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A multi-omics atlas of the plant nuclear envelope

ABSTRACT: The nuclear envelope (NE) proteins play a pivotal role in maintaining nuclear integrity and orchestrating nucleocytoplasmic communication. Increasing evidence suggests that NE proteins interact with a wide array of other proteins, implying functions far beyond membrane compartmentalization. However, the full composition and functional landscape of plant NE proteins remain largely uncharted. Here, we used proximity-labeling proteomics to generate a comprehensive map of the Arabidopsis NE proteome, identifying nearly 700 unique integral and associated NE proteins. Compositional analyses revealed that the NE not only functions as a hub for chromatin organization and transcriptional regulation but also tied to mRNA processing, membrane trafficking, and lipid metabolism. By integrating these proteomic data with single-cell and single-nucleus RNA sequencing, we uncovered a range of NE-associated functional modules exhibiting specificity across tissues, cell types, and developmental stages. Together, our results highlight the fundamental and multifaceted roles of the plant NE and provide new insights into its conserved and lineage-specific functions across eukaryotic evolution.

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling

SUBMITTER: Yiling Fang

LAB HEAD: Yangnan Gu

PROVIDER: PXD071667 | Pride | 2026-03-06

REPOSITORIES: Pride

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Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors. To determine the global in vivo binding sites of FHY3, we performed ChIP-seq analysis using 35S:3FLAG-FHY3-3HA fhy3-4 transgenic lines in which the 3FLAG-FHY3-3HA fusion proteins could largely rescue the long hypocotyl phenotype of the fhy3-4 mutants The seedlings were grown in D or continuous FR light conditions for 4 days, and then chromatin fragments were prepared using the commercially monoclonal anti-FLAG antibodies. We then generated two DNA libraries, one for D and one for FR -grown samples, which were then subjected to ultra-high throughput Solexa (Illumina) sequencing

			Action	DRS
	MS190849_COL.msf	Msf
	MS190849_COL_1.raw	Raw
	MS190849_COL_2.raw	Raw
	MS190849_COL_3.raw	Raw
	MS190849_MSBP1.msf	Msf

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A multi-omics atlas of the plant nuclear envelope

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