Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming

Abstract

Identification of functionally relevant differences between induced pluripotent stem cells (iPSC) and reference embryonic stem cells (ESC) remains a central question for therapeutic applications. Differences in gene expression between iPSC and ESC have been examined by microarray and more recently with RNA-SEQ technologies. We here report an in depth analyses of nuclear and cytoplasmic transcriptomes, using the CAGE (cap analysis of gene expression) technology, for 5 iPSC clones derived from mouse lymphocytes B and 3 ESC lines. This approach reveals nuclear transcriptomes significantly more complex in ESC than in iPSC. Hundreds of yet not annotated putative non-coding RNAs and enhancer-associated transcripts specifically transcribed in ESC have been detected and supported with epigenetic and chromatin-chromatin interactions data. We identified super-enhancers transcriptionally active specifically in ESC and associated with genes implicated in the maintenance of pluripotency. Similarly, we detected non-coding transcripts of yet unknown function being regulated by ESC specific super-enhancers. Taken together, these results demonstrate that current protocols of iPSC reprogramming do not trigger activation of numerous cis-regulatory regions. It thus reinforces the need for already suggested deeper monitoring of the non-coding transcriptome when characterizing iPSC clones. Such differences in regulatory transcript expression may indeed impact their potential for clinical applications.

Keywords:

• iPS
• lncRNAs
• non-coding RNA
• pluripotency
• Stem cells
• super-enhancers
• transcriptome

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Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Accession Code

All sequencing data have been deposited at the DNA Data Bank of Japan (DDBJ) under accession DRA000914 and DRA002621.

Funding

This work was supported by a grant to P.C. from the Japan Society for the Promotion of Science (JSPS) through the Funding Program for Next-Generation World-Leading Researchers (NEXT) initiated by the Council for Science and Technology Policy (CSTP), by a grand-in-aid for scientific research from JSPS to P.C. and A.F., and by a research grant from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT) to the RIKEN Center for Life Science Technologies. A.F. was supported by a Swiss National Science Foundation (SNSF) Fellowship for Advanced Researchers (PA00P3_142122) and a SNSF Ambizione grant (PZ00P3–154728). K.H. was supported by European Union Framework Program 7 (MODHEP project) for P.C. D.Y. and H.K. were supported by the Japan Science and Technology Agency CREST. The authors thank the RIKEN GeNAS sequencing platform for sequencing of the libraries.

Supplemental Material

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