HSFA1a modulates plant heat stress responses and alters the 3D chromatin organization of enhancer-promoter interactions

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Янв. 28, 2023

Abstract The complex and dynamic three-dimensional organization of chromatin within the nucleus makes understanding control gene expression challenging, but also opens up possible ways to epigenetically modulate expression. Because plants are sessile, they evolved sophisticated rapidly in response environmental stress, that thought be coordinated by changes conformation mediate specific cellular physiological responses. However, what extent how stress induces reorganization remains poorly understood. Here, we comprehensively investigated genome-wide associated with transcriptional reprogramming heat tomato. Our data show rapid architecture, leading transient formation promoter-enhancer contacts, likely driving heat-stress responsive genes. Furthermore, demonstrate spatial requires HSFA1a, a transcription factor (TF) essential for tolerance In light our findings, propose TFs play key role controlling responses through 3D reconfiguration contacts.

Язык: Английский

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Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

Nature Reviews Molecular Cell Biology, Год журнала: 2024, Номер 25(7), С. 574 - 591

Опубликована: Фев. 27, 2024

Язык: Английский

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Cell Type–Specific Whole-Genome Landscape of ΔFOSB Binding in the Nucleus Accumbens After Chronic Cocaine Exposure

Biological Psychiatry, Год журнала: 2023, Номер 94(5), С. 367 - 377

Опубликована: Янв. 2, 2023

Язык: Английский

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Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(3), С. 2855 - 2855

Опубликована: Фев. 2, 2023

In higher eukaryotes, the regulation of developmental gene expression is determined by enhancers, which are often located at a large distance from promoters they regulate. Therefore, architecture chromosomes and mechanisms that determine functional interaction between enhancers decisive importance in development organisms. Mammals model animal Drosophila have homologous key architectural proteins similar organization chromosome architecture. This review describes current progress understanding formation long-range interactions three well-studied regulatory loci Drosophila.

Язык: Английский

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CLAVATA signaling in plant–environment interactions

PLANT PHYSIOLOGY, Год журнала: 2023, Номер 194(3), С. 1336 - 1357

Опубликована: Ноя. 1, 2023

Abstract Plants must rapidly and dynamically adapt to changes in their environment. Upon sensing environmental signals, plants convert them into cellular which elicit physiological or developmental that allow respond various abiotic biotic cues. Because can be simultaneously exposed multiple cues, signal integration between plant cells, tissues, organs is necessary induce specific responses. Recently, CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides cognate CLAVATA-type receptors received increased attention for roles plant–environment interactions. CLE are mobile signaling molecules, many of induced by a variety stimuli. Secreted perceived receptor complexes on the surface target often include leucine-rich repeat receptor-like kinase CLAVATA1. Receptor activation then results cell-type and/or environment-specific This review summarizes our current understanding diverse environment-regulated modulating responses We highlight how signals regulate physiology fine-tuning plant–microbe interactions, nutrient homeostasis, carbon allocation. Finally, we describe role CLAVATA perception environment-induced discuss CLE-CLAVATA modules may integrate with development.

Язык: Английский

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Bovine enhancer-regulated circSGCB acts as a ceRNA to regulate skeletal muscle development via enhancing KLF3 expression

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 261, С. 129779 - 129779

Опубликована: Янв. 28, 2024

Язык: Английский

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C2H2 proteins: Evolutionary aspects of domain architecture and diversification

BioEssays, Год журнала: 2024, Номер 46(8)

Опубликована: Июнь 14, 2024

The largest group of transcription factors in higher eukaryotes are C2H2 proteins, which contain C2H2-type zinc finger domains that specifically bind to DNA. Few well-studied however, demonstrate their key role the control gene expression and chromosome architecture. Here we review features domain architecture proteins likely origin fingers. A comprehensive investigation proteomes for presence with multiple clustered has revealed a difference between groups organisms. Unlike plants, metazoans clusters typically separated by linker TGEKP consensus sequence. average size varies substantially, even genomes metazoans, tendency increase combination SCAN, especially KRAB domains, reflecting increasing complexity regulatory networks.

Язык: Английский

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Mechanisms of enhancer-promoter communication and chromosomal architecture in mammals and Drosophila

Frontiers in Genetics, Год журнала: 2022, Номер 13

Опубликована: Дек. 1, 2022

The spatial organization of chromosomes is involved in regulating the majority intranuclear processes higher eukaryotes, including gene expression. Drosophila was used as a model to discover many transcription factors whose homologs play key role regulation expression mammals. According modern views, cohesin complex mostly determines architecture mammalian by forming chromatin loops on anchors created CTCF DNA-binding architectural protein. chromosome poorly understood Drosophila, and merely one proteins with proven potential organize specific long-range interactions between regulatory elements genome. review compares mechanisms responsible for mammals Drosophila.

Язык: Английский

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Regulatory non-coding somatic mutations as drivers of neuroblastoma

British Journal of Cancer, Год журнала: 2025, Номер unknown

Опубликована: Янв. 23, 2025

Abstract Background Emerging evidence suggests that non-coding somatic single nucleotide variants (SNVs) in cis -regulatory elements (CREs) contribute to cancer by disrupting gene expression networks. However, the role of SNVs cancer, particularly neuroblastoma, remains largely unclear. Methods effect on CREs activity was evaluated luciferase assays. Motif analysis and ChIP-qPCR experiments were employed reveal transcription factors (TFs) involved these processes. We exploited CRISPR-Cas9 elucidate target genes expression. Cell proliferation invasion assays performed assess their neuroblastoma tumorigenesis. Results Our findings demonstrate modify transcriptional two altering binding STAT3 SIN3A. Therefore, reduce CTTNBP2 MCF2L . act as tumor suppressor neuroblastoma. These pathogenetic may serve oncogenic drivers impairing programs essential for neuronal development differentiation which both investigated TFs are involved. Conclusion Overall, understanding functional elucidates impact tumorigenesis can uncover new potential targets therapeutic strategies.

Язык: Английский

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Epigene functional diversity: isoform usage, disordered domain content, and variable binding partners

Epigenetics & Chromatin, Год журнала: 2025, Номер 18(1)

Опубликована: Фев. 1, 2025

Epigenes are defined as proteins that perform post-translational modification of histones or DNA, reading modifications, form complexes with epigenetic factors changing the general structure chromatin. This specialized group is responsible for controlling organization genomic DNA in a cell-type specific fashion, normal development spatial and temporal fashion. Moreover, mutations epigenes have been implicated causal germline pediatric disorders driver cancer. Despite their importance to human disease, date, there has not systematic analysis sources functional diversity at large. Epigenes' unique functions require assembly pools within nucleus suggest amino acid composition would enriched features enable efficient chromatin transcription, splicing, modifications. In this study, we assess stemming from gene structure, isoforms, protein domains, multiprotein complex formation drive established epigenes. We found structural variable roles depending on cellular environmental context. First, significantly larger more exons compared non-epigenes which contributes increased isoform diversity. Second participate multimeric than non-epigenes. Thirdly, given proposed membraneless organelles, show substantially intrinsically disordered regions (IDRs). Additionally, assessed specificity expression profiles showed ubiquitously expressed consistent enrichment syndromes intellectual disability, multiorgan dysfunction, developmental delay. Finally, L1000 dataset, identify drugs can potentially be used modulate these genes. Here significant differences usage, domain content, binding partners between using various genomics datasets Ensembl, ENCODE, GTEx, HPO, LINCS L1000, BrainSpan. Our results contribute new knowledge growing field focused developing targeted therapies diseases caused by epigene mutations, such chromatinopathies cancers.

Язык: Английский

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