Multi‐Omics Analysis Reveals Adaptation Strategies of Marine Diatom to Long‐Term Ocean Warming: Resource Allocation Trade‐Offs and Epigenetic Regulation

Plant Cell & Environment, Год журнала: 2025, Номер unknown

Опубликована: Март 30, 2025

ABSTRACT High CO 2 emissions originating from anthropogenic sources have resulted in ocean warming (OW), posing a severe threat to marine organisms and ecosystems. Recent evidence has shown that phytoplankton may acclimate adapt long‐term OW. Whether how diatoms—a functional group of contributes 40% primary production—can OW remains virtually unknown. The model diatom Phaeodactylum tricornutum was subjected thermal stress (25°C, compared the Control at 20°C) for 400 days (~400 generations), physiological, transcriptomic, genetic epigenetic analyses were performed reveal adaptation mechanisms under During adaptation, regulation resource allocation (e.g., photosynthesis, nitrogen metabolism, ribosomal synthesis translation, carbon metabolism heat shock response) transcriptional levels linked accumulated proteins, carbohydrates particulate organic carbon, reduced lipid content, enlarged cell size. Integrated histone modification (H3K27me3) transcriptome data sets revealed potential role transposable elements via P. stress. These mechanistic insights facilitate modelling prediction OW‐induced impacts on future.

Язык: Английский

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MER57E3 transposable element subfamily co-opted for gene regulation in human early neural development

Research Square (Research Square), Год журнала: 2025, Номер unknown

Опубликована: Апрель 7, 2025

Background Long dismissed as mere genomic parasites, transposable elements (TEs) are now recognized major drivers of genome evolution. TEs serve a source cell-type specific cis-regulatory elements, influencing gene expression and observable phenotypes. However, the precise TE regulatory roles in different contexts remain largely unexplored impact on transcriptional networks contribution to disease risk is likely deeply underestimated. Results Using multimapper-aware strategy, we systematically characterised epigenetic profile brain. This analysis revealed that MER57E3, primate-specific subfamily, exhibits strong enrichment for active, absence repressive, histone modifications across six brain cell types. MER57E3 copies predominantly located near zinc finger genes enriched homeodomain motifs by brain-specific transcription factors, including GBX1 BSX. Upon CRISPR interference (CRISPRi) targeting copies, RNA-seq demonstrated downregulation key neurogenesis-related PAX6 NEUROG2. Conclusions Our data indicate members subfamily regulate critical neurogenesis during neural progenitor (NPC) development. Moreover, this study emphasises importance characterising TEs, offering new insights into how their dysregulation may contribute pathogenesis neurodevelopmental disorders.

Язык: Английский

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Alternative silencing states of Transposable Elements in Arabidopsis

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 16, 2024

Abstract The DNA methylation/H3K9me2 and Polycomb-group proteins (PcG)-H3K27me3 pathways have long been considered mutually exclusive specific to TEs genes, respectively. However, H3K27me3 can be recruited many in the absence of methylation machinery sometimes also co-occur with methylation. In this study, we show that solely targeted by wild-type Arabidopsis plants. These H3K27me3-marked not only comprise degenerate relics but seemingly intact copies display epigenetic features responsive PcG target genes as well an active regulation. We deposited on newly inserted transgenic TE sequences a TE-specific manner indicating silencing is determined cis . Finally, comparison natural accessions reveals existence category - which refer “ bifrons ” are marked or depending ecotype. This variation linked intrinsic trans acting factors, change status across lifespan. Our study sheds light alternative mode associated instead flowering It suggests dynamic switching between two marks at species level, new paradigm might extend other multicellular eukaryotes.

Язык: Английский

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Small‐RNA‐guided histone modifications and somatic genome elimination in ciliates

Wiley Interdisciplinary Reviews - RNA, Год журнала: 2024, Номер 15(2)

Опубликована: Март 1, 2024

Abstract Transposable elements and other repeats are repressed by small‐RNA‐guided histone modifications in fungi, plants animals. The specificity of silencing is achieved through base‐pairing small RNAs corresponding to the these genomic loci nascent noncoding RNAs, which allows recruitment methyltransferases that methylate H3 on lysine 9. Self‐reinforcing feedback loops enhance RNA production ensure robust heritable repression. In unicellular ciliate Paramecium tetraurelia , lead elimination transposable their remnants, a definitive form this organism, germline somatic functions separated within two types nuclei with different genomes. At each sexual cycle, development genome accompanied reproducible removal approximately third genome. Instead recruiting H3K9 methyltransferase, eliminated sequences tether Polycomb Repressive Complex 2, ciliates has unique property catalyzing both 9 27 trimethylation H3. These crucial for thought guide endonuclease complex, triggers double‐strand breaks at specific loci. comparison between eukaryotes underscores importance investigating small‐RNAs‐directed chromatin diverse range organisms. This article categorized under: Regulatory RNAs/RNAi/Riboswitches > RNAi: Mechanisms Action

Язык: Английский

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From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements

Seminars in Cell and Developmental Biology, Год журнала: 2024, Номер 164, С. 1 - 12

Опубликована: Май 31, 2024

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if harm the host. However, numerous studies have shown that TEs, though typically harmful, also fuel for adaptation. This is code functional sequences be useful host which reside. In this review, I summarize "how" "why" adaptation enabled by between TEs hosts. addition, focusing on mechanisms TE control small piwi-interacting RNAs (piRNAs), highlight an indirect form conflict. case, defense regulate been redeployed endogenous gene regulation. propose released meiosis early eukaryotes may important because, among other reasons, it spurred evolutionary innovation multiple interwoven trajectories - part hosts embedded parasites. evolution function as complexity generating engine was critical player eukaryotic evolution.

