scholarly journals Epitranscriptomics: A New Layer of microRNA Regulation in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (13) ◽  
pp. 3372
Author(s):  
Veronica De Paolis ◽  
Elisa Lorefice ◽  
Elisa Orecchini ◽  
Claudia Carissimi ◽  
Ilaria Laudadio ◽  
...  
Keyword(s):  
Gene Expression ◽  
Potential Role ◽  
Fine Tuning ◽  
Cancer Development ◽  
Transcriptional Level ◽  
Rna Modifications ◽  
Gene Expressions ◽  
Microrna Regulation ◽  
Non Coding Rnas

MicroRNAs are pervasive regulators of gene expression at the post-transcriptional level in metazoan, playing key roles in several physiological and pathological processes. Accordingly, these small non-coding RNAs are also involved in cancer development and progression. Furthermore, miRNAs represent valuable diagnostic and prognostic biomarkers in malignancies. In the last twenty years, the role of RNA modifications in fine-tuning gene expressions at several levels has been unraveled. All RNA species may undergo post-transcriptional modifications, collectively referred to as epitranscriptomic modifications, which, in many instances, affect RNA molecule properties. miRNAs are not an exception, in this respect, and they have been shown to undergo several post-transcriptional modifications. In this review, we will summarize the recent findings concerning miRNA epitranscriptomic modifications, focusing on their potential role in cancer development and progression.

scholarly journals Pesticide application has little influence on coding and non-coding gene expressions in rice

2019 ◽  
Author(s):  
Sajid Muhammad ◽  
Jingai Tan ◽  
Pingchuan Deng ◽  
Tingting Li ◽  
Haohua He ◽  
...  
Keyword(s):  
Gene Expression ◽  
Potential Role ◽  
Insect Pests ◽  
Host Gene Expression ◽  
Pesticide Application ◽  
Gene Expressions ◽  
Number Of Genes ◽  
Non Coding Rnas ◽  
Transcriptomic Changes

Abstract Background Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment and ecosystem; however, there is lack of knowledge whether it could influence the physiology and metabolic processes in plants. Results Here, we systemically analyzed the transcriptomic changes in rice after a spray of two commercial pesticides, Abamectin (ABM) and Thiamethoxam (TXM). We found only a limited number of genes were altered by two pesticide applications, indicating that pesticides cannot dramatically affect the performance of rice. Nevertheless, we characterized some Differentially Expressed Genes (DEGs) and long non-coding RNAs (lncRNAs) that can be impacted by both two pesticides, suggesting their certain involvement in response to farm chemicals. Moreover, we detected several alternative splicing (AS) alterations accompanied by host gene expression, illustrating a potential role of AS in control of gene transcription during insecticide spraying. Finally, a couple of transposons were identified significantly changed with pesticides treatment, leading to a variation in adjacent coding or non-coding transcripts. Conclusions Altogether, our results provide valuable insights into pest management through appropriate timing and balanced mixture over sustainable application of field drugs.

scholarly journals Pesticide application has little influence on coding and non-coding gene expressions in rice

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Sajid Muhammad ◽  
Jingai Tan ◽  
Pingchuan Deng ◽  
Tingting Li ◽  
Haohua He ◽  
...  
Keyword(s):  
Potential Role ◽  
Insect Pests ◽  
Pesticide Application ◽  
Gene Expressions ◽  
Number Of Genes ◽  
Non Coding Rnas ◽  
Transcriptomic Changes ◽  
Harmful Effects ◽  
Host Genes

Abstract Background Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment and ecosystem; however, there is lack of knowledge whether it could influence the physiology and metabolic processes in plants. Results Here, we systemically analyzed the transcriptomic changes in rice after a spray of two commercial pesticides, Abamectin (ABM) and Thiamethoxam (TXM). We found only a limited number of genes (0.91%) and (1.24%) were altered by ABM and TXM respectively, indicating that these pesticides cannot dramatically affect the performance of rice. Nevertheless, we characterized 1140 Differentially Expressed Genes (DEGs) interacting with 105 long non-coding RNAs (lncRNAs) that can be impacted by the two pesticides, suggesting their certain involvement in response to farm chemicals. Moreover, we detected 274 alternative splicing (AS) alterations accompanied by host genes expressions, elucidating a potential role of AS in control of gene transcription during insecticide spraying. Finally, we identified 488 transposons that were significantly changed with pesticides treatment, leading to a variation in adjacent coding or non-coding transcripts. Conclusion Altogether, our results provide valuable insights into pest management through appropriate timing and balanced mixture, these pesticides have no harmful effects on crop physiology over sustainable application of field drugs.

scholarly journals MiR-147: Functions and Implications in Inflammation and Diseases

