Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes.
Super-enhancers are tissue-specific cis-regulatory elements that drive expression of genes associated with cell identity and malignancy. A cardinal feature of super-enhancers is that they are transcribed to produce enhancer-derived RNAs (eRNAs). It remains unclear whether super-enhancers robustly activate genes in situ and whether their functions are attributable to eRNAs or the DNA element. CRISPR/Cas9 was used to systematically delete three discrete super-enhancers at the Nanog locus in embryonic stem cells, revealing functional differences in Nanog transcriptional regulation. One distal super-enhancer 45 kb upstream of Nanog (-45 enhancer) regulates both nearest neighbor genes, Nanog and Dppa3. Interestingly, eRNAs produced at the -45 enhancer specifically regulate Dppa3 expression by stabilizing looping of the -45 enhancer and Dppa3. Our work illustrates that genomic editing is required to determine enhancer function and points to a method to selectively target a subset of super-enhancer-regulated genes by depleting eRNAs.
Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA.
Steven
S
Blinka
Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA.
Michael H
MH
Reimer
Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA.
Kirthi
K
Pulakanti
Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Blood Research Institute, BloodCenter of Wisconsin, Milwaukee, WI 53226, USA; Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA. Electronic address: sridhar.rao@bcw.edu.
Sridhar
S
Rao
D000818:Animals; D064113:CRISPR-Cas Systems; D002868:Chromosomal Proteins, Non-Histone; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D004720:Endonucleases / Q000235:genetics / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D000072669:Gene Editing; D005786:Gene Expression Regulation; D000066449:Human Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D006801:Humans; D051379:Mice; D041681:NIH 3T3 Cells; D000071317:Nanog Homeobox Protein / Q000235:genetics* / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism*; D061251:Primary Cell Culture; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic
D002868:Chromosomal Proteins, Non-Histone; C466105:DPPA3 protein, human; C486780:NANOG protein, human; D000071317:Nanog Homeobox Protein; D011506:Proteins; D062085:RNA, Long Noncoding; D004720:Endonucleases
eRNAs; embryonic stem cells; long non-coding RNAs; super-enhancers; transcriptional regulation
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