Ago2-Dependent Processing Allows miR-451 to Evade the Global MicroRNA Turnover Elicited during Erythropoiesis.

MicroRNAs (miRNAs) are sequentially processed by two RNase III enzymes, Drosha and Dicer. miR-451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute-2 (Ago2). miR-451 is highly conserved in vertebrates and regulates erythrocyte maturation, where it becomes the most abundant miRNA. However, the basis for the non-canonical biogenesis of miR-451 is unclear. Here, we show that Ago2 is less efficient than Dicer in processing pre-miRNAs, but this deficit is overcome when miR-144 represses Dicer in a negative-feedback loop during erythropoiesis. Loss of miR-144-mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR-451 maturation. Overexpression of Ago2 rescues some of the defects of miR-451 processing. Thus, the evolution of Ago2-dependent processing allows miR-451 to circumvent the global repression of canonical miRNAs elicited, in part, by the miR-144 targeting of Dicer during erythropoiesis.

Recruitment of CTCF to an Fto enhancer is responsible for transgenerational inheritance of BPA-induced obesity.

The mechanisms by which environmentally-induced epiphenotypes are transmitted transgenerationally in mammals are poorly understood. Here we show that exposure of pregnant mouse females to bisphenol A (BPA) results in obesity in the F2 progeny due to increased food intake. This epiphenotype can be transmitted up to the F6 generation. Analysis of chromatin accessibility in sperm of the F1-F6 generations reveals alterations at sites containing binding motifs for CCCTC-binding factor (CTCF) at two cis-regulatory elements (CREs) of the Fto gene that correlate with transmission of obesity. These CREs show increased interactions in sperm of obese mice with the Irx3 and Irx5 genes, which are involved in the differentiation of appetite-controlling neurons. Deletion of the CTCF site in Fto results in mice that have normal food intake and fail to become obese when ancestrally exposed to BPA. The results suggest that epigenetic alterations of Fto can lead to the same phenotypes as genetic variants.

Practical considerations for continuous glucose monitoring in elite athletes with type 1 diabetes mellitus: A narrative review.

Type 1 diabetes mellitus (T1DM) refers to a metabolic condition where a lack of insulin impairs the usual homeostatic mechanisms to control blood glucose levels. Historically, participation in competitive sport has posed a challenge for those with T1DM, where the dynamic changes in blood glucose during exercise can result in dangerously high (hyperglycaemia) or low blood glucoses (hypoglycaemia) levels. Over the last decade, research and technological development has enhanced the methods of monitoring and managing blood glucose levels, thus reducing the chances of experiencing hyper- or hypoglycaemia during exercise. The introduction of continuous glucose monitoring (CGM) systems means that glucose can be monitored conveniently, without the need for frequent fingerpick glucose checks. CGM devices include a fine sensor inserted under the skin, measuring levels of glucose in the interstitial fluid. Readings can be synchronized to a reader or mobile phone app as often as every 1-5 min. Use of CGM devices is associated with lower HbA1c and a reduction in hypoglycaemic events, promoting overall health and athletic performance. However, there are limitations to CGM, which must be considered when being used by an athlete with T1DM. These limitations can be addressed by individualized education plans, using protective equipment to prevent sensor dislodgement, as well as further research aiming to: (i) account for disparities between CGM and true blood glucose levels during vigorous exercise; (ii) investigate the effects of temperature and altitude on CGM accuracy, and (iii) explore of the sociological impact of CGM use amongst sportspeople without diabetes on those with T1DM.

Dysregulated mitochondrial and cytosolic tRNA m1A methylation in Alzheimer's disease.

