Hypoxia-induced alteration of RNA modifications in the mouse testis and sperm

2021 ◽  
Author(s):  
Tong He ◽  
Huanping Guo ◽  
Xipeng Shen ◽  
Xiao Wu ◽  
Lin Xia ◽  
...  
Keyword(s):  
Hypobaric Hypoxia ◽  
Environmental Changes ◽  
Epigenetic Inheritance ◽  
Transcriptional Regulators ◽  
Extreme Environment ◽  
Mouse Testis ◽  
Rna Modification ◽  
Rna Modifications ◽  
Sperm Counts ◽  
Health Studies

Abstract Hypobaric hypoxia as an extreme environment in a plateau may have deleterious effects on human health. Studies have indicated that rush entry into a plateau may reduce male fertility and manifest in decreased sperm counts and weakened sperm motility. RNA modifications are sensitive to environmental changes and have recently emerged as novel post-transcriptional regulators in male spermatogenesis and intergenerational epigenetic inheritance. In the present study, we generated a mouse hypoxia model simulating the environment of 5500 meters in altitude for 35 days, which led to compromised spermatogenesis, decreased sperm counts, and an increased sperm deformation rate. Using this hypoxia model, we further applied our recently developed high-throughput RNA modification quantification platform based on LC–MS/MS, which exhibited the capacity to simultaneously examine 25 types of RNA modifications. Our results revealed an altered sperm RNA modifications signature in the testis (6 types) and mature sperm (11 types) under the hypoxia model, with 4 types showing overlap (Am, Gm, m7G, and m22G). Our data first drew the signature of RNA modification profiles and comprehensively analyzed the alteration of RNA modification levels in mouse testis and sperm under a mouse hypoxia model. These data may be highly related to human conditions under a similar hypoxia environment.

RNA N-6-methyladenosine enzymes and resistance of cancer cells to chemotherapy and radiotherapy

Epigenomics ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 801-809 ◽  
Author(s):  
Meiyi Xiang ◽  
Wensu Liu ◽  
Wei Tian ◽  
Abin You ◽  
Dajun Deng
Keyword(s):  
Drug Resistance ◽  
Cancer Cells ◽  
Environmental Changes ◽  
Experimental Studies ◽  
Rna Modification ◽  
Rna Modifications ◽  
Resistance Development ◽  
Development Of Resistance ◽  
Promising Target ◽  
Adaptive Mechanisms

Aim: As one of the early adaptive mechanisms by which cells respond to environmental changes, RNA modification appears to be a very promising target for cancer treatment. Results: RNA modifications are currently a hot topic in epigenetic research. Emerging experimental studies show that expression alterations of multiple m6A enzymes, including demethylase FTO, methyltransferase METTL3 and WTAP, mediate the development of resistance of cancer cells to various treatments. A set of small molecular chemical drugs targeted to these m6A enzymes are under development. Intervention of RNA m6A methylation is a possible therapeutic strategy to overcome drug resistance. Conclusions: RNA m6A methylation may play a crucial role in drug resistance development and intervention in cancer cells.

scholarly journals RNA Modification Level Estimation with pulseR

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 619
Author(s):  
Etienne Boileau ◽  
Christoph Dieterich
Keyword(s):  
Experimental Approach ◽  
High Efficiency ◽  
Rna Modification ◽  
Model Parameters ◽  
Metabolic Labeling ◽  
Rna Seq ◽  
Rna Modifications ◽  
Log Odds ◽  
Pros And Cons ◽  
Wide Scale

RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m6A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale. Our workflow centers around the pulseR package, which was originally developed for the analysis of metabolic labeling experiments. We demonstrate how to analyze data without external normalization (i.e., in the absence of spike-ins), given high efficiency of separation, and how, alternatively, scaling factors can be derived from unmodified spike-ins. Importantly, our workflow provides an estimate of uncertainty of modification levels in terms of confidence intervals for model parameters, such as gene expression and RNA modification levels. We also compare alternative model parametrizations, log-odds, or the proportion of the modified molecules and discuss the pros and cons of each representation. In summary, our workflow is a versatile approach to RNA modification level estimation, which is open to any read-count-based experimental approach.

scholarly journals The architecture of SARS-CoV-2 transcriptome

2020 ◽  
Author(s):  
Dongwan Kim ◽  
Joo-Yeon Lee ◽  
Jeong-Sun Yang ◽  
Jun Won Kim ◽  
V. Narry Kim ◽  
...  
Keyword(s):  
High Resolution ◽  
Rna Sequencing ◽  
Rna Modification ◽  
List Type ◽  
Rna Modifications ◽  
Subgenomic Rnas ◽  
Frequent Motif ◽  
High Resolution Map ◽  
Functional Investigation ◽  
Resolution Map

