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1. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies

   https://doi.org/10.1093/nar/gkaa1262  

   Xu, Jing; Zhao, Xiaolu; Mao, Fengbiao; Basrur, Venkatesha; Ueberheide, Beatrix; Chait, Brian T; Allis, C David; Taverna, Sean D; Gao, Shan; Wang, Wei; et al (January 2021, Nucleic Acids Research)

   Abstract Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1—another PcG protein interacting with the EZL1 complex—reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome. 

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2. Chromatin architectural proteins regulate flowering time by precluding gene looping

   https://doi.org/10.1126/sciadv.abg3097  

   Zhao, Bo; Xi, Yanpeng; Kim, Junghyun; Sung, Sibum (June 2021, Science Advances)

   null (Ed.)

   Chromatin structure is critical for gene expression and many other cellular processes. In Arabidopsis thaliana , the floral repressor FLC adopts a self-loop chromatin structure via bridging of its flanking regions. This local gene loop is necessary for active FLC expression. However, the molecular mechanism underlying the formation of this class of gene loops is unknown. Here, we report the characterization of a group of linker histone-like proteins, named the GH1-HMGA family in Arabidopsis , which act as chromatin architecture modulators. We demonstrate that these family members redundantly promote the floral transition through the repression of FLC . A genome-wide study revealed that this family preferentially binds to the 5′ and 3′ ends of gene bodies. The loss of this binding increases FLC expression by stabilizing the FLC 5′ to 3′ gene looping. Our study provides mechanistic insights into how a family of evolutionarily conserved proteins regulates the formation of local gene loops. 

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3. DEK domain‐containing proteins control flowering time in Arabidopsis

   https://doi.org/10.1111/nph.17366  

   Zong, Wei; Zhao, Bo; Xi, Yanpeng; Bordiya, Yogendra; Mun, Hyungwon; Cerda, Nicholas A.; Kim, Dong‐Hwan; Sung, Sibum (May 2021, New Phytologist)

   Summary Evolutionarily conserved DEK domain‐containing proteins have been implicated in multiple chromatin‐related processes, mRNA splicing and transcriptional regulation in eukaryotes.Here, we show that two DEK proteins, DEK3 and DEK4, control the floral transition inArabidopsis. DEK3 and DEK4 directly associate with chromatin of related flowering repressors,FLOWERING LOCUS C(FLC), and its two homologs,MADS AFFECTING FLOWERING4(MAF4) andMAF5, to promote their expression.The binding of DEK3 and DEK4 to a histone octamerin vivoaffects histone modifications atFLC,MAF4andMAF5loci. In addition, DEK3 and DEK4 interact with RNA polymerase II and promote the association of RNA polymerase II withFLC,MAF4andMAF5chromatin to promote their expression.Our results show that DEK3 and DEK4 directly interact with chromatin to facilitate the transcription of key flowering repressors and thus prevent precocious flowering inArabidopsis. 

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4. Dynamic control of H2A.Zub and H3K27me3 by ambient temperature during cell fate determination in Arabidopsis

   https://doi.org/10.1016/j.devcel.2025.04.002  

   Zhu, Kehui; Chen, Jinchao; Zhao, Long; Lu, Fangfang; Deng, Jia; Lin, Xuelei; He, Chongsheng; Wagner, Doris; Xiao, Jun (April 2025, Developmental Cell)

   Crucial to plant development, ambient temperature triggers intricate mechanisms enabling adaptive responses to temperature variations. The precise coordination of chromatin modifications in shaping cell developmental fate under diverse temperatures remains elusive. Our study, integrating comprehensive transcriptome, epigenome profiling, and genetics, demonstrates that lower ambient temperature (16°C) partially restores developmental defects caused by H3K27me3 loss in prc2 mutants by specifically depositing H2A.Zub at ectopically expressed embryonic genes in Arabidopsis, such as ABA INSENSITIVE 3 (ABI3) and LEAFY COTYLEDON 1 (LEC1). This deposition leads to downregulation of these genes and compensates for H3K27me3 depletion. Polycomb-repressive complex 1 (PRC1)-catalyzed H2A.Zub and PRC2-catalyzed H3K27me3 play roles in silencing transcription of embryonic genes for post-germination development. Low-temperature-induced reduction of TOE1 protein level decelerates H2A.Z turnover at specific loci, sustaining repression of embryonic genes and alleviating requirement for PRC2-H3K27me3 at post-germination stage. Our findings offer mechanistic insights into the cooperative epigenetic layers, facilitating plant adaptation to varying environmental temperatures. 

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5. Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

   https://doi.org/10.1111/tpj.14817  

   Xi, Yanpeng; Park, Sung‐Rye; Kim, Dong‐Hwan; Kim, Eun‐Deok; Sung, Sibum (June 2020, The Plant Journal)

   Summary Vernalization accelerates flowering after prolonged winter cold. Transcriptional and epigenetic changes are known to be involved in the regulation of the vernalization response. Despite intensive applications of next‐generation sequencing in diverse aspects of plant research, genome‐wide transcriptome and epigenome profiling during the vernalization response has not been conducted. In this work, to our knowledge, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process inArabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold exposure. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development‐related transcription factors, which resulted in either inhibition of transcription or a bivalent status of the genes. Lastly,FLC‐like andVIN3‐like genes were identified that appear to be novel components of the vernalization pathway. 

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