Natural antisense transcripts are significantly involved in regulation of drought stress in maize

Xu, Jie; Wang, Qi; Freeling, M.; Zhang, Xuecai; Xu, Yunbi; Mao, Yan; Tang, Xin; Wu, Fengkai; Long, Hai; Cao, Mengji; Tang, Rong; Lisch, Damon; Lu, Yanli

doi:10.1093/nar/gkx085

Cited by 50 publications

(42 citation statements)

References 98 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More recently, the development of the next sequence generation technology and the gaining of knowledge on the gene silencing, contribute to change this opinion revealing that an extensive number of NATs have a functional role. NATs have been surveyed in Arabidopsis [108], rice [109], wheat [110] and several legumes [111] and involved in response of abiotic stresses [112,113] and developmental transitions [114][115][116]. The mechanism of action of NATs are still not fully understood [117], although in many cases their role is in the repression of their sense cognate transcripts [118].…”

Section: The Genetic Control Of Apomixismentioning

confidence: 99%

“…Our findings show that apomixis-linked genes are expressed as sense and antisense transcripts in cell lineages of sexual ovules, whereas their expression of both transcripts was strongly down regulated in the same cells of apomictic ovules. Coordinated down or up regulation of both sense and antisense transcripts derived from NAT pairs has been reported under water stress conditions in maize [112], suggesting that "sexual" and "apomictic" alleles may interact each other as NAT gene pairs (i.e., gene pairs that express transcripts that are overlapping and complementary). The nature of this interaction is generally poorly understood, although a possible link between antisense transcripts and chromatin modification has been proposed [108,119].…”

Section: The Genetic Control Of Apomixismentioning

confidence: 99%

See 1 more Smart Citation

A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

Barcaccia

Palumbo

Sgorbati

et al. 2020

Genes

View full text Add to dashboard Cite

Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.

show abstract

Section: The Genetic Control Of Apomixismentioning

confidence: 99%

Section: The Genetic Control Of Apomixismentioning

confidence: 99%

A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

Barcaccia

Palumbo

Sgorbati

et al. 2020

Genes

View full text Add to dashboard Cite

show abstract

“…Among the transcripts clustered by WGCNA were lncRNAs. lncRNAs are proposed to function as gene expression regulators, particularly in organisms experiencing stress [36]. In this study, the two Eutrema salsugineum ecotypes display different transcriptional responses to water deficits.…”

Section: Discussionmentioning

confidence: 98%

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

et al. 2020

View full text Add to dashboard Cite

Background: The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has become an important objective for crop improvement. Some wild crop relatives have adapted to extreme osmotic stresses and can provide valuable insights into traits and genetic signatures that can guide efforts to improve crop tolerance to water deficits. Eutrema salsugineum, a close relative of many cruciferous crops, is a halophytic plant and extremophyte model for abiotic stress research. Results: Using comparative transcriptomics, we show that two E. salsugineum ecotypes display significantly different transcriptional responses towards a two-stage drought treatment. Even before visibly wilting, water deficit led to the differential expression of almost 1,100 genes for an ecotype from the semi-arid, sub-arctic Yukon, Canada, but only 63 genes for an ecotype from the semi-tropical, monsoonal, Shandong, China. After recovery and a second drought treatment, about 5,000 differentially expressed genes were detected in Shandong plants versus 1,900 genes in Yukon plants. Only 13 genes displayed similar drought-responsive patterns for both ecotypes. We detected 1,007 long non-protein coding RNAs (lncRNAs), 8% were only expressed in stress-treated plants, a surprising outcome given the documented association between lncRNA expression and stress. Co-expression network analysis of the transcriptomes identified eight gene clusters where at least half of the genes in each cluster were differentially expressed. While many gene clusters were correlated to drought treatments, only a single cluster significantly correlated to drought exposure in both ecotypes. Conclusion: Extensive, ecotype-specific transcriptional reprogramming with drought was unexpected given that both ecotypes are adapted to saline habitats providing persistent exposure to osmotic stress. This ecotype-specific

show abstract

“…A previous study reported a method that was developed to express sgRNA with RNA polymerase II promoter by using self-cleaving ribozymes and tRNA 26 . In addition, sgRNA-shRNA structure has been also introduced to the multiplex genome engineering by using U6 promoter 27 .…”

Section: Discussionmentioning

confidence: 99%

SgRNA Expression of CRIPSR-Cas9 System Based on MiRNA Polycistrons as a Versatile Tool to Manipulate Multiple and Tissue-Specific Genome Editing

Xie

Chen

Wang

et al. 2017

Sci Rep

View full text Add to dashboard Cite

CRISPR/Cas9-mediated genome editing is a next-generation strategy for genetic modifications. Typically, sgRNA is constitutively expressed relying on RNA polymerase III promoters. Polymerase II promoters initiate transcription in a flexible manner, but sgRNAs generated by RNA polymerase II promoter lost their nuclease activity. To express sgRNAs in a tissue-specific fashion and endow CRISPR with more versatile function, a novel system was established in a polycistron, where miRNAs (or shRNAs) and sgRNAs alternately emerged and co-expressed under the control of a single polymerase II promoter. Effective expression and further processing of functional miRNAs and sgRNAs were achieved. The redundant nucleotides adjacent to sgRNA were degraded, and 5′- cap structure was responsible for the compromised nuclease capacity of sgRNA: Cas9 complex. Furthermore, this strategy fulfilled conducting multiplex genome editing, as well as executing neural- specific genome editing and enhancing the proportion of homologous recombination via inhibiting NHEJ pathway by shRNA. In summary, we designed a new construction for efficient expression of sgRNAs with miRNAs (shRNAs) by virtue of RNA polymerase II promoters, which will spur the development of safer, more controllable/regulable and powerful CRISPR/Cas9 system-mediated genome editing in a wide variety of further biomedical applications.

show abstract

Natural antisense transcripts are significantly involved in regulation of drought stress in maize

Cited by 50 publications

References 98 publications

A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

Coding and long non-coding RNAs provide evidence of distinct transcriptional reprogramming for two ecotypes of the extremophile plant Eutrema salsugineum undergoing water deficit stress

SgRNA Expression of CRIPSR-Cas9 System Based on MiRNA Polycistrons as a Versatile Tool to Manipulate Multiple and Tissue-Specific Genome Editing

Contact Info

Product

Resources

About