Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates DOI Creative Commons
James M. Gahan, Lily W. Helfrich, Laura A. Wetzel

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 30, 2024

Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate possibility, here we examine gene features closest relatives animals, choanoflagellates. Using Salpingoeca rosetta as a model system, examined chromatin accessibility and histone modifications at genome scale compared these expression. We first observed accessible regions are primarily associated with promoters found no distal elements resembling enhancers deploy regulate developmental Remarkably, modification deposited by polycomb repressive complex 2, H3 lysine 27 trimethylation (H3K27me3), appeared function similarly S. its role because decorated genes type-specific Additionally, H3K27me3 marked transposons, retaining what appears be an ancestral regulating elements. further uncovered putative new bivalent state consists 4 mono-methylation (H3K4me1). Together, our discoveries support scenario gene-associated states underpin emerged before evolution multicellularity.

Language: Английский

Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3 DOI Creative Commons

Valentin Hure,

Florence Piron‐Prunier,

Tamara Yehouessi

et al.

Genome biology, Journal Year: 2025, Volume and Issue: 26(1)

Published: Jan. 20, 2025

Language: Английский

Citations

2
Mind the gap: Epigenetic regulation of chromatin accessibility in plants DOI Creative Commons
Joan Candela-Ferre, Borja Diego‐Martin, Jaime Pérez-Alemany

et al.

PLANT PHYSIOLOGY, Journal Year: 2024, Volume and Issue: 194(4), P. 1998 - 2016

Published: Jan. 17, 2024

Abstract Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central these processes, determining chromatin accessibility by limiting access to DNA various proteins acting as important signaling hubs. The association histones with nucleosomes folding into higher-order structures strongly influenced variety epigenetic marks, including methylation, histone variants, post-translational modifications. Additionally, wide array chaperones ATP-dependent remodelers regulate aspects nucleosome biology, assembly, deposition, positioning. This review provides an overview recent advances our mechanistic understanding how organization regulated marks plants. Furthermore, we present current technologies profiling organization.

Language: Английский

Citations

13
Cold stress induces rapid gene-specific changes in the levels of H3K4me3 and H3K27me3 in Arabidopsis thaliana DOI Creative Commons
Léa Faivre,

Nathalie-Francesca Kinscher,

Ana Belén Kuhlmann

et al.

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: April 15, 2024

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 only weakly correlates changes expression. Interestingly, 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.

Language: Английский

Citations

8
A dual histone code specifies the binding of heterochromatin protein Rhino to a subset of piRNA source loci DOI Creative Commons
Abdou Akkouche, Emma Kneuss, Susanne Bornelöv

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 11, 2024

ABSTRACT Animal germ cells deploy a specialized small RNA-based silencing system, called the PIWI-interacting RNA (piRNA) pathway, to prevent unwanted expression of transposable elements and maintain genome integrity. In Drosophila cells, majority piRNA populations originate from dual-strand clusters, genomic regions highly enriched in transposon fragments, via an elaborate protein machinery centred on heterochromatin 1 homolog, Rhino. Although Rhino binds peptides carrying trimethylated H3K9 vitro, it is not fully understood why vivo only fraction H3K9me3-decorated occupied by Recent work uncovered that recruited subset clusters zinc finger Kipferl. Here we identify Kipferl-independent mode targeting dependent histone H3 lysine 27 methyltransferase Enhancer Zeste presence H3K9me3 H3K27me3 marks. At sites, find Rhino, through its dimeric chromodomain, specifically loci marked both H3K27me3. These results expand our understanding characteristic binding profile Our reveals role for dual modifications defining specificity chromatin protein.

Language: Английский

Citations

7
DNA methylation enables recurrent endogenization of giant viruses in an animal relative DOI Creative Commons
Luke A. Sarre, Iana V. Kim, Vladimir Ovchinnikov

et al.

Science Advances, Journal Year: 2024, Volume and Issue: 10(28)

Published: July 12, 2024

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet also been lost many lineages. The causes for retention and its consequences are still poorly understood. Here, we show the protist closely related to animals Amoebidium appalachense features both transposon body methylation, pattern reminiscent of invertebrates plants. Unexpectedly, hypermethylated regions derive from viral insertions, including hundreds endogenized giant viruses, contributing 14% proteome. Using combination inhibitors assays, demonstrate silences these virus insertions. Moreover, alternative isolates polymorphic highlighting dynamic process infection, endogenization, purging. Our results indicate critical controlled coexistence newly acquired DNA into eukaryotic genomes, making unique model understand hybrid origins DNA.

