FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

Célia Jeronimo; Andrew Angel; Vu Q. Nguyen; Jee Min Kim; Christian Poitras; Elie Lambert; Pierre Collin; Jane Mellor; Carl Wu; François Robert

doi:10.1016/j.molcel.2021.07.010

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

Célia Jeronimo
, Andrew Angel
, Vu Q. Nguyen
, Jee Min Kim
, Christian Poitras
, Elie Lambert
, Pierre Collin
, Jane Mellor
, Carl Wu
, François Robert^* (Corresponding Author)

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

50 Citations (Scopus)

Abstract

The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

Original language	English
Pages (from-to)	3542-3559.e11
Number of pages	30
Journal	Molecular Cell
Volume	81
Issue number	17
DOIs	https://doi.org/10.1016/j.molcel.2021.07.010
Publication status	Published - 2 Sept 2021
Externally published	Yes

Bibliographical note

Funding Information:
We are grateful to N. Francis for critical reading of the manuscript and the Robert lab members for comments. We also thank A. Bataille for advice about ChIP-exo library preparation and analysis; M. Sarsenova and O. Rocheleau-Leclair for help generating some strains; and T. Formosa, D. Stillman, R.A. Young, S. Hahn, S. Buratowski, F. Winston, S. Churchman, A. Lusser, and K. Förstemann for sharing reagents. This work was funded by grants from the Canadian Institutes of Health Research (CIHR; MOP-162334) and the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2018-04519) to F.R. and from the National Institutes of Health (GM132290-01) to C.W. This research was also enabled in part by support provided by Calcul Québec (https://www.calculquebec.ca) and Compute Canada (https://www.computecanada.ca). A.A. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) grant to J.M. (BB/S009035/1), J.M.K. by a Korean Foundation for Advanced Studies fellowship, and E.L. by an Alexander Graham Bell Canada Doctoral Scholarship from NSERC. F.R. holds a Research Chair from Fonds de Recherche Québec – Santé (FRQS). F.R. and C.J. conceived the study and designed experiments. C.J. performed most genomic experiments. A.A. performed the mathematical modeling. V.Q.N. and J.M.K. performed the SMT experiments and analyses. E.L. performed the ChIP experiments in Drosophila cells. P.C. performed some ChIP-chip experiments in Figures 1E and S2. C.P. and F.R. performed genomic data analyses. F.R. supervised research. C.W. supervised SMT. J.M. supervised modeling. F.R. C.W. and J.M. provided funding. F.R. and C.J. wrote the manuscript with input from all authors. The authors declare no competing interests.

Data Availability Statement

Data and code availability
•
The microarray (ChIP-chip) and DNA sequencing (ChIP-exo and MNase-ChIP-seq) data generated during this study are available at the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE155144.

•
The single-molecule tracking data generated during this study are available in Mendeley Data, https://doi.org/10.17632/rnf4nc3g6y.1 (https://data.mendeley.com/datasets/rnf4nc3g6y/1).

•
The in-house scripts used to generate some of the analyses during this study are available at https://github.com/francoisrobertlab.

•
The code related to the mathematical modeling of the MNase-ChIP-seq data is available at https://github.com/aangel-code/FACT-inchworm-model.

Funding

We are grateful to N. Francis for critical reading of the manuscript and the Robert lab members for comments. We also thank A. Bataille for advice about ChIP-exo library preparation and analysis; M. Sarsenova and O. Rocheleau-Leclair for help generating some strains; and T. Formosa, D. Stillman, R.A. Young, S. Hahn, S. Buratowski, F. Winston, S. Churchman, A. Lusser, and K. Förstemann for sharing reagents. This work was funded by grants from the Canadian Institutes of Health Research (CIHR; MOP-162334) and the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2018-04519) to F.R. and from the National Institutes of Health (GM132290-01) to C.W. This research was also enabled in part by support provided by Calcul Québec (https://www.calculquebec.ca) and Compute Canada (https://www.computecanada.ca). A.A. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) grant to J.M. (BB/S009035/1), J.M.K. by a Korean Foundation for Advanced Studies fellowship, and E.L. by an Alexander Graham Bell Canada Doctoral Scholarship from NSERC. F.R. holds a Research Chair from Fonds de Recherche Québec – Santé (FRQS). F.R. and C.J. conceived the study and designed experiments. C.J. performed most genomic experiments. A.A. performed the mathematical modeling. V.Q.N. and J.M.K. performed the SMT experiments and analyses. E.L. performed the ChIP experiments in Drosophila cells. P.C. performed some ChIP-chip experiments in Figures 1E and S2. C.P. and F.R. performed genomic data analyses. F.R. supervised research. C.W. supervised SMT. J.M. supervised modeling. F.R. C.W. and J.M. provided funding. F.R. and C.J. wrote the manuscript with input from all authors. The authors declare no competing interests. We are grateful to N. Francis for critical reading of the manuscript and the Robert lab members for comments. We also thank A. Bataille for advice about ChIP-exo library preparation and analysis; M. Sarsenova and O. Rocheleau-Leclair for help generating some strains; and T. Formosa, D. Stillman, R.A. Young, S. Hahn, S. Buratowski, F. Winston, S. Churchman, A. Lusser, and K. Förstemann for sharing reagents. This work was funded by grants from the Canadian Institutes of Health Research (CIHR; MOP-162334 ) and the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2018-04519 ) to F.R. and from the National Institutes of Health ( GM132290-01 ) to C.W. This research was also enabled in part by support provided by Calcul Québec ( https://www.calculquebec.ca ) and Compute Canada ( https://www.computecanada.ca ). A.A. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) grant to J.M. ( BB/S009035/1 ), J.M.K. by a Korean Foundation for Advanced Studies fellowship, and E.L. by an Alexander Graham Bell Canada Doctoral Scholarship from NSERC . F.R. holds a Research Chair from Fonds de Recherche Québec – Santé (FRQS).

