Abstract
Transcriptional repression of Nanog is an important hallmark of stem cell differentiation. Chromatin modifications have been linked to the epigenetic profile of the Nanog gene, but whether chromatin organization actually plays a causal role in Nanog regulation is still unclear. Here, we report that the formation of a chromatin loop in the Nanog locus is concomitant to its transcriptional downregulation during human NTERA-2 cell differentiation. We found that two Alu elements flanking the Nanog gene were bound by the aryl hydrocarbon receptor (AhR) and the insulator protein CTCF during cell differentiation. Such binding altered the profile of repressive histone modifications near Nanog likely leading to gene insulation through the formation of a chromatin loop between the two Alu elements. Using a dCAS9-guided proteomic screening, we found that interaction of the histone methyltransferase PRMT1 and the chromatin assembly factor CHAF1B with the Alu elements flanking Nanog was required for chromatin loop formation and Nanog repression. Therefore, our results uncover a chromatin-driven, retrotransposon-regulated mechanism for the control of Nanog expression during cell differentiation.
Highlights
Cellular differentiation is a key process during embryonic development [1, 2] and in adult stem cell homeostasis [3] whose alteration can lead to pathological states including cancer [4, 5]
Our main conclusion is that a molecular complex, composed by aryl hydrocarbon receptor (AhR), PRMT1, CHAF1B and CTCF, interacts with Alu elements modifying the epigenetic profile and generating a chromatin loop around the Nanog gene that will lead to its repression during retinoic acid (RA)-mediated differentiation
Following the same bioinformatic algorithm used to analyze the mouse heterologous of these human repetitive elements (e.g., B1 family) [35], we have extracted those Alu retrotransposons located in human gene promoters that have an AhR binding site and an E-Box binding site separated by a conserved nucleotide sequence (Additional file 1: Figure S1A)
Summary
Cellular differentiation is a key process during embryonic development [1, 2] and in adult stem cell homeostasis [3] whose alteration can lead to pathological states including cancer [4, 5]. Alu-generated transcripts in differentiated cells were able to repress Nanog and Oct expression by a mechanism involving the miRNA machinery [17]. These results are in agreement with the proposed roles for repetitive elements as enhancer–promoter insulators and/or chromatin barriers and architecture [29,30,31,32,33,34]. We have investigated if Alu retrotransposons located near pluripotency genes could participate in human stem cell differentiation by modulating chromatin structure and dynamics. Impairing the interaction between AhR and PRMT1 with the Alu elements restored Nanog expression in differentiation-induced cells
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