RNA modifications shed new light on DNA's older brother

Epigenetics, which literally means ‘on top of genetics’, is a term that describes factors that influence gene expression and are mitotically heritable, but potentially reversible. Recently, N6methyladenosine (m6A) has been identified as a reversible RNA modification that is widespread in mRNA. This is just one of hundreds of modifications to RNA. These exciting findings led to the birth of ‘epitranscriptomics’- the study of reversible RNA modifications. We discuss specific examples of how epigenetic and epitranscriptomic, mechanisms interact to collectively modify genomic output and highlight how these two intertwined forms of gene regulation contribute to homeostasis and stress adaptation.

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N6-methyladenosine in poly(A) tails stabilize VSG transcripts

10.1101/2020.01.30.925776 ◽

2020 ◽

Author(s):

Idalio J. Viegas ◽

Juan Pereira de Macedo ◽

Mariana De Niz ◽

João A. Rodrigues ◽

Francisco Aresta-Branco ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Trypanosoma Brucei ◽

Mrna Degradation ◽

Surface Glycoprotein ◽

Variant Surface Glycoprotein ◽

Rna Modification ◽

Rna Modifications ◽

Genetic Tools ◽

Cis Acting

SummaryRNA modifications are important regulators of gene expression. In Trypanosoma brucei, transcription is polycistronic and thus most regulation happens post-transcriptionally. N6-methyladenosine (m6A) has been detected in this parasite, but its function remains unknown. Here we show that ∼50% of the m6A is located in the poly(A) tail of the monoallelically expressed Variant Surface Glycoprotein (VSG) transcript. m6A residues are removed from the VSG poly(A) tail prior to deadenylation and mRNA degradation. Using genetic tools, we identified a 16-mer motif in the 3’UTR of VSG that acts as a cis-acting motif required for inclusion of m6A in the poly(A) tail. Removal of this motif from the VSG 3’ UTR results in poly(A) tails lacking m6A, rapid deadenylation and mRNA degradation. To our knowledge this is the first identification of an RNA modification in the poly(A) tail of any eukaryote, uncovering a novel post-transcriptional mechanism of gene regulation.

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Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

The Journal of Cell Biology ◽

10.1083/jcb.201511041 ◽

2016 ◽

Vol 213 (1) ◽

pp. 15-22 ◽

Cited By ~ 66

Author(s):

Konstantin Licht ◽

Michael F. Jantsch

Keyword(s):

Gene Expression ◽

Mass Spectrometry ◽

Rna Editing ◽

Messenger Rna ◽

Gene Expression Regulation ◽

Rna Modification ◽

Rna Modifications ◽

Transcriptome Regulation ◽

Affect Gene Expression ◽

Generation Sequencing

Advances in next-generation sequencing and mass spectrometry have revealed widespread messenger RNA modifications and RNA editing, with dramatic effects on mammalian transcriptomes. Factors introducing, deleting, or interpreting specific modifications have been identified, and analogous with epigenetic terminology, have been designated “writers,” “erasers,” and “readers.” Such modifications in the transcriptome are referred to as epitranscriptomic changes and represent a fascinating new layer of gene expression regulation that has only recently been appreciated. Here, we outline how RNA editing and RNA modification can rapidly affect gene expression, making both processes as well suited to respond to cellular stress and to regulate the transcriptome during development or circadian periods.

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Emerging roles of RNA modifications in genome integrity

Briefings in Functional Genomics ◽

10.1093/bfgp/elaa022 ◽

2020 ◽

Author(s):

Seo Yun Lee ◽

Jae Jin Kim ◽

Kyle M Miller

Keyword(s):

Gene Expression ◽

Dna Damage ◽

Dna Repair ◽

Genome Stability ◽

Strand Break ◽

Human Diseases ◽

Genome Integrity ◽

Rna Modification ◽

Rna Modifications ◽

Dna Double Strand Break

Abstract Post-translational modifications of proteins are well-established participants in DNA damage response (DDR) pathways, which function in the maintenance of genome integrity. Emerging evidence is starting to reveal the involvement of modifications on RNA in the DDR. RNA modifications are known regulators of gene expression but how and if they participate in DNA repair and genome maintenance has been poorly understood. Here, we review several studies that have now established RNA modifications as key components of DNA damage responses. RNA modifying enzymes and the binding proteins that recognize these modifications localize to and participate in the repair of UV-induced and DNA double-strand break lesions. RNA modifications have a profound effect on DNA–RNA hybrids (R-loops) at DNA damage sites, a structure known to be involved in DNA repair and genome stability. Given the importance of the DDR in suppressing mutations and human diseases such as neurodegeneration, immunodeficiencies, cancer and aging, RNA modification pathways may be involved in human diseases not solely through their roles in gene expression but also by their ability to impact DNA repair and genome stability.

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Faculty Opinions recommendation of Dynamic RNA modifications in gene expression regulation.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727721904.793541904 ◽

2018 ◽

Author(s):

Jeffrey Kieft ◽

Daniel Eiler

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Expression Regulation ◽

Rna Modifications

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Base-Pair Opening Dynamics Study of Fluoride Riboswitch in the Bacillus cereus CrcB Gene

International Journal of Molecular Sciences ◽

10.3390/ijms22063234 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3234

Author(s):

Juhyun Lee ◽

Si-Eun Sung ◽

Janghyun Lee ◽

Jin Young Kang ◽

Joon-Hwa Lee ◽

...

