Chromatin architectural proteins regulate flowering time by precluding gene looping
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA687751 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13316009_1.fastq.gz | Fastqsanger.gz | |||
| SRR13316009_2.fastq.gz | Fastqsanger.gz | |||
| SRR13316010_1.fastq.gz | Fastqsanger.gz | |||
| SRR13316010_2.fastq.gz | Fastqsanger.gz | |||
| SRR13316011_1.fastq.gz | Fastqsanger.gz |
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Project description:Architectural proteins alter the shape of DNA. Some distort the double helix by introducing sharp kinks. This can serve to relieve strain in tightly-bent DNA structures. Here, we design and test artificial architectural proteins based on a sequence-specific Transcription Activator-like Effector (TALE) protein, either alone or fused to a eukaryotic high mobility group B (HMGB) DNA-bending domain. We hypothesized that TALE protein binding would stiffen DNA to bending and twisting, acting as an architectural protein that antagonizes the formation of small DNA loops. In contrast, fusion to an HMGB domain was hypothesized to generate a targeted DNA-bending architectural protein that facilitates DNA looping. We provide evidence from Escherichia coli Lac repressor gene regulatory loops supporting these hypotheses in living bacteria. Both data fitting to a thermodynamic DNA looping model and sophisticated molecular modeling support the interpretation of these results. We find that TALE protein binding inhibits looping by stiffening DNA to bending and twisting, while the Nhp6A domain enhances looping by bending DNA without introducing twisting flexibility. Our work illustrates artificial approaches to sculpt DNA geometry with functional consequences. Similar approaches may be applicable to tune the stability of small DNA loops in eukaryotes.
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Project description:The timing of flowering is a critical agronomic trait governed by a number of different internal and external events, such as temperature, light and photoperiod. Despite a firm understanding of flowering time from a genetic standpoint, there exists a limited understanding of how post-translational modifications may influence flowering, and what molecular PTM machinery is responsible for catalyzing these events. Here, we identify and characterize a novel B4 Raf-like MAPKKK protein kinase called RAF24, which exhibits an early flowering phenotype. Analysis of closely-related B4 Raf-like MAPKKK protein kinases RAF18 and RAF20, indicate that RAF24 is the only B4 RAF to possess an early flowering phenotype. Through quantitative proteomics, we then found that RAF24 impacts the phosphorylation status of numerous flowering related proteins related to the autonomous flowering pathway, with changes in the phosphorylation status of HISTONE MONO-UBIQUITINATION 2 (HUB2) representing the largest fold-change. Subsequent analysis of the HUB2 protein interactome by quantitative affinity purification mass spectrometry (AP-MS) revealed a relationship between HUB2 phosphorylation at S314 phosphorylation status and HUB2 function that manifest as changes in activity and protein-protein interactions. Use of phospho-memetic and -ablative mutants validate the importance of S314, directly linking this HUB2 phosphorylation event to the proper control of flowering time. Collectively, our findings implicate RAF24 as a higher-order regulator of flowering, while further implicating HUB2 as a centerpiece of flowering time regulation in plants.
2025-05-09 | PXD038688 | Pride
Project description:This study investigated the effect of autophagy on flowering time in rice. Results provide important information of the response of flowering time to autophagy, such as specific flowerig time genes, up- or down-regulated specific flowering time functions.
2022-05-06 | GSE175519 | GEO
Project description:In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. In contrast, dCP enhancers are marked by H3K4me1, associated with chromatin loop anchors and are more commonly associated with single TSS-contacts. dCP enhancers are depleted of the hkCP-specific architectural proteins and show an enrichment for Fs(1)h-L and Rad21 instead. Thus, our data supports the model that the unique occupancy of architectural proteins in the distinct enhancer classes are key contributors to the types of interactions that enhancers can mediate genome-wide, ultimately affecting enhancer-promoter specificity.
2016-11-16 | GSE80701 | GEO
Project description:In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. In contrast, dCP enhancers are marked by H3K4me1, associated with chromatin loop anchors and are more commonly associated with single TSS-contacts. dCP enhancers are depleted of the hkCP-specific architectural proteins and show an enrichment for Fs(1)h-L and Rad21 instead. Thus, our data supports the model that the unique occupancy of architectural proteins in the distinct enhancer classes are key contributors to the types of interactions that enhancers can mediate genome-wide, ultimately affecting enhancer-promoter specificity.
