The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes

Amigo, Roberto; Farkas, Carlos; Gidi, Cristian; Hepp, Matías I.; Cartes, Natalia; Tarifeno, Estefania; Workman, Jerry L.; Gutiérrez, José L.

doi:10.1016/j.bbagrm.2021.194781

Cited by 7 publications

(5 citation statements)

References 49 publications

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“…The ISW1a and RSC complexes were obtained by tandem affinity purification from Ioc3-TAP and Rsc2-TAP S. cerevisiae strains, respectively (Open Biosystems), as previously described [27]. The purified complexes were analyzed as previously reported by us [28]. For each complex, an aliquot of a purification was extensively concentrated (Microcon Ultracel YM-10, Amicon-Millipore), quantified by SDS-PAGE followed by Coomassie staining and then used as standard for Western blot quantification of the purified complex in that and further purifications.…”

Section: Recombinant Proteins and Protein Complexesmentioning

confidence: 99%

General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex

Oyarzún-Cisterna,

Gidi,

Raiqueo

et al. 2024

Biol Res

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Background Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown. Results Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome. Conclusions Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.

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Section: Recombinant Proteins and Protein Complexesmentioning

confidence: 99%

General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex

Oyarzún-Cisterna,

Gidi,

Raiqueo

et al. 2024

Biol Res

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“…The linker histone H1, however, is not well conserved across species, with only 37% of shared sequence identity between humans and budding yeast, while fission yeast lacks a linker histone altogether. S. cerevisiae chromatin is also organized by the high mobility group box family protein Hmo1 which performs similar but not fully overlapping roles to histone H1 [14]. While budding and fission yeasts can serve as excellent models for the core histones due to their high level of conservation with mammalian histone proteins, this is not true of histone H1, so we do not focus on the linker histone in this review.…”

Section: Histones and Nucleosomes In Humans And Yeastmentioning

confidence: 99%

Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model

Zhang,

Fawwal,

Spangle

et al. 2023

JoF

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Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into “oncohistones”. Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.

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“…The S. cerevisiae ISW1a and RSC complexes were obtained by tandem affinity purification from Ioc3-TAP and Rsc2-TAP strains, respectively (Table S2), as previously described [57]. Purified complexes were analyzed as detailed in our previous report [58]. For both complexes, a portion of a purification was extensively concentrated (Microcon Ultracel YM-10, Amicon-Millipore, Burlington, MA, USA), quantified by SDS-PAGE/Coomassie staining and then used as standard for Western blot quantification of the purified complex in that and further purifications.…”

Section: Protein Complexesmentioning

confidence: 99%

Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects

Amigo,

Raiqueo,

Tarifeño

et al. 2023

IJMS

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The establishment and maintenance of nucleosome-free regions (NFRs) are prominent processes within chromatin dynamics. Transcription factors, ATP-dependent chromatin remodeling complexes (CRCs) and DNA sequences are the main factors involved. In Saccharomyces cerevisiae, CRCs such as RSC contribute to chromatin opening at NFRs, while other complexes, including ISW1a, contribute to NFR shrinking. Regarding DNA sequences, growing evidence points to poly(dA:dT) tracts as playing a direct role in active processes involved in nucleosome positioning dynamics. Intriguingly, poly(dA:dT)-tract-containing NFRs span asymmetrically relative to the location of the tract by a currently unknown mechanism. In order to obtain insight into the role of poly(dA:dT) tracts in nucleosome remodeling, we performed a systematic analysis of their influence on the activity of ISW1a and RSC complexes. Our results show that poly(dA:dT) tracts differentially affect the activity of these CRCs. Moreover, we found differences between the effects exerted by the two alternative tract orientations. Remarkably, tract-containing linker DNA is taken as exit DNA for nucleosome sliding catalyzed by RSC. Our findings show that defined DNA sequences, when present in linker DNA, can dictate in which direction a remodeling complex has to slide nucleosomes and shed light into the mechanisms underlying asymmetrical chromatin opening around poly(dA:dT) tracts.

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The linker histone Hho1 modulates the activity of ATP-dependent chromatin remodeling complexes

Cited by 7 publications

References 49 publications

General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex

General regulatory factors exert differential effects on nucleosome sliding activity of the ISW1a complex

Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model

Poly(dA:dT) Tracts Differentially Modulate Nucleosome Remodeling Activity of RSC and ISW1a Complexes, Exerting Tract Orientation-Dependent and -Independent Effects

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