Single-Cell Transcriptome Analysis Reveals Dynamic Changes in lncRNA Expression during Reprogramming
Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential functions in reprogramming cell fate have been largely unexplored. We used single-cell RNA sequencing to characterize the expression patterns of over 16,000 genes, including 437 lncRNAs, during defined stages of reprogramming to pluripotency. Self-organizing maps (SOMs) were used as an intuitive way to structure and interrogate transcriptome data at the single-cell level. Early molecular events during reprogramming involved the activation of Ras signaling pathways, along with hundreds of lncRNAs. Loss-of-function studies showed that activated lncRNAs can repress lineage-specific genes, while lncRNAs activated in multiple reprogramming cell types can regulate metabolic gene expression. Our findings demonstrate that reprogramming cells activate defined sets of functionally relevant lncRNAs and provide a resource to further investigate how dynamic changes in the transcriptome reprogram cell state.
Additional Information© 2015 Elsevier Inc. Received: February 7, 2014. Revised: October 21, 2014. Accepted: November 10, 2014. Published: January 8, 2015. We thank Ellen Rothenberg, Paul Sternberg, and Chuck Murry for helpful discussions; Jorge Mata and Scott Wang for tail tip excision; Josh Verceles, Diana Perez, and Rochelle Diamond for cell sorting; Igor Antoshechkin for sequencing; Henry Amrhein and Diane Trout for data curation; Shujun Luo for single-cell protocol development; and Maria Moon and Hank Huang for illustration and graphic design. D.H.K. was supported by a Fellowship Award from the Damon Runyon Cancer Research Foundation and the Beckman Fellows Program at the California Institute of Technology. G.P.S. is an employee and shareholder of Illumina. M.B.E. is an Investigator of the Howard Hughes Medical Institute. This work was supported by NIH R01HD075605A and HFSP.RGP0200 funding to M.B.E.; Gordon and Betty Moore Foundation Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative; and the Bren Chair, Caltech Beckman Institute, and NIH NHGRI funding to B.J.W. Sequencing data have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus under accession number GSE55291.
Accepted Version - nihms-642325.pdf
Supplemental Material - mmc1.pdf
Supplemental Material - mmc2.xlsx