<scp>SLIDE</scp>, The Protein Interacting Domain of Imitation Switch Remodelers, Binds <scp>DDT</scp>‐<scp>D</scp>omain Proteins of Different Subfamilies in Chromatin Remodeling Complexes

Dong, Jiaqiang; Gao, Zheng; Liu, S.; Li, Guang; Yang, Zhong‐Nan; Huang, Hai; Xu, Lin

doi:10.1111/jipb.12069

Cited by 25 publications

(22 citation statements)

References 32 publications

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“…The DDT class is characterized by a DDT domain, which is found in numerous other factors involved in chromatin regulation, and binds to the SLIDE domain in ISWI chromatin remodeling factors (Doerks et al 2001 ; Dong et al 2013 ). DDT class HD proteins contain additional conserved domains named D-TOXA to D-TOXH, and WSD, named because of the sequence conservation to BAZ/Williams syndrome transcription factor (WSTF) chromodomain proteins (Mukherjee et al 2009 ).…”

Section: Hd Sequence and Classificationmentioning

confidence: 99%

Homeodomain proteins: an update

2015

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Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MATα2.Electronic supplementary materialThe online version of this article (doi:10.1007/s00412-015-0543-8) contains supplementary material, which is available to authorized users.

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Section: Hd Sequence and Classificationmentioning

confidence: 99%

Homeodomain proteins: an update

2015

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“…In Arabidopsis, CHR11 and CHR17 (CHR11/17), two closely related ISWI chromatin remodelers, function redundantly and are required for gametic and zygotic development (Huanca-Mamani et al, 2005;Li et al, 2012;Smaczniak et al, 2012). A family of DTT domaincontaining proteins interact with CHR11/17 and thus form ISWI complexes (Li et al, 2012;Dong et al, 2013). The closely related DTT domain-containing proteins RLT1 and RLT2 function together with CHR11/17 and are required for the regulation of development and flowering time (Li et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

A plant‐specific SWR1 chromatin‐remodeling complex couples histone H2A.Z deposition with nucleosome sliding

et al. 2020

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Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin‐remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant‐specific SWR1 components: MBD9, a methyl‐CpG‐binding domain‐containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co‐regulating gene expression, development, and flowering time.

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“…The imitation switch (ISWI)-type chromatin remodeling factors belong to a subfamily of these remodelers, and the Arabidopsis thaliana ISWI (AtISWI) proteins CHROMATIN REMODELING 11 (CHR11) and CHR17 are involved in multiple developmental processes, including female gametogenesis (Huanca-Mamani et al, 2005), flowering time control (Li et al, 2012a) and flower development (Smaczniak et al, 2012). In addition, AtISWI has been shown to form complexes with the AtDDT-domain proteins for regulating specific target genes (Aravind and Iyer, 2012;Li et al, 2012a;Smaczniak et al, 2012;Dong et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

ISWI proteins participate in the genome‐wide nucleosome distribution in Arabidopsis

et al. 2014

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SUMMARYChromatin is a highly organized structure with repetitive nucleosome subunits. Nucleosome distribution patterns, which contain information on epigenetic controls, are dynamically affected by ATP-dependent chromatin remodeling factors (remodelers). However, whether plants have specific nucleosome distribution patterns and how plant remodelers contribute to the pattern formation are not clear. In this study we used the micrococcal nuclease digestion followed by deep sequencing (MNase-seq) assay to show the genome-wide nucleosome pattern in Arabidopsis thaliana. We demonstrated that the nucleosome distribution patterns of Arabidopsis are associated with the gene expression level, and have several specific characteristics that are different from those of animals and yeast. In addition, we found that remodelers in the A. thaliana imitation switch (AtISWI) subfamily are important for the formation of the nucleosome distribution pattern. Double mutations in the AtISWI genes, CHROMATIN REMODELING 11 (CHR11) and CHR17, resulted in the loss of the evenly spaced nucleosome pattern in gene bodies, but did not affect nucleosome density, supporting a previous idea that the primary role of ISWI is to slide nucleosomes in gene bodies for pattern formation.

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SLIDE, The Protein Interacting Domain of Imitation Switch Remodelers, Binds DDT‐Domain Proteins of Different Subfamilies in Chromatin Remodeling Complexes

Cited by 25 publications

References 32 publications

Homeodomain proteins: an update

Homeodomain proteins: an update

A plant‐specific SWR1 chromatin‐remodeling complex couples histone H2A.Z deposition with nucleosome sliding

ISWI proteins participate in the genome‐wide nucleosome distribution in Arabidopsis

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