Keyword(s):

Gene Expression ◽

Gene Regulation ◽

Nmr Spectroscopy ◽

Bacillus Cereus ◽

Base Pair ◽

Noncoding Rna ◽

Hydrogen Exchange ◽

Magnesium Ion ◽

Fluoride Ion ◽

Base Pair Opening

Riboswitches are segments of noncoding RNA that bind with metabolites, resulting in a change in gene expression. To understand the molecular mechanism of gene regulation in a fluoride riboswitch, a base-pair opening dynamics study was performed with and without ligands using the Bacillus cereus fluoride riboswitch. We demonstrate that the structural stability of the fluoride riboswitch is caused by two steps depending on ligands. Upon binding of a magnesium ion, significant changes in a conformation of the riboswitch occur, resulting in the greatest increase in their stability and changes in dynamics by a fluoride ion. Examining hydrogen exchange dynamics through NMR spectroscopy, we reveal that the stabilization of the U45·A37 base-pair due to the binding of the fluoride ion, by changing the dynamics while maintaining the structure, results in transcription regulation. Our results demonstrate that the opening dynamics and stabilities of a fluoride riboswitch in different ion states are essential for the genetic switching mechanism.

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N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosis

Journal of Translational Medicine ◽

10.1186/s12967-021-02981-5 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Fei Ye ◽

Tianzhu Wang ◽

Xiaoxin Wu ◽

Jie Liang ◽

Jiaoxing Li ◽

...

Keyword(s):

Gene Expression ◽

Multiple Sclerosis ◽

Clustering Analysis ◽

Roc Curves ◽

Progressive Multiple Sclerosis ◽

Rna Modification ◽

Diagnostic Model ◽

Consensus Clustering ◽

Rna Methylation ◽

M6a Rna Methylation

Abstract Background Progressive multiple sclerosis (PMS) is an uncommon and severe subtype of MS that worsens gradually and leads to irreversible disabilities in young adults. Currently, there are no applicable or reliable biomarkers to distinguish PMS from relapsing–remitting multiple sclerosis (RRMS). Previous studies have demonstrated that dysfunction of N6-methyladenosine (m6A) RNA modification is relevant to many neurological disorders. Thus, the aim of this study was to explore the diagnostic biomarkers for PMS based on m6A regulatory genes in the cerebrospinal fluid (CSF). Methods Gene expression matrices were downloaded from the ArrayExpress database. Then, we identified differentially expressed m6A regulatory genes between MS and non-MS patients. MS clusters were identified by consensus clustering analysis. Next, we analyzed the correlation between clusters and clinical characteristics. The random forest (RF) algorithm was applied to select key m6A-related genes. The support vector machine (SVM) was then used to construct a diagnostic gene signature. Receiver operating characteristic (ROC) curves were plotted to evaluate the accuracy of the diagnostic model. In addition, CSF samples from MS and non-MS patients were collected and used for external validation, as evaluated by an m6A RNA Methylation Quantification Kit and by real-time quantitative polymerase chain reaction. Results The 13 central m6A RNA methylation regulators were all upregulated in MS patients when compared with non-MS patients. Consensus clustering analysis identified two clusters, both of which were significantly associated with MS subtypes. Next, we divided 61 MS patients into a training set (n = 41) and a test set (n = 20). The RF algorithm identified eight feature genes, and the SVM method was successfully applied to construct a diagnostic model. ROC curves revealed good performance. Finally, the analysis of 11 CSF samples demonstrated that RRMS samples exhibited significantly higher levels of m6A RNA methylation and higher gene expression levels of m6A-related genes than PMS samples. Conclusions The dynamic modification of m6A RNA methylation is involved in the progression of MS and could potentially represent a novel CSF biomarker for diagnosing MS and distinguishing PMS from RRMS in the early stages of the disease.

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CFTR Cooperative Cis-Regulatory Elements in Intestinal Cells

International Journal of Molecular Sciences ◽

10.3390/ijms22052599 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2599

Author(s):

Mégane Collobert ◽

Ozvan Bocher ◽

Anaïs Le Nabec ◽

Emmanuelle Génin ◽

Claude Férec ◽

...

Keyword(s):

Gene Expression ◽

Cystic Fibrosis ◽

Gene Regulation ◽

Genetic Diseases ◽

Regulatory Elements ◽

Cftr Gene ◽

Intestinal Cells ◽

Cooperative Effects ◽

Cis Acting ◽

Study Techniques

About 8% of the human genome is covered with candidate cis-regulatory elements (cCREs). Disruptions of CREs, described as “cis-ruptions” have been identified as being involved in various genetic diseases. Thanks to the development of chromatin conformation study techniques, several long-range cystic fibrosis transmembrane conductance regulator (CFTR) regulatory elements were identified, but the regulatory mechanisms of the CFTR gene have yet to be fully elucidated. The aim of this work is to improve our knowledge of the CFTR gene regulation, and to identity factors that could impact the CFTR gene expression, and potentially account for the variability of the clinical presentation of cystic fibrosis as well as CFTR-related disorders. Here, we apply the robust GWAS3D score to determine which of the CFTR introns could be involved in gene regulation. This approach highlights four particular CFTR introns of interest. Using reporter gene constructs in intestinal cells, we show that two new introns display strong cooperative effects in intestinal cells. Chromatin immunoprecipitation analyses further demonstrate fixation of transcription factors network. These results provide new insights into our understanding of the CFTR gene regulation and allow us to suggest a 3D CFTR locus structure in intestinal cells. A better understand of regulation mechanisms of the CFTR gene could elucidate cases of patients where the phenotype is not yet explained by the genotype. This would thus help in better diagnosis and therefore better management. These cis-acting regions may be a therapeutic challenge that could lead to the development of specific molecules capable of modulating gene expression in the future.

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