MicroRNA ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Ling Lin ◽  
Kebin Hu
Keyword(s):  
Gene Expression ◽  
Infectious Disease ◽  
Neurodegenerative Disorder ◽  
Mrna Translation ◽  
Transcriptional Level ◽  
Regulate Gene Expression ◽  
Inflammatory Bowel ◽  
Non Coding Rnas ◽  
Regulate Gene

: MicroRNAs (miRNAs) are small non-coding RNAs (19~25 nucleotides) that regulate gene expression at a post-transcriptional level through repression of mRNA translation or mRNA decay. miR-147, which was initially discovered in mouse spleen and macrophages, has been shown to correlate with coronary atherogenesis and inflammatory bowel disease and modulate macrophage functions and inflammation through TLR-4. The altered miR-147 level has been shown in various human diseases, including infectious disease, cancer, cardiovascular disease, a neurodegenerative disorder, etc. This review will focus on the current understanding regarding the role of miR-147 in inflammation and diseases.

Non-coding RNAs: what are we missing?

2020 ◽  
Vol 98 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Cristina Carvalho Barbosa ◽  
Sydnee H. Calhoun ◽  
Hans-Joachim Wieden
Keyword(s):  
Gene Expression ◽  
External Stress ◽  
Fine Tuning ◽  
Transcriptional Level ◽  
Control Of Gene Expression ◽  
Cell Responses ◽  
The Past ◽  
Domains Of Life ◽  
Non Coding Rnas

Over the past two decades, the importance of small non-coding RNAs (sncRNAs) as regulatory molecules has become apparent in all three domains of life (archaea, bacteria, eukaryotes). In fact, sncRNAs play an important role in the control of gene expression at both the transcriptional and the post-transcriptional level, with crucial roles in fine-tuning cell responses during internal and external stress. Multiple pathways for sncRNA biogenesis and diverse mechanisms of regulation have been reported, and although biogenesis and mechanisms of sncRNAs in prokaryotes and eukaryotes are different, remarkable similarities exist. Here, we briefly review and compare the major sncRNA classes that act post-transcriptionally, and focus on recent discoveries regarding the ribosome as a target of regulation and the conservation of these mechanisms between prokaryotes and eukaryotes.

scholarly journals The Critical Role of miRNAs in Regulation of Flowering Time and Flower Development

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 319
Author(s):  
Saquib Waheed ◽  
Lihui Zeng
Keyword(s):  
Gene Expression ◽  
Flower Development ◽  
Critical Role ◽  
Transcriptional Level ◽  
Control Of Gene Expression ◽  
Non Coding Rnas ◽  
Time Of Year ◽  
Acting In Concert ◽  
Flowering Process

Flowering is an important biological process for plants that ensures reproductive success. The onset of flowering needs to be coordinated with an appropriate time of year, which requires tight control of gene expression acting in concert to form a regulatory network. MicroRNAs (miRNAs) are non-coding RNAs known as master modulators of gene expression at the post-transcriptional level. Many different miRNA families are involved in flowering-related processes such as the induction of floral competence, floral patterning, and the development of floral organs. This review highlights the diverse roles of miRNAs in controlling the flowering process and flower development, in combination with potential biotechnological applications for miRNAs implicated in flower regulation.

scholarly journals Regulation of gene transcription in the epididymis

Reproduction ◽  
2001 ◽  
pp. 41-48 ◽  
Author(s):  
CM Rodriguez ◽  
JL Kirby ◽  
BT Hinton
Keyword(s):  
Gene Expression ◽  
Transcriptional Control ◽  
Potential Role ◽  
Transcriptional Level ◽  
Spatial And Temporal Patterns ◽  
Critical Control Points ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Dna Elements

The epididymis exhibits region-specific as well as cell-specific patterns of gene expression within the epithelium. The spatial and temporal patterns of gene expression originate during development and are critical to the formation and maintenance of a fully functional epididymis. Despite the number of mechanisms reported to contribute to the regulation of eukaryotic gene expression, little is known about the specific mechanisms involved in the control of epididymal gene expression. This review will outline some of the cis-DNA elements and associated transcription factors that have been identified in the epididymis, in addition to discussing the potential role of co-regulator molecules and changes in chromatin structure as critical control points of gene expression. Although gene expression can be controlled at several points, discussion will focus on gene regulation at the transcriptional level. The role of post-transcriptional control, with particular attention to mRNA stability, will also be discussed.

scholarly journals The role of m6A, m5C and Ψ RNA modifications in cancer: Novel therapeutic opportunities

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Paz Nombela ◽  
Borja Miguel-López ◽  
Sandra Blanco
Keyword(s):  
Gene Expression ◽  
Rna Processing ◽  
Therapeutic Potential ◽  
Biological Processes ◽  
Rna Modifications ◽  
Non Coding Rna ◽  
Non Coding Rnas ◽  
And Function ◽  
Made In