AbstractSARS-CoV-2 is a betacoronavirus that is responsible for the COVID-19 pandemic. The genome of SARS-CoV-2 was reported recently, but its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we here present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical. In addition to the genomic RNA and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces a large number of transcripts encoding unknown ORFs with fusion, deletion, and/or frameshift. Using nanopore direct RNA sequencing, we further find at least 41 RNA modification sites on viral transcripts, with the most frequent motif being AAGAA. Modified RNAs have shorter poly(A) tails than unmodified RNAs, suggesting a link between the internal modification and the 3′ tail. Functional investigation of the unknown ORFs and RNA modifications discovered in this study will open new directions to our understanding of the life cycle and pathogenicity of SARS-CoV-2.HighlightsWe provide a high-resolution map of SARS-CoV-2 transcriptome and epitranscriptome using nanopore direct RNA sequencing and DNA nanoball sequencing.The transcriptome is highly complex owing to numerous recombination events, both canonical and noncanonical.In addition to the genomic and subgenomic RNAs common in all coronaviruses, SARS-CoV-2 produces transcripts encoding unknown ORFs.We discover at least 41 potential RNA modification sites with an AAGAA motif.

RNA modifications in hematopoietic malignancies: A new research frontier

Blood ◽  
2021 ◽  
Author(s):  
Ying Qing ◽  
Rui Su ◽  
Jianjun Chen
Keyword(s):  
Myeloid Leukemia ◽  
Therapeutic Potential ◽  
Rna Modification ◽  
Biological Functions ◽  
Rna Modifications ◽  
Aberrant Expression ◽  
Protein Coding ◽  
Hematopoietic Malignancies ◽  
Underlying Mechanisms ◽  
New Research

Both protein-coding and noncoding RNAs can be decorated with a wealth of chemical modifications and such modifications coordinately orchestrate gene expression during normal hematopoietic differentiation and development. However, aberrant expression and/or dysfunction of the relevant RNA modification modulators/regulators ("writers", "erasers", and "readers") drive the initiation and progression of hematopoietic malignancies, and targeting these dysregulated modulators holds potent therapeutic potential for the treatment of hematopoietic malignancies. In this review, we summarize current progress in the understanding of the biological functions and underlying mechanisms of RNA modifications in normal and malignant hematopoiesis, with a focus on the N6-methyladenosine (m6A) modification, and discuss the therapeutic potential of targeting RNA modifications for the treatment of hematopoietic malignancies, especially acute myeloid leukemia (AML).

scholarly journals Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 26 ◽  
Author(s):  
Kayla Borland ◽  
Jan Diesend ◽  
Taku Ito-Kureha ◽  
Vigo Heissmeyer ◽  
Christian Hammann ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Isotope Labeling ◽  
Rna Stability ◽  
Internal Standard ◽  
Modified Nucleosides ◽  
Rna Modification ◽  
Mouse Tissue ◽  
Rna Modifications ◽  
Internal Standards ◽  
Translation Fidelity

Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.

scholarly journals Nucleotide resolution profiling of m3C RNA modification by HAC-seq

2020 ◽  
Author(s):  
Jia Cui ◽  
Qi Liu ◽  
Erdem Sendinc ◽  
Yang Shi ◽  
Richard I Gregory
Keyword(s):  
Rna Modification ◽  
Rna Modifications ◽  
Mcf7 Cells ◽  
Single Nucleotide ◽  
Novel Method ◽  
Specific Mapping ◽  
Nucleotide Resolution ◽  
And Function ◽  
Trna Isoacceptors ◽  
Single Nucleotide Resolution

Abstract Cellular RNAs are subject to a myriad of different chemical modifications that play important roles in controlling RNA expression and function. Dysregulation of certain RNA modifications, the so-called ‘epitranscriptome’, contributes to human disease. One limitation in studying the functional, physiological, and pathological roles of the epitranscriptome is the availability of methods for the precise mapping of individual RNA modifications throughout the transcriptome. 3-Methylcytidine (m3C) modification of certain tRNAs is well established and was also recently detected in mRNA. However, methods for the specific mapping of m3C throughout the transcriptome are lacking. Here, we developed a m3C-specific technique, Hydrazine-Aniline Cleavage sequencing (HAC-seq), to profile the m3C methylome at single-nucleotide resolution. We applied HAC-seq to analyze ribosomal RNA (rRNA)-depleted total RNAs in human cells. We found that tRNAs are the predominant m3C-modified RNA species, with 17 m3C modification sites on 11 cytoplasmic and 2 mitochondrial tRNA isoacceptors in MCF7 cells. We found no evidence for m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNAs in these cells. HAC-seq provides a novel method for the unbiased, transcriptome-wide identification of m3C RNA modification at single-nucleotide resolution, and could be widely applied to reveal the m3C methylome in different cells and tissues.

scholarly journals RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis

2020 ◽  
Vol 49 (D1) ◽  
pp. D1396-D1404 ◽  
Author(s):  
Kunqi Chen ◽  
Bowen Song ◽  
Yujiao Tang ◽  
Zhen Wei ◽  
Qingru Xu ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Relevant Information ◽  
Rna Modification ◽  
Rna Modifications ◽  
Single Nucleotide Variants ◽  
Binding Interaction ◽  
Essential Information ◽  
Regulatory Circuits

