The ISWI remodeler in plants: protein complexes, biochemical functions, and developmental roles

Abstract

Imitation Switch (ISWI) is a member of the ATP-dependent chromatin remodeling factor family, whose members move or restructure nucleosomes using energy derived from ATP hydrolysis. ISWI proteins are conserved in eukaryotes and usually form complexes with DDT (DNA-binding homeobox and different transcription factors)-domain proteins. Here, we review recent research on ISWI in the model plant Arabidopsis thaliana (AtISWI). AtISWI forms complexes with AtDDT-domain proteins, many of which have domain structures that differ from those of DDT-domain proteins in yeast and animals. This might suggest that plant ISWI complexes have unique roles. In vivo studies have shown that AtISWI is involved in the formation of the evenly spaced pattern of nucleosome arrangement in gene bodies—this pattern is associated with high transcriptional levels of genes. In addition, AtISWI and the AtDDT-domain protein RINGLET (RLT) are involved in many developmental processes in A. thaliana, including meristem fate transition and organ formation. Studies on the functions of AtISWI may shed light on how chromatin remodeling functions in plants and also provide new information about the evolution of ISWI remodeling complexes in eukaryotes.

Glossary of domains and motifs in ISWI complexes

SWI2/SNF2-family ATPase

ATP hydrolysis to provide energy for changing contacts between histones and DNA (Bork and Koonin 1993; Clapier and Cairns 2009; Gorbalenya et al. 1988; Zhou et al. 2016)

HAND

DNA binding (Dang and Bartholomew 2007); dimerization (Racki and Narlikar 2008; Strohner et al. 2005)

SANT

DNA binding (Dang and Bartholomew 2007; Yamada et al. 2011); interaction with histone tail (Boyer et al. 2002; Boyer et al. 2004; Grune et al. 2003)

SLIDE

Interaction with DDT-domain proteins (Aravind and Iyer 2012; Dong et al. 2013); interaction with Ioc3 (Yamada et al. 2011); DNA binding (Dang and Bartholomew 2007; Grune et al. 2003; Yamada et al. 2011)

PHD

Interaction with methylated histones (Wysocka et al. 2006)

Bromo

Interaction with acetylated histones (Dhalluin et al. 1999)

WAC

DNA binding (Fyodorov and Kadonaga 2002)

DDT + WHIM

Interaction with SLIDE domain (Aravind and Iyer 2012; Doerks et al. 2001; Dong et al. 2013)

HD

Putative binding activity with DNA cis elements (Mukherjee et al. 2009)

Peptidase M50

Involved in proteolytic cleavage of PTM in response to retrograde signals (Sun et al. 2011)

HARE-HTH

Unknown, possibly involved in chromatin regulation (Aravind and Iyer 2012)

D-TOX A, B, ZF, G, H

Unknown (Dong et al. 2013; Mukherjee et al. 2009)