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Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

ABSTRACT: Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

PROVIDER: PRJNA818631 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18430263_1.fastq.gz	Fastqsanger.gz
	SRR18430263_2.fastq.gz	Fastqsanger.gz
	SRR18430264_1.fastq.gz	Fastqsanger.gz
	SRR18430264_2.fastq.gz	Fastqsanger.gz
	SRR18430265_1.fastq.gz	Fastqsanger.gz

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Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice.

Project description:Purpose: To understand the miRNAome changes during coleoptile senescence, small RNA libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. Total four small RNA libraries of coleoptile senescence were constructed and high-throughput sequencing was performed using Illumina GA IIx system . . Results: Small RNA sequencing identified forty-one known and twenty-one novel miRNAs that were differentially expressed during coleoptile senescence. Integration of expression data of transcriptome and miRNAome identified 148 miRNA-mRNA modules, mainly comprised of miRNAs regulating TFs, signaling-associated factors and transporters, thereby demonstrating multi-tiered regulation of coleoptile senescence. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

2022-07-21 | GSE199238 | GEO

Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

Project description:Purpose: To understand the transcriptional changes during coleoptile senescence, transcriptome libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. mRNA libraries were generated and sequenced as 101 bp paired-end reads by using Illumina Hiseq 4000. Results: Our analysis revealed that 3166 transcripts were differentially expressed in senescing coleoptile (Day 2) samples as compared to the control. Furthermore, 44 and 273 transcripts showed specific expression in control and day 2 samples, respectively. From the functional category analysis, we observed that 197, 182, 99 and 88 transcripts belonging to signalling, transcription factors, hormone signalling and transporters respectively were differentially expressed during coleoptile senescence . And 15, 12, 3, and 6 transcripts showed senescence specific expression patterns in the transporters, transcription factors, signalling and hormone signalling categories respectively. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

2022-07-21 | GSE199139 | GEO

Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice.

Project description:Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice.

| PRJNA819015 | ENA

Integrated transcriptomics and miRNAomics provide insights into the complex multi-tiered regulatory networks associated with coleoptile senescence in rice.

Project description:Coleoptile is the small conical, short-lived, sheath-like organ that safeguards the first leaf and shoot apex in cereals. It is also the first leaf-like organ to senesce that provides nutrition to the developing shoot and is, therefore, believed to play a crucial role in seedling establishment in rice and other grasses. Though histochemical studies have helped in understanding the pattern of cell death in senescing rice coleoptiles, genome-wide expression changes during coleoptile senescence have not yet been explored. With an aim to investigate the gene regulation underlying the coleoptile senescence (CS), we performed a combinatorial whole genome expression analysis by sequencing transcriptome and miRNAome of senescing coleoptiles. Transcriptome analysis revealed extensive reprogramming of 3439 genes belonging to several categories, the most prominent of which encoded for transporters, transcription factors (TFs), signaling components, cell wall organization enzymes, redox homeostasis, stress response and hormone metabolism. Small RNA sequencing identified 41 known and 21 novel miRNAs that were differentially expressed during CS. Comparison of gene expression and miRNA profiles generated for CS with publicly available leaf senescence (LS) datasets revealed that the two aging programs are remarkably distinct at molecular level in rice. Integration of expression data of transcriptome and miRNAome identified high confidence 140 miRNA-mRNA pairs forming 42 modules, thereby demonstrating multi-tiered regulation of CS. The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

| S-EPMC9597502 | biostudies-literature

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

Project description:Normally, rice can elongate the coleoptile under submerged condition. However, reduced adh activity (rad) mutant cannot elongate the coleoptile under submergence. To investigate the change in gene expression, we performed microarray analysis. In this analysis, we used 1 day old seedling of rice. But it is difficult to isolate only coleoptile from rice embryo without any contamination in this stage. Therefore, we applied laser microdissection (LM) technique to this microarray. By use of LM, we isolated coleoptile from rice embryo and use for microarray analysis. As the results, we found that the differences in the gene expression profiles of coleoptile between wild type and rad mutant.

2011-04-07 | GSE26632 | GEO

Transcriptome profiles of the rice coleoptile of wild type and reduced adh activity (rad) mutant

2011-04-07 | E-GEOD-26632 | biostudies-arrayexpress

Transcript Profiling of the Aerobic and Anoxic Rice Coleoptile

Project description:Rice (Oryza sativa L.) seeds can germinate in complete absence of oxygen. Under anoxia, the rice coleoptile elongates, reaching a length greater than that of the aerobic one. In this series, we compare the transcriptome of rice coleoptiles grown under aerobic and anaerobic conditions. Lasanthi-Kudahettige, R, et. al. Plant Physiology (2007). Transcript Profiling of the Anoxic Rice Coleoptile. Keywords: stress response

2007-03-19 | GSE6908 | GEO

The effect of Ras on the signalling networks in senescence

Project description:Activated Ha-ras was introduced to HMF3A cells. HMF3A cells are conditionally immortalised human mammary fibroblasts. They undergo co-ordinated senescence upon inactivation of LT antigen, when cultured at 39C. The introduction of Ras did not prevent this but affected the molecular profile. Keywords = Senescence Keywords = fibroblast Keywords = Ras Keywords = immortalization Keywords = transformation

2010-06-09 | E-GEOD-979 | biostudies-arrayexpress

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots.

Project description:Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice's cold-stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold-stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold-stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

| S-EPMC7369714 | biostudies-literature

Integrated multi-omics approach revealed cellular senescence landscape

Project description:Cellular senescence is a complex multifactorial biological phenomenon that plays essential roles in aging, and aging-related diseases. During this process, the senescent cells undergo gene expression altering and chromatin structure remodeling. However, studies on the epigenetic landscape of senescence using integrated multi-omics approaches are limited. In this research, we performed ATAC-seq, RNA-seq, and ChIP-seq on different senescent types to reveal the landscape of senescence and identify the prime regulatory elements.

2022-08-15 | GSE210285 | GEO

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