Regulation of Gene Expression during Seed Development in Flowering Plants

Arabidopsis seed development involves maternal small interfering RNAs (siRNAs) that induce RNA-directed DNA methylation (RdDM) through the NRPD1-mediated pathway. To investigate their biological functions, we characterized siRNAs in the endosperm and seed coat that were separated by laser-capture microdissection (LCM) in reciprocal genetic crosses with an nrpd1 mutant. We also monitored the spatial-temporal activity of the NRPD1-mediated pathway on seed development using the AGO4:GFP::AGO4 (promoter:GFP::protein) reporter and promoter:GUS sensors of siRNA-mediated silencing. From these approaches, we identified four distinct groups of siRNA loci dependent on or independent of the maternal NRPD1 allele in the endosperm or seed coat. A group of maternally expressed NRPD1-siRNA loci targets endosperm-preferred genes, including those encoding AGAMOUS-LIKE (AGL) transcription factors. Using translational promoter:AGL::GUS constructs as sensors, we demonstrate that spatial and temporal expression patterns of these genes in the endosperm are regulated by the NRPD1-mediated pathway irrespective of complete silencing (AGL91) or incomplete silencing (AGL40) of these target genes. Moreover, altered expression of these siRNA-targeted genes affects seed size. We propose that the corresponding maternal siRNAs could account for parent-of-origin effects on the endosperm in interploidy and hybrid crosses. These analyses reconcile previous studies on siRNAs and imprinted gene expression during seed development.

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Correction for Kirkbride et al., Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development inArabidopsis

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1904996116 ◽

2019 ◽

Vol 116 (17) ◽

pp. 8633-8633

Keyword(s):

Gene Expression ◽

Seed Development ◽

Small Rnas ◽

Regulation Of Gene Expression ◽

Temporal Regulation

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Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales) reveal dynamic expression of DNA and histone methylation modifiers

10.1101/2021.04.04.438399 ◽

2021 ◽

Author(s):

Rebecca A. Povilus ◽

William E. Friedman

Keyword(s):

Gene Expression ◽

Seed Development ◽

Histone Methylation ◽

Expression Patterns ◽

Flowering Plants ◽

Model Systems ◽

Crop Species ◽

Water Lily ◽

Angiosperm Evolution ◽

Genetic Imprinting

AbstractStudies of gene expression during seed development have been performed for a growing collection of species from a phylogenetically broad sampling of flowering plants (angiosperms). However, attention has mostly been focused on crop species or a small number of ‘model’ systems. Information on gene expression during seed development is minimal for those angiosperm lineages whose origins predate the divergence of monocots and eudicots. In order to provide a new perspective on the early evolution of seed development in flowering plants, we sequenced transcriptomes of whole ovules and seeds from three key stages of reproductive development in the waterlily Nymphaea thermarum, an experimentally-tractable member of the Nymphaeales. We first explore general patterns of gene expression, beginning with mature ovules and continuing through fertilization into early- and mid-seed development. We then examine the expression of genes associated with DNA and histone methylation – processes known to be essential for development in distantly-related and structurally-divergent monocots and eudicots. Around 60% of transcripts putatively homologous to DNA and histone methylation modifiers are differentially expressed during seed development in N. thermarum, suggesting that the importance of dynamic epigenetic patterning during seed development dates to the earliest phases of angiosperm evolution. However, genes involved in establishing, maintaining, and removing methylation marks associated with genetic imprinting show a mix of conserved and unique expression patterns between N. thermarum and other flowering plants. Our data suggests that the regulation of imprinting has likely changed throughout angiosperm evolution, and furthermore identifies genes that merit further characterization in any angiosperm system.

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Regulation of Gene Expression Programs during Arabidopsis Seed Development: Roles of the ABI3 Locus and of Endogenous Abscisic Acid

The Plant Cell ◽

10.2307/3869944 ◽

1994 ◽

Vol 6 (11) ◽

pp. 1567 ◽

Cited By ~ 4

Author(s):

Francois Parcy ◽

Christiane Valon ◽

Monique Raynal ◽

Pascale Gaubier-Comella ◽

Michel Delseny ◽

...

Keyword(s):

Gene Expression ◽

Abscisic Acid ◽

Seed Development ◽

Regulation Of Gene Expression ◽

Arabidopsis Seed ◽

Endogenous Abscisic Acid

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Linking transcription, RNA polymerase II elongation and alternative splicing

Biochemical Journal ◽

10.1042/bcj20200475 ◽

2020 ◽

Vol 477 (16) ◽

pp. 3091-3104 ◽

Cited By ~ 1

Author(s):

Luciana E. Giono ◽

Alberto R. Kornblihtt

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Rna Polymerase Ii ◽

Environmental Changes ◽

Transcription Elongation ◽

Single Gene ◽

Regulation Of Gene Expression ◽

Regulation Of Transcription ◽

Stepping Stones ◽

Eukaryotic Transcription

Gene expression is an intricately regulated process that is at the basis of cell differentiation, the maintenance of cell identity and the cellular responses to environmental changes. Alternative splicing, the process by which multiple functionally distinct transcripts are generated from a single gene, is one of the main mechanisms that contribute to expand the coding capacity of genomes and help explain the level of complexity achieved by higher organisms. Eukaryotic transcription is subject to multiple layers of regulation both intrinsic — such as promoter structure — and dynamic, allowing the cell to respond to internal and external signals. Similarly, alternative splicing choices are affected by all of these aspects, mainly through the regulation of transcription elongation, making it a regulatory knob on a par with the regulation of gene expression levels. This review aims to recapitulate some of the history and stepping-stones that led to the paradigms held today about transcription and splicing regulation, with major focus on transcription elongation and its effect on alternative splicing.

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