Transcription factor activity and nucleosome organisation in mitosis

Abstract

Mitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and understand the function of BFs: first, formaldehyde has been suggested to be unable to efficiently capture these transient interactions, leading to profound contradictions in the literature; second, if BFs are not permanently bound to their targets during mitosis, it becomes unclear how they convey regulatory information to daughter cells. Here, comparing formaldehyde to alternative fixatives we clarify the nature of the chromosomal association of previously proposed BFs in embryonic stem cells: while Esrrb can be considered as a canonical BF that binds at selected regulatory regions in mitosis, Sox2 and Oct4 establish DNA sequence independent interactions with the mitotic chromosomes, either throughout the chromosomal arms (Sox2) or at pericentromeric regions (Oct4). Moreover, we show that ordered nucleosomal arrays are retained during mitosis at Esrrb bookmarked sites, whereas regions losing transcription factor binding display a profound loss of order. By maintaining nucleosome positioning during mitosis, Esrrb might ensure the rapid postmitotic re-establishment of functional regulatory complexes at selected enhancers and promoters. Our results provide a mechanistic framework that reconciles dynamic mitotic binding with the transmission of gene regulatory information across cell division. mitotic bookmarking | mitosis | nucleosome | transcription factor | fixationCorrespondence: pnavarro@pasteur.fr

Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells

“…9). Our results support the emerging view that TF association with mitotic chromosomes detected by live-cell imaging is to large extent driven by nonspecific interactions (Festuccia et al 2019;Raccaud et al 2019). However, to what extent the lack of sequence-specific binding observed with Brn2 can be extended to other mitotic chromosome binding TFs must be examined in the future.…”

“…However, to what extent the lack of sequence-specific binding observed with Brn2 can be extended to other mitotic chromosome binding TFs must be examined in the future. Of note, the Brn2 case finds precedent in a recent study showing that association of Sox2 with mitotic chromatin in ES cells also occurs in the absence of sequence-specific binding (Festuccia et al 2019).…”

“…Enhancer usage, and the establishment of enhancer-promoter loops, has been observed as early as anaphase (Palozola et al 2017;Abramo et al 2019;Zhang et al 2019). A role for TFs in regulating chromatin accessibility during this period has been recently shown (Festuccia et al 2019;Friman et al 2019;Owens et al 2019); however, a clear link between canonical TF activity and timing of gene reactivation has remained elusive. Addressing this requires the ability to knock down the function of TFs specifically during mitosis, a task made more difficult with Brn2, by the coexpression of redundant POU3f family members in neural stem/progenitor cells (Sugitani et al 2002).…”

“…TF binding to regulatory regions may therefore mark a subset of genes for efficient reactivation upon mitotic exit (Festuccia et al 2017;Palozola et al 2018a). One possibility is that occupancy of regulatory regions by TFs maintains nucleosome positioning, counteracting large chromatin rearrangements characteristic of mitosis, as shown in recent studies (Festuccia et al 2019;Owens et al 2019). Nevertheless, the basis and impact of mitotic chromosome binding by TFs to gene regulatory events remain poorly understood.…”

Mitotic chromosome binding predicts transcription factor properties in interphase

“…Both non-specific and specific DNA binding of TFs to mitotic chromosomes have been described. However, the often small number of specifically-bound loci on mitotic chromosomes (Caravaca et al, 2013;Deluz et al, 2016;Festuccia et al, 2018;Kadauke et al, 2012), the mild or null sensitivity to alterations of specific DNA binding properties (Caravaca et al, 2013;Festuccia et al, 2016), and the absence of quantitative relationship between mitotic ChIPseq datasets and fluorescence microscopy (Festuccia et al, 2018) suggest that the co-localization of TFs with mitotic chromosomes observed by microscopy is mainly due to non-specific DNA interactions. Converging evidence from the literature further corroborates this view.…”