scholarly journals Novel insights into the pervasive role of RNA structure in post-transcriptional regulation of gene expression in plants

2021 ◽  
Vol 49 (4) ◽  
pp. 1829-1839
Author(s):  
Huakun Zhang ◽  
Yiliang Ding
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Rna Structure ◽  
Environmental Changes ◽  
Regulation Of Gene Expression ◽  
Intrinsic Property ◽  
Rna Degradation ◽  
Mrna Maturation ◽  
Recent Developments ◽  
Post Transcriptional Regulation

RNA folding is an intrinsic property of RNA that serves a key role in every step of post-transcriptional regulation of gene expression, from RNA maturation to translation in plants. Recent developments of genome-wide RNA structure profiling methods have transformed research in this area enabling focus to shift from individual molecules to the study of tens of thousands of RNAs. Here, we provide a comprehensive review of recent advances in the field. We discuss these new insights of RNA structure functionality within the context of post-transcriptional regulation including mRNA maturation, translation, and RNA degradation in plants. Notably, we also provide an overview of how plants exhibit different RNA structures in response to environmental changes.

scholarly journals Distinct Hypoxia-induced Translational Profiles of Embryonic and Adult-derived Macrophages

2021 ◽  
Author(s):  
Nicholas S. Wilcox ◽  
Timur O. Yarovinsky ◽  
Prakruti Pandya ◽  
Vinod S. Ramgolam ◽  
Albertomaria Moro ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Rna Binding ◽  
Environmental Changes ◽  
Rna Binding Proteins ◽  
Fetal Liver ◽  
Affinity Purification ◽  
Regulation Of Gene Expression ◽  
Translation Rate ◽  
Post Transcriptional Regulation

SummaryTissue homeostasis and repair are orchestrated by resident and newly recruited macrophages that alter their gene expression program in response to changes in tissue microenvironment. Embryonic macrophages, such as fetal liver derived macrophages (FLDM) seed the organs, including heart and lung during embryonic development and persist throughout the adult lifetime, while bone marrow-derived macrophages (BMDM) are recruited following an acute perturbation. Transcriptome analyses of FLDM and BMDM identified differences between them at the level of RNA expression, which correlates imperfectly with protein levels. Post-transcriptional regulation by microRNAs (miRNAs) and RNA-binding proteins determines mRNA stability and translation rate and may override transcriptional cues in response to environmental changes, such as hypoxia. To identify distinct features of FLDM and BMDM response to hypoxia at the level of translation, we employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA. RNA-seq profiling of translated RNA identified distinct hypoxia-induced translational signature of BMDM (Ly6e, vimentin and glycolysis-associated enzymes Pgk1, Tpi1, Aldoa, Ldha) and FLDM (chemokines Ccl7 and Ccl2). By translational profiling of BMDM and FLDM with deletion of the RNA-binding protein HuR, we identified transcripts that were dependent on HuR. These findings highlight the importance of HuR and identify its distinct targets for post-transcriptional regulation of gene expression in embryonic vs. adult-derived macrophages.

Post-transcriptional regulation of gene expression

Methods ◽  
2017 ◽  
Vol 126 ◽  
pp. 1-2 ◽  
Author(s):  
Howard D. Lipshitz ◽  
Julie M. Claycomb ◽  
Craig A. Smibert
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Post Transcriptional Regulation

scholarly journals Post-transcriptional regulation of gene expression by degradation of messenger RNAs

2003 ◽  
Vol 195 (3) ◽  
pp. 356-372 ◽  
Author(s):  
Annamaria Bevilacqua ◽  
Maria Cristina Ceriani ◽  
Sergio Capaccioli ◽  
Angelo Nicolin
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Regulation Of Gene Expression ◽  
Messenger Rnas ◽  
Post Transcriptional Regulation

scholarly journals Regulatory signals in messenger RNA: determinants of nutrient–gene interaction and metabolic compartmentation

1998 ◽  
Vol 80 (4) ◽  
pp. 307-321
Author(s):  
John E. Hesketh ◽  
M. Helena Vasconcelos ◽  
Giovanna Bermano
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Mrna Stability ◽  
Transcriptional Control ◽  
Regulation Of Gene Expression ◽  
Untranslated Regions ◽  
Nutritional Requirements ◽  
Control Of Gene Expression ◽  
Metabolic Compartmentation ◽  
Post Transcriptional Regulation

Nutrition has marked influences on gene expression and an understanding of the interaction between nutrients and gene expression is important in order to provide a basis for determining the nutritional requirements on an individual basis. The effects of nutrition can be exerted at many stages between transcription of the genetic sequence and production of a functional protein. This review focuses on the role of post-transcriptional control, particularly mRNA stability, translation and localization, in the interactions of nutrients with gene expression. The effects of both macronutrients and micronutrients on regulation of gene expression by post-transcriptional mechanisms are presented and the post-transcriptional regulation of specific genes of nutritional relevance (glucose transporters, transferrin, selenoenzymes, metallothionein, lipoproteins) is described in detail. The function of the regulatory signals in the untranslated regions of the mRNA is highlighted in relation to control of mRNA stability, translation and localization and the importance of these mRNA regions to regulation by nutrients is illustrated by reference to specific examples. The localization of mRNA by signals in the untranslated regions and its function in the spatial organization of protein synthesis is described; the potential of such mechanisms to play a key part in nutrient channelling and metabolic compartmentation is discussed. It is concluded that nutrients can influence gene expression through control of the regulatory signals in these untranslated regions and that the post-transcriptional regulation of gene expression by these mechanisms may influence nutritional requirements. It is emphasized that in studies of nutritional control of gene expression it is important not to focus only on regulation through gene promoters but also to consider the possibility of post-transcriptional control.

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