Язык: Английский

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Development of a rapamycin-inducible protein-knockdown system in the unicellular red alga Cyanidioschyzon merolae

PLANT PHYSIOLOGY, Год журнала: 2024, Номер 196(1), С. 77 - 94

Опубликована: Июнь 4, 2024

Abstract An inducible protein-knockdown system is highly effective for investigating the functions of proteins and mechanisms essential survival growth organisms. However, this technique not available in photosynthetic eukaryotes. The unicellular red alga Cyanidioschyzon merolae possesses a very simple cellular genomic architecture genetically tractable but lacks RNA interference machinery. In study, we developed alga. constitutive utilizes destabilizing activity FK506-binding protein 12 (FKBP12)-rapamycin-binding (FRB) domain human target rapamycin kinase or its derivatives to knock down proteins. system, treatment induces heterodimerization FRB fused with FKBP S-phase kinase-associated 1 Cullin 1, subunits SCF E3 ubiquitin ligase. This results rapid degradation through ubiquitin-proteasome pathway. With successfully degraded endogenous such as chloroplast division dynamin-related 5B E2 transcription factor, regulator G1/S transition, within 2 3 h after administration, enabling assessment resulting phenotypes. rapamycin-inducible contributes functional analysis genes whose disruption leads lethality.

Язык: Английский

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The evolutionary consequences of interactions between the epigenome, the genome and the environment

Evolutionary Applications, Год журнала: 2024, Номер 17(7)

Опубликована: Июль 1, 2024

Abstract The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns development, phenotypic plasticity gene regulation, in part due its responsiveness environmental stimuli. There increasing interest understanding functional evolutionary importance this sensitivity under ecologically realistic conditions. Observations epigenetic variation abounds natural populations have prompted speculation it may facilitate responses rapid perturbations, such as those occurring climate change. A frequent point contention whether variants reflect genetic or are independent it. genome often appear tightly linked interdependent. While many changes genetically determined, converse also true, with DNA sequence influenced by presence marks. Understanding how epigenome, environment interact one another therefore an essential step explaining broader consequences epigenomic variation. Drawing on results from experimental comparative studies carried out diverse plant animal species, we synthesize our current these factors populations, a focus identifying similarities differences between taxonomic groups. We describe main components they vary within taxa. review interacts features determinants, role transposable elements (TEs) integrating environment. And look at recent investigating interactions. Although differentiation nature likely result drift selection stochastic epimutations, there growing evidence significant fraction can be stably inherited could contribute evolution independently

Язык: Английский

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Insights into the molecular bases of multicellular development from brown algae

Development, Год журнала: 2024, Номер 151(20)

Опубликована: Сен. 20, 2024

ABSTRACT The transition from simple to complex multicellularity represents a major evolutionary step that occurred in only few eukaryotic lineages. Comparative analyses of these lineages provide insights into the molecular and cellular mechanisms driving this transition, but limited understanding biology some multicellular lineages, such as brown algae, has hampered progress. This Review explores how recent advances genetic genomic technologies now allow detailed investigations bases algae development. We highlight forward techniques have identified mutants enhance our pattern formation sexual differentiation organisms. Additionally, existence nature morphogens potential influence microbiome key developmental processes are examined. Outstanding questions, identity master regulators, definition characterization cell types, plasticity discussed, with technical could answers. Overall, highlights emerging alternative model organisms, contributing evolution life diversity body plans.

Язык: Английский

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Cold stress induces a rapid redistribution of the antagonistic marks H3K4me3 and H3K27me3 inArabidopsis thaliana

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 3, 2024

Abstract When exposed to low temperatures, plants undergo a drastic reprogramming of their transcriptome in order adapt new environmental conditions, which primes them for potential freezing temperatures. While the involvement transcription factors this process, termed cold acclimation, has been deeply investigated, contribution chromatin regulation remains largely unclear. A large proportion cold-inducible genes carries repressive mark histone 3 lysine 27 trimethylation (H3K27me3), hypothesized as maintaining silenced state absence stress, but would need be removed or counteracted upon stress perception. However, fate H3K27me3 during exposure not studied genome-wide. In study, we offer an epigenome profiling and its antagonistic active H3K4me3 short-term exposure. Both marks rapid redistribution exposure, however, gene sets undergoing differential methylation are distinct, refuting simplistic idea that activation relies on switch from repressed form enriched H3K4me3. Coupling ChIP-seq experiments with reveals correlates changes expression. Interestingly, only subset cold-regulated lose induction, indicating is obstacle transcriptional activation. methyltransferase curly leaf (clf) mutant, many regulated display reduced levels activity altered prior suggesting may serve more intricate role response than simply repressing naïve conditions.

Язык: Английский

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Activity and Silencing of Transposable Elements in C. elegans

DNA, Год журнала: 2024, Номер 4(2), С. 129 - 140

Опубликована: Апрель 2, 2024

Since the discovery of transposable elements (TEs) in maize 1940s by Barbara McClintock have been described as junk, selfish with no benefit to host, and more recently major determinants genome structure evolution. TEs are DNA sequences that capable moving new sites making additional copies themselves while doing so. To limit propagation TEs, host silencing mechanisms directed at transposon-encoded genes required for mobilization. The mutagenic properties potential form affect gene expression, together mechanisms, shape eukaryotic genomes drive While constitute than half many higher eukaryotes, nematode C. elegans a relatively small proportion (approximately 15%). Genetic studies transposon silencing, RNA interference (RNAi) elegans, propelled Caenorhabditis (C. elegans) forefront RNA-based silence TEs. Here, I will review present active genome, defense these elements.

Язык: Английский

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