu Wang⁴, Qi Li¹, Xinglan An¹, Sheng Zhang¹, Ziyi Li⁵

Affiliations

¹ Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China.
² College of Animal Science, Jilin University, Changchun, China.
³ Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China.
⁴ Shenzhen University Affiliated South China Hospital, Shenzhen, China.
⁵ Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China. Electronic address: ziyi@jlu.edu.cn.

PMID: 38772516
DOI: 10.1016/j.gene.2024.148590

Abstract

Long noncoding RNAs (lncRNAs) are implicated in a number of regulatory functions in eukaryotic genomes. In humans, KCNQ1OT1 is a 91 kb imprinted lncRNA that inhibits multiple surrounding genes in cis. Among them, CDKN1C is closely related to KCNQ1OT1 and is involved in multiple epigenetic disorders. Here, we found that pigs also had a relatively conserved paternal allele expressing KCNQ1OT1 and had a shorter 5' end (∼27 kb) compared to human KCNQ1OT1. Knockdown of KCNQ1OT1 using antisense oligonucleotides (ASO) showed that upregulation of CDKN1C expression in pigs. However, porcine KCNQ1OT1 did not affect the DNA methylation status of the CpG islands in the promoters of KCNQ1OT1 and CDKN1C. Inhibition of DNA methyltransferase using Decitabine treatment resulted in a significant increase in both KCNQ1OT1 and CDKN1C expression, suggesting that the regulation between KCNQ1OT1 and CDKN1C may not be dependent on RNA interference. Further use of chromosome conformation capture and reverse transcription-associated trap detection in the region where CDKN1C was located revealed that KCNQ1OT1 bound to the CDKN1C promoter and affected chromosome folding. Phenotypically, inhibition of KCNQ1OT1 at the cumulus-oocyte complex promoted cumulus cell transformation, and to upregulated the expression of ALPL at the early stage of osteogenic differentiation of porcine bone marrow mesenchymal stem cells. Our results confirm that the expression of KCNQ1OT1 imprinting in pigs as well as porcine KCNQ1OT1 regulates the expression of CDKN1C through direct promoter binding and chromatin folding alteration. And this regulatory mechanism played an important role in cell differentiation.

Keywords: Chromosome folding; DNA methylation; Imprinted gene; Long-noncoding RNA; Pigs.