ISWI chromatin remodeling: one primary actor or a coordinated effort?

Abstract

The ISWI family of ATP-dependent chromatin remodelers regulates transcription of coding and noncoding RNA by mobilizing nucleosomes and controlling the length of linker DNA separating nucleosomes (spacing). Nucleosome movement is tightly coupled to the DNA translocation activity of the helicase domain in the catalytic subunit. There may be other domains besides the helicase domain needed to move DNA in and out of nucleosomes. The C terminus of the ISWI catalytic subunit with the conserved HAND, SANT, and SLIDE domains may be involved in nucleosome spacing. There are several models of how the C terminus may facilitate in ISWI remodeling such as regulating the activity of the helicase domain and causing the helicase domain to translocate more efficiently on DNA or to enhance its selectivity for nucleosomes. Another possibility is that domains like SLIDE promote linker DNA entering into nucleosomes in a coordinated manner with the helicase domain.

Figure 1. ISWI family of chromatin remodelers in Saccharomyces cerevisiae and mammals

The subunits are represented as ellipses and conserved protein motifs as rectangles. HSS is the HAND, SANT and SLIDE domains. Some of the conserved proteins domains bind to modified sites in histones such as the bromo, PHD and PWWP domain; and others are involved in subunit-subunit interactions like the WAC and DTT domains.

Figure 2. Interactions of Isw2 with nucleosomes

(A) Three DNA sites probed by crosslinking are in red and the regions of Isw2 crosslinked to them in magenta. The helicase, HAND and SLIDE domains are labeled. The region in the helicase domain crosslinked to DNA cannot be seen in this orientation. (B) The crystal structure of the Sulfulobus Rad54 helicase domain (green) with DNA (orange) bound is shown on the left. In the middle is the overlay of the model of Isw2 with the known crystal structure of Rad54. On the right is Isw2 (blue) with DNA bound similar to that shown for Rad54 and the region crosslinked to DNA in magenta. (C) On the left is shown the predicted electrostatic surface potential for the HAND-SANT-SLIDE domains and on the right the regions shown to crosslink DNA in magenta. These structures are rotated by 90° to more fully visualize the conserved basic patch in blue.

Figure 3. Nucleosome dynamics and ISW2

Nucleosome energetics were measured using the single molecule approach shown on the left in which the two ends of DNA are fixed and then progressively unzipped. A typical profile of these experiments is shown on the right and the position where the helicase domain is bound. Above the plot is shown the progressive movement of DNA in (left) and out (right) of nucleosomes by ISW2 using smFRET.

Figure 4. Roles for the HAND-SANT-SLIDE domains in ISWI remodeling

The three ways that these domains might be involved in mobilizing nucleosomes are recruitment, modulating the helicase domain activity, and coordinating the movement of DNA in nucleosomes. The helicase domain is represented in blue, histone octamer in orange, and HSS or SLIDE domains in green.