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Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

ABSTRACT: Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

PROVIDER: PRJNA888981 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21851124_1.fastq.gz	Fastqsanger.gz
	SRR21851124_2.fastq.gz	Fastqsanger.gz
	SRR21851125_1.fastq.gz	Fastqsanger.gz
	SRR21851125_2.fastq.gz	Fastqsanger.gz
	SRR21851126_1.fastq.gz	Fastqsanger.gz

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Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

Project description:The nuclear matrix was identified as a nuclear fraction in eukaryotic cells that offers a supporting scaffold for chromatin. While the structure is known in plant nuclei for decades, the distribution of regions attaching at plant nuclei, and how the nuclear matrix influences chromatin status is largely unkown. Here, we identify novel proteins, FRS7 (FAR1 RELATED SEQUENCE 7) and FRS12, attaching chromatin regions at the nuclear matrix in Arabidopsis thaliana. We found the above two proteins cooperate with AHL22 (AT-hook Motif Nuclear Localized 22) in repress hypocotyl elongation, by recruiting chromatin regions and histone deacetylases to the nuclear matrix and silence the genes. These findings shed light on understanding regulation and roles of the nuclear matrix influence in epigenetic and transcriptional regulation in Arabidopsis.

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Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

Project description:Identification of novel proteins attaching chromatin regions at the nuclear matrix in Arabidopsis thaliana.

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Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5. Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day. Seedlings were then collected during periods of hypocotyl elongation and stasis for three days. There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates. In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study. Each sample consists of multiple pooled seedlings.

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Project description:Hypocotyl elongation is extensively controlled by hormone signaling networks. In particular, auxin metabolism and signaling play key roles in light-dependent hypocotyl growth. The nuclear matrix facilitates organization of DNA within the nucleus, and dynamic interactions between nuclear matrix and DNA are related to gene regulation. Conserved scaffold/matrix attachment regions (S/MARs) are anchored to the nuclear matrix by the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) proteins in Arabidopsis. Here, we found that ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 redundantly regulate auxin biosynthesis in the control of hypocotyl elongation. The light-inducible AHL proteins bind directly to an S/MAR region of the YUCCA 9 (YUC9) promoter and suppress its expression to inhibit hypocotyl growth in light-grown seedlings. In addition, they recruit the SWI2/SNF2-RELATED 1 (SWR1) complex and promote exchange of H2A with the histone variant H2A.Z at the YUC9 locus to further elaborately control auxin biosynthesis. Consistent with these results, the long hypocotyl phenotypes of light-grown genetic mutants of the AHLs and H2A.Z-exchanging components were suppressed by potent chemical inhibitors of auxin transport and YUC enzymes. These results suggest that the coordination of matrix attachment and chromatin modification underlies auxin biosynthesis in light-dependent hypocotyl growth.

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