Kidney Week

Abstract: FR-PO918

Comprehensive Analysis of Chromatin Signature and Transcriptome Uncovers Functional lncRNAs Expressed in Nephron Progenitor Cells

Session Information

• Development, Stem Cells, Regenerative Medicine - II
  October 26, 2018 | Location: Exhibit Hall, San Diego Convention Center
  Abstract Time: 10:00 AM - 12:00 PM

Category: Development, Stem Cells, and Regenerative Medicine

• 501 Development, Stem Cells, and Regenerative Medicine: Basic

Authors

• Nishikawa, Masaki, University of California, Los Angeles, California, United States

Masaki Nishikawa,

• Yuri, Shunsuke, Nara Institute of Science & Technology, Nara, Japan

Shunsuke Yuri,

• Kimura, Hiroshi, Tokai University, Hiratsuka, Japan

Hiroshi Kimura,

• Yanagawa, Naomi, University of California, Los Angeles, California, United States

Naomi Yanagawa,

• Hamon, Morgan, University of California, Los Angeles, California, United States

Morgan Hamon,

• Hauser, Peter V., University of California, Los Angeles, California, United States

Peter V. Hauser,

• Zhao, Lifu, University of California, Los Angeles, California, United States

Lifu Zhao,

• Jo, Oak Dong, University of California, Los Angeles, California, United States

Oak Dong Jo,

• Yanagawa, Norimoto, University of California, Los Angeles, California, United States

Norimoto Yanagawa,

Group or Team Name

• Renal Regeneration Laboratory

Background

Emerging evidence from recent studies has unraveled the roles of long noncoding RNAs (lncRNAs) in the function of various tissues. However, little is known about the roles of lncRNAs in kidney development. In our present study, we aimed to identify functional lncRNAs in one of the three lineages of kidney progenitor cells, i.e., metanephric mesenchymal (MM) cells.

Methods

MM cells were purified by FACS from Cited1^nuc-TagRFP-T mouse embryonic kidneys, and comprehensive analyses of the chromatin signature and transcriptome were conducted by RNA-seq and ChIP-seq.

Results

We found seventeen lncRNAs that were expressed specifically in MM cells with an active chromatin signature, while remaining silenced in a bivalent chromatin state in non-MM cells. Out of these MM specific lncRNAs, we identified a lncRNA, Gm29418, in a distal enhancer region of Six2, a key regulatory gene of MM cells. We further identified three transcript variants of Gm29418 by Rapid Amplification of cDNA Ends (RACE), and confirmed that the transcription-start-sites (TSSs) of these variants were consistent with the result of Cap Analysis Gene Expression (CAGE). In support of the enhancer-like function of Gm29418 on Six2 expression, we found that knock-down of Gm29418 by two independent anti-sense locked nucleic acid (LNA) phosphorothioate gapmers suppressed Six2 mRNA expression levels in MM cells. We also found that over-expression of Gm29418 led to an increase in Six2 mRNA expression levels in a mouse MM cell line.

Conclusion

In conclusion, we demonstrated in our present study that a comprehensive analysis of chromatin signature and transcriptome can be a powerful tool in screening lncRNAs in various tissues, which led us to identify a lncRNA, Gm29418, in renal progenitor cells that has an enhancer-like function on a key regulatory gene, Six2.

Funding

• Private Foundation Support