MicroRNA functions in plant embryos

2014 ◽  
Vol 42 (2) ◽  
pp. 352-357 ◽  
Author(s):  
Divya Vashisht ◽  
Michael D. Nodine
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Cellular Differentiation ◽  
Early Embryogenesis ◽  
Plant Mirnas ◽  
Plant Body ◽  
Basic Plant ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Embryonic Pattern Formation

Plant miRNAs are short non-coding RNAs that mediate the repression of hundreds of genes. The basic plant body plan is established during early embryogenesis, and recent results have demonstrated that miRNAs play pivotal roles during both embryonic pattern formation and developmental timing. Multiple miRNAs appear to specifically repress transcription factor families during early embryogenesis. Therefore miRNAs probably have a large influence on the gene regulatory networks that contribute to the earliest cellular differentiation events in plants.

scholarly journals A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Miguel Casanova ◽  
Madeleine Moscatelli ◽  
Louis Édouard Chauvière ◽  
Christophe Huret ◽  
Julia Samson ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Endogenous Retroviruses ◽  
X Chromosomes ◽  
Regulatory Pathways ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Specific Regulation ◽  
Species Specific ◽  
And Function

AbstractTransposable elements (TEs) have been proposed to play an important role in driving the expansion of gene regulatory networks during mammalian evolution, notably by contributing to the evolution and function of long non-coding RNAs (lncRNAs). XACT is a primate-specific TE-derived lncRNA that coats active X chromosomes in pluripotent cells and may contribute to species-specific regulation of X-chromosome inactivation. Here we explore how different families of TEs have contributed to shaping the XACT locus and coupling its expression to pluripotency. Through a combination of sequence analysis across primates, transcriptional interference, and genome editing, we identify a critical enhancer for the regulation of the XACT locus that evolved from an ancestral group of mammalian endogenous retroviruses (ERVs), prior to the emergence of XACT. This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.

Prioritizing candidate disease-related long non-coding RNAs by walking on the heterogeneous lncRNA and disease network

2015 ◽  
Vol 11 (3) ◽  
pp. 760-769 ◽  
Author(s):  
Meng Zhou ◽  
Xiaojun Wang ◽  
Jiawei Li ◽  
Dapeng Hao ◽  
Zhenzhen Wang ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Biological Processes ◽  
Disease Network ◽  
Wide Range ◽  
Gene Regulatory ◽  
Non Coding Rnas

Accumulated evidence has shown that long non-coding RNAs (lncRNA) act as a widespread layer in gene regulatory networks and are involved in a wide range of biological processes.

scholarly journals Non-Coding RNAs and their Integrated Networks

2019 ◽  
Vol 16 (3) ◽  
Author(s):  
Peijing Zhang ◽  
Wenyi Wu ◽  
Qi Chen ◽  
Ming Chen
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Protein Coding ◽  
Integrated Networks ◽  
Cellular Processes ◽  
Sequencing Technologies ◽  
Different Types ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Eukaryotic Genomes

AbstractEukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs’ essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

scholarly journals Molecular Mediators of RNA Loading into Extracellular Vesicles

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3355
Author(s):  
Chiara Corrado ◽  
Maria Magdalena Barreca ◽  
Chiara Zichittella ◽  
Riccardo Alessandro ◽  
Alice Conigliaro
Keyword(s):  
Gene Expression ◽  
Extracellular Vesicles ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Translation Regulation ◽  
Circular Rnas ◽  
Non Coding Rna ◽  
Gene Regulatory ◽  
Non Coding Rnas ◽  
Different Levels

In the last decade, an increasing number of studies have demonstrated that non-coding RNA (ncRNAs) cooperate in the gene regulatory networks with other biomolecules, including coding RNAs, DNAs and proteins. Among them, microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are involved in transcriptional and translation regulation at different levels. Intriguingly, ncRNAs can be packed in vesicles, released in the extracellular space, and finally internalized by receiving cells, thus affecting gene expression also at distance. This review focuses on the mechanisms through which the ncRNAs can be selectively packaged into extracellular vesicles (EVs).

scholarly journals Structural and Functional Analyses of Hub MicroRNAs in an Integrated Gene Regulatory Network of Arabidopsis

2020 ◽  
Author(s):  
Zhaoxu Gao ◽  
Jun Li ◽  
Li Li ◽  
Yanzhi Yang ◽  
Jian Li ◽  
...  
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Individual Plant ◽  
Plant Mirnas ◽  
Control Logic ◽  
Small Regulatory Rnas ◽  
Gene Regulatory ◽  
Regulatory Rnas ◽  
Functional Analyses ◽  
And Control

AbstractMicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoires of cellular mRNA available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions reanalyzed from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those in which the miRNAs are intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlighted the prevalence and importance of miRNA-containing FFLs to provide new insights into the design principles and control logic of miRNA regulatory networks governing gene expression programs in plants.

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