RNA modifications affect many aspects of RNA metabolism and are involved in the regulation of many different biological processes. Mono-methylation of adenosine in the N1 position, N1-methyladensoine (m1A), is a reversible modification that is known to target rRNAs and tRNAs. m1A has been shown to increase tRNA structural stability and induce correct tRNA folding. Recent studies have begun to associate the dysregulation of epitranscriptomic control with age-related disorders such as Alzheimer's disease. Here, we applied the newly developed m1A-quant-seq approach to map the brain abundant m1A RNA modification in the cortex of an Alzheimer's disease mouse model, 5XFAD. We observed hypomethylation in both mitochondrial and cytosolic tRNAs in 5XFAD mice compared with wild type. Furthermore, the main enzymes responsible for the addition of m1A in mitochondrial (TRMT10C, HSD17B10) and cytosolic tRNAs (TRMT61A) displayed decreased expression in 5XFAD compared with wild-type mice. Knockdown of these enzymes results in a more severe phenotype in a Drosophila tau model, and differential m1A methylation is correlated with differences in mature mitochondrial tRNA expression. Collectively, this work suggests that hypo m1A modification in tRNAs may play a role in Alzheimer's disease pathogenesis.

METTL3 Gains R/W Access to the Epitranscriptome.

Epitranscriptomic marks are dynamically placed on mRNA by "writer" or "eraser" enzymes, while "readers" modulate their function accordingly. Lin et al. (2016) now report that the N6-methyladenosine:RNA methyltransferase METTL3 is both a writer and a reader, directly enhancing mRNA translation.

Differential RNA methylation analysis for MeRIP-seq data under general experimental design.

MOTIVATION: RNA epigenetics is an emerging field to study the post-transcriptional gene regulation. The dynamics of RNA epigenetic modification have been reported to associate with many human diseases. Recently developed high-throughput technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables the transcriptome-wide profiling of N6-methyladenosine (m6A) modification and comparison of RNA epigenetic modifications. There are a few computational methods for the comparison of mRNA modifications under different conditions but they all suffer from serious limitations. RESULTS: In this work, we develop a novel statistical method to detect differentially methylated mRNA regions from MeRIP-seq data. We model the sequence count data by a hierarchical negative binomial model that accounts for various sources of variations and derive parameter estimation and statistical testing procedures for flexible statistical inferences under general experimental designs. Extensive benchmark evaluations in simulation and real data analyses demonstrate that our method is more accurate, robust and flexible compared to existing methods. AVAILABILITY AND IMPLEMENTATION: Our method TRESS is implemented as an R/Bioconductor package and is available at https://bioconductor.org/packages/devel/TRESS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Epitranscriptomic dynamics in brain development and disease.

Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.

Expansion of Human-Specific GGC Repeat in Neuronal Intranuclear Inclusion Disease-Related Disorders.

Neuronal intranuclear inclusion disease (NIID) is a slowly progressing neurodegenerative disease characterized by eosinophilic intranuclear inclusions in the nervous system and multiple visceral organs. The clinical manifestation of NIID varies widely, and both familial and sporadic cases have been reported. Here we have performed genetic linkage analysis and mapped the disease locus to 1p13.3-q23.1; however, whole-exome sequencing revealed no potential disease-causing mutations. We then performed long-read genome sequencing and identified a large GGC repeat expansion within human-specific NOTCH2NLC. Expanded GGC repeats as the cause of NIID was further confirmed in an additional three NIID-affected families as well as five sporadic NIID-affected case subjects. Moreover, given the clinical heterogeneity of NIID, we examined the size of the GGC repeat among 456 families with a variety of neurological conditions with the known pathogenic genes excluded. Surprisingly, GGC repeat expansion was observed in two Alzheimer disease (AD)-affected families and three parkinsonism-affected families, implicating that the GGC repeat expansions in NOTCH2NLC could also contribute to the pathogenesis of both AD and PD. Therefore, we suggest defining a term NIID-related disorders (NIIDRD), which will include NIID and other related neurodegenerative diseases caused by the expanded GGC repeat within human-specific NOTCH2NLC.

Detecting m6A methylation regions from Methylated RNA Immunoprecipitation Sequencing.

