Biology subjects

Zander, M.

Publications and source records attributed to Zander, M..

7 recordsLinked to original sources

bioRxiv2026

Jasmonate-induced expansion of the MYC2 cistrome occurs within a preconfigured chromatin landscape

The transcription factor (TF) MYC2 is a central regulator of jasmonate (JA) signaling, yet its genome-wide occupancy has primarily been characterized using transgenic lines expressing tagged MYC2 proteins, leaving the dynamics of the native MYC2 cistrome unresolved. Here, using a MYC2-specific antibody, we define the wildtype MYC2 cistrome in Arabidopsis thaliana under basal and JA-induced conditions. Native MYC2 showed minimal genome-wide occupancy under control conditions but underwent a pronounced expansion following JA treatment, resulting in more than 3,000 binding sites enriched at core components of the JA signaling network. Cistrome expansion coincided with increased MYC2 protein abundance, while elevated basal MYC2 levels in a transgenic line were associated with extensive MYC2 occupancy even in the absence of JA, supporting a dosage-dependent relationship between MYC2 abundance and genome-wide binding. Despite this extensive cistrome expansion and transcriptional reprogramming, ATAC-seq revealed remarkably limited remodeling of chromatin accessibility following JA treatment. MYC2 recruitment occurred predominantly within pre-existing accessible chromatin regions that remained largely intact in myc2 myc3 myc4 mutants. Together, our findings reveal that JA-dependent expansion of the native MYC2 cistrome occurs within a largely pre-established accessome and identify MYC2 dosage as an important determinant of the extent of genome-wide occupancy.

plant biology↗

bioRxiv2026

Dynamic histone hyperacetylation shapes environmentally responsive chromatin states

Transcription factors (TFs) orchestrate environmental responses by activating target genes, yet how they reshape epigenome architecture to coordinate gene expression remains poorly understood. We previously identified SIENA (Stimulus-Induced ENhancer Acetylation) domains as large regions of jasmonic acid (JA)-induced H3K9 hyperacetylation surrounding MYC2 TF binding sites in Arabidopsis and tomato. However, the mechanisms underlying the formation of SIENA domains (SIENAs) and their functional significance remained unknown. Here, we show that SIENAs also form at major JA-responsive genes and gene clusters in soybean, extending this phenomenon to an evolutionarily distant crop species. Comprehensive chromatin profiling revealed that SIENAs accumulate multiple histone acetylation marks, including H3K9ac, H3K27ac, H3K56ac, H2BK20ac, and H2A.Zac, establishing them as regions of broad histone hyperacetylation. Pharmacological disruption of proteasomal turnover and histone acetylation dynamics compromised SIENA formation. Chromatin accessibility analyses further showed that inducible accessibility within SIENAs is tightly associated with MYC2 binding sites, supporting a model in which MYCs nucleate localized chromatin reprogramming events. Together, our findings establish SIENAs as MYC2-dependent chromatin-organizing domains and identify histone hyperacetylation as a central feature of MYC2-mediated gene activation.

Plant Biology↗

bioRxiv2023

Transcription Factor Dynamics in Cross-Regulation of Plant Hormone Signaling Pathways

Cross-regulation between hormone signaling pathways is indispensable for plant growth and development. However, the molecular mechanisms by which multiple hormones interact and co-ordinate activity need to be understood. Here, we generated a cross-regulation network explaining how hormone signals are integrated from multiple pathways in etiolated Arabidopsis (Arabidopsis thaliana) seedlings. To do so we comprehensively characterized transcription factor activity during plant hormone responses and reconstructed dynamic transcriptional regulatory models for six hormones; abscisic acid, brassinosteroid, ethylene, jasmonic acid, salicylic acid and strigolactone/karrikin. These models incorporated target data for hundreds of transcription factors and thousands of protein-protein interactions. Each hormone recruited different combinations of transcription factors, a subset of which were shared between hormones. Hub target genes existed within hormone transcriptional networks, exhibiting transcription factor activity themselves. In addition, a group of MITOGEN-ACTIVATED PROTEIN KINASES (MPKs) were identified as potential key points of cross-regulation between multiple hormones. Accordingly, the loss of function of one of these (MPK6) disrupted the global proteome, phosphoproteome and transcriptome during hormone responses. Lastly, we determined that all hormones drive substantial alternative splicing that has distinct effects on the transcriptome compared with differential gene expression, acting in early hormone responses. These results provide a comprehensive understanding of the common features of plant transcriptional regulatory pathways and how cross-regulation between hormones acts upon gene expression.

