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Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

ABSTRACT: We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE49382 | GEO | 2013/12/23

SECONDARY ACCESSION(S): PRJNA213871

REPOSITORIES: GEO

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Dynamic changes of Arabidopsis cis-NAT pairs during de-etiolation

Project description:We systematically identified long noncoding natural antisense transcripts (lncNATs), defined as lncRNAs transcribed from the opposite DNA strand of coding or noncoding genes. We identified in total 37,238 sense-antisense transcript pairs and found 70% mRNAs are associated with antisense transcripts in Arabidopsis. To investigate the role of NATs in response to white light treatment, we designed an Agilent custom array, ATH NAT array, and analyzed WT seedlings grown in the dark (0h) and seedlings undergoing de-etiolation in continuous white light for 1h and 6h. To obtain information on organ-specific transcriptome profiles, we further dissected seedlings into cotyledons, hypocotyls and roots. We examined the abundance of NATs in etiolated seedlings and seedlings undergoing de-etiolation in continuous white light for 1/6h. Seedlings were further dissected into cotyledons, hypocotyls and roots. RNAs from 3 biological replicates of each of the 3 organs were separately hybridized to ATH NAT arrays to profile light-regulated NAT pairs.

2013-12-23 | E-GEOD-49382 | biostudies-arrayexpress

Expression data from Arabidopsis during de-etiolation

Project description:Arabidopsis fc2-1 mutants fail to properly de-etiolate after a prolonged period in the dark. Our goal was to monitor whole genome expression during the first 2 hours of de-etiolation to determine the cuase of this growth arrest. In comparison with other mutants that also affect de-etiolation, we identified a subset of genes specifically regulated by FC2 function during de-etiolation. Seedlings were grown in the dark for 4 days and then exposed to white light for 30 or 120 minutes to initiate de-etiolation and photomorphogenesis

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Project description:Long intergenic noncoding RNAs (lincRNAs), Natural Antisense Transcripts (NATs), and microRNAs (miRNAs) play important roles in many biological processes. To profile circadian regulated long noncoding RNAs (lncRNAs), we grow Arabidopsis plants (Col-0) under short day SD (8h light/16h dark) condition and used the ATH lincRNA v1 array to profile lincRNA, NAT and miRNA gene expression under continuous light condition. Using JTK_CYCLE to search for cycling expression pattern of genes, we found ~900 genes encoding lincRNAs, NATs and miRNAs showed significant cycling expression patterns (Adjusted P-value < 0.05).

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Tissue specific light response during Arabidopsis de-etiolation

Project description:The time between seed germination and the development of the first true leaves is crucial for plants success. Depending on the environmental light conditions a plant must decide which developmental program to use. If light is limited, the seedling will use etiolated growth characterized by an elongated hypocotyl and tightly-closed, underdeveloped cotyledons, thus allowing it to reach a light source as quickly as possible. In contrast, seedlings that are grown in unlimited light will use de-etiolation growth, that is characterized by inhibited hypocotyl growth and unhooked, unfolded and fully expanded cotyledons. These seedlings become photosynthetic and increase their chances for reproduction. Interestingly, the outcome of the light signal varies between the seedling’s different organs, e.g. hypocotyl growth is inhibited by light whereas cotyledon expansion is induced. Separating the cotyledons and hypocotyls of de-etiolated seedlings during their first 12 hours of white light exposure, enabled us to perform individual transcriptome analyses of each organ and to examine what causes this variation in light responsiveness.

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Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots

2013-12-23 | GSE49381 | GEO

Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots

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Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [RNA-seq]

Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.

2019-03-28 | GSE115584 | GEO

Light releases the TCP4-SAUR16/50 transcription module from the repression of PIF3 to facilitate cotyledon opening during de-etiolation [ChIP-Seq]

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Transcriptome Analyses of Two Hybrid Citrus Cultivars in Seedlings Etiolation

Project description:Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30 (sequencing error rate, 0.1%). 124,952 unigenes were finally generated with a mean length of 1,189 bp. Of these unigenes, 98,904 (79.15%), 105,408 (84.35%), 42,016 (33.62%), 78,872 (63.12%), 72,068 (57.67%), 72,464 (57.99%), 72464 (57.99%) and 46,308 (37.06%) had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes (DEGs) in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Functional classification of the DEGs in two cultivars using GO term indicated that biological process, cellular component and molecular function were three major groups. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan, and advance our knowledge of the genes involved in the complex regulatory networks of seedling etiolation.

2017-06-13 | GSE90935 | GEO

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Project description:Naturally occurring Antisense Transcripts (NATs) compose an emerging group of regulatory RNAs. These regulatory elements appear in all organisms examined, but little is known about global expression of NATs in fungi. Analysis of currently available EST sequences suggests that 352 cis NATs are present in Aspergillus flavus. An Affymetrix GeneChip® microarray containing probes for these cis NATs, as well as all predicted genes in A. flavus, allowed a whole genome expression analysis of these elements in response to two ecologically important temperatures for the fungus. RNA expression analysis showed that 32 NATs and 2709 genes were differentially expressed between 37°C, the optimum temperature for growth, and 28°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. These NATs correspond to sense genes with diverse functions including transcription initiation, carbohydrate processing and binding, temperature sensitive morphogenesis, and secondary metabolism. This is the first report of a whole genome transcriptional analysis of NAT expression in a fungus and shows that although less than 10% of putative NATs are differentially expressed in response to temperature, some of the NAT-cis gene interactions are likely to be important. Keywords: temperature response

2009-03-25 | GSE12594 | GEO

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