Histone variants shape chromatin states in Arabidopsis

Jamge, Bhagyshree; Lorković, Zdravko J.; Axelsson, Elin; Osakabe, Akihisa; Shukla, Vikas; Yelagandula, Ramesh; Akimcheva, Svetlana; Khuen, Annika Luisa; Berger, Frédéric

doi:10.1101/2023.03.08.531698

Cited by 8 publications

(18 citation statements)

References 97 publications

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“…Consistent with ours (Fang et al 2020) and other reports (Qi et al 2022) among the top-hits we also found FLD (Figure 2A). Interestingly, one of the highest hits was the histone H2A.W.7, a variant exclusively found on constitutive heterochromatin (Lorković et al 2017, Jamge et al 2023, suggesting a generic role for APRF1 in co-transcriptional gene repression. Given this robust APRF1-LD interaction, we considered if LD could be the homolog of one of the yeast Swd2 partners in the CPF or the APT phosphatase modules (Casanal et al 2017, Lidschreiber et al 2018).…”

Section: Ref2/pnutsmentioning

confidence: 99%

A CPF-like phosphatase module links transcription termination to chromatin silencing

Mateo-Bonmatí

Fang

Maple

et al. 2023

Preprint

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RNA-mediated chromatin silencing plays important roles in development and environmental response in many organisms. However, it is still unclear how the RNA, and/or the transcriptional processes producing them, trigger chromatin silencing. Through the study of developmental timing in plants we have found co-transcriptional RNA processing modulates a chromatin regulatory mechanism controlling quantitative expression of Arabidopsis FLOWERING LOCUS C (FLC). Here, we show that the phosphatase module of the mRNA 3′ processing CPSF complex is central to this mechanism. The phosphatase module components APRF1 (yeast Swd2/human WDR82), TOPP4 (Glc7/PP1) and LD (which we show is functionally equivalent to Ref2/PNUTS) all function genetically downstream of the CPSF-mediated cleavage and polyadenylation and are necessary for chromatin modification that results in FLC transcriptional silencing. LD has been previously shown to stoichiometrically co-associate in vivo with the histone demethylase FLD. We show both proteins result in removal of H3K4 monomethylation in the central section of the FLC locus. This links transcription termination to delivery of chromatin modifications that then influence subsequent transcription. Thus, physical association of the CPSF phosphatase module with chromatin modifiers generates a transcription-coupled silencing mechanism. The conservation of the factors involved suggest this mechanism may be generally relevant to transcription-mediated chromatin silencing.

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Section: Ref2/pnutsmentioning

confidence: 99%

A CPF-like phosphatase module links transcription termination to chromatin silencing

Mateo-Bonmatí

Fang

Maple

et al. 2023

Preprint

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“…1, C and D). To further substantiate this perspective, we examined the accumulation of different histone marks and histone variants at Paf1C target genes (Jamge et al, 2023). Paf1C target genes were enriched in histone marks associated with active gene transcription, such as H3K4me3 and H3K36me3, while being depleted of the Polycomb -based H3K27me3 mark (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…ChIP-seq reads of H3, H3K4me3, H3K36me3, H3K27me3, and H2A.Z (GSE231408; samples GSM7075958, GSM7075959, GSM7075961, GSM7075962, GSM7075963, GSM7075964, GSM7075985, GSM7075986 and GSM7075990) (Jamge et al, 2023) were analysed as described in ChIP-seq analysis. MNase-seq reads of wild type Col-0 (GSE205110; samples GSM6205325 and GSM6205326) (Diego-Martín et al, 2022) were downloaded, processed and aligned as described in ChIP-seq analysis.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide evidence of the role of Paf1C in transcription elongation and histone H2B monoubiquitination inArabidopsis

Blanco-Touriñán,

Pérez-Alemany,

Bourbousse

et al. 2023

Preprint

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The evolutionarily conserved Paf1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNAPII progression through chromatin remodeling. To obtain evidence that Paf1C acts in transcription elongation inArabidopsis, we examined the genomic distribution of the ELF7 and VIP3 subunits of Paf1C. The occupancy of both subunits was confined to thousands of gene bodies and positively correlated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome-wide inelf7seedlings. Genome-wide profiling of RNAPII revealed that inelf7mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest that there is a direct functional link between Paf1C activity, mono-ubiquitination of histone H2B, and the transition of RNPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stably than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.

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“…For instance, those representing RNAP IV subunits or components of the microtubule assembly machinery typically have only one DEG in most species examined (Figure 3 and Figure S4). Importantly, histone variants are emerging as modulators of chromatin architecture (Borg et al, 2021;Bhagyshree et al, 2023). The histone proteins that we identified in this conserved cluster of enriched OGs are therefore strong candidates for determining the specific chromatin state of the endosperm.…”

Section: The Conserved Transcriptional Network Of the Angiosperm Seed...mentioning

confidence: 86%

“…Histone variants contribute to the definition of chromatin states and gene expression patterns. By modifying chromatin structure, they regulate the accessibility of DNA, influence gene expression, contribute to epigenetic inheritance, and participate in plant responses to environmental cues and developmental processes (Borg et al, 2021;Bhagyshree et al, 2023). Interestingly, histone variants were exclusively present in the shared protein network and not in any of the private sets of proteins specific to particular plant clades.…”

Section: Conserved Transcriptional Features Of the Angiosperm Endospermmentioning

confidence: 99%

Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants

Florez-Rueda,

Miguel,

Figueiredo

2023

Preprint

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SummaryThe evolutionary and ecological success of Spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the pre-development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world’s population. Here, using orthogroup inference, we provide a comparative transcriptomic analysis of seed nourishing tissues from representative species of all main angiosperm clades, including those of early diverging basal angiosperms, and of two gymnosperm representatives. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are exclusive to each clade, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in new functional studies.Significance StatementWithin seeds a specialized structure is responsible for nourishing the embryo, and is thus analogous to the mammalian placenta. Moreover, these nourishing tissues are also important sources of staple foods and feed. Here, we provide novel gene expression datasets of nourishing tissues of early diverging angiosperms, and use this information for a meta-analysis to identify pathways conserved, or divergent, throughout evolution. Thus, we aim to provide a resource for gene discovery for seed biology studies.

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Histone variants shape chromatin states in Arabidopsis

Cited by 8 publications

References 97 publications

A CPF-like phosphatase module links transcription termination to chromatin silencing

A CPF-like phosphatase module links transcription termination to chromatin silencing

Genome-wide evidence of the role of Paf1C in transcription elongation and histone H2B monoubiquitination inArabidopsis

Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants

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