Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

Montgomery, Sean A.; Tanizawa, Yasuhiro; Gálik, Bence; Wang, Nan; Ito, Tasuku; Mochizuki, Takako; Akimcheva, Svetlana; Bowman, John L.; Cognat, Valérie; Maréchal-Drouard, Laurence; Ekker, Heinz; Hong, Syuan Fei; Kohchi, Takayuki; Lin, Shih Shun; Liu, Li Yu Daisy; Nakamura, Yasukazu; Valeeva, Lia R.; Shakirov, Eugene V.; Shippen, Dorothy E.; Wei, Wei Lun; Yagura, Masaru; Yamaoka, Shohei; Yamato, Katsuyuki T.; Liu, Chang; Berger, Frédéric

doi:10.1016/j.cub.2019.12.015

Cited by 176 publications

(186 citation statements)

References 113 publications

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“…An intriguing puzzle to solve in the near future is how H3K27me3 can confer instability on a molecular level, and why this mechanism evolved over evolutionary timescales. While functional studies on the molecular mechanism are still lacking, a recent study on early land plants suggested that H3K27me3 together with H3K9me3 might represent an ancient form of genome defense mechanism against transposons [156]. Regions enriched with H3K9me2/3 and DNA cytosine methylation are usually AT-and repeat-rich, and movement of H3K27me3 to these regions in absence of H3K9me3 hints to a compensatory genome defense mechanism that was previously proposed to act in animals [152].…”

Section: Evolution Of H3k27me3-dependent Transcriptional Silencing Frmentioning

confidence: 99%

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Ridenour

Möller

Freitag

2020

Genes

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Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.

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Section: Evolution Of H3k27me3-dependent Transcriptional Silencing Frmentioning

confidence: 99%

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Ridenour

Möller

Freitag

2020

Genes

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“…TEs are maintained in silent form either by changes in the chromatin structure or directly by cytosine methylation of their sequences in CG, CHG and CHH contexts [52]. DNA methylation in a CHH context is the signature of RNA-directed DNA methylation, RdDM [53,54].…”

Section: Consequences Of Te Location and Sirna Production Nearby In Gmentioning

confidence: 99%

Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

Guyot

Bocs

et al. 2020

IJMS

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The natural rubber biosynthetic pathway is well described in Hevea, although the final stages of rubber elongation are still poorly understood. Small Rubber Particle Proteins and Rubber Elongation Factors (SRPPs and REFs) are proteins with major function in rubber particle formation and stabilization. Their corresponding genes are clustered on a scaffold1222 of the reference genomic sequence of the Hevea brasiliensis genome. Apart from gene expression by transcriptomic analyses, to date, no deep analyses have been carried out for the genomic environment of SRPPs and REFs loci. By integrative analyses on transposable element annotation, small RNAs production and gene expression, we analysed their role in the control of the transcription of rubber biosynthetic genes. The first in-depth annotation of TEs (Transposable Elements) and their capacity to produce TE-derived siRNAs (small interfering RNAs) is presented, only possible in the Hevea brasiliensis clone PB 260 for which all data are available. We observed that 11% of genes are located near TEs and their presence may interfere in their transcription at both genetic and epigenetic level. We hypothesized that the genomic environment of rubber biosynthesis genes has been shaped by TE and TE-derived siRNAs with possible transcriptional interference on their gene expression. We discussed possible functionalization of TEs as enhancers and as donors of alternative transcription start sites in promoter sequences, possibly through the modelling of genetic and epigenetic landscapes.

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“…We followed the nomenclature of genes, proteins, and mutants of Marchantia reported in Bowman et al 66 . Gene IDs were taken from MarpolBase (http://marchantia.info/), genome version 3.1 and version 5.1 27,67 .…”

mentioning

confidence: 99%

The liverwort oil body is formed by redirection of the secretory pathway

et al. 2020

Self Cite

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Eukaryotic cells acquired novel organelles during evolution through mechanisms that remain largely obscure. The existence of the unique oil body compartment is a synapomorphy of liverworts that represents lineage-specific acquisition of this organelle during evolution, although its origin, biogenesis, and physiological function are yet unknown. We find that two paralogous syntaxin-1 homologs in the liverwort Marchantia polymorpha are distinctly targeted to forming cell plates and the oil body, suggesting that these structures share some developmental similarity. Oil body formation is regulated by an ERF/AP2-type transcription factor and loss of the oil body increases M. polymorpha herbivory. These findings highlight a common strategy for the acquisition of organelles with distinct functions in plants, via periodical redirection of the secretory pathway depending on cellular phase transition.

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Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

Cited by 176 publications

References 113 publications

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi

Structural and Functional Annotation of Transposable Elements Revealed a Potential Regulation of Genes Involved in Rubber Biosynthesis by TE-Derived siRNA Interference in Hevea brasiliensis

The liverwort oil body is formed by redirection of the secretory pathway

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