Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Genomic DNA from Mature Seed Tissues

Iwasaki, Mayumi; Lopez‐Molina, Luis

doi:10.1007/978-1-0716-1134-0_22

Cited by 3 publications

(4 citation statements)

References 9 publications

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“…Isolation of embryos from seeds was performed as described by ref. 72 with minor modifications. Germinating seeds were placed between two microscope slides with a small drop of water which were rotated and squeezed together with gentle force until the embryos were released from within the seed.…”

Section: Methodsmentioning

confidence: 99%

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Tremblay,

Santini,

Cheng

et al. 2024

Nat Commun

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Translation of seed stored mRNAs is essential to trigger germination. However, when RNAPII re-engages RNA synthesis during the seed-to-seedling transition has remained in question. Combining csRNA-seq, ATAC-seq and smFISH in Arabidopsis thaliana we demonstrate that active transcription initiation is detectable during the entire germination process. Features of non-coding regulation such as dynamic changes in chromatin accessible regions, antisense transcription, as well as bidirectional non-coding promoters are widespread throughout the Arabidopsis genome. We show that sensitivity to exogenous ABSCISIC ACID (ABA) during germination depends on proximal promoter accessibility at ABA-responsive genes. Moreover, we provide genetic validation of the existence of divergent transcription in plants. Our results reveal that active enhancer elements are transcribed producing non-coding enhancer RNAs (eRNAs) as widely documented in metazoans. In sum, this study defining the extent and role of coding and non-coding transcription during key stages of germination expands our understanding of transcriptional mechanisms underlying plant developmental transitions.

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Section: Methodsmentioning

confidence: 99%

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Tremblay,

Santini,

Cheng

et al. 2024

Nat Commun

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“…RNA was extracted using RNeasy Plant Mini Kit (Qiagen, 74904). To extract RNA from mature and imbibed endosperm, 0.05 g seeds were imbibed for 1 (mature) or 24 h (24HAI), prior to purification of endosperm-enriched tissues as previously described 46 . In brief, seeds were squeezed with glass slides after imbibition.…”

Section: Methodsmentioning

confidence: 99%

A VEL3 histone deacetylase complex establishes a maternal epigenetic state controlling progeny seed dormancy

et al. 2023

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Mother plants play an important role in the control of dormancy and dispersal characters of their progeny. In Arabidopsis seed dormancy is imposed by the embryo-surrounding tissues of the endosperm and seed coat. Here we show that VERNALIZATION5/VIN3-LIKE 3 (VEL3) maintains maternal control over progeny seed dormancy by establishing an epigenetic state in the central cell that primes the depth of primary seed dormancy later established during seed maturation. VEL3 colocalises with MSI1 in the nucleolus and associates with a histone deacetylase complex. Furthermore, VEL3 preferentially associates with pericentromeric chromatin and is required for deacetylation and H3K27me3 deposition established in the central cell. The epigenetic state established by maternal VEL3 is retained in mature seeds, and controls seed dormancy in part through repression of programmed cell death-associated gene ORE1. Our data demonstrates a mechanism by which maternal control of progeny seed physiology persists post-shedding, maintaining parental control of seed behaviour.

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“…RNA was extracted using RNeasy Plant Mini Kit (Qiagen, 74904). To extract RNA from mature and imbibed endosperm, 0.5g seeds were imbibed for 1hour (mature) or 24hours (24HAI), prior to purification of endosperm enriched tissues as previously described 47 . RNA was extracted using the borate method 48 .…”

Section: Methodsmentioning

confidence: 99%

“…For H3K27me3 ChIP-seq, at maturation stage, endosperm of Col0 and vel3-1 was purified from 0.5g seeds after 1 hour imbibition as previously described 47 . Endosperm tissue were cross-linked in 1% formaldehyde solution for 15min and quenched with 0.125M glycine for 5min.…”

Section: Chip-seq and Chip-qpcrmentioning

confidence: 99%

A histone deacetylase complex establishes a transgenerationally inherited maternal epigenetic state controlling progeny seed dormancy

Chen

MacGregor

Stefanato

et al. 2022

Preprint

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Mother plants play an important role in the control of dormancy and dispersal characters of their progeny. In Arabidopsis seed dormancy is imposed by the embryo-surrounding tissues of the endosperm and seed coat. Here we show that the VERNALIZATION5/VIN3-LIKE 3 (VEL3) gene maintains maternal control over progeny seed dormancy by establishing an epigenetic state early in endosperm development that primes the depth of primary seed dormancy later established during seed maturation. VEL3 relocates MSI1 to the nucleolus and associates with other components of the histone deacetylase complex (HDAC), and is required for gene repression via PRC2 and HDAC at pericentromeric regions established in the central cell. Interestingly, the epigenetic state established by the maternal VEL3 is retained trans-generationally in mature seeds, and controls seed dormancy through the repression of programmed cell death-associated gene ORE1. Our data demonstrates a novel mechanism by which maternal control of progeny seed physiology persists post-shedding, maintaining parental control of seed behaviour.

show abstract

Arabidopsis thaliana Mature Endosperm Dissection and Isolation of Genomic DNA from Mature Seed Tissues

Cited by 3 publications

References 9 publications

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

A VEL3 histone deacetylase complex establishes a maternal epigenetic state controlling progeny seed dormancy

A histone deacetylase complex establishes a transgenerationally inherited maternal epigenetic state controlling progeny seed dormancy

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