Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodelling complexes are multi-protein machineries that control gene expression by regulating chromatin structure in eukaryotes. However, the full subunit composition of SWI/SNF complexes in plants remains unclear. Here we report that in Arabidopsis thaliana, two homologous glioma tumour suppressor candidate region domain-containing proteins, named BRAHMA-interacting proteins 1 (BRIP1) and BRIP2, are core subunits of plant SWI/SNF complexes. brip1 brip2 double mutants exhibit developmental phenotypes and a transcriptome remarkably similar to those of BRAHMA (BRM) mutants. Genetic interaction tests indicated that BRIP1 and BRIP2 act together with BRM to regulate gene expression. Furthermore, BRIP1 and BRIP2 physically interact with BRM-containing SWI/SNF complexes and extensively co-localize with BRM on chromatin. Simultaneous mutation of BRIP1 and BRIP2 results in decreased BRM occupancy at almost all BRM target loci and substantially reduced abundance of the SWI/SNF assemblies. Together, our work identifies new core subunits of BRM-containing SWI/SNF complexes in plants and uncovers the essential role of these subunits in maintaining the abundance of SWI/SNF complexes in plants.
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Data availability
The ChIP–seq and RNA-seq datasets have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE142369. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium under the dataset identifier PXD018815. Source data are provided with this paper.
References
Hargreaves, D. C. & Crabtree, G. R. ATP-dependent chromatin remodeling: genetics, genomics and mechanisms. Cell Res. 21, 396–420 (2011).
Clapier, C. R. & Cairns, B. R. The biology of chromatin remodeling complexes. Annu. Rev. Biochem. 78, 273–304 (2009).
Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017).
Ryan, D. P. & Owen-Hughes, T. Snf2-family proteins: chromatin remodellers for any occasion. Curr. Opin. Chem. Biol. 15, 649–656 (2011).
Ho, L. & Crabtree, G. R. Chromatin remodelling during development. Nature 463, 474–484 (2010).
Sarnowska, E. et al. The role of SWI/SNF chromatin remodeling complexes in hormone crosstalk. Trends Plant Sci. 21, 594–608 (2016).
Han, S. K., Wu, M. F., Cui, S. & Wagner, D. Roles and activities of chromatin remodeling ATPases in plants. Plant J. 83, 62–77 (2015).
Jerzmanowski, A. SWI/SNF chromatin remodeling and linker histones in plants. Biochim. Biophys. Acta 1769, 330–345 (2007).
Vercruyssen, L. et al. ANGUSTIFOLIA3 binds to SWI/SNF chromatin remodeling complexes to regulate transcription during Arabidopsis leaf development. Plant Cell 26, 210–229 (2014).
Nelissen, H. et al. Dynamic changes in ANGUSTIFOLIA3 complex composition reveal a growth regulatory mechanism in the maize Leaf. Plant Cell 27, 1605–1619 (2015).
Li, C. et al. Concerted genomic targeting of H3K27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis. Nat. Genet. 48, 687–693 (2016).
Li, C. et al. The Arabidopsis SWI2/SNF2 chromatin remodeler BRAHMA regulates polycomb function during vegetative development and directly activates the flowering repressor gene SVP. PLoS Genet. 11, e1004944 (2015).
Yang, S. et al. The Arabidopsis SWI2/SNF2 chromatin remodeling ATPase BRAHMA targets directly to PINs and is required for root stem cell niche maintenance. Plant Cell 27, 1670–1680 (2015).
Reyes, J. C. The many faces of plant SWI/SNF complex. Mol. Plant 7, 454–458 (2014).
Han, S. K. et al. The SWI2/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. Plant Cell 24, 4892–4906 (2012).
Farrona, S., Hurtado, L., Bowman, J. L. & Reyes, J. C. The Arabidopsis thaliana SNF2 homolog AtBRM controls shoot development and flowering. Development 131, 4965–4975 (2004).
Tang, X. et al. The Arabidopsis BRAHMA chromatin-remodeling ATPase is involved in repression of seed maturation genes in leaves. Plant Physiol. 147, 1143–1157 (2008).
Wu, M. F. et al. SWI2/SNF2 chromatin remodeling ATPases overcome polycomb repression and control floral organ identity with the LEAFY and SEPALLATA3 transcription factors. Proc. Natl Acad. Sci. USA 109, 3576–3581 (2012).