MOTIVATION: The post-transcriptional epigenetic modification on mRNA is an emerging field to study the gene regulatory mechanism and their association with diseases. Recently developed high-throughput sequencing technology named Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) enables one to profile mRNA epigenetic modification transcriptome wide. A few computational methods are available to identify transcriptome-wide mRNA modification, but they are either limited by over-simplified model ignoring the biological variance across replicates or suffer from low accuracy and efficiency. RESULTS: In this work, we develop a novel statistical method, based on an empirical Bayesian hierarchical model, to identify mRNA epigenetic modification regions from MeRIP-seq data. Our method accounts for various sources of variations in the data through rigorous modeling and applies shrinkage estimation by borrowing information from transcriptome-wide data to stabilize the parameter estimation. Simulation and real data analyses demonstrate that our method is more accurate, robust and efficient than the existing peak calling methods. AVAILABILITY AND IMPLEMENTATION: Our method TRES is implemented as an R package and is freely available on Github at https://github.com/ZhenxingGuo0015/TRES. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The emerging epitranscriptomics of long noncoding RNAs.

The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.

Sport-related concussion knowledge and attitudes of staff working in English elite women's football: a survey-based study.

BACKGROUND: Sport-related concussion (SRC) remains an injury of concern in sport, including football(soccer). There has been little investigation into SRC knowledge and attitudes of support staff working in the professional setting. METHODS: An amended version of the Rosenbaum Concussion Knowledge and Attitudes Survey(RoCKAS) was distributed online to coaching staff, and medical and performance staff, working at clubs in the English Football Association Women's SuperLeague (WSL) and Championship. Completion of the survey generated two scores: concussion knowledge index (CKI) and concussion attitudes index (CAI). RESULTS: Sixty-three completed surveys were returned. Eighteen respondents were coaching staff, and 45 were medical and performance staff. The median CKI in medical and performance staff was significantly greater than in coaching staff. There was no significant difference in CAIbetween coaching staff and medical and performance staff. There was no correlation between CKI and CAI across all staff. CONCLUSION: Medical and performance staff working in elite women's football have greater knowledge of SRC than coaching staff. However, this does not always translate into safe behaviours on the field. Education should continue to be mandated across the professional game amongst support staff in order to maximise player welfare and enhance injury outcomes, whilst also reinforcing present SRC guidance.

Analyzing mRNA Epigenetic Sequencing Data with TRESS.

RNA epigenetics has emerged as an active topic to study gene regulation mechanisms. In this regard, the MeRIP-seq technology allows profiling transcriptome-wide mRNA modifications, in particular m6A. The primary goals for the analysis of MeRIP-seq data are the identification of m6A-methylated regions under each condition and across different biological conditions. Here we describe detailed procedures to guide researchers in MeRIP-seq data analyses by providing step-by-step instructions of the dedicated bioconductor package TRESS.

Sport-related concussion attitudes and knowledge in elite English female footballers.

BACKGROUND: Sport-related concussions (SRC) are more common and more severe in women's football than men's yet the knowledge and attitudes of SRC in the women's game are not well understood. The objective of this study was to assess the SRC knowledge and attitude in elite female footballers. METHODS: An online questionnaire was sent to all registered players in the English Football Association Women's Super League (WSL) and Championship. Respondents completed an amended version of the Rosenbaum Concussion Knowledge and Attitudes Survey (RoCKAS). Concussion Knowledge Index (CKI) and Concussion Attitudes Index (CAI) scores were derived for all respondents. RESULTS: One hundred and twenty-three players completed the survey with 111 fitting the inclusion criteria. The mean CKI score was 20.5 ± 2.3 and the mean CAI score was 63.3 ± 6.3. A weak positive correlation was shown between the CKI and CAI (r = 0.20; p = 0.03). Previous concussion education had a significant impact on increased knowledge (U = 1198; p = 0.04). There was no significant difference in concussion attitudes and knowledge between the WSL and Championship or in those with a previous concussion history and no previous concussion (p > 0.05). CONCLUSION: Previous SRC education demonstrated an increased knowledge around concussion but a limited impact towards concussion attitudes. It is suggested that concussion education should be mandated across the professional game to enhance player welfare.