plant biology↗

bioRxiv2019

Polycomb-mediated repression compensates for loss of postnatal DNA methylation in excitatory neurons

Two epigenetic pathways of repression, DNA methylation and Polycomb repressive complex 2 (PRC2) mediated gene silencing, regulate neuron development and function, but their respective contributions are unknown. We found that conditional loss of the de novo DNA methyltransferase Dnmt3a in mouse excitatory neurons altered expression of synapse-related genes, stunted synapse maturation, and impaired working memory and social interest. Loss of Dnmt3a abolished postnatal accumulation of CG and non-CG DNA methylation, leaving neurons with an unmethylated, fetal-like epigenomic pattern at -140,000 genomic regions. The PRC2-associated histone modification H3K27me3 increased at many of these sites, partially compensating for the loss of DNA methylation. Our data support a dynamic interaction between two fundamental modes of epigenetic repression during postnatal maturation of excitatory neurons, which together confer robustness on neuronal regulation.

neuroscience↗

bioRxiv2019

PHYTOCHROME INTERACTING FACTORs trigger environmentally responsive chromatin dynamics

The pivotal interplay between light receptors and PHYTOCHROME INTERACTING FACTORs (PIFs) serves as an essential regulatory hub that perceives and integrates environmental cues into the plants transcriptional networks. A critical control component of environmentally-responsive gene networks is the histone variant H2A.Z which provides transcriptional plasticity and prevents undesired gene activation. However, the functional relationship between PIF transcription factors and H2A.Z is only poorly understood. Here, we describe a genomic approach that utilizes the rapid and reversible light-mediated manipulation of PIF7 activity to visualize PIF7 DNA binding and H2A.Z occupancy kinetics. Strikingly, PIFs shape the H2A.Z landscape in a light quality-dependent manner. In addition, we observed that PIFs initiate H2A.Z eviction through direct interaction with EIN6 ENHANCER (EEN), a subunit of INO80 chromatin remodeling complex. These studies uncover a previously unknown PIF-INO80 regulatory module controlling plant growth in response to rapid environmental changes.\n\nOne-sentence summaryA PIF-INO80 module controls light quality-dependent H2A.Z dynamics.

genomics↗

bioRxiv2019

Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA that spans from the activity of master and secondary-regulatory transcription factors, through gene expression outputs and alternative splicing to protein abundance changes, protein phosphorylation and chromatin remodeling. We integrated time series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enable us to predict previously unknown points of crosstalk from JA to other signaling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behavior, the general principles of which provide a framework for analysis of cross-regulation between other hormone and stress signaling pathways.

plant biology↗

bioRxiv2018

The complex architecture of plant transgene insertions

Over the last 35 years the soil bacterium Agrobacterium tumefaciens has been the workhorse tool for plant genome engineering. Replacement of native tumor-inducing (Ti) plasmid elements with customizable cassettes enabled insertion of a sequence of interest called Transfer DNA (T-DNA) into any plant genome. Although these T-DNA transfer mechanisms are well understood, detailed understanding of structure and epigenomic status of insertion events was limited by current technologies. To fill this gap, we analyzed transgenic Arabidopsis thaliana lines from three widely used collections (SALK, SAIL and WISC) with two single molecule technologies, optical genome mapping and nanopore sequencing. Optical maps for four randomly selected T-DNA lines revealed between one and seven insertions/rearrangements, and for the first time the actual length of individual transgene insertions from 27 to 236 kilobases. De novo nanopore sequencing-based genome assemblies for two segregating lines resolved T-DNA structures up to 36 kb into the insertions and revealed large-scale T-DNA associated translocations and exchange of chromosome arm ends. The multiple internally rearranged nature of T-DNA arrays made full assembly impossible, even with long nanopore reads. For the current TAIR10 reference genome, nanopore contigs corrected 83% of non-centromeric misassemblies. This unprecedented nucleotide-level definition of T-DNA insertions enabled the mapping of epigenome data. We identify variable small RNA transgene targeting and DNA methylation. SALK_059379 T-DNA insertions were enriched for 24nt siRNAs and contained dense cytosine DNA methylation. Transgene silencing via the RNA-directed DNA methylation pathway was confirmed by in planta assays. In contrast, SAIL_232 T-DNA insertions are predominantly targeted by 21/22nt siRNAs, with DNA methylation and silencing limited to a reporter, but not the resistance gene. With the emergence of genome editing technologies that rely on Agrobacterium for gene delivery, this study provides new insights into the structural impact of engineering plant genomes and demonstrates the utility of state-of-the-art long-range sequencing technologies to rapidly identify unanticipated genomic changes.

plant biology↗