Zhang, D., Li, Y., Zhang, X., Zha, P. & Lin, R. The SWI2/SNF2 chromatin-remodeling ATPase BRAHMA regulates chlorophyll biosynthesis in Arabidopsis. Mol. Plant 10, 155–167 (2017).
Vicente, J. et al. The Cys-Arg/N-End rule pathway is a general sensor of abiotic stress in flowering plants. Curr. Biol. 27, 3183–3190 (2017).
Xu, Y. et al. Regulation of vegetative phase change by SWI2/SNF2 chromatin remodeling ATPase BRAHMA. Plant Physiol. 172, 2416–2428 (2016).
Wu, M. F. et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. eLife 4, e09269 (2015).
Efroni, I. et al. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. Dev. Cell 24, 438–445 (2013).
Zhao, M. et al. Arabidopsis BREVIPEDICELLUS interacts with the SWI2/SNF2 chromatin remodeling ATPase BRAHMA to regulate KNAT2 and KNAT6 expression in control of inflorescence architecture. PLoS Genet. 11, e1005125 (2015).
Brzezinka, K. et al. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 5, e17061 (2016).
Sarnowski, T. J. et al. SWI3 subunits of putative SWI/SNF chromatin-remodeling complexes play distinct roles during Arabidopsis development. Plant Cell 17, 2454–2472 (2005).
Saez, A., Rodrigues, A., Santiago, J., Rubio, S. & Rodriguez, P. L. HAB1-SWI3B interaction reveals a link between abscisic acid signaling and putative SWI/SNF chromatin-remodeling complexes in Arabidopsis. Plant Cell 20, 2972–2988 (2008).
Archacki, R. et al. Genetic analysis of functional redundancy of BRM ATPase and ATSWI3C subunits of Arabidopsis SWI/SNF chromatin remodelling complexes. Planta 229, 1281–1292 (2009).
Sacharowski, S. P. et al. SWP73 subunits of Arabidopsis SWI/SNF chromatin remodeling complexes play distinct roles in leaf and flower development. Plant Cell 27, 1889–1906 (2015).
Buszewicz, D. et al. HD2C histone deacetylase and a SWI/SNF chromatin remodelling complex interact and both are involved in mediating the heat stress response in Arabidopsis. Plant Cell Environ. 39, 2108–2122 (2016).
Jegu, T. et al. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biol. 18, 114 (2017).
Oh, E., Zhu, J. Y. & Wang, Z. Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–809 (2012).
Zhang, J. et al. A SUMO ligase AtMMS21 regulates the stability of the chromatin remodeler BRAHMA in root development. Plant Physiol. 173, 1574–1582 (2017).
Hurtado, L., Farrona, S. & Reyes, J. C. The putative SWI/SNF complex subunit BRAHMA activates flower homeotic genes in Arabidopsis thaliana. Plant Mol. Biol. 62, 291–304 (2006).
Perez-Perez, J. M., Candela, H. & Micol, J. L. Understanding synergy in genetic interactions. Trends Genet. 25, 368–376 (2009).
Alpsoy, A. & Dykhuizen, E. C. Glioma tumor suppressor candidate region gene 1 (GLTSCR1) and its paralog GLTSCR1-like form SWI/SNF chromatin remodeling subcomplexes. J. Biol. Chem. 293, 3892–3903 (2018).
Ho, L. et al. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl Acad. Sci. USA 106, 5181–5186 (2009).
Middeljans, E. et al. SS18 together with animal-specific tactors defines human BAF-type SWI/SNF complexes. PLoS ONE 7, e33834 (2012).
Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes. Cell 175, 1272–1288 (2018).
Gatchalian, J. et al. A non-canonical BRD9-containing BAF chromatin remodeling complex regulates naive pluripotency in mouse embryonic stem cells. Nat. Commun. 9, 5139 (2018).
Michel, B. C. et al. A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation. Nat. Cell Biol. 20, 1410–1420 (2018).
Archacki, R. et al. Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression. Nucleic Acids Res. 45, 3116–3129 (2017).
Torres, E. S. & Deal, R. B. The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis. Plant J. 99, 144–162 (2019).
Ho, L. et al. esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat. Cell Biol. 13, 903–913 (2011).
Horiguchi, G., Kim, G. T. & Tsukaya, H. The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana. Plant J. 43, 68–78 (2005).
