FACT mediates cohesin function on chromatin

Abstract

Cohesin is a regulator of genome architecture with roles in sister chromatid cohesion and chromosome compaction. The recruitment and mobility of cohesin complexes on DNA is restricted by nucleosomes. Here, we show that the role of cohesin in chromosome organization requires the histone chaperone FACT (‘facilitates chromatin transcription’) in Saccharomyces cerevisiae. We find that FACT interacts directly with cohesin, and is dynamically required for its localization on chromatin. Depletion of FACT in metaphase cells prevents cohesin accumulation at pericentric regions and causes reduced binding on chromosome arms. Using the Hi-C technique, we show that cohesin-dependent TAD (topological associated domain)-like structures in G1 and metaphase chromosomes are reduced in the absence of FACT. Sister chromatid cohesion is intact in FACT-depleted cells, although chromosome segregation failure is observed. Our data show that FACT contributes to the formation of cohesin-dependent TADs, thus uncovering a new role for this complex in nuclear organization during interphase and mitotic chromosome folding.

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Fig. 1: The cohesin complex interacts physically with FACT.
Fig. 2: FACT is necessary for the localization of cohesins in metaphase chromosomes.
Fig. 3: FACT inactivation causes defects in chromosome organization but not sister chromatid cohesion.
Fig. 4: FACT function is important for the establishment cohesin-dependent TAD-like domains.
Fig. 5: Analysis of chromosome segregation in the absence of FACT.

Data availability

ChIP-seq and MNase-seq data supporting the findings of this study have been deposited in the GEO database and are accessible through accession no. GSE118534. Hi-C raw sequences are accessible via the SRA database through accession no. PRJNA486513. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD014896. Source data for Figs. 1b,c, 3d and 5 are available online. Any further data that support the findings of this study are available from the corresponding authors upon request.

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Acknowledgements

We thank the members of the L.A., R.K. and P.A. laboratories for fruitful discussions and advice. The work in the L.A. laboratory was supported by a Wellcome Trust Senior Investigator award to L.A. (100955, ‘Functional dissection of mitotic chromatin’) and the London Institute of Medical Research (LMS), which receives its core funding from the UK Medical Research Council. This research was further supported by funding from The European Research Council (R.K.), Agence Nationale pour la Recherche (R.K.) and the the Spanish Ministerio de Economía, Industria y Competitividad (BFU2017-89622-P; F.A.).

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Contributions

J.G.-L. performed all yeast experiments, providing samples for nucleosome mapping, HiC and sequencing. J.G.-L. performed IP and cell biology experiments. L.L.-S. and A.T. performed Hi-C experiments and analysis. A.C. analyzed Hi-C data. A.G., S.G. and M.S. performed and analyzed nucleosome position experiments. M.D. and M.M.K. performed bioinformatic analysis. P.G.-E. performed experiments related to the pulldowns for mass spectrometry and analyzed results data. H.K. and A.M. performed technical mass spectrometry analysis. A.J. performed molecular biology experiments to generate constructs. J.G.-L. and L.A. conceived the project. L.A. wrote the manuscript. L.A., F.A. and R.K. revised the manuscript.

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Correspondence to Romain Koszul or Luis Aragon.

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Peer review information Anke Sparmann was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Integrated supplementary information

Supplementary Figure 1 Auxin-mediated degradation of Spt16 in G2–M arrested cells.

Cells carrying either SMC1-6HA or SMC1-6HA SPT16-AID (which allows auxin-mediated degradation of Spt16) were arrested in metaphase (G2–M-nocodazole) and exposed to auxin to degrade Spt16. Nuclear and cellular morphology was used following auxin addition to confirm that the cell population remained arrested in metaphase (top). Western analysis for Spt16 confirms its degradation in SPT16-AID cells upon auxin addition (bottom). The bar graph data show the mean and error bars the s.d. of three independent experiments.

Supplementary Figure 2 Auxin-mediated degradation of Sth1 in G2–M arrested cells.

Cells carrying either SMC1-6HA or SMC1-6HA STH1-AID (which allows auxin-mediated degradation of Sth1) were arrested in metaphase (G2–M-nocodazole) and exposed to auxin to degrade Sth1. Western analysis for Sth1 confirms its degradation in STH1-AID cells upon auxin addition.

Supplementary Figure 3 FACT function in chromosome organization.

The 16 yeast chromosomes are displayed on Hi-C maps (10 kb bins) obtained from G2–M arrests in the presence of auxin of SMC1-6HA (wild-type, bottom left) and SMC1-6HA SPT16-AID (Spt16-aid) cells (top right). Black to white color scales reflect high to low contact frequencies, respectively (log2). Inset: Magnifications of chr7.

Supplementary Figure 4 FACT function in the establishment of cohesin-dependent structures in G1.

The 16 yeast chromosomes are displayed on Hi-C maps (10 kb bins) obtained from G1 arrests overexpressing MCD1 from the GAL1-10 promoter in the presence of auxin of wild-type (bottom left) and SPT16-AID (Spt16-aid) cells (top right). Black to white color scales reflect high to low contact frequencies, respectively (log2). Inset: magnifications of chr7.

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Supplementary Information

Supplementary Figs. 1–4, Supplementary Table 1 and Supplementary Data Set 1

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Garcia-Luis, J., Lazar-Stefanita, L., Gutierrez-Escribano, P. et al. FACT mediates cohesin function on chromatin. Nat Struct Mol Biol 26, 970–979 (2019). https://doi.org/10.1038/s41594-019-0307-x

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