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ABSTRACT: rice cold treatment RNA-seq

PROVIDER: PRJNA1102144 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28741178_1.fastq.gz	Fastqsanger.gz
	SRR28741178_2.fastq.gz	Fastqsanger.gz
	SRR28741179_1.fastq.gz	Fastqsanger.gz
	SRR28741179_2.fastq.gz	Fastqsanger.gz
	SRR28741180_1.fastq.gz	Fastqsanger.gz

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Project description:Cold is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in plants. R-loops can function in a series of biological processes, including normal development and stress responses, in plants. However, how R-loops function in cold responses is still largely unknown in plants, especially in cold sensitive rice. Herein, we conducted DRIP-seq in combination with other newly generated omics data (RNA-seq, DNase-seq, ChIP-seq and MNase-seq) in rice with or without cold treatment. We found that cold treatment caused R-loop dynamics across the genome, indicating that R-loops are cold sensitive non-B DNA structures. Moreover, cold biased R-loops had high GC content and novel motifs the binding of distinct TFs as compared to CK biased R-loops, indicative of occurrence of differential biological implications of R-loop dynamics in response to cold stress. More importantly, we for the first time to provide evidence showing that, in addition to the direct involvement of R-loops in the regulation of cold-responsive gene transcription, R-loops can indirectly modulate transcription of subsets of cold-responsive genes through R-loop overlapping TF-centered or cis-regulatory element related regulatory networks and lncRNAs in rice. Thus, our study for the first time provides evidence showing functions of R-loop dynamics in rice cold responses. It also provides some potential R-loop loci for genetic and epigenetic manipulation towards breeding of enhanced cold tolerance rice varieties.

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Project description:Purpose: In this study, RNA-seq was used to analyzed the molecular mechanism of cold tolerance in rice Methods: Rice 9311 (cold intolerant) and DC907 (cold tolerant) were used as experimental materials for transcriptome sequencing on Illumina HIseq platform. Fastq is used to evaluate the quality of the original data, and NGS QC Toolkit is used to filter the original data to obtain clean reads. Clean reads were compared to the rice 9311 reference genome using HISAT2 software. Put the genome mapping results of all sequenced reads data together, assemble them with cufflinks, and then compare them with known gene models with cuffcompare. The gene expression level of each sample was analyzed by HTSeq software. All treatments were analyzed for differential expression using DEseq. Results: A total of 36 samples were used for RNA sequencing analysis, with three biological replicates per treatment. Each sample generates at least 2G data. The genes regulated by cold stress treatment (1,3 days) and recovery treatment (1,3 days) were determined by comparative analysis.

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