Identification of cold-inducible microRNAs in plants by transcriptome analysis

Zhou, Xuefeng; Wang, Guandong; Sutoh, Keita; Zhu, Jian‐Kang; Zhang, Weixiong

doi:10.1016/j.bbagrm.2008.04.005

Cited by 281 publications

(202 citation statements)

References 71 publications

Supporting

Mentioning

192

Contrasting

Unclassified

Order By: Relevance

“…Baldwin, unpublished data), suggesting smRNA-mediated regulation of WRKY TFs. Conversely, several miRNA gene promoters are highly abundant in W box sequences, implicating WRKY TFs in their activation/repression (Zhou et al, 2008). Further evidence of a WRKY-smRNA interactome comes from our studies on AtWRKY18 and -40 in modulating responses to powdery mildew (S.P.…”

Section: Regulation Via Other Tfs and Proteinsmentioning

confidence: 84%

The Role of WRKY Transcription Factors in Plant Immunity

2009

View full text Add to dashboard Cite

Section: Regulation Via Other Tfs and Proteinsmentioning

confidence: 84%

The Role of WRKY Transcription Factors in Plant Immunity

2009

View full text Add to dashboard Cite

“…In addition, RNAs appearing only under extreme environmental conditions may well have escaped previous annotation efforts. Especially in the light of the growing appreciation of the roles of non-coding RNAs, a more unbiased detection of stress-induced changes of the Arabidopsis transcriptome is of great importance (Sunkar and Zhu, 2004;FrancoZorrilla et al, 2007;Reyes and Chua, 2007;Liu et al, 2008;Zhou et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

et al. 2009

View full text Add to dashboard Cite

SUMMARYThe responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.

show abstract

“…Recently, expression profiles of all known miRNAs under cold stress in Arabidopsis, poplar and rice were validated with microarray analyses. [19,24,28] Zhou et al [7] established a machinelearning transcriptome-based approach for annotating cold-inducible miRNAs in Arabidopsis. They found that miR165/166, miR169, miR172, miR393, miR396 and miR397 were over expressed in cold stress.…”

Section: Introductionmentioning

confidence: 99%

Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars

Koç

Filiz

Tombuloğlu

2015

Biotechnology & Biotechnological Equipment

View full text Add to dashboard Cite

MircroRNAs (miRNAs) are small non-coding RNAs about 21 nt in length. These short transcripts regulate developmental and stress responses in plants. Cold stress is one of the most restraining abiotic factors adversely affecting the plant yield. In the present study, some cold stress-related miRNAs (miR167, miR169, miR172, miR393 and miR397) in tomato (Solanum lycopersicum) were assessed at early time points (0, 1, 4 and 16 h) of cold exposure. Relative expression of miRNAs was measured by stemÀloop quantitative reverse transcription polymerase chain reaction. The results showed that miR167, miR169, miR172 and miR393 were activated in the early time points of cold treatment. Especially, miR172 was found to have highest expression level. Furthermore, target genes of selected miRNAs were identified and their expression profiles were assessed between cold-sensitive and cold-tolerant cultivars of tomato. It was found that inferred expression patterns of target genes were differentiated between the cultivars. Analysis of cis-acting elements showed that miRNAs had stress-responsive elements. Meanwhile, since no miR393 sequence is available, putative miR393 sequence and its secondary structure were predicted in tomato. These results may provide a framework for further analysis in terms of understanding the response of miRNAs against cold stress in tomato.

show abstract

Identification of cold-inducible microRNAs in plants by transcriptome analysis

Cited by 281 publications

References 71 publications

The Role of WRKY Transcription Factors in Plant Immunity

The Role of WRKY Transcription Factors in Plant Immunity

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

Assessment of miRNA expression profile and differential expression pattern of target genes in cold-tolerant and cold-sensitive tomato cultivars

Contact Info

Product

Resources

About