skip to main content

Explore Research Products in the NSF-PAR

Title: Chromatin architectural proteins regulate flowering time by precluding gene looping
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.  more » « less
Award ID(s):
1656764
NSF-PAR ID:
10293781
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
Science Advances
Volume:
7
Issue:
24
ISSN:
2375-2548
Page Range / eLocation ID:
eabg3097
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ( , The Plant Journal)
    SUMMARY

    The transition from vegetative to reproductive development (floral transition) is a costly process in annual plants requiring increased investments in metabolic resources. TheArabidopsis thaliana(Arabidopsis) PHD finger protein EDM2 and RRM domain proteins EDM3 and IBM2 are known to form chromatin‐associated complexes controlling transcript processing. We are reporting that distinct splice isoforms of EDM3 and IBM2 cooperate in the coordination of the floral transition with basal immune responses. These cooperating splice isoforms, termed EDM3L and IBM2L, control the intensity of basal immunity and, via a separate pathway, the timing of the floral transition. During the developmental phase prior to the floral transition expression of EDM3L and IBM2L strongly and gradually increases, while these isoforms simultaneously down‐regulate expression of the floral suppressor geneFLCand promote the transition to reproductive growth. At the same time these accumulating EDM3 and IBM2 splice isoforms gradually suppress basal immunity against the virulent Noco2 isolate of the pathogenic oomyceteHyaloperonospora arabidopsidisand down‐regulate expression of a set of defense‐associated genes and immune receptor genes. We are providing clear evidence for a functional link between the floral transition and basal immunity in the annual plant Arabidopsis. Coordination of these two biological processes, which compete for metabolic resources, is likely critical for plant survival and reproductive success.

     
    more » « less
  2. ; ; ; ; ; ; ; ( , 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.

     
    more » « less
  3. ; ; ( , PLOS genetics)
    The long noncoding RNA COLDAIR is necessary for the repression of a floral repressor FLOWERING LOCUS C (FLC) during vernalization in Arabidopsis thaliana. The repression of FLC is mediated by increased enrichment of Polycomb Repressive Complex 2 (PRC2) and subsequent trimethylation of Histone H3 Lysine 27 (H3K27me3) at FLC chromatin. In this study we found that the association of COLDAIR with chromatin occurs only at the FLC locus and that the central region of the COLDAIR transcript is critical for this interaction. A modular motif in COLDAIR is responsible for the association with PRC2 in vitro, and the mutations within the motif that reduced the association of COLDAIR with PRC2 resulted in vernalization insensitivity. The vernalization insensitivity caused by mutant COLDAIR was rescued by the ectopic expression of the wild-type COLDAIR. Our study reveals the molecular framework in which COLDAIR lncRNA mediates the PRC2-mediated repression of FLC during vernalization. 
    more » « less
  4. ; ; ; ; ; ; ( , Plant, Cell & Environment)
    Abstract

    Blue light triggers the opening of stomata in the morning to allow CO2uptake and water loss through transpiration. During the day, plants may experience periodic drought and accumulate abscisic acid (ABA). ABA antagonizes blue light signalling through phosphatidic acid and reduces stomatal aperture. This study reveals a molecular mechanism by which two light signalling proteins interact to repress ABA signalling in the control of stomatal aperture. Ahypersensitive to red and blue 2(hrb2) mutant has a defective ATP‐dependent chromatin‐remodelling factor, PKL, in the chromodomain/helicase/DNA binding family. HRB2 enhances the light‐induced expression of a B‐box transcription factor gene,BBX21. BBX21 binds a T/G box in theABI5promoter and recruits HRB2 to modulate the chromatin structure at theABI5locus. Mutation in eitherHRB2orBBX21led to reduced water loss and ABA hypersensitivity. This hypersensitivity to ABA was well explained by the enhanced expression of the ABA signalling geneABI5in both mutants. Indeed, stomatal aperture was significantly reduced byABI5overexpression in the absence or presence of ABA under monochromatic light conditions. Overall, we present a regulatory loop in which two light signalling proteins repress ABA signalling to sustain gas exchange when plants experience periodic drought.

     
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al ( , The Plant Journal)
    SUMMARY

    Flowering of the reference legumeMedicago truncatulais promoted by winter cold (vernalization) followed by long‐day photoperiods (VLD) similar to winter annual Arabidopsis. However, Medicago lacksFLCandCO, key regulators of Arabidopsis VLD flowering.Most plants have twoINHIBITOR OF GROWTH(ING) genes (ING1andING2), encoding proteins with an ING domain with two anti‐parallel alpha‐helices and a plant homeodomain (PHD) finger, but their genetic role has not been previously described.In Medicago,Mting1gene‐edited mutants developed and flowered normally, but anMting2‐1 Tnt1insertion mutant and gene‐editedMting2mutants had developmental abnormalities including delayed flowering particularly in VLD, compact architecture, abnormal leaves with extra leaflets but no trichomes, and smaller seeds and barrels.Mting2mutants had reduced expression of activators of flowering, including theFT‐like geneMtFTa1, and increased expression of the candidate repressorMtTFL1c, consistent with the delayed flowering of the mutant.MtING2overexpression complementedMting2‐1, but did not accelerate flowering in wild type. The MtING2 PHD finger bound H3K4me2/3 peptides weaklyin vitro, but analysis of gene‐edited mutants indicated that it was dispensable to MtING2 function in wild‐type plants. RNA sequencing experiments indicated that >7000 genes are mis‐expressed in theMting2‐1mutant, consistent with its strong mutant phenotypes. Interestingly, ChIP‐seq analysis identified >5000 novel H3K4me3 locations in the genome ofMting2‐1mutants compared to wild type R108. Overall, our mutant study has uncovered an important physiological role of a plantING2gene in development, flowering, and gene expression, which likely involves an epigenetic mechanism.

     
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email