Regulating the chromatin landscape: structural and mechanistic perspectives

Abstract

A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).

Keywords: ATRX; CHD; INO80; ISWI; SWI/SNF; SWR1; cancer; differentiation; epigenetics; histone; nucleosome; transcription.

Figure 1

Properties and domain organization of ATP-dependent chromatin remodelers. (a) The SF2 (top) and Snf2 (bottom) motifs found in the helicase domain, along with the insertion sites. The purple and light blue regions correspond to the two RecA-like regions, and the magenta regions correspond to the protusion and linker regions. The domain organization of the catalytic subunit for each of the five major classes of remodelers is shown. (b) Remodelers have four distinct properties. In the exchange reaction, the different H2A variant containing dimers are represented in gold and blue. The red oval in the assembly reaction represents the newly assembled nucleosome. (c) This model for the ATP-dependent movement of the helicase domain along DNA is based on crystal structures of PcrA. The purple and blue ovals represent the protein contacts with DNA from lobes 1 and 2, respectively. Abbreviations: ATRX, α-thalassemia mental retardation syndrome X-linked; HSA, helicase/SANT-associated; PHD, plant homeodomain; Pi, inorganic phosphate; SnAC, SNF ATP coupling.

Figure 2

Approaches for studying the dynamics of nucleosome remodeling and the interactions of remodelers with nucleosomes. (a–d) Single-molecule approaches. (a) DNA unzipping is used to precisely measure the strength of histone--DNA interactions throughout nucleosomes with near-base-pair resolution (159). (b) The magnetic tweezer and (c) dual optical trap techniques are used to measure the DNA translocation properties of nucleosome remodelers such as rates, processivity, and the ability to move against an opposing force. (d) Single-molecule fluorescence resonance energy transfer (smFRET) tracks the movement of DNA relative to the histone octamer by measuring the rate at which a modified site in the histone octamer (Cy3) is moved from a different modified site in DNA (Cy5) by changes in FRET efficiencies. Individual nucleosomes are observed through the technique of total internal reflection fluorescence (TIRF). (e–g) Site-directed cross-linking approaches. (e) In the first approach, photoreactive groups are incorporated at specific locations in DNA through either a nucleotide base or the phosphate backbone, and a DNA radiolabel is transferred to its protein target following cross-linking. The two other approaches incorporate different types of photoreactive groups into the histone octamer. (f) The photoreactive group is radioiodinated and is designed to cleave and transfer the radiolabel to the target by disulfide bond reduction. (g) This approach incorporates the photoreactive group at a histone site that is close to DNA and is intended to covalently link histone to DNA. Such cross-links can be used to cleave the DNA at the cross-linked site to determine the location of the cross-link. Abbreviation: PEG, polyethylene glycol.

Figure 3

Structural aspects of the ISW2, ISW1a, and SWI/SNF complexes. (a) This model of the interactions between the C terminus (gray) and helicase domain (blue) of Isw2 and the nucleosome is based on site-directed cross-linking between DNA and a remodeler, as depicted in Figure 2e (26). The HAND, SLIDE, and helicase domains are cross-linked to three regions in DNA. The cross-linked regions are colored magneta, and the red dots in the DNA indicate the sites of the DNA cross-linker. Because of the orientation, the region of the helicase domain cross-linked to DNA 17 and 18 bp from the dyad axis is not visible. (b) Two DNA molecules bind Ioc3 (purple) and the C terminus of Isw1 (pink). This binding is the basis for the suggestions that ISW1a binds external and internal linker DNA in a dinucleosome. (c) As demonstrated by cryo--electron microscopy yeast SWI/SNF contains a trough region (TB) flanked by a high wall (HW) and a low wall (LW), and blocked at one end by another wall (BW). (d–f) This model of a nucleosome bound into the trough region of SWI/SNF is based in part on the finding that SWI/SNF protects nearly one gyre of DNA (red) when bound (f). The SWI/SNF/nucleosome complex (d–e). (g) Four different subunits of SWI/SNF cross-link to different parts of the histone octamer when SWI/SNF binds to nucleosomes. (h) The interactions between specific subunits of SWI/SNF and nucleosomes in terms of the DNA gyre (red dotted line) and the histone octamer face (green circle). The colored dots represent specific sites that were probed by site-directed cross-linking (28). Panel h is based on the model depicted in panels e and f.

Figure 4

Mechanisms for mobilizing nucleosomes. (a) The nucleosomal region where DNA gaps interfere. Two black lines represent DNA and the breaks in the black line represent the single—base pair gaps that interfere with NURF, ISW2 and SWI/SNF remodeling. The green box represents the location of the helicase domain. (b) The orientation of the helicase domain on nucleosomes is either on the exposed side of nucleosomal DNA (pull only) or between the DNA gyre and the histone octamer (pull and wedge). When the helicase domain tracks through DNA, there are two expected outcomes. (c) The dual helicase model, in which only one of the two helicases (blue) is bound at a time, depending on the linker DNA available at either side of the nucleosome. The arrows indicate the direction in which DNA moves. (d) The two strands of DNA are colored gold and blue, and the helicase domain is colored pink. First, the helicase domain moves DNA out of the exit side in 1-bp increments until a total of 7 bp has been moved. This movement causes a DNA strain between the helicase domain and the entry site, as demonstrated by underwinding DNA. The next step is the passage of 3 bp of DNA from the entry site, which releases some of the torsional strain. (e) The SLIDE domain is colored green, the helicase domain is colored blue, and additional protein--DNA contacts are colored gray. The movements of the helicase domain and the SLIDE domain are coordinated by two actions; the helicase domain pulling DNA and the SLIDE domain pushing DNA into nucleosomes. Abbreviation: SHL2, superhelical location 2.

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