Genome-wide interaction target profiling reveals a novel Peblr20-eRNA activation pathway to control stem cell pluripotency

Abstract

Background: Long non-coding RNAs (lncRNAs) constitute an important component of the regulatory apparatus that controls stem cell pluripotency. However, the specific mechanisms utilized by these lncRNAs in the control of pluripotency are not fully characterized.Methods: We utilized a RNA reverse transcription-associated trap sequencing (RAT-seq) approach to profile the mouse genome-wide interaction targets for lncRNAs that are screened by RNA-seq.Results: We identified Peblr20 (Pou5F1 enhancer binding lncRNA 20) as a novel lncRNA that is associated with stem cell reprogramming. Peblr20 was differentially transcribed in fibroblasts compared to induced pluripotent stem cells (iPSCs). Notably, we found that Peblr20 utilized a trans mechanism to interact with the regulatory elements of multiple stemness genes. Using gain- and loss-of-function experiments, we showed that knockdown of Peblr20 caused iPSCs to exit from pluripotency, while overexpression of Peblr20 activated endogenous Pou5F1 expression. We further showed that Peblr20 promoted pluripotent reprogramming. Mechanistically, we demonstrated that Peblr20 activated endogenous Pou5F1 by binding to the Pou5F1 enhancer in trans, recruiting TET2 demethylase and activating the enhancer-transcribed RNAs.Conclusions: Our data reveal a novel epigenetic mechanism by which a lncRNA controls the fate of stem cells by trans-regulating the Pou5F1 enhancer RNA pathway. We demonstrate the potential for leveraging lncRNA biology to enhance the generation of stem cells for regenerative medicine.

Ribosomes: An Exciting Avenue in Stem Cell Research

“…Numerous studies have shown that the presence of long noncoding RNAs (lncRNAs) promote the maintenance of stem cell function [ 173 ]. LncRNAs, such as Peblr20 and SNHG14, significantly improve reprogramming efficiency [ 174 , 175 ]. This review focuses on the diversity of ribosomes associated with the translational control of stem gene expression and identification of specific recognition elements in the mRNAs associated with stemness.…”

LncRNA Functions as a New Emerging Epigenetic Factor in Determining the Fate of Stem Cells

“…Oplr16 enhanced reprograming epigenetically by coordinating intrachromosomal looping and DNA methylation in the Oct4 promoter. Wang et al (2020) used CRIST-seq to identify Peblr20 (Pou5F1 enhancer binding lncRNA 20) as another reprogramingassociated lncRNA. Notably, Peblr20 binds to the Oct4 enhancers, where it recruits TET2 demethylase and activates the enhancer RNA (eRNA) pathway.…”

“…Some pluripotent reprograming regulatory lncRNAs have been recently identified using CRIST-seq (Zhang et al, 2019). They form a regulatory network around the Oct4 and Sox2 promoters and affect reprograming through epigenetic pathways, including coordination of intrachromosomal loops, alteration of the methylation levels, and activation of the eRNA pathway for stemness genes (Jia et al, 2020;Wang et al, 2020). It is interesting to explore whether these lncRNAs work in coordination, and what their spatial and temporal specialties are in regulating the fate of stem cells.…”

Non-Coding RNAs and Nucleosome Remodeling Complexes: An Intricate Regulatory Relationship

“…Traditionally, RNA transcripts generated from non-protein-coding regions of the genome were thought of as transcriptional noise sometimes referred to as "junk". However, more recent research has shown non-protein-coding, or non-coding RNAs (ncRNAs), are numerous, diverse in form, and serve significant biological function [9,10]. ncRNAs are sorted into classes defined by functionality, length, or from the genomic element from which they originate.…”