Mitotic chromosome binding predicts transcription factor properties in interphase

Mahé Raccaud,Timo Kuhn,Andrea B Alber,J Christof M Gebhardt,Harsha Agarwal,David M Suter,Cédric Deluz,Elias T Friman

doi:10.1038/s41467-019-08417-5

Mahé Raccaud, Timo Kuhn + Show 6 more

Open Access

https://doi.org/10.1038/s41467-019-08417-5

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Abstract

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequence-specific/non-specific DNA binding. How these properties affect their ability to occupy specific genomic sites and modify the epigenetic landscape is unclear. The association of TFs with mitotic chromosomes observed by fluorescence microscopy is largely mediated by non-specific DNA interactions and differs broadly between TFs. Here we combine quantitative measurements of mitotic chromosome binding (MCB) of 501 TFs, TF mobility measurements by fluorescence recovery after photobleaching, single molecule imaging of DNA binding, and mapping of TF binding and chromatin accessibility. TFs associating to mitotic chromosomes are enriched in DNA-rich compartments in interphase and display slower mobility in interphase and mitosis. Remarkably, MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times. This suggests that non-specific DNA binding properties of TFs regulate their search efficiency and occupancy of specific genomic sites.

Highlights

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequencespecific/non-specific DNA binding
Cells were seeded in 96-well plates and treated with dox to induce expression of TF-YPet fusion proteins. and the day they were imaged by wide-field fluorescence microscopy
We asked whether Mitotic Bound Fraction (MBF) values depend on overexpression levels, in at least 19 individual cells for each of 21 different TFs spanning a broad range of MBF

Summary

Introduction

Mammalian transcription factors (TFs) differ broadly in their nuclear mobility and sequencespecific/non-specific DNA binding. MCB correlates with relative TF on-rates and genome-wide specific site occupancy, but not with TF residence times This suggests that non-specific DNA binding properties of TFs regulate their search efficiency and occupancy of specific genomic sites. While ChIP-seq essentially identifies sequence-specific DNA binding, fluorescence microscopy allows quantifying mitotic chromosome association independently of enrichment on specific genomic sites[26]. The often small number of -bound loci on mitotic chromosomes[31,32,33,34], the mild or null sensitivity to alterations of specific DNA binding properties[31,35], and the absence of quantitative relationship between mitotic ChIP-seq datasets and fluorescence microscopy[33] suggest that co-localization of TFs with mitotic chromosomes as observed by microscopy is largely due to nonspecific DNA interactions. The existence of a common molecular mechanism underlying mitotic chromosome binding and pioneer activity remains uncertain

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