title: Enhancer transcribed RNAs arise from hypomethylated, Tet-occupied genomic regions.
abstract: Enhancers are cis-acting elements capable of regulating transcription in a distance and orientation-independent manner. A subset of enhancers are occupied by RNA polymerase II (RNAP II) and transcribed to produce long non-coding RNAs termed eRNAs. We thoroughly investigated the association between eRNA productivity and various chromatin marks and transcriptional regulators in mouse embryonic stem cells (ESCs) through an integrative approach. We found that eRNA-producing enhancers exhibited elevated levels of the active mark H3K27Ac, decreased DNA methylation, and enrichment for the DNA hydroxylase Tet1. Many eRNA-producing enhancers have recently been characterized as "super-enhancers," suggesting an important role in the maintenance of pluripotency. Using experimental methods, we focally investigated a well-characterized enhancer linked to the Nanog locus and confirmed its exclusive eRNA productivity in ESCs. We further demonstrate that the binding of Sall4 and Tet family proteins were required for eRNA productivity at this locus. Collectively, we demonstrate that Tet1 binding and DNA hypomethylation are hallmarks of eRNA production.
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA.
authors.forename: Kirthi
authors.initials: K
authors.lastname: Pulakanti
authors.affiliation: Dana-Farber Cancer Institute and Harvard School of Public Health; Boston, MA USA.
authors.forename: Luca
authors.initials: L
authors.lastname: Pinello
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA.
authors.forename: Cary
authors.initials: C
authors.lastname: Stelloh
authors.affiliation: Medical College of Wisconsin; Milwaukee, WI USA; Departments of Cell Biology, Neurobiology, and Anatomy; Medical College of Wisconsin; Milwaukee, WI USA.
authors.forename: Steven
authors.initials: S
authors.lastname: Blinka
authors.affiliation: Medical College of Wisconsin; Milwaukee, WI USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Allred
authors.affiliation: Medical College of Wisconsin; Milwaukee, WI USA; Department of Pediatrics; Medical College of Wisconsin; Milwaukee, WI USA.
authors.forename: Samuel
authors.initials: S
authors.lastname: Milanovich
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA.
authors.forename: Sid
authors.initials: S
authors.lastname: Kiblawi
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Peterson
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Wang
authors.affiliation: Dana-Farber Cancer Institute and Harvard School of Public Health; Boston, MA USA.
authors.forename: Guo-Cheng
authors.initials: GC
authors.lastname: Yuan
authors.affiliation: BloodCenter of Wisconsin; Blood Research Institute; Milwaukee, WI USA; Medical College of Wisconsin; Milwaukee, WI USA; Departments of Cell Biology, Neurobiology, and Anatomy; Medical College of Wisconsin; Milwaukee, WI USA; Department of Pediatrics; Medical College of Wisconsin; Milwaukee, WI USA.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Rao
mesh_terms: D000818:Animals; D002460:Cell Line; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000378:metabolism; D004742:Enhancer Elements, Genetic; D018398:Homeodomain Proteins / Q000235:genetics / Q000378:metabolism; D051379:Mice; D041681:NIH 3T3 Cells; D000071317:Nanog Homeobox Protein; D011401:Promoter Regions, Genetic; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism*; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D000071317:Nanog Homeobox Protein; C475540:Nanog protein, mouse; D011518:Proto-Oncogene Proteins; C540839:TET1 protein, mouse; D012313:RNA; D004248:DNA (Cytosine-5-)-Methyltransferases
keywords: DNA methylation; Enhancer Transcribed RNAs (eRNAs); Tet-proteins; non-coding RNA; transcriptional enhancers