Language: Английский

Citations

7
Retrotransposon-driven environmental regulation of FLC leads to adaptive response to herbicide DOI

Mathieu Raingeval,

Basile Leduque,

Pierre Baduel

et al.

Nature Plants, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 27, 2024

Language: Английский

Citations

7
DNA methylation enables recurrent endogenization of giant viruses in an animal relative DOI Creative Commons
Luke A. Sarre, Iana V. Kim, Vladimir Ovchinnikov

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 8, 2024

Abstract 5-methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. However, in many eukaryotes 5mC has gained complex roles gene regulation beyond parasite control. Animals are quintessential case for evolution, as they show variability across lineages, ranging from and transposable element control to loss of this base modification. Here we the protist closely related animals Amoebidium appalachense features both transposon body methylation, pattern reminiscent invertebrates plants. Unexpectedly, large hypermethylated regions genome derive viral insertions, including hundreds endogenized giant viruses contributing 14% encoded genes, an extent never reported before any eukaryotic genome. Using combination inhibitors functional assays, demonstrate silences these virus insertions. Moreover, alternative isolates polymorphic highlighting dynamic process infection, endogenization purging. Our results indicate critical controlled co-existence newly acquired DNA into genomes, making unique model understand hybrid origins genomes.

Language: Английский

Citations

6
Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing DOI Creative Commons

Basile Leduque,

Alejandro Edera, Clémentine Vitte

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(11), P. 6285 - 6297

Published: April 27, 2024

Abstract Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions cannot detect multiple features simultaneously. Here, we performed Simultaneous Accessibility Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks the use long-read nanopore sequencing, SAM-seq enables high-resolution m6A-tagged accessibility together with endogenous cytosine in plants. Analysis naked revealed significant sequence preference biases m6A-MTases, controllable through a normalisation step. By applying Arabidopsis maize nuclei obtained fine-grained landscapes genome-wide. We uncovered crosstalk between within nucleosomes genes, TEs, centromeric repeats. also detects footprints over cis-regulatory regions. Furthermore, using single-molecule information provided by identified extensive cellular heterogeneity at domains antagonistic marks, suggesting that bivalency reflects cell-specific regulations. is powerful approach simultaneously study epigenetic unique sequences, opening new opportunities for investigation mechanisms.

Language: Английский

Citations

5
Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1 DOI Creative Commons
Bastiaan de Potter, Maximilian W. D. Raas, Michael Seidl

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Nov. 10, 2023

Polycomb group proteins, as part of the repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation histone H2A non-canonical PRC1 and tri-methylation H3K27 PRC2. Despite prevalent models emphasizing tight functional coupling between PRC2, it remains unclear whether this paradigm indeed reflects evolution functioning these complexes. Here, we conduct a comprehensive analysis presence or absence cPRC1, nPRC1 PRC2 across entire eukaryotic tree life, find that both complexes were present Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% organisms contain only showing their since LECA is largely uncoupled. The identification ncPRC1-defining subunits unicellular relatives animals fungi suggests ncPRC1 originated before propose scenario for cPRC1 from ncPRC1. Together, our results suggest crosstalk secondary development evolution.

Language: Английский

Citations

12
Proteins and DNA Sequences Interacting with Tanshinones and Tanshinone Derivatives DOI Open Access
Piotr Szymczyk, M. Majewska, Jadwiga Nowak

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(2), P. 848 - 848

Published: Jan. 20, 2025

Tanshinones, biologically active diterpene compounds derived from Salvia miltiorrhiza, interact with specific proteins and DNA sequences, influencing signaling pathways in animals humans. This study highlights tanshinone–protein interactions observed at concentrations achievable vivo, ensuring greater physiological relevance compared to vitro studies that often employ supraphysiological ligand levels. Experimental data suggest while tanshinones multiple proteomic targets, only a few enzymes are significantly affected relevant concentrations. apparent paradox may be resolved by tanshinones’ ability bind influence involved gene expression or mRNA stability, such as RNA polymerase II human antigen R protein. These trigger secondary, widespread changes expression, leading complex alterations. Although the current understanding of remains incomplete, this provides foundation for deciphering molecular mechanisms underlying therapeutic effects S. miltiorrhiza diterpenes. Additionally, numerous tanshinone derivatives have been developed enhance pharmacokinetic properties biological activity. However, their safety profiles remain poorly characterized, limiting comprehensive insights into medicinal potential. Further investigation is essential fully elucidate toxicological both native modified tanshinones.

Language: Английский

Citations

0