Keywords

Chd1
chromatin remodeling
FACT
histone chaperone
mathematical modeling
nucleosome unwrapping
Pob3
RNA polymerase II
single-molecule tracking
Spt16

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Cite this

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title = "FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner",

abstract = "The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.",

keywords = "Chd1, chromatin remodeling, FACT, histone chaperone, mathematical modeling, nucleosome unwrapping, Pob3, RNA polymerase II, single-molecule tracking, Spt16",

author = "C{\'e}lia Jeronimo and Andrew Angel and Nguyen, \{Vu Q.\} and Kim, \{Jee Min\} and Christian Poitras and Elie Lambert and Pierre Collin and Jane Mellor and Carl Wu and Fran{\c c}ois Robert",

note = "Funding Information: We are grateful to N. Francis for critical reading of the manuscript and the Robert lab members for comments. We also thank A. Bataille for advice about ChIP-exo library preparation and analysis; M. Sarsenova and O. Rocheleau-Leclair for help generating some strains; and T. Formosa, D. Stillman, R.A. Young, S. Hahn, S. Buratowski, F. Winston, S. Churchman, A. Lusser, and K. F{\"o}rstemann for sharing reagents. This work was funded by grants from the Canadian Institutes of Health Research (CIHR; MOP-162334) and the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2018-04519) to F.R. and from the National Institutes of Health (GM132290-01) to C.W. This research was also enabled in part by support provided by Calcul Qu{\'e}bec (https://www.calculquebec.ca) and Compute Canada (https://www.computecanada.ca). A.A. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) grant to J.M. (BB/S009035/1), J.M.K. by a Korean Foundation for Advanced Studies fellowship, and E.L. by an Alexander Graham Bell Canada Doctoral Scholarship from NSERC. F.R. holds a Research Chair from Fonds de Recherche Qu{\'e}bec – Sant{\'e} (FRQS). F.R. and C.J. conceived the study and designed experiments. C.J. performed most genomic experiments. A.A. performed the mathematical modeling. V.Q.N. and J.M.K. performed the SMT experiments and analyses. E.L. performed the ChIP experiments in Drosophila cells. P.C. performed some ChIP-chip experiments in Figures 1E and S2. C.P. and F.R. performed genomic data analyses. F.R. supervised research. C.W. supervised SMT. J.M. supervised modeling. F.R. C.W. and J.M. provided funding. F.R. and C.J. wrote the manuscript with input from all authors. The authors declare no competing interests. ",

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doi = "10.1016/j.molcel.2021.07.010",

language = "English",

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T1 - FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

AU - Jeronimo, Célia

AU - Angel, Andrew

AU - Nguyen, Vu Q.

AU - Kim, Jee Min

AU - Poitras, Christian

AU - Lambert, Elie

AU - Collin, Pierre

AU - Mellor, Jane

AU - Wu, Carl

AU - Robert, François

N1 - Funding Information: We are grateful to N. Francis for critical reading of the manuscript and the Robert lab members for comments. We also thank A. Bataille for advice about ChIP-exo library preparation and analysis; M. Sarsenova and O. Rocheleau-Leclair for help generating some strains; and T. Formosa, D. Stillman, R.A. Young, S. Hahn, S. Buratowski, F. Winston, S. Churchman, A. Lusser, and K. Förstemann for sharing reagents. This work was funded by grants from the Canadian Institutes of Health Research (CIHR; MOP-162334) and the Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2018-04519) to F.R. and from the National Institutes of Health (GM132290-01) to C.W. This research was also enabled in part by support provided by Calcul Québec (https://www.calculquebec.ca) and Compute Canada (https://www.computecanada.ca). A.A. was supported by a Biotechnology and Biological Sciences Research Council (BBSRC) grant to J.M. (BB/S009035/1), J.M.K. by a Korean Foundation for Advanced Studies fellowship, and E.L. by an Alexander Graham Bell Canada Doctoral Scholarship from NSERC. F.R. holds a Research Chair from Fonds de Recherche Québec – Santé (FRQS). F.R. and C.J. conceived the study and designed experiments. C.J. performed most genomic experiments. A.A. performed the mathematical modeling. V.Q.N. and J.M.K. performed the SMT experiments and analyses. E.L. performed the ChIP experiments in Drosophila cells. P.C. performed some ChIP-chip experiments in Figures 1E and S2. C.P. and F.R. performed genomic data analyses. F.R. supervised research. C.W. supervised SMT. J.M. supervised modeling. F.R. C.W. and J.M. provided funding. F.R. and C.J. wrote the manuscript with input from all authors. The authors declare no competing interests.

PY - 2021/9/2

Y1 - 2021/9/2

N2 - The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

AB - The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

KW - Chd1

KW - chromatin remodeling

KW - FACT

KW - histone chaperone

KW - mathematical modeling

KW - nucleosome unwrapping

KW - Pob3

KW - RNA polymerase II

KW - single-molecule tracking

KW - Spt16

UR - https://www.scopus.com/pages/publications/85114019429

U2 - 10.1016/j.molcel.2021.07.010

DO - 10.1016/j.molcel.2021.07.010

M3 - Article

C2 - 34380014

AN - SCOPUS:85114019429

SN - 1097-2765

VL - 81

SP - 3542-3559.e11

JO - Molecular Cell

JF - Molecular Cell

IS - 17

ER -

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner

Abstract

Bibliographical note

Data Availability Statement

Funding

Keywords

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