AbstractRNA modifications have recently emerged as critical posttranscriptional regulators of gene expression programmes. Significant advances have been made in understanding the functional role of RNA modifications in regulating coding and non-coding RNA processing and function, which in turn thoroughly shape distinct gene expression programmes. They affect diverse biological processes, and the correct deposition of many of these modifications is required for normal development. Alterations of their deposition are implicated in several diseases, including cancer. In this Review, we focus on the occurrence of N6-methyladenosine (m6A), 5-methylcytosine (m5C) and pseudouridine (Ψ) in coding and non-coding RNAs and describe their physiopathological role in cancer. We will highlight the latest insights into the mechanisms of how these posttranscriptional modifications influence tumour development, maintenance, and progression. Finally, we will summarize the latest advances on the development of small molecule inhibitors that target specific writers or erasers to rewind the epitranscriptome of a cancer cell and their therapeutic potential.

scholarly journals The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Alejandra Monserrat Retis-Resendiz ◽  
Ixchel Nayeli González-García ◽  
Moisés León-Juárez ◽  
Ignacio Camacho-Arroyo ◽  
Marco Cerbón ◽  
...  
Keyword(s):  
Gene Expression ◽  
Menstrual Cycle ◽  
Fine Tuning ◽  
Cycle Phase ◽  
Transcriptional Networks ◽  
Epigenetic Mechanisms ◽  
Cell Type ◽  
Expression Of Genes ◽  
Non Coding Rnas

Abstract Background The human endometrium is a highly dynamic tissue whose function is mainly regulated by the ovarian steroid hormones estradiol and progesterone. The serum levels of these and other hormones are associated with three specific phases that compose the endometrial cycle: menstrual, proliferative, and secretory. Throughout this cycle, the endometrium exhibits different transcriptional networks according to the genes expressed in each phase. Epigenetic mechanisms are crucial in the fine-tuning of gene expression to generate such transcriptional networks. The present review aims to provide an overview of current research focused on the epigenetic mechanisms that regulate gene expression in the cyclical endometrium and discuss the technical and clinical perspectives regarding this topic. Main body The main epigenetic mechanisms reported are DNA methylation, histone post-translational modifications, and non-coding RNAs. These epigenetic mechanisms induce the expression of genes associated with transcriptional regulation, endometrial epithelial growth, angiogenesis, and stromal cell proliferation during the proliferative phase. During the secretory phase, epigenetic mechanisms promote the expression of genes associated with hormone response, insulin signaling, decidualization, and embryo implantation. Furthermore, the global content of specific epigenetic modifications and the gene expression of non-coding RNAs and epigenetic modifiers vary according to the menstrual cycle phase. In vitro and cell type-specific studies have demonstrated that epithelial and stromal cells undergo particular epigenetic changes that modulate their transcriptional networks to accomplish their function during decidualization and implantation. Conclusion and perspectives Epigenetic mechanisms are emerging as key players in regulating transcriptional networks associated with key processes and functions of the cyclical endometrium. Further studies using next-generation sequencing and single-cell technology are warranted to explore the role of other epigenetic mechanisms in each cell type that composes the endometrium throughout the menstrual cycle. The application of this knowledge will definitively provide essential information to understand the pathological mechanisms of endometrial diseases, such as endometriosis and endometrial cancer, and to identify potential therapeutic targets and improve women’s health.

scholarly journals Micro-ribonucleic acid and carcinogenesis: breast cancer as an example

2015 ◽  
Author(s):  
Manal Al-Khanbashi ◽  
Mansour Al-Moundhri
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cell Cycle ◽  
Ribonucleic Acid ◽  
Cell Cycle Regulation ◽  
Potential Role ◽  
Disease Status ◽  
Transcriptional Level ◽  
Non Coding Rnas ◽  
Cycle Regulation

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have unique functions at post-transcriptional level (epigenetics). MiRNAs play a pivotal role in controlling gene expression at various levels including differentiation, cell-cycle regulation, apoptosis and many others in mammals as well as in many organisms. Recently, there has been greater understanding of the contribution of dysregulation of miRNA into disease status in particular carcinogenesis. In this review, we will discuss miRNA discovery, nomenclature, function, contribution of their dysregulation into disease status in particular carcinogenesis and their potential role as biomarkers.

scholarly journals RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 627
Author(s):  
Amber Willbanks ◽  
Shaun Wood ◽  
Jason X. Cheng
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Fine Tuning ◽  
Human Diseases ◽  
Rna Modifications ◽  
Regulate Gene Expression ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Fine Tune

Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases.

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