Target-Specific Profiling of RNA m5C Methylation Level Using Amplicon Sequencing.

Mapping the position and quantifying the level of 5-methylcytosine (m5C) as a modification in different types of cellular RNA is an important objective in the field of epitranscriptomics. Bisulfite conversion has long been the gold standard for the detection of m5C in DNA, but it can also be applied to RNA. Here, we detail methods for bisulfite treatment of RNA, locus-specific PCR amplification, and detection of candidate sites by sequencing on the Illumina MiSeq platform.

N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease.

BACKGROUND: N6-methyladenosine (m6A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain. RESULTS: We show that m6A modification displays temporal and spatial dynamics during neurodevelopment and aging. Genes that are temporally differentially methylated are more prone to have mRNA expression changes and affect many pathways associated with nervous system development. Furthermore, m6A shows a distinct tissue-specific methylation profile, which is most pronounced in the hypothalamus. Tissue-specific methylation is associated with an increase in mRNA expression and is associated with tissue-specific developmental processes. During the aging process, we observe significantly more m6A sites as age increases, in both mouse and human. We show a high level of overlap between mouse and human; however, humans at both young and old ages consistently show more m6A sites compared to mice. Differential m6A sites are found to be enriched in alternative untranslated regions of genes that affect aging-related pathways. These m6A sites are associated with a strong negative effect on mRNA expression. We also show that many Alzheimer-related transcripts exhibit decreased m6A methylation in a mouse model of Alzheimer's disease, which is correlated with reduced protein levels. CONCLUSIONS: Our results suggest that m6A exerts a critical function in both early and late brain development in a spatio-temporal fashion. Furthermore, m6A controls protein levels of key genes involved in Alzheimer's disease-associated pathways, suggesting that m6A plays an important role in aging and neurodegenerative disease.

Dynamic N6-methyladenosine RNA methylation in brain and diseases.

N6-methyladenosine (m6A) is a dynamic RNA modification that regulates various aspects of RNA metabolism and has been implicated in many biological processes and transitions. m6A is highly abundant in the brain; however, only recently has the role of m6A in brain development been a focus. The machinery that controls m6A is critically important for proper neurodevelopment, and the precise mechanisms by which m6A regulates these processes are starting to emerge. However, the role of m6A in neurodegenerative and neuropsychiatric diseases still requires much elucidation. This review discusses and summarizes the current body of knowledge surrounding the function of the m6A modification in regulating normal brain development, neurodegenerative diseases and outlines possible future directions.

Recommendations for return to sport during the SARS-CoV-2 pandemic.

In this viewpoint we make specific recommendations that can assist and make the return to sport/exercise as safe as possible for all those impacted - from the recreational athlete to the elite athlete. We acknowledge that there are varying rules and regulations around the world, not to mention the varying philosophies and numerous schools of thought as it relates to return to sport/exercise and we have been cognisant of this in our recommendations. Despite the varying rules and circumstances around the world, we believe it is essential to provide some helpful and consistent guidance for return to training and sport for sport and exercise physicians around the world at this most difficult time. The present viewpoint provides practical and medical recommendations on the resumption to sport process.

Assessing miR-451 Activity and Its Role in Erythropoiesis.

The ability to microinject small RNAs and mRNAs into zebrafish embryos, of different genetic backgrounds, allows for the precise dissection of microRNA processing pathways at the molecular level, while simultaneously provides insight into their physiologic role. Here, we apply such an approach to determine the impact of Argonaute 2 in the processing of miR-451, a vertebrate-specific microRNA required for terminal erythrocyte differentiation. This was achieved using fluorescent microRNA reporter sensor assays and phenotype rescue experiments.