Sakamoto, T., Tsujimoto-Inui, Y. & Sotta, N. Proteasomal degradation of BRAHMA promotes boron tolerance in Arabidopsis. Nat. Commun. 9, 5285 (2018).
Pan, J., McKenzie, Z. M., D’Avino, A. R., Mashtalir, N. & Lareau, C. A. The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting. Nat. Genet. 51, 618–626 (2019).
Farrona, S., Hurtado, L. & Reyes, J. C. A nucleosome interaction module is required for normal function of Arabidopsis thaliana BRAHMA. J. Mol. Biol. 373, 240–250 (2007).
Curtis, M. D. & Grossniklaus, U. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462–469 (2003).
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
Liu, X. et al. The NF-YC-RGL2 module integrates GA and ABA signalling to regulate seed germination in Arabidopsis. Nat. Commun. 7, 12768 (2016).
Adachi, S., Nobusawa, T. & Umeda, M. Quantitative and cell type-specific transcriptional regulation of A-type cyclin-dependent kinase in Arabidopsis thaliana. Dev. Biol. 329, 306–314 (2009).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(-Delta Delta C) method. Methods 25, 402–408 (2001).
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
Saeed, A. I. et al. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34, 374–378 (2003).
Metsalu, T. & Vilo, J. ClustVis: a web tool for visualizing clustering of multivariate data using principal component analysis and heatmap. Nucleic Acids Res. 43, W566–W570 (2015).
Gendrel, A. V., Lippman, Z., Martienssen, R. & Colot, V. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2, 213–218 (2005).
Chen, C. et al. Cytosolic acetyl-CoA promotes histone acetylation predominantly at H3K27 in Arabidopsis. Nat. Plants 3, 814–824 (2017).
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Zhang, Y. et al. Model-based analysis of ChIP–Seq (MACS). Genome Biol. 9, R137 (2008).
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP–seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Thorvaldsdottir, H., Robinson, J. T. & Mesirov, J. P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief. Bioinform. 14, 178–192 (2013).
Yu, G., Wang, L. G. & He, Q. Y. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).
Hulsen, T., de Vlieg, J. & Alkema, W. BioVenn—a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 9, 488 (2008).
Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–393 (2012).
Zhou, Y. Y. et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat. Commun. 10, 1523 (2019).
Lu, Q. et al. Arabidopsis homolog of the yeast TREX-2 mRNA export complex: components and anchoring nucleoporin. Plant J. 61, 259–270 (2010).
Li, J. F., Zhang, D. D. & Sheen, J. Epitope-tagged protein-based artificial miRNA screens for optimized gene silencing in plants. Nat. Protoc. 9, 939–949 (2014).
Liu, Y. C. et al. LjCOCH interplays with LjAPP1 to maintain the nodule development in Lotus japonicus. Plant Growth Regul. 85, 267–279 (2018).
Yoo, S. D., Cho, Y. H. & Sheen, J. Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis. Nat. Protoc. 2, 1565–1572 (2007).
Yang, Z. L. et al. EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis. Nat. Genet. 50, 1247–1253 (2018).
Perez-Riverol, Y. et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 47, D442–D450 (2019).
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729 (2013).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
Heger, A., Webber, C., Goodson, M., Ponting, C. P. & Lunter, G. GAT: a simulation framework for testing the association of genomic intervals. Bioinformatics 29, 2046–2048 (2013).
Acknowledgements
We thank the ABRC for seeds of tDNA insertion lines, S. Yang and X. Hou (Chinese Academy of Sciences) for the pEAQ-BRM-N-GFP vector and pZPY122-FLAG vector, respectively, and J. Li (Sun Yat-sen University) for the pHBT-HA vector. This work was supported by the National Natural Science Foundation of China to C.L. (no. 31870289) and the Natural Science and Engineering Council of Canada to Y.C. (no. RGPIN/04625-2017).
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Y.Y. and C.L. conceived the project. Y.Y. performed most of the experiments. Wenqun Fu constructed the GUS reporter lines. Y.Y., Z.L., L.Y. and C.L. conducted bioinformatics analysis. Y.Y., Z.L., X.S., Wei Fu, Y.L., L.Y., J.X., J.R., C.C., Y.C. and S.H. analysed data. Y.Y. and C.L. wrote the manuscript.
