Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA98687 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The transcription factor HY5 acts downstream of multiple families of the photoreceptors and promotes photomorphogenesis. Although it is well accepted that HY5 acts to regulate target gene expression, in vivo binding of HY5 to any of its target gene promoters has yet to be demonstrated. Here we used a chromatin immunoprecipitation procedure to verify suspected in vivo HY5 binding sites. We demonstrated that in vivo association of HY5 with promoter targets is not altered under distinct light qualities or during light-to-dark transition. Coupled with DNA chip hybridization using high density 60-nucleotide oligomer microarray that contains one probe for every 500 nucleotides over the entire Arabidopsis genome, we mapped genome wide in vivo HY5 binding sites. This analysis showed that HY5 binds preferentially to promoter regions in vivo and revealed over 3 thousand chromosomal sites as putative HY5 binding targets. HY5 binding targets tend to be enriched in the early light responsive genes and transcription factor genes. Our data thus supports a model in which HY5 is a high hierarchical regulator of the transcriptional cascades for photomorphogenesis. Keywords: ChIP-chip
2007-03-01 | GSE6510 | GEO
Project description:Cryptochromes (CRYs) is known as the key blue light receptors that promote photomorphogenesis in Arabidopsis, but to date, the underlying mechanisms are still not fully understood. Through interrogating the CRY2 interactome, we identified MOS4-ASSOCIATED COMPLEX subunits 3A and 3B (MAC3A and MAC3B) as blue light-independent CRY2 interacting partners. MAC3A/B proteins could be assembled into liquid nuclear condensates of CRYs in a blue light-dependent manner. Hypocotyl elongation is markedly repressed in mac3ab double knock-out mutants under various light conditions, which uncovers a previously unknown role of MAC3A/B as negative regulators in plant photomorphogenesis. Our results also uncover the noncanonical activities of MAC3A as the DNA-binding proteins that regulate transcription. Genome-wide mapping of MAC3A-binding sites reveals that blue light facilitates the binding of MAC3A to its targets, which is weakened in cry1cry2 mutants, suggesting that CRYs may enhance MAC3A activities in blue light to negatively influence photomorphogenesis. Interestingly, we observe that the genomic binding sites of MAC3A and HY5 are largely overlapped, and physical interactions between MAC3A and HY5 are detected as well. In addition, the in vitro DNA-binding assay shows that both proteins compete for the same DNA probe. These results indicate that MAC3A may antagonize the function of HY5 by competing for the common binding sites across the genome. Taken together, we propose that cryptochromes may fine-tune Arabidopsis photomorphogenesis by balancing the positive and negative effects on HY5 activities.
2023-08-21 | GSE220945 | GEO
Project description:NFYA5, a CCAAT binding transcription factor important for drought resistance in Arabidopsis
| PRJNA113307 | ENA
Project description:RGA binding sites in Arabidopsis thaliana seedlings
| PRJNA254703 | ENA
Project description:Genome-wide binding sites for Arabidopsis REPLUMLESS
| PRJNA313326 | ENA
Project description:Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes
| PRJNA212013 | ENA
Project description:A biophysical DNA binding model for the LEAFY transcription factor reveals the evolutionary fluidity of its binding sites
| PRJNA132641 | ENA
Project description:Analysis of genes regulated by an Arabidopsis transcription factor, Dof3.2
| PRJNA248784 | ENA
Project description:Injured plant somatic tissues regenerate themselves by establishing the shoot or root meristems. In Arabidopsis (Arabidopsis thaliana) a two-step culture system ensures regeneration by first promoting the acquisition of pluripotency and subsequently specifying the fate of new meristems. Although previous studies have reported the importance of phytohormones auxin and cytokinin in determining the fate of new meristems, it remains elusive whether and how the environmental factors influence this process. In this study, we investigated the impact of light signals on shoot regeneration using Arabidopsis hypocotyl as explants. We found that light signals promote shoot regeneration while inhibiting root formation. ELONGATED HYPOCOTYL 5 (HY5), the pivotal transcriptional factor in light signaling, plays a central role in this process by mediating the expression of key genes controlling the fate of new meristems. Specifically, HY5 directly represses root development genes and activates shoot meristem genes, leading to the establishment of shoot progenitor from pluripotent callus. We further demonstrated that the early activation of photosynthesis is critical for shoot initiation, and this is transcriptionally regulated downstream of the HY5-dependent pathways. In conclusion, we uncovered the intricate molecular mechanisms by which light signals control the establishment of new meristem through the regulatory network governed by HY5, thus, highlighting the influence of light signals on plant developmental plasticity.
2024-09-16 | GSE236147 | GEO
Project description:Identification of LEC1 binding sites in Arabidopsis seedlings
| PRJNA388705 | ENA