Mitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network

Abstract

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate post-mitotic gene reactivation. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the significance and importance of their bookmarking function. Here, we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover an unexpected redundancy among members of the protein superfamily of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ESRRB is essential for mouse pluripotency, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly the most rapidly and strongly reactivated ones. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially by nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.

Nr5a2is essential for morula development

“…The FDR for the differential expression of each gene is plotted alongside. (C) NR5A2 and ESRRB binding in ES cells (12 , 13) in proximity of the subtelomeric region near Tcstv3 on Chr13. Note the presence of clusters of degenerate NR5A2/ESRRB binding sites.…”

“…Tracks from the input are shown in support of the specificity of the signal observed. (D) Nr5a2 and Esrrb binding at the same sub-telomeric regions as in C, assessed by ChIP q-PCR in ES cells in which NR5A2 and ESRRB can be depleted by addition of Auxin (13) . N.b.…”

“…While directed against NR5A2, SR1848 strongly inhibits NR2C2 (11) and possibly more nuclear receptors expressed at the 2C stage (26). Given that these TFs often share the same DNA binding motif, and that we have shown a high redundancy in their chromatin association (12,13), it is possible that this class of TFs represents, as a whole, the first example of a so far elusive sequence specific activity essential to jumpstart zygotic transcription in mammals. In this regard, it is noteworthy that the motif identified at genes responding to NR5A2 in 2C stage embryos, which matches SINE B1/Alu repeats, is constituted of a direct tandem of two basic nuclear receptor response elements.…”

“…The potential involvement of NR5A2, in combination with ESRRB (two related nuclear receptors), in preimplantation development is of interest given the established role of these two TFs in the control of pluripotency in mouse Embryonic Stem (ES) cells (12) . Indeed, they conjunctly control thousands of regulatory elements, in interphase but also during mitosis (13) , to confer robustness to the expression and activity of major regulators of pluripotency such as OCT4, SOX2 and NANOG. Hence, NR5A2 and ESRRB could represent global regulators of early mouse embryogenesis, controlling events linking ZGA to the formation of the blastocyst.…”

MYC and MAX drive the reactivation of the genome after mitosis

“…While the number of mitotic bookmarking TFs has increased considerably over the last years, none has been shown to play a determinant role in the efficient and global reactivation of the genome following mitosis. This is particularly true in mouse pluripotent Em-bryonic Stem (ES) cells, where several mitotic bookmarking TFs have been recently identified but only some shown to assist gene reactivation of particular sets of genes 4,7,[16][17][18] . Since these self-renewing cells display an almost inexistent G1 phase and start replication almost immediately after undergoing mitosis 4,19 , more efficient and global mechanisms are thus to be expected to drive a very rapid and accurate post-mitotic gene reactivation.…”