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Extended data
Extended Data Fig. 1 Physical interaction among BRIP1, BRIP2 and SWI/SNF complex.
a, Bimolecular Fluorescence Complementation assay (BiFC) showing that BRIP1 and BRIP2 interact with SWI/SNF complex core members. An unrelated nuclear protein encoded by AT3G60390 was used as a negative control. error bar = 20 μm. b, Co-immunoprecipitation of BRIP1 with BRM-N (N-terminal of BRM, 1-952 amino acids). BRM-N-GFP was immunoprecipitated by an anti-HA-Agarose antibody from protoplasts co-transfected with BRM-N-GFP and BRIP1-HA. The antibodies used for immunoblot are indicated on the left, and the sizes of the protein markers are indicated on the right. c, Yeast-two hybrid assay to examine the region of BRM that interacts with BRIP1/2. Growth of transformed yeast is shown on permissive SD -Ade/-His/-Leu/-Trp medium.
Extended Data Fig. 2 Gene structures and Genetic materials.
a, Schematic illustration of the conserved domain of BRIP1 and BRIP2. The numbers indicate the positions of amino acids. At the bottom, the alignment of the sequences of the GLTSCR domain of BRIP1/2 proteins. The amino acids same in both proteins are marked by red. b, Schematic illustration of the locations of the T-DNA insertion sites (dark arrow) of the two brip mutants. The GLTSCR domains are red marked. c, Genotyping of brip1 and brip2 by using the three primers method (LBb1.3+LP + RP). Wild-type (Col-0) was used as a control. d, The mRNA levels of BRIP1 and BRIP2 were determined by RT-PCR in brip1, brip2 and Col-0. GAPDH was amplified as an internal control. Error bars represent s.d. of three biological replicates, as determined by the post hoc Tukey’s HSD test.
Extended Data Fig. 3 Phenotype of brip1, brip2, brip1 brip2 and brm mutants.
a, Leaf phenotype of 14-day-old seedlings. Scale bars, 5 mm. b, Confocal images of root tips showing nuclear localization of the BRIP1-GFP and BRIP2-GFP in brip1 brip2 double mutant background. The red fluorescent signal is from propidium iodide staining. Scale bars, 50 μm. c, Number of rosette leaf of different plant materials at flowering. d, Silique phenotypes of different materials. Scale bars, 1 cm. Lowercase letters indicate significant differences between genetic backgrounds, as determined by the post hoc Tukey’s HSD test. The number of ‘n = ’ indicates the number of plants that were used. Data are presented as mean values +/− SD.
Extended Data Fig. 4 brip1brip2 mutants had similar transcriptome to brm mutants.
a, Summary of up- and down-regulated genes in different mutants compared to WT. The number indicates the concrete number of up- and down-regulated genes and the Y-axis showing the percentage of up- and down-regulated genes of all mis-regulated genes. b, Venn diagrams showing statistically significant overlaps between genes up- or down-regulated in brm-3 and those in brip1 brip2. p = 0, Hypergeometric test. c, Scatterplot of FPKM log2 fold change over WT of indicated mutants (y-axis) vs. brm-3 or brm-1 (x-axis) at brm-3 or brm-1 differentially expressed genes. Red lines indicate the line of best fit, and adjusted R value is indicated. Dots are mean values from three biologically independent experiments.
Extended Data Fig. 5 Plants expressing GFP-tagged BRIP1 or BRIP2 in their respective single mutant background.
a, Pictures showing 21-day-old plants. Scale bars, 1 cm. b, Confocal images of root tips showing nuclear localization of the BRIP1-GFP and BRIP2-GFP in their single mutant background. The red fluorescent signal is from propidium iodide staining. Scale bars, 50 μm. c, Western blot analysis using an anti-GFP antibody shows the accumulation of BRIP1 and BRIP2. For each plot, the antibody used is indicated on the left, and the sizes of the protein markers are indicated on the right. H3 serves as a loading control.
Extended Data Fig. 6 BRIP1, BRIP2 and BRM show a similar binding pattern.
a, Pie charts showing the distribution of BRM, BRIP1 and BRIP2 peaks at annotated genic and intergenic regions in the genome. b, The average enrichment of BRM, BRIP1 or BRIP2 at its target genes, respectively (n = 7,767, 5,035 and 7,023, respectively). Plotting regions were scaled to the same length as follows: 5′ ends (−3.0 kb to transcription starting site (TSS)) and 3′ ends (transcription stop site (TTS) to downstream 3.0 kb), and the gene body was scaled to 3 kb. Two biological replicates were included. c, GO analysis for biological processes associated with genes occupied by BRM, BRIP1 or BRIP2.
