Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis

Nature Communications, Год журнала: 2020, Номер 11(1)

Опубликована: Апрель 20, 2020

In higher eukaryotes, heterochromatin is mainly composed of transposable elements (TEs) silenced by epigenetic mechanisms. But, the silencing certain heterochromatin-associated TEs disrupted heat stress. By comparing genome-wide high-resolution chromatin packing patterns under normal or conditions obtained through Hi-C analysis, we show here that stress causes global rearrangement 3D genome in Arabidopsis thaliana. Contacts between pericentromeric regions and distal chromosome arms, as well proximal intra-chromosomal interactions along chromosomes, are enhanced. However, within pericentromeres those decreased. Many inter-chromosomal interactions, including KNOT, also reduced. Furthermore, activation exhibits a high correlation with reduction chromosomal involving pericentromeres, knob, upstream downstream flanking activated TEs. Together, our results provide insights into relationship TE reorganization.

Язык: Английский

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Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters

Nature Plants, Год журнала: 2021, Номер 7(6), С. 842 - 855

Опубликована: Июнь 3, 2021

Язык: Английский

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Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Genome biology, Год журнала: 2021, Номер 22(1)

Опубликована: Янв. 14, 2021

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies plants have investigated AS response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, comprehensive study contrasting stress-response tissue-specific patterns directly comparing them with those animal models still missing. Results We generate massive resource for Arabidopsis thaliana , PastDB comprising expression quantifications across tissues, development including abiotic biotic stresses. Harmonized analysis these datasets reveals A. shows high levels AS, similar fruitflies, that, compared animals, disproportionately uses stress responses. identify core sets genes regulated specifically by either or transcription upon stresses among specialization tightly mirrored the genomic features genes. Unexpectedly, non-intron events, exon skipping, are overrepresented being also largely involved modulating through NMD uORF inclusion. Conclusions Non-intron events likely been functionally underrated plants. constitutes distinct layer controlling internal external stimuli whose target master regulators hardwired at level undergo post-transcriptional regulation. Given higher relevance different when this molecular hardwiring required proper .

Язык: Английский

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The Arabidopsis Information Resource in 2024

Genetics, Год журнала: 2024, Номер 227(1)

Опубликована: Март 8, 2024

Since 1999, The Arabidopsis Information Resource (www.arabidopsis.org) has been curating data about the thaliana genome. Its primary focus is integrating experimental gene function information from peer-reviewed literature and codifying it as controlled vocabulary annotations. Our goal to produce a "gold standard" functional annotation set that reflects current state of knowledge At same time, resource serves nexus for community-based collaborations aimed at improving quality, access, reuse. For past decade, our work made possible by subscriptions global user base. This update covers ongoing biocuration work, some modernization efforts contribute first major infrastructure overhaul since 2011, introduction JBrowse2, resource's role in community activities such organizing structural reannotation assessment, we used ontology annotations metric evaluate: (1) what currently known (2) "unknown" genes. Currently, 74% proteome annotated least one term. Of those loci, half have support following aspects: molecular function, biological process, or cellular component. sheds light on genes which not yet identified any published no annotation. Drawing attention these unknown highlights gaps potential sources novel discoveries.

Язык: Английский

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Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration

Developmental Cell, Год журнала: 2022, Номер 57(4), С. 526 - 542.e7

Опубликована: Янв. 20, 2022

Highlights•The dynamic chromatin state landscape during shoot regeneration is revealed•Collapse of pluripotency in the absence cytokinin signaling•Generation a catalog regulatory sequences regeneration•A cohort transcription factors involved outlinedSummaryShoot mediated by sequential action two phytohormones, auxin and cytokinin. However, landscapes underlying this response have not yet been studied. In study, we jointly profiled accessibility, histone modifications, transcriptomes to demonstrate that high auxin/cytokinin ratio environment primes Arabidopsis increasing accessibility gene loci associated with fate determination. Cytokinin signaling only triggers commitment progenitor at later stages but also allows maintain identity genes priming stage. Our analysis transcriptional dynamics further identifies cis-elements dedicated cell transitions uncovers important roles BES1, MYC, IDD, PIF regeneration. results, thus, provide comprehensive resource for studying reprogramming plants potential targets improving future efficiency.Graphical abstract

Язык: Английский

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