Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of Telomere Repeat Binding factors

Epigenetic regulators shape chromatin landscapes, allowing cells to express distinct gene sets depending on cell-type, developmental stage or environmental cues. These regulatory complexes rely on interactions with sequence-specific DNA binding proteins, such as the small family of TELOMERE REPEAT BINDING FACTORS (TRBs). TRBs are components of chromatin regulatory complexes with opposing functions, such as the epigenetic repressors Polycomb Repressive Complex 2 (PRC2) and a JMJ14/NAC complex that respectively add and removes the repressive H3K27me3 and positive H3K4me3 modification, but also with the plant-specific PEAT complex that is linked to histone acetylation and gene activation. We dissected the partial redundancy between TRB1, TRB2 and TRB3 in target gene selection and interaction with different chromatin regulatory complexes. High redundancy of TRBs is suggested by major phenotypic changes that are only observed trb triple mutants; however, we found different target site prefer..., Plant material and growth conditions Plants were grown in greenhouse conditions or growth chambers as indicated under long day (LD) (16h light, 8h dark) photoperiod at 22°C ambient temperature. Plants were randomized within trays for phenotypic analyses. Plants for RNA-seq analysis were grown in growth chambers. Three biological replicates were grown in 1 week intervals in the same chamber, material was collected at ZT10 from 14-day-old seedlings. For ChIP-seq, plants were grown in tissue culture on GM plates in LD conditions at 21°C. Material from replicated plates was collected from 14-day-old-seedling at ZT10 as biological replicates. The trb1-2 (Salk_001540) and trb3-2 (Salk_134641) alleles are previously described T-DNA insertion lines, trb2-2 and trb2-3 are CRISPR/Cas9 edited alleles as previously described except that the editing transgene was removed by segregation (1). Double and triple mutants were generated by crosses. Transgenic lines TRB2pro-TRB2-YFP and TRB3pro-TRB3-YFP we..., # Epigenetic gene regulation is controlled by distinct regulatory complexes utilizing specialized paralogs of Telomere Repeat Binding factors Dataset DOI: [10.5061/dryad.gtht76j2r](https://doi.org/10.5061/dryad.gtht76j2r) ## Description of the data and file structure ## Description of file repository This repository contains raw data files, intermediate analysis files and scripts that allow recapitulating the analyses presented in the PLOS Genetics manuscript `PGENETICS-D-25-01278` Some larger items, such as raw read data for RNAseq and ChIPseq and the raw proteomics data, are not included as they have been deposited in public databases. The ChIPseq and RNAseq data that support the findings of this study are publicly available from the European Nucleotide Archive (ENA) with the identifier [PRJEB63124](https://www.ebi.ac.uk/ena/browser/view/PRJEB63124). The proteomics data that support the findings of this study are publicly available from the Proteome Xchange database with the id..., ,