Extended Data Fig. 7 Loss of BRM causes the genome-wide decrease of BRIP1/2 occupancy.
a, On the top, Plot representation of the mean density of BRIP1 or BRIP2 occupancy at all BRIP1 or BRIP2 sites in brm-1 compared with WT. The average BRIP1/2 binding signal within 3 kb genomic regions flanking the summit of BRIP1/2 peaks are shown. Bottom, Heat-map representation of the occupancy of BRIP1 or BRIP1 in WT and brm-1. b, IGV views of BRIP1/2 occupancy at selected loci in WT and brm-1 background. The scale was identical for the different tracks, and gene structures are shown underneath each panel. The gene IDs and the ‘START and END’ positions on the chromosome are shown below. The y-axis scales represent shifted merged MACS2 tag counts for every 10-bp window.
Extended Data Fig. 8 The number of unique peptides identified by Mass spectrometry analyses.
a, Mass spectrometry results showing the total number of unique peptides in the input or IP samples of SWI3C-3×FLAG BRM-GFP brm-1 and SWI3C-3×FLAG BRM-GFP brm-1 brip1 brip2. b, The number of unique peptides of five representative proteins (named by UniProt) in the input samples SWI3C-3×FLAG BRM-GFP brm-1 before FLAG immunoprecipitation was similar to that in SWI3C-3×FLAG BRM-GFP brm-1 brip1 brip2. c, The number of unique peptides of five representative proteins (named by UniProt) in the input samples SWI3C-3×FLAG BRM-GFP brm-1 before GFP immunoprecipitation was similar to that in SWI3C-3×FLAG BRM-GFP brm-1 brip1 brip2. Error bars are presented as mean values from three biological replicates, +/− SD. N.S., not significant (Unpaired, two-tailed Student’s t-test).
Extended Data Fig. 9 Loss of GLTSCR domain impairs the function of BRIP2.
a, qRT-PCR analyses showing the mRNA level of BRIP2∆GLTSCR-GFP and full length BRIP2-GFP. The expression level of each gene was normalized to that of GAPDH. Error bars are presented as mean values from three biological replicates, +/− SD. ** p < 0.01 (Unpaired, two-tailed Student’s t-test). b, Morphological phenotypes of pBRIP2:BRIP2-GFP brip1 brip2 and pBRIP2:BRIP2∆ GLTSCR-GFP brip1 brip2. Photographs of 35-day-old plants are shown. Scale bar, 1 cm. c, Silique phenotypes of different materials. Scale bars, 1 cm. Lowercase letters indicate significant differences between genetic backgrounds, as determined by the post hoc Tukey’s HSD test. The number of ‘n = ’ indicates the number of plants that were used. Data are presented as mean values +/− SD.
Extended Data Fig. 10 Phylogenetic analysis of GLTSCR domain-containing proteins among different species.
a, The phylogenetic tree was constructed using the amino-acid sequences of the GLTSCR domain from different species, including Amborella trichopoda, Physcomitrella patens, Arabidopsis thaliana, Arabidopsis lyrate, Brassica napus, Oryza sativa Japonica, Triticum aestivum, Hordeum vulgare subsp. Vulgare, Zea mays, Homo sapiens, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Mus musculus. The scale length in the tree is indicated. b, The alignment of sequences of GLTSCR domain across different species. Conserved amino acids are marked in red (100%), green (≥75%), and purple (≥ 50%), respectively.
Supplementary information
Supplementary Information
Supplementary Figs. 1–4.
Supplementary Tables
Supplementary Table 1: Summary of SWI/SNF complex core members according to the IP/MS results for BRM. Supplementary Table 2: List of genes misregulated in different mutants. Supplementary Table 3: List of genes occupied by BRM, BRIP1 or BRIP2 in Arabidopsis seedlings. Supplementary Table 4: Summary of IP–MS data. Supplementary Table 5: Oligonucleotides used in this study. Supplementary Table 6: Summary of mapped reads in ChIP–seq.
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Yu, Y., Liang, Z., Song, X. et al. BRAHMA-interacting proteins BRIP1 and BRIP2 are core subunits of Arabidopsis SWI/SNF complexes. Nat. Plants 6, 996–1007 (2020). https://doi.org/10.1038/s41477-020-0734-z
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DOI: https://doi.org/10.1038/s41477-020-0734-z
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