Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

Pang, Mingxiong; Woodward, Andrew W.; Agarwal, Vikram; Guan, Xueying; Ha, Misook; Ramachandran, Vanitharani; Chen, Xuemei; Triplett, Barbara A.; Stelly, David M.; Chen, Z Jeffrey

doi:10.1186/gb-2009-10-11-r122

Cited by 137 publications

(163 citation statements)

References 73 publications

(124 reference statements)

Supporting

Mentioning

147

Contrasting

Order By: Relevance

“…S1 in the supplementary material, RNAs isolated from wildtype (Ler) and lug-3 inflorescence tissues were enriched for small RNAs, labeled with Cy5, and hybridized to a custom-designed miRNA chip as described (Pang et al, 2009). Average expression values were first normalized against internal positive controls (tRNAs) before they were compared between wild type and lug-3.…”

Section: Rna Expressionmentioning

confidence: 99%

LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers

et al. 2011

Self Cite

View full text Add to dashboard Cite

SUMMARYCentral to the ABCE model of flower development is the antagonistic interaction between class A and class C genes. The molecular mechanisms underlying the A-C antagonism are not completely understood. In Arabidopsis thaliana, miR172 is expressed in the inner floral whorls where it downregulates the class A gene APETALA 2 (AP2). However, what controls this predominantly inner whorl-specific expression of miR172 is not known. We show that the LEUNIG (LUG) and SEUSS (SEU) corepressors repress miR172 expression in the outer whorls of A. thaliana flowers. The recruitment of LUG/SEU to the miR172 promoters is dependent on AP2, suggesting that AP2 represses the expression of its cognate microRNA. Our study provides new insights into the molecular mechanisms underlying the A-C antagonism and shed light on the transcriptional regulation of miR172 during flower development.

show abstract

Section: Rna Expressionmentioning

confidence: 99%

LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers

et al. 2011

Self Cite

View full text Add to dashboard Cite

show abstract

“…Numerous studies have investigated cotton miRNAs and their regulatory functions in developmental processes of cotton fibers [6][7][8][9][10]. Especially, the high throughput RNA-sequence technology was employed to identify 562 candidate miRNAs from 7-DPA fibers of allotetraploid cotton [9], while cotton DD-genome shotgun sequences were examined to annotate 348 miRNA candidate sequences [2].…”

mentioning

confidence: 99%

High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

Wang

Ding

et al. 2015

Sci. China Life Sci.

View full text Add to dashboard Cite

MicroRNAs (miRNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of miRNAs have been identified in cotton fibers, the functions of miRNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis (DPA) and was subjected to high-throughput sequencing. A total of 95 known miRNAs were detected to be expressed in cotton seeds. The expression pattern of these identified miRNAs was profiled and 48 known miRNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel miRNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known miRNAs were successfully predicted and 900 expressed sequence tag (EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, miRNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5′ RACE. This study is the first to show the regulatory network of miRNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these miRNAs in seed development.Gossypium hirsutum, seed development, microRNA (miRNA), target gene, GO annotation, high-throughput sequencing Citation:Wang YM, Ding Y, Yu DW, Xue W, Liu JY. High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds. Sci China Life Sci, 2015, 58: 778 -786,

show abstract

“…Using Illumina sequencing, Morin et al (2008b) identified 334 known plus 104 novel miRNA genes expressed in human embryonic stem cells, while Glazov et al (2008) detected 449 novel and all known chicken miRNAs in the chicken embryo. In addition, small RNA profilings in locust, Xenopus tropicalis (Armisen et al, 2009), C. elegans embryos (Stoeckius et al, 2009) and Gossypium hirsutum L (Pang et al, 2009) have also been reported.…”

Section: Small Rna Analysismentioning

confidence: 98%

The next-generation sequencing technology and application

et al. 2010

View full text Add to dashboard Cite

As one of the key technologies in biomedical research, DNA sequencing has not only improved its productivity with an exponential growth rate but also been applied to new areas of application over the past few years. This is largely due to the advent of newer generations of sequencing platforms, offering ever-faster and cheaper ways to analyze sequences. In our previous review, we looked into technical characteristics of the nextgeneration sequencers and provided prospective insights into their future development. In this article, we present a brief overview of the advantages and shortcomings of key commercially available platforms with a focus on their suitability for a broad range of applications.

show abstract

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

Abstract: Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.

Cited by 137 publications

References 73 publications

LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers

LEUNIG and SEUSS co-repressors regulate miR172 expression in Arabidopsis flowers

High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds

The next-generation sequencing technology and application

Contact Info

Product

Resources

About