Plant isomiRs: origins, biogenesis, and biological functions

Fard, Ehsan Mohseni; Moradi, Sharif; Salekdeh, Nava Nikpay; Oghan, Hassan Amiri; Ghaffari, Mohammad Reza; Zeinalabedini, Mehrshad; Salekdeh, Ghasem Hosseini

doi:10.1016/j.ygeno.2020.06.019

Cited by 12 publications

(7 citation statements)

References 152 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It exemplified by several isomiRs with a length bias of 18 or 19 nt were only differentially expressed in roots and had more diversified targets, such as two targets for miR399c, eight targets for miR395c-5 , and 10 targets for miR482-5 (Supplementary Table 9). Recent evidence suggests that isomiR production is differentially modulated at different developmental stages and by adverse environmental signals (Hackenberg et al, 2013;Balyan et al, 2020;Fard et al, 2020). For example, Shao et al (2015) found that the abundance of iso-osa-miR528-5p in AGO1 complexes was higher than that of its canonical osa-miR528-5p in rice.…”

Section: Srna Length Patterns and Potential Roles In Betula Luminiferamentioning

confidence: 99%

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera

Zhang

Lin

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

Inorganic phosphate (Pi) is often lacking in natural and agro-climatic environments, which impedes the growth of economically important woody species. Plants have developed strategies to cope with low Pi (LP) availability. MicroRNAs (miRNAs) play important roles in responses to abiotic stresses, including nutrition stress, by regulating target gene expression. However, the miRNA-mediated regulation of these adaptive responses and their underlying coordinating signals are still poorly understood in forestry trees such as Betula luminifera. Transcriptomic libraries, small RNA (sRNA) libraries, and a mixed degradome cDNA library of B. luminifera roots and shoots treated under LP and normal conditions (CK) were constructed and sequenced using next-generation deep sequencing. A comprehensive B. luminifera transcriptome derived from its roots and shoots was constructed, and a total of 76,899 unigenes were generated. Analysis of the transcriptome identified 8,095 and 5,584 differentially expressed genes in roots and shoots, respectively, under LP conditions. sRNA sequencing analyses indicated that 66 and 60 miRNAs were differentially expressed in roots and shoots, respectively, under LP conditions. A total of 109 and 112 miRNA–target pairs were further validated in the roots and shoots, respectively, using degradome sequencing. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differential miRNA targets indicated that the “ascorbate and aldarate metabolism” pathway responded to LP, suggesting miRNA-target pairs might participating in the removing of reactive oxidative species under LP stress. Moreover, a putative network of miRNA–target interactions involved in responses to LP stress in B. luminifera is proposed. Taken together, these findings provide useful information to decipher miRNA functions and establish a framework for exploring P signaling networks regulated by miRNAs in B. luminifera and other woody plants. It may provide new insights into the genetic engineering of high use efficiency of Pi in forestry trees.

show abstract

Section: Srna Length Patterns and Potential Roles In Betula Luminiferamentioning

confidence: 99%

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera

Zhang

Lin

et al. 2021

Front. Genet.

View full text Add to dashboard Cite

show abstract

“…Most miRNAs with a length of 21 nt bind to AGO1 and AGO2 while 24 nt miRNAs bind to AGO4 [ 84 ]. Therefore, it is suggested that the isomiRs length variation may be related to the strategy of target differentiation by assigning isomiRs to different AGO complexes [ 85 ].…”

Section: Discussionmentioning

confidence: 99%

Barley Seeds miRNome Stability during Long-Term Storage and Aging

Puchta

Groszyk

Małecka

et al. 2021

IJMS

View full text Add to dashboard Cite

Seed aging is a complex biological process that has been attracting scientists’ attention for many years. High-throughput small RNA sequencing was applied to examine microRNAs contribution in barley seeds senescence. Unique samples of seeds that, despite having the same genetic makeup, differed in viability after over 45 years of storage in a dry state were investigated. In total, 61 known and 81 novel miRNA were identified in dry seeds. The highest level of expression was found in four conserved miRNA families, i.e., miR159, miR156, miR166, and miR168. However, the most astonishing result was the lack of significant differences in the level of almost all miRNAs in seed samples with significantly different viability. This result reveals that miRNAs in dry seeds are extremely stable. This is also the first identified RNA fraction that is not deteriorating along with the loss of seed viability. Moreover, the novel miRNA hvu-new41, with higher expression in seeds with the lowest viability as detected by RT-qPCR, has the potential to become an indicator of the decreasing viability of seeds during storage in a dry state.

show abstract

“…MicroRNAs as the Regulatory Switches during Scar Formation MicroRNAs are small noncoding RNA molecules serving as the posttranscriptional gene expression regulators, thereby modulating virtually all biological processes and developmental pathways [124][125][126][127][128]. The evidence is constantly mounting that microRNAs are capable of regulating different aspects of wound healing, and their dysregulation is linked to aberrant wound repair and scar formation.…”

Section: Noncoding Rnas In Scar Formationmentioning

confidence: 99%

The Emerging Therapeutic Targets for Scar Management: Genetic and Epigenetic Landscapes

Amjadian

Moradi

Mohammadi

2022

Skin Pharmacol Physiol

Self Cite

View full text Add to dashboard Cite

Wound healing is a complex process including hemostasis, inflammation, proliferation, and remodeling during which an orchestrated array of biological and molecular events occurs to promote skin regeneration. Abnormalities in each step of the wound healing process lead to reparative rather than regenerative responses, thereby driving the formation of cutaneous scar. Patients suffering from scars represent serious health problems such as contractures, functional and aesthetic concerns as well as painful, thick, and itchy complications, which generally decrease the quality of life and impose high medical costs. Therefore, therapies reducing cutaneous scarring are necessary to improve patients' rehabilitation. Current approaches to remove scars, including surgical and non-surgical methods are not efficient enough, which is in principle due to our limited knowledge about underlying mechanisms of pathological as well as the physiological wound healing process. Thus, therapeutic interventions focused on basic science including genetic and epigenetic knowledge are recently taken into consideration as promising approaches for scar management, since they have the potential to provide targeted therapies and improve the conventional treatments as well as present opportunities for combination therapy. In this review, we highlight the recent advances in skin regenerative medicine through genetic and epigenetic approaches to achieve novel insights for the development of safe, efficient, and reproducible therapies and discuss promising approaches for scar management.

show abstract

Plant isomiRs: origins, biogenesis, and biological functions

Cited by 12 publications

References 152 publications

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera

Profiling of MicroRNAs and Their Targets in Roots and Shoots Reveals a Potential MiRNA-Mediated Interaction Network in Response to Phosphate Deficiency in the Forestry Tree Betula luminifera

Barley Seeds miRNome Stability during Long-Term Storage and Aging

The Emerging Therapeutic Targets for Scar Management: Genetic and Epigenetic Landscapes

Contact Info

Product

Resources

About