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1. H2A.X promotes endosperm-specific DNA methylation in Arabidopsis thaliana

   https://doi.org/10.1186/s12870-023-04596-y  

   Frost, Jennifer M. ; Lee, Jaehoon ; Hsieh, Ping-Hung ; Lin, Samuel J. H. ; Min, Yunsook ; Bauer, Matthew ; Runkel, Anne M. ; Cho, Hyung-Taeg ; Hsieh, Tzung-Fu ; Fischer, Robert L. ; et al ( November 2023 , BMC Plant Biology)

   H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci inArabidopsis thalianafemale gametophytes during reproduction. Here, we sought to investigate whether H2A.X is involved in DME- and FACT-mediated DNA demethylation during reproduction.

   H2A.X is encoded by two genes in Arabidopsis genome,HTA3andHTA5. We generatedh2a.xdouble mutants, which displayed a normal growth profile, whereby flowering time, seed development, and root tip organization, S-phase progression and proliferation were all normal. However,h2a.xmutants were more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to Green Fluorescent Protein (GFP) under theH2A.Xpromoter was highly expressed especially in newly developing Arabidopsis tissues, including in male and female gametophytes, where DME is also expressed. We examined DNA methylation inh2a.xdeveloping seeds and seedlings using whole genome bisulfite sequencing, and found that CG DNA methylation is decreased genome-wide inh2a.xmutant endosperm. Hypomethylation was most striking in transposon bodies, and occurred on both parental alleles in the developing endosperm, but not the embryo or seedling.h2a.x-mediated hypomethylated sites overlapped DME targets, but also included other loci, predominately located in heterochromatic transposons and intergenic DNA.

   Our genome-wide methylation analyses suggest that H2A.X could function in preventing access of the DME demethylase to non-canonical sites. Overall, our data suggest that H2A.X is required to maintain DNA methylation homeostasis in the unique chromatin environment of the Arabidopsis endosperm.

    

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2. Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

   https://doi.org/10.1093/genetics/iyaa003  

   Noshay, Jaclyn M ; Marand, Alexandre P ; Anderson, Sarah N ; Zhou, Peng ; Mejia Guerra, Maria Katherine ; Lu, Zefu ; O’Connor, Christine H ; Crisp, Peter A ; Hirsch, Candice N ; Schmitz, Robert J ; et al ( January 2021 , Genetics)

   Bomblies, K (Ed.)

   Abstract Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes. 

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3. Arabidopsis ‐expressing lysine‐null SUMO1 reveals a non‐essential role for secondary SUMO modifications in plants

   https://doi.org/10.1002/pld3.506  

   Rytz, Thérèse C. ; Feng, Juanjuan ; Barros, Jessica A. S. ; Vierstra, Richard D. ( July 2023 , Plant Direct)

   The reversible conjugation of small ubiquitin‐like modifier (SUMO) to other proteins has pervasive roles in various aspects of plant development and stress defense through its selective attachment to numerous intracellular substrates. An intriguing aspect of SUMO is that it can be further modified by SUMOylation and ubiquitylation, which isopeptide‐link either or both polypeptides to internal lysines within previously bound SUMOs. Although detectable by mass spectrometry, the functions of these secondary modifications remain obscure. Here, we generated transgenicArabidopsisthat replaced the two related and essential SUMO isoforms (SUMO1 and SUMO2) with a lysine‐null SUMO1 variant (K0) immune to further SUMOylation/ubiquitylation at these residues. Remarkably, homozygousSUMO1(K0) sumo1 sumo2plants developed normally, were not hypersensitive to heat stress, and have nearly unaltered SUMOylation profiles during heat shock. However, subtle changes in tolerance to salt, paraquat, and the DNA‐damaging agents bleomycin and methane methylsulfonate were evident, as were increased sensitivities to ABA and the gibberellic acid biosynthesis inhibitor paclobutrazol, suggesting roles for these secondary modifications in stress defense, DNA repair, and hormone signaling. We also generated viablesumo1 sumo2lines expressing a SUMO1(K0) variant specifically designed to help isolate SUMO conjugates and map SUMOylation sites, thus offering a new tool for investigating SUMOin planta.

    

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4. Maize unstable factor for orange1 encodes a nuclear protein that affects redox accumulation during kernel development

   https://doi.org/10.1093/plcell/koae301  

   Chatterjee, Debamalya ; Zhang, Ziru ; Lin, Pei-Yu ; Wang, Po-Hao ; Sidhu, Gurpreet K ; Yennawar, Neela H ; Hsieh, Jo-Wei Allison ; Chen, Pao-Yang ; Song, Rentao ; Meyers, Blake C ; et al ( November 2024 , The Plant Cell)

   Meyers, Blake (Ed.)

   The basal endosperm transfer layer (BETL) of the maize (Zea mays L.) kernel is composed of transfer cells for nutrient transport to nourish the developing kernel. To understand the spatiotemporal processes required for BETL development, we characterized 2 unstable factor for orange1 (Zmufo1) mutant alleles. The BETL defects in these mutants were associated with high levels of reactive oxygen species, oxidative DNA damage, and cell death. Interestingly, antioxidant supplementation in in vitro cultured kernels alleviated the cellular defects in mutants. Transcriptome analysis of the loss-of-function Zmufo1 allele showed differential expression of tricarboxylic acid cycle, redox homeostasis, and BETL-related genes. The basal endosperms of the mutant alleles had high levels of acetyl-CoA and elevated histone acetyltransferase activity. The BETL cell nuclei showed reduced electron-dense regions, indicating sparse heterochromatin distribution in the mutants compared with wild-type. Zmufo1 overexpression further reduced histone methylation marks in the enhancer and gene body regions of the pericarp color1 (Zmp1) reporter gene. Zmufo1 encodes an intrinsically disordered nuclear protein with very low sequence similarity to known proteins. Yeast two-hybrid and luciferase complementation assays established that ZmUFO1 interacts with proteins that play a role in chromatin remodeling, nuclear transport, and transcriptional regulation. This study establishes the critical function of Zmufo1 during basal endosperm development in maize kernels.

    

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5. Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis

   https://doi.org/10.1073/pnas.1807621116  

   Kirkbride, Ryan C. ; Lu, Jie ; Zhang, Changqing ; Mosher, Rebecca A. ; Baulcombe, David C. ; Chen, Z. Jeffrey ( February 2019 , Proceedings of the National Academy of Sciences)

   Arabidopsisseed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through theNRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with annrpd1mutant. We also monitored the spatial-temporal activity of theNRPD1-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternalNRPD1allele in the endosperm or seed coat. A group of maternally expressedNRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by theNRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

    

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