FACT Creates a Transiently Accessible Nucleosome Structure Through Integrated Reorganization Mechanism

Yasuo Tsunaka* and Kosuke Morikawa

Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-konoemachi, Sakyoku, Kyoto, Japan

*Corresponding Author:
Dr. Yasuo Tsunaka
Department of Gene Mechanisms, Graduate School of Biostudies
Kyoto University, Yoshida-konoemachi, Sakyo-ku, Kyoto 606- 8501, Japan
Tel: 81757537531
E-mail: [email protected]

Received Date: December 18, 2016; Accepted Date: December 29, 2016; Published Date: December 31, 2016

Citation: Tsunaka Y, Morikawa K. FACT Creates a Transiently Accessible Nucleosome Structure Through Integrated Reorganization Mechanism. Biochem Mol Biol J. 2016, 2:3.DOI: 10.21767/2471-8084.100029

 
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Abstract

Nucleosomes act as a barrier in nuclear processes, such as DNA transcription, replication, and repair. Facilitates chromatin transcription (FACT) plays essential roles in nucleosome dynamics during these processes. Two different mechanisms so far have been proposed for nucleosome reorganization by FACT. However, these interpretations have left some unsolved problems in terms of FACTmediated eviction and exchange of histones within nucleosome. Most recently, we have proposed the integrated reorganization mechanism, in which FACT retains nucleosome in transiently loosened structures. This accessible structure allows us to explain most reasonably about how FACT directs further disruption of nucleosome and histone replacement in concert with other factors.

Keywords

Nucleosomes; Histone; Transcription

Description

Eukaryotic genomes are highly condensed in chromatin, which is dominated by arrays of the basic repeating units termed nucleosome [1,2]. This packaging limits the accessibility of DNA, thus creating a barrier that plays a major role in regulating nuclear processes such as DNA transcription, replication, and repair. The orchestrated actions of histone chaperones and ATP-dependent chromatin remodelers rearrange the barrier at nucleosome or higher order levels, thereby playing critical roles in gene regulation linked to epigenetics [3-8]. Facilitates chromatin transcription (FACT) is an essential and highly conserved histone chaperone that facilitates histone replacement, nucleosome assembly and nucleosome disassembly; thus highlighting that it can both stabilize and destabilize the barrier [5-13]. In fact, Drosophila FACT counteracts the spreading of silent chromatin through histone replacement at the boundary between heterochromatin and euchromatin [10].

FACT is a heterodimer consisting of Spt16 and SSRP1 (Pob3 in yeast) proteins, each organized by several structural domains [14]. In yeast, the functions of FACT are supported by the HMG protein, Nhp6 [15,16]. Intriguingly, the FACT subunits participate in a broad range of processes including DNA transcription, replication and repair [6,13,17-19]. In spite of this broad functional spectrum, every eukaryotic species contains only one ortholog of the FACT complex, suggesting that FACT should conduct universal actions in terms of nucleosome dynamics.

Initially, human FACT promotes the eviction of an H2A-H2B dimer from histone octamer, thereby forming hexasome, which consists of an H3-H4 tetramer and one H2A-H2B dimer (Figure 1: dimer displacement mechanism) [9]. Hexasomes are proposed to facilitate transcription, which is followed by the reassembly of octameric nucleosomes. On the other hand, yeast FACT can increase nuclease sensitivity throughout nucleosome without displacing a dimer [15]. FACT also competes with DNA for binding to H2A-H2B [20,21]. Therefore, FACT is considered to enhance unwrapping of nucleosomal DNA, by blocking its contacts with H2A–H2B. These findings suggested that FACT reorganizes nucleosomes to increase DNA accessibility, while tethering the eight histone components together [21] (Figure 1). In another word, FACT interferes with histone-DNA contacts, while preserving histone-histone interactions [22]. Whereas this nicely explains how FACT prevents histone loss, it does not appear to clearly explain how the same molecule causes further disruption of nucleosome and histone variant replacement.

