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ABSTRACT: ATAC analysis of Disanthus cercidifolius var. longipes

PROVIDER: PRJNA1223964 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32355289_1.fastq.gz	Fastqsanger.gz
	SRR32355289_2.fastq.gz	Fastqsanger.gz
	SRR32355290_1.fastq.gz	Fastqsanger.gz
	SRR32355290_2.fastq.gz	Fastqsanger.gz

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Integration of Transcriptomic and Metabolomic Analysis Reveals Possible Molecular Mechanisms of Leaf Growth and Development in Disanthus cercidifolius var. longipes

Project description:Disanthus cercidifolius var. longipes is an important but rare tree species used in plant studies due to its highly ornamental leaves. However, its sciophilous nature and low photosynthetic efficiency make it difficult to cultivate on a large scale. In this study, we collected leaves of D. cercidifolius var. longipes at three developmental stages to assess its photosynthetic capacity and photoprotection mechanisms. Primary metabolites were quantified and separate and joint analyses of the transcriptome and metabolome were carried out. Our results revealed significant changes in the contents of flavonoids, free amino acids, and other substances during development. Metabolome and transcriptome analyses showed that the photosynthesis-related pathways changed rapidly, increasing at first and then decreasing. Under low photosynthetic capacity, flavonoids and anthocyanins were synthesized to achieve photoprotection, with synthesis of these compounds and other pathway-related genes and metabolites showing a significant increase. Total flavonoids also followed this trend. Our findings provide insights into the shade-loving plant's photoprotection mechanisms and nutrient synthesis strategy, which involve quick nutrient production over a short period. This study could aid in developing D. cercidifolius var. longipes into a street or foliage tree through selective breeding.

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Integration of Transcriptomic and Metabolomic Analysis Reveals Possible Molecular Mechanisms of Leaf Growth and Development in Disanthus cercidifolius var. longipes

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Exploring the var gene interactome with CRISPR/dCas9

Project description:Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum. var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown. Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus. Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.

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