Abstract Deciphering the biological impacts of millions of single nucleotide variants remains a major challenge. Recent studies suggest that RNA modifications play versatile roles in essential biological mechanisms, and are closely related to the progression of various diseases including multiple cancers. To comprehensively unveil the association between disease-associated variants and their epitranscriptome disturbance, we built RMDisease, a database of genetic variants that can affect RNA modifications. By integrating the prediction results of 18 different RNA modification prediction tools and also 303,426 experimentally-validated RNA modification sites, RMDisease identified a total of 202,307 human SNPs that may affect (add or remove) sites of eight types of RNA modifications (m6A, m5C, m1A, m5U, Ψ, m6Am, m7G and Nm). These include 4,289 disease-associated variants that may imply disease pathogenesis functioning at the epitranscriptome layer. These SNPs were further annotated with essential information such as post-transcriptional regulations (sites for miRNA binding, interaction with RNA-binding proteins and alternative splicing) revealing putative regulatory circuits. A convenient graphical user interface was constructed to support the query, exploration and download of the relevant information. RMDisease should make a useful resource for studying the epitranscriptome impact of genetic variants via multiple RNA modifications with emphasis on their potential disease relevance. RMDisease is freely accessible at: www.xjtlu.edu.cn/biologicalsciences/rmd.

scholarly journals Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

2019 ◽  
Author(s):  
Oguzhan Begik ◽  
Morghan C. Lucas ◽  
Huanle Liu ◽  
Jose Miguel Ramirez ◽  
John S. Mattick ◽  
...  
Keyword(s):  
Cancer Research ◽  
Expression Patterns ◽  
Rna Modification ◽  
Cancer Type ◽  
Evolutionary Analysis ◽  
Rna Modifications ◽  
Human Samples ◽  
Mammalian Tissues ◽  
Normal Human ◽  
Cancer Types

ABSTRACTBackgroundRNA modifications play central roles in cellular fate and differentiation. These features have placed the epitranscriptome in the forefront of developmental biology and cancer research. However, the machinery responsible for placing, removing and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification–related proteins (RMPs) may be dysregulated in each cancer type.ResultsHere we have performed a comprehensive annotation and evolutionary analysis of human RMPs as well as an integrative analysis of their expression patterns across 32 tissues, 10 species and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. Moreover, through the analysis of paired tumor-normal human samples we uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO, are not significantly up-regulated in most cancer types, once the sample is properly scaled and normalized to the full dataset, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers.ConclusionsOur analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues, and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviours that are orchestrated by RNA modifications.

scholarly journals RPS27A is a Poor Prognostic Predictor for Hepatocellular Carcinoma via Interacting with METTL3-Mediated RNA Modifications

2021 ◽  
Author(s):  
Huiying Liu ◽  
Jianjun Zhu ◽  
Xiaoxia Kou ◽  
Lingling Guo ◽  
Hongjuan Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Quantitative Pcr ◽  
Cell Lines ◽  
Disease Free Survival ◽  
Rna Modification ◽  
Ppi Network ◽  
Rna Modifications ◽  
Pcr Assay ◽  
Prognostic Predictor ◽  
Quantitative Pcr Assay

Abstract Background: Increasing evidence has pointed to the involvement of RNA modifications in the pathogenesis of human cancers. However, they are rarely studied in hepatocellular carcinoma (HCC). Method: We summarized multiple types of RNA modification-related genes (RMRGs) from public references, and identified differentially expressed RMRGs (DEGs) between HCC tissues and matched normal samples, where their genetic variation were then investigated. The potential hub genes in the protein-protein interaction (PPI) network constructed by co-expression genes of RMRGs were recognized and verified in METTL3-knockdown HCC cell lines by quantitative PCR assay.Results: Seventy-six RMRGs, including six writers, seven readers, and seven erasers, were collected, of which 34 were identified and validated as DEGs. YTHDC2 exhibited the highest mutation rate, while ADAT2 showed widespread deletions. High correlations were observed between the expressions of 34 RMRGs. The PPI network constructed by 1080 co-expression DEGs related to RNA regulations consisted of 513 nodes and 11557 edges, with RPS27A presented the most directed edges and maximum closeness centrality. Patients with high expression of RPS27A showed worse overall survival (P < 0.01) and disease-free survival (P = 0.019). Moreover, RPS27A was found upregulated on high-risk metastatic and recurrent HCC tissues. Quantitative PCR assay indicated that RPS27A was significantly decreased in cancer cell lines when METTL3 was knocked down. Conclusions: Remarkable differences were observed for RNA modifications between HCC and normal samples, and RPS27A could be a poor prognostic predictor for HCC via interacting with METTL3-mediated RNA modifications.

scholarly journals RNA modifications shed new light on DNA's older brother

2017 ◽  
Vol 39 (5) ◽  
pp. 16-19
Author(s):  
Keir H. Murison ◽  
Michelle L. Holland
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Rna Modification ◽  
Stress Adaptation ◽  
Rna Modifications ◽  
Influence Gene Expression

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.

Sign in / Sign up

Export Citation Format

Share Document