biochem-molbio-Potential-mechanisms

Figure 1: Potential mechanisms for nucleosome reorganization by FACT. In dimer displacement mechanism [9], an H2A-H2B dimer (yellow and red) is displaced from the nucleosome by FACT (magenta), forming hexasome. FACT then reassembles the displaced dimer in the wake of the polymerase. In nucleosome breathing mechanism [21,22], FACT competes away H2BDNA interactions, peeling off the first 30 base pairs of nucleosome DNA (light sea green) without H2A-H2B displacement. In integrated reorganization mechanism [23], the AID segment of FACT interacts with the H2B N-tail detached from the nucleosomal DNA. Next, the hMid domain of FACT correctly binds to an H3-H4 tetramer (blue and green) of the nucleosome. Thus, FACT displaces an H2A-H2B dimer from the nucleosome for a time, but the H2A-H2B dimer remains tethered to nucleosome via FACT. Consequently, the complex between FACT and the hexasome strips ~30 bp of the nucleosomal DNA from histones.

Our recent studies revealed the integrated molecular mechanism of nucleosome reorganization involving H2A-H2B displacement by human FACT [23] (Figure 1). Initially, the acidic intrinsically disordered (AID) segment of FACT interacts with a highly basic region in the H2B N-tail (HBR) detached from the nucleosomal DNA. This local disruption of DNA-histone contact may be aided by DNA torsional strain, generated by elongating polymerases [24,25], and also most likely by ATP-dependent chromatin remodelers, which create DNA loops or bulges on nucleosomes during DNA translocation [8,26,27]. Next, the rigid Mid domain of FACT correctly binds to the H2A docking surface of nucleosome. Thus, FACT displaces an H2A-H2B dimer from nucleosome for a time through steric collisions on the H2A docking surface of an H3-H4 tetramer, but the H2A-H2B dimer remains tethered to nucleosome via FACT; presumably, through transient interaction retained between the FACT AID segment and the HBR region of H2B. Consequently, the complex between FACT and hexasome strips approximately 30-bp of the nucleosomal DNA from histones. The DNA stripping may facilitate the invasion of polymerases, which must surmount the barriers against their progress [28,29]. After the relevant processes have concluded, FACT immediately reassembles the tethered dimer into nucleosome, thus remaining the eight histone components during the processes. In addition, the accessible nucleosome configuration would provide a comprehensive explanation for how FACT causes further disruption of nucleosome and edits histone variant contents through cooperation with histone chaperones, such as Asf1, HIRA, CAL1/HJURP, CAF1, Spt6, and MCM2 [10-13,30-33].

Universality of this integrated mechanism is strongly supported by some recent studies. First, Kemble et al. [34] and Valievahas et al. [16] have proposed a similar mechanism in which yeast FACT remains in the reorganized nucleosome complex and is likely to interact with both the uncoiled nucleosomal DNA and core histones, thereby replacing both of the DNA-histone and histonehistone interactions. Second, the integrated mechanism indicates that the H2B N-tail is essential for both of H2A-H2B displacement and deposition by FACT. This is verified by recent studies that the HBR region in the H2B N-tail is important for nucleosome disassembly [35] as well as assembly [36] by yeast FACT.

In conclusion, the integrated reorganization mechanism rationalizes how FACT operates to create a stable and dynamic nucleosome structure without entire nucleosome disassembly, so as to ensure chromatin integrity. However, FACT retains nucleosome in partially loosened structures by two transient interactions, in which Mid and AID of FACT bind to a H3-H4 tetramer and HBR of H2A-H2B, respectively, thereby replacing histone-histone interactions within nucleosome [23]. Therefore, it may act in concert with other factors to facilitate histone eviction and exchange.

Acknowledgment

This work was supported by Grants-in-Aid for Scientific Research (A) (JSPS KAKENHI Grant Number 23247016 and 26251008) and PRESTO, JST.

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