Reactome | ATP-dependent chromatin remodelers

ATP-dependent chromatin remodelers

Stable Identifier

R-HSA-9932444

DOI

10.3180/R-HSA-9932444.1

Type

Pathway

Species

Homo sapiens

ReviewStatus

5/5

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ATP-dependent chromatin remodelers use the energy from ATP hydrolysis to organize or rearrange nucleosomes by altering histone-DNA contacts (reviewed in de la Serna et al, 2006; Hargreaves and Crabtree, 2011; Narlikar et al, 2013; Clapier et al, 2017; Eustermann et al, 2024). There are four main classes of mammalian ATP-dependent chromatin remodellers: SWI/SNF (for switch/sucrose non-fermenting, initially characterized in S. cerevisiae); ISWI (imitation switch), chromodomain helicase DNA-binding (CHD) and INO80 (inositol requiring mutant 80). Each of these complexes is characterized by a SWI2/SNF2-family ATPase domain that contributes the catalytic function and translocates the DNA along the histone core of the nucleosome (reviewed in Narlikar et al, 2013; Clapier et al, 2017; Eustermann et al, 2024). The remainder of the 1 - 1.5MDa complexes are made up of accessory proteins that modulate ATPase activity and contribute to target recognition and specificity by interacting with nucleosomes and histone tails (reviewed in Hargreaves and Crabtree, 2011; Narlikar et al, 2013; Clapier et al, 2017; Eustermann et al, 2024).
Human SWI/SNF ATPases bind acetylated nucleosomes through the bromodomains of their two alternative catalytic subunits, SMARCA2 (also known as BRM) or SMARCA4 (BRG1) (Hassan et al, 2002; Singh et al, 2006; Singh et al, 2007; reviewed in Euskirchen et al 2012). Histone and DNA contacts are also mediated by other protein components of the SWI/SNF complex (reviewed in Euskirchen et al, 2012; Cenik and Shilatifard, 2021). SWI/SNF chromatin remodellers are generally involved in gene activation or repression and provide access to chromatin by repositioning or ejecting nucleosomes (reviewed in Eustermann et al, 2024).
Human CHD family ATPases contain one of nine catalytic CHD protein paralogs. DNA-binding is mediated by contacts between methylated histones and the chromodomain of CHD1-9, as well as through other protein constituents of the ATPase complex (Bannister et al, 2001; Lachner et al, 2001; Flanagan et al, 2005; Sims et al, 2005; reviewed in Eustermann et al, 2024). CHD family ATPases are involved in diverse chromatin remodelling activities, including nucleosome assembly and spacing, access to regulatory elements and changes to histone composition (reviewed in Clapier et al, 2017).
Human ISWI family ATPases contain one of two potential catalytic subunits, SMARCA5 (also known as SNF2H) or SMARCA1 (SNF2L), that interact with unmodified histone tails through their SANT domains (Grune et al, 2003; Boyer et al, 2004). ISWI complexes are generally involved in nucleosome maturation and regulation of spacing and assembly, often resulting in repressive gene states, but some are also involved in transcriptional activation (Xiao et al, 2001; reviewed in Clapier et al, 2017; Eustermann et al, 2024).
Human INO80 family ATPases contain one of three catalytic subunits, INO80, SRCAP or EP400. INO80 complexes generally contribute more to histone exchange than to nucleosome spacing, assembly or access (reviewed in Clapier et al, 2017; Eustermann et al, 2024).

Literature References

PubMed ID	Title	Journal	Year
11583616	Dual functions of largest NURF subunit NURF301 in nucleosome sliding and transcription factor interactions Xiao, H, Sandaltzopoulos, R, Wang, HM, Hamiche, A, Ranallo, R, Lee, KM, Fu, D, Wu, C	Mol Cell	2001
16708073	Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers de la Serna, IL, Ohkawa, Y, Imbalzano, AN	Nat Rev Genet	2006
16263726	Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains Sims, RJ, Chen, CF, Santos-Rosa, H, Kouzarides, T, Patel, SS, Reinberg, D	J Biol Chem	2005
28512350	Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes Clapier, CR, Iwasa, J, Cairns, BR, Peterson, CL	Nat Rev Mol Cell Biol	2017
22952240	SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions Euskirchen, G, Auerbach, RK, Snyder, M	J Biol Chem	2012
16372014	Double chromodomains cooperate to recognize the methylated histone H3 tail Flanagan, JF, Mi, LZ, Chruszcz, M, Cymborowski, M, Clines, KL, Kim, Y, Minor, W, Rastinejad, F, Khorasanizadeh, S	Nature	2005
38081975	Energy-driven genome regulation by ATP-dependent chromatin remodellers Eustermann, S, Patel, AB, Hopfner, KP, He, Y, Korber, P	Nat Rev Mol Cell Biol	2024
32958894	COMPASS and SWI/SNF complexes in development and disease Cenik, BK, Shilatifard, A	Nat Rev Genet	2021
15040448	The SANT domain: a unique histone-tail-binding module? Boyer, LA, Latek, RR, Peterson, CL	Nat Rev Mol Cell Biol	2004
17081121	DNA-binding properties of the recombinant high-mobility-group-like AT-hook-containing region from human BRG1 protein Singh, M, D'Silva, L, Holak, TA	Biol Chem	2006
11242053	Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins Lachner, M, O'Carroll, D, Rea, S, Mechtler, K, Jenuwein, T	Nature	2001
11242054	Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain Bannister, AJ, Zegerman, P, Partridge, JF, Miska, EA, Thomas, JO, Allshire, RC, Kouzarides, T	Nature	2001
12419247	Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes Hassan, AH, Prochasson, P, Neely, KE, Galasinski, SC, Chandy, M, Carrozza, MJ, Workman, JL	Cell	2002
14536084	Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI Grüne, T, Brzeski, J, Eberharter, A, Clapier, CR, Corona, DF, Becker, PB, Müller, CW	Mol Cell	2003
21358755	ATP-dependent chromatin remodeling: genetics, genomics and mechanisms Hargreaves, DC, Crabtree, GR	Cell Res	2011
23911317	Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes Narlikar, GJ, Sundaramoorthy, R, Owen-Hughes, T	Cell	2013
17582821	Structural ramification for acetyl-lysine recognition by the bromodomain of human BRG1 protein, a central ATPase of the SWI/SNF remodeling complex Singh, M, Popowicz, GM, Krajewski, M, Holak, TA	Chembiochem	2007