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Project description:Flowering in plants is a very dynamic and synchronized process where various cues including age, day-length, temperature and endogenous hormones fine-tune the timing of flowering for reproductive success. Arabidopsis thaliana is a facultative long day plant where long-day (LD) photoperiod promotes flowering. Arabidopsis still flowers under short-day (SD) conditions, albeit much later than LD conditions. Although, factors regulating the photoperiodic LD pathway have been extensively investigated, the SD pathway is much less understood. Here we identified a critical transcription factor called bHLH93 (basic Helix-Loop-Helix 93) that is essential to induce flowering specifically under SD conditions in Arabidopsis. bhlh93 mutants do not flower from primary meristem under SD conditions, but flowers similar to wild type under LD conditions. The late flowering phenotype is rescued by exogenous application of GA, suggesting that bHLH93 acts upstream of GA pathway to promote flowering. Double mutant studies showed that bhlh93 is epistatic to phyB and soc1 genes under SD conditions. bHLH93 is expressed at the meristematic regions and its expression peaks at 8 hours after dawn under SD conditions. As expected, the bHLH93 is localized in the nucleus. Taken together, these data suggest that bHLH93 is a key transcription factor necessary for Arabidopsis thaliana to evolve as a facultative plant.
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Project description:Ubiquitylated H2A.Z nucleosomes are associated with nuclear architectural proteins and global transcriptional silencing
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Project description:Mammalian genomes are folded into tens of thousands of long-range looping interactions1,2. The cause and effect relationship between looping and genome function is poorly understood, and the extent to which chromatin loops are dynamic on short time scales remains a fundamental unanswered question. Currently available strategies for loop engineering involve synthetic transcription factors tethered to dCas93,4or zinc fingers5,6, which are constitutively expressed5,6or induced on long time scales by the presence of a small molecule3.Here we report a new class of 3D optoepigenetic toolsfor the directed rearrangement of 3D chromatin looping on short time scales using blue light. We create synthetic architectural proteins by fusing the CIBN protein subunit from Arabidopsis thaliana with enzymatically dead Cas9 (dCas9). We target our light-activated dynamic looping system (LADL) to two genomic anchors with CRISPR guide RNAs and engineer their spatial co-localization via light-induced heterodimerization of the cryptochrome 2 (CRY2) protein with dCas9-CIBN. We apply LADL to redirect a stretch enhancer(SE)away from its endogenous Klf4target gene and to the Zfp462promoter. Looping changes occur as early as four hours after light induction. Using single molecule RNA FISH, we observe a LADL-induced increase in the total nascent Zfp462transcripts and the number of Zfp462 alleles expressing simultaneously per cell.Moreover, LADL also increased synchronous Sox2 expression after reinforcement of a known Sox2-SElooping interaction. LADL facilitates loop synchronization across a large population of cells without exogenous chemical cofactors and can enable future efforts to engineer reversible and oscillatory looping on short time scales.
2019-06-24 | GSE115963 | GEO
Project description:Plants flower in an appropriate season to allow sufficient vegetative development and position flower development in favorable environments. In Arabidopsis, CONSTANS (CO) and FLAVIN-BINDING KELCH REPEAT F-BOX1 (FKF1) promote flowering by inducing FLOWER LOCUS T (FT) expression in the long-day afternoon. The CO protein is present in the morning but could not activate FT expression due to unknown negative mechanisms, which prevent premature flowering before the day length reaches a threshold. Here, we report that TARGET OF EAT1 (TOE1) and related proteins interact with the activation domain of CO and CO-like (COL) proteins and inhibit CO activity. TOE1 binds to the FT promoter near the CO-binding site, and reducing TOE function results in a morning peak of the FT mRNA. In addition, TOE1 interacts with the LOV domain of FKF1 and likely interferes with the FKF1-CO interaction, resulting in partial degradation of the CO protein in the afternoon to prevent premature flowering.
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