The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis

Abstract

Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of this SWI/SNF complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcription start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and transcription start site determination.

Organization, genomic targeting and assembly of three distinct SWI/SNF chromatin remodeling complexes inArabidopsis

“…In contrast, the SYD-containing complexes selectively contain paralog SWI3D but not SWI3A/B/C, and include a complex-specific subunit, encoded by S YD sub- S WI/SNF Interacting P rotein 1/2/3 ( SSIP1 , SSIP2, or SSIP3 ). Finally, consistent with the recent report (Diego-Martin et al, 2022), the MINU- containing complexes do not contain the GIF2 subunit (SS18 paralogs) found in both BRM- and SYD-containing complexes, incorporate selective paralogs (that is, SWI3A/B but not SWI3C and SWI3D) and include a number of complex-specific subunits, including BSH, BRD5, SHH2, TPF1/2, OPF1/2, PSA1, and PSA2.…”

“…For example, for SAS complexes, the three SSIPs (SSIP1, SSIP2, SSIP3) are separately incorporated into the SAS complexes (Figure 1B). Similarly, OPF1, the MAS-specific subunit, did not exist in the OPF2-containing MAS complexes (Diego-Martin et al, 2022). Finally, BAS- specific subunit BRIP1 cannot co-immunoprecipitated with BRIP2, and BRD1 cannot co-immunoprecipitated with BRD2 and BRD13 (Figure 1B).…”

“…In addition, we recently biochemically isolated novel subunits of the BRM-containing SWI/SNF complexes in Arabidopsis, including two BRM-interacting proteins (BRIP1 and BRIP2) and three bromodomain-containing proteins, BRD1, BRD12, and BRD13 (Yu et al, 2020; Yu et al, 2021). More recently, MINU-containing SWI/SNF complexes were also reported (Diego-Martin et al, 2022). Plant SWI/SNF subunits serve critical roles in cell differentiation, development, and response to various environmental signals, and their mutations result in severe defects in leaf development, root stem cell maintenance, flower patterning and timing, embryo development, and vegetative to adult phase transition (Sarnowski et al, 2005; Ho and Crabtree, 2010; Li et al, 2015; Wu et al, 2015; Yang et al, 2015; Zhao et al, 2015; Sarnowska et al, 2016; Xu et al, 2016).…”

Arabidopsis LFR, a SWI/SNF complex component, interacts with ICE1 and activates ICE1 and CBF3 expression in cold acclimation

“…In the model plant Arabidopsis ( Arabidopsis thaliana ), the SWI/SNF CRC is a multi-subunit machine containing four core catalytic ATPases [BRAHMA (BRM), SPLAYED (SYD), Chromatin Remodeling Factor 12/MINUSCULE 1 (CHR12/MINU1), and CHR23/MINU2] ( Wagner and Meyerowitz, 2002 ; Farrona et al., 2004 ; Bezhani et al., 2007 ; Sang et al., 2012 ), a single SNF5 subunit called BUSHY (BSH) ( Brzeski et al., 1999 ), four SWI3 proteins (SWI3A, SWI3B, SWI3C, and SWI3D) ( Sarnowski et al., 2005 ), two SWI/SNF ASSOCIATED PROTEINS 73 (SWP73A and SWP73B) ( Jégu et al., 2014 ; Sacharowski et al., 2015 ; Jégu et al., 2017 ), two ACTIN-RELATED PROTEINS (ARP4 and ARP7) ( Kandasamy et al., 2003 ), and a single Leaf and Flower Related (LFR) protein ( Wang et al., 2009 ; Lin et al., 2021 ). In addition, two homologous BRM‐interacting proteins (BRIP1 and BRIP2) ( Yu et al., 2020 ), three bromodomain‐containing proteins (BRD1, BRD2, and BRD13) ( Jarończyk et al., 2021 ; Yu et al., 2021 ), ANGUSTIFOLIA3 ( Vercruyssen et al., 2014 ), and two TRIPLE PHD FINGERS proteins (TPF1 and TFP2) ( Diego-Martin et al., 2022 ) have been identified as components of the SWI/SNF CRC.…”

“…The LFR gene is essential for leaf and flower development in Arabidopsis ( Wang et al., 2012 ; Lin et al., 2018 ; Lin et al., 2021 ). LFR encodes an Armadillo (ARM)-repeat domain-containing protein that is predicted to be a subunit of the SWI/SNF CRC ( Wang et al., 2009 ; Lin et al., 2021 ; Diego-Martin et al., 2022 ; Shang and He, 2022 ). In this study, we found that the disruption of LFR led to reduced freezing tolerance in Arabidopsis.…”