KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-H3K27me1 | Active Motif | Cat#61015 |
| Rabbit polyclonal anti-H3 | Abcam | Cat#Ab1791 |
| Rabbit polyclonal anti-H4K16ac | EMD millipore | Cat#07-329 |
| Rabbit polyclonal anti-H4 | Abcam | Cat#ab10158 |
| GFP-trap magnetic agarose beads | ChromoTek | Cat#gtma-10 |
| RFP-trap magnetic agarose beads | ChromoTek | Cat#rtma-10 |
| Rabbit polyclonal anti-GFP | Thermo Fisher scientific | Cat#A-11122 |
| Polyclonal anti-DDM1 | This paper | N/A |
| Rabbit polyclonal anti-RFP | Rockland | Cat#600-401-379 |
| Goat anti-mouse Alexa Fluor 488 | Thermo Fisher scientific | Cat#A-10680 |
| Chemicals, peptides, and recombinant proteins | ||
| His-TEV-DDM1 | This paper | N/A |
| His-TEV-DDM1(Δ1–132) | This paper | N/A |
| Critical commercial assays | ||
| ChIP DNA clean and concentrator kit | Zymo Research | Cat#D5205 |
| KAPA SYBR FAST qPCR Master Mix | Kapa Biosystems | Cat#KK4600 |
| NEBNext Ultra II DNA Library Prep Kit for Illumina | New England Biolabs | Cat#E7645S |
| Nucleon PhytoPure Genomic DNA Extraction Kits | Cytiva | Cat#RPN8510 |
| NEXTFLEX Bisulfite Library Prep Kit | PerkinElmer | Cat#NOVA-5119-01 |
| Deposited data | ||
| Raw and analyzed data | This paper | GEO: GSE231563 |
| Coordinates map of DDM1-nucleosome complex | This paper | PDB: 7UX9 |
| cryoEM microscopy data | This paper | EMD-26855 |
| Raw data | Stroud et al.40 | GEO: GSE34840 |
| Raw data | Borg et al.47 | GEO: GSE120664 |
| Atomic model of SWI/SNF nucleosome complex | Han et al.118 | PDB: 6UXW |
| Experimental models: Organisms/strains | ||
| E. coli: BL21-CodonPlus (DE3)-RIPL | Agilent | Cat#230280 |
| A. thaliana: htr4 htr5 htr8/+ | Wollman et al.55 | N/A |
| A. thaliana: pHTR3:HTR3-GFP | Otero et al.39 | N/A |
| A. thaliana: pHTR5:HTR5-RFP | Otero et al.39 | N/A |
| A. thaliana: pHTR13:HTR13-CFP | Ingouff et al.104 | N/A |
| A. thaliana: pMGH3:MGH3-GFP | Leblanc et al.103 | N/A |
| A. thaliana: pDDM1:DDM1-GFP | Slotkin et al.44 | N/A |
| A. thaliana: See Table S2 for lines used | This paper | N/A |
| Oligonucleotides | ||
| See Table S3 for primers used | This paper | N/A |
| Recombinant DNA | ||
| pB7WG-pDDM1:DDM1-mCherry | This paper | N/A |
| pB7WG-pDDM1:DDM1(K233Q)-mCherry | This paper | N/A |
| pBiFC2-DDM1 | This paper | N/A |
| pBiFC4-MET1 | This paper | N/A |
| Software and algorithms | ||
| cutadapt | Martin107 | https://cutadapt.readthedocs.io/en/stable/ |
| bowtie2 | Langmead et al.108 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| samtools | Li et al.109 | http://www.htslib.org/ |
| Deeptools | Ramirez et al.95 | https://deeptools.readthedocs.io/en/develop/ |
| Bismark | Krueger et al.112 | https://www.bioinformatics.babraham.ac.uk/projects/bismark/ |
| R | R Core Team | https://www.r-project.org/ |
| DMRcaller | Catoni et al.113 | https://bioconductor.org/packages/release/bioc/html/DMRcaller.html |
| ggplot2 | Wickham110 | https://ggplot2.tidyverse.org |
| GViz | Hahne and Ivanek111 | https://bioconductor.org/packages/release/bioc/html/Gviz.html |
| WARP version 1.0.9 | Tegunov and Cramer96 | http://www.warpem.com/warp/ |
| cryoSPARC v3.2.0+210831 | Punjani et al.97 | https://cryosparc.com/ |
| Coot version 0.9.2-pre | Emsley et al.120 | https://pemsley.github.io/coot/ |
| Phenix version 1.19.2-4158-000 | Liebschner et al.122 | https://phenix-online.org/documentation/index.html |
| Resolve | Terwilliger et al.121 | https://phenix-online.org/documentation/reference/resolve_cryo_em.html |
| MolProbity version 4.5.1 | Williams et al.123 | http://molprobity.biochem.duke.edu/ |
| ChimeraX version 1.2.5 | Pettersen et al.124 | https://www.cgl.ucsf.edu/chimerax/download.html |
| APBS | Jurrus et al.100 | https://www.poissonboltzmann.org/ |
| DALI | Holm125 | http://ekhidna2.biocenter.helsinki.fi/dali/ |
| Consurf | Ashkenazi et al.98 | https://consurf.tau.ac.il/2016/overview.php |
| Original code | This study | https://github.com/rnartienssenlab/DDM1-manuscript |