#epitranscriptomics

[didanawisgi]

[owlservice]

Last night I was rereading my notes on nervous system changes during hibernation, and came across RNA motif binding protein 3 (RMBP3), which is posited as the potential master switch allowing hibernation to occur. Long story short, I found out about epitranscriptomics. I knew about epigenetics, and I knew about post translational modifications, and I knew about mRNA splicing variants, but I didn't know about post transcriptional modifications of the mRNA transcript at the level of the nucleotide. Did you guys know about this... It was never mentioned in my degree

[biotechscientist]

Transcriptomics is the branch of molecular biology that focuses on the study of RNA transcripts produced by the genome under specific conditions. It provides insights into gene expression patterns, regulatory mechanisms, and cellular responses at a given time.

Key Techniques in Transcriptomics

RNA Sequencing (RNA-Seq) – A high-throughput method to analyze the complete transcriptome using next-generation sequencing (NGS).

Microarrays – A hybridization-based method that detects specific RNA sequences using complementary probes.

qRT-PCR (Quantitative Reverse Transcription PCR) – Used for precise quantification of specific mRNA levels.

Northern Blotting – A traditional method to detect specific RNA molecules.

Single-cell RNA-Seq (scRNA-Seq) – Studies transcriptomics at a single-cell resolution, helping to understand cellular heterogeneity.

Applications of Transcriptomics

Disease Biomarker Discovery – Identifying gene expression changes in diseases like cancer, diabetes, and neurodegenerative disorders.

Drug Development – Assessing how drugs influence gene expression at the cellular level.

Precision Medicine – Personalized treatment strategies based on an individual's transcriptomic profile.

Systems Biology – Understanding how genes interact in biological networks.

Functional Genomics – Linking transcriptome data with gene function and phenotype.

Challenges in Transcriptomics

Data Complexity – Large datasets require advanced bioinformatics tools for analysis.

RNA Stability – RNA is more prone to degradation than DNA, requiring careful handling.

High Cost – RNA-Seq, especially at single-cell resolution, remains expensive.

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[medicomunicare]

It's a supplement aFTOr all: how tocopherol acetate VESsels for anticancer defences

Epigenetics and epitranscriptomics play a crucial role in modifying gene expression without altering gene sequence. N6-methyladenosine (m6A) is one such mechanism, where methyl groups are added to the N6 position of adenosine on RNA. Adding these methyl groups enhances RNA stability; however, their removal by enzymes can promote development of tumors. High levels of fat mass and…

[healthcaremarketanalysis]

Exploring the Epigenetics Market: Trends, Growth, and Future Prospects

The epigenetics market is gaining significant momentum in the life sciences and healthcare sectors. This field, which studies heritable changes in gene expression without altering the DNA sequence, is instrumental in understanding complex biological processes and diseases. From drug discovery to personalized medicine, epigenetics offers transformative potential, making it a crucial area of research and development.

In this blog, we’ll delve into the key trends, market dynamics, applications, and growth drivers shaping the epigenetics market.

Understanding Epigenetics

Epigenetics refers to modifications on DNA or associated proteins that regulate gene activity without changing the underlying sequence. These modifications include:

DNA Methylation – The addition of methyl groups to DNA, often silencing gene expression.

Histone Modification – Changes in proteins around which DNA is wrapped, affecting gene accessibility.

Non-Coding RNAs – Molecules that influence gene expression post-transcriptionally.

Epigenetic mechanisms are reversible, making them attractive therapeutic targets for diseases like cancer, neurodegenerative disorders, and autoimmune conditions.

Market Overview

Market Size and Growth

The global epigenetics market was valued at approximately $1.4 billion in 2023 and is projected to grow at a CAGR of 15-18% over the next decade. This growth is driven by increasing research in gene therapy, rising cancer prevalence, and advancements in epigenetic technologies.

Key Market Segments

The market can be categorized into the following:

Products:

Reagents

Kits

Instruments (e.g., sequencers, microarrays)

Software

Applications:

Oncology

Developmental Biology

Metabolic Disorders

Neurology

End Users:

Academic Research Institutions

Pharmaceutical and Biotechnology Companies

Contract Research Organizations (CROs)

Drivers of Market Growth

1. Rising Prevalence of Cancer

Cancer is a leading application area for epigenetic research. Abnormal epigenetic modifications are closely linked to tumorigenesis. Epigenetic therapies, such as DNA methylation inhibitors and histone deacetylase (HDAC) inhibitors, are showing promising results in cancer treatment.

2. Advances in Epigenomics Technologies

The development of high-throughput sequencing and microarray platforms has made it possible to study epigenetic changes on a genome-wide scale. Tools like CRISPR-based epigenome editing are expanding research possibilities.

3. Increasing Focus on Personalized Medicine

Epigenetics plays a critical role in tailoring therapies based on individual genetic and epigenetic profiles. This approach is gaining traction, especially in oncology and chronic disease management.

4. Government and Private Funding

Governments worldwide are investing heavily in genomics and epigenetics research. For instance, the National Institutes of Health (NIH) in the U.S. allocates substantial grants for epigenetics projects. Private investments and collaborations are also fueling market growth.

Challenges in the Epigenetics Market

1. High Costs of Research and Equipment

Epigenetic research requires advanced instruments and reagents, which can be cost-prohibitive for smaller organizations.

2. Complexity of Epigenetic Mechanisms

The dynamic and reversible nature of epigenetic changes makes it challenging to pinpoint causal relationships between modifications and diseases.

3. Regulatory and Ethical Issues

Using epigenetic data in personalized medicine raises concerns about data privacy and ethical implications.

Emerging Trends in the Epigenetics Market

1. Integration of AI and Big Data

Artificial Intelligence (AI) and machine learning algorithms are being used to analyze complex epigenomic datasets, accelerating discoveries.

2. Focus on Epitranscriptomics

This subfield studies modifications in RNA rather than DNA, opening new avenues for understanding gene regulation.

3. Development of Epigenetic Biomarkers

Biomarkers are being developed for early diagnosis, prognosis, and treatment monitoring in diseases like cancer, Alzheimer’s, and diabetes.

4. Expansion of Non-Oncology Applications

While oncology dominates the market, epigenetics is increasingly applied in neurodegenerative diseases, cardiovascular disorders, and metabolic syndromes.

Competitive Landscape

Key players in the epigenetics market include:

Illumina, Inc. – Leading in sequencing technologies.

Thermo Fisher Scientific, Inc. – Offering comprehensive epigenetics solutions.

Abcam plc – Specializing in antibodies and kits for epigenetic research.

Qiagen – Providing tools for epigenomic studies.

Merck KGaA – Known for its advanced reagents and inhibitors.

Collaborations, acquisitions, and product launches are common strategies adopted by these players to strengthen their market position.

Applications of Epigenetics

1. Cancer Research and Therapy

Epigenetic drugs are used to reprogram cancer cells, making them more susceptible to traditional therapies.

2. Developmental Biology

Epigenetics helps unravel how environmental factors influence gene expression during development.

3. Neurology

Research in conditions like Alzheimer’s and Parkinson’s diseases focuses on epigenetic mechanisms underlying neuronal dysfunction.

4. Agriculture and Veterinary Science

Epigenetic studies in plants and animals aim to enhance productivity and disease resistance.

Future Prospects

The future of the epigenetics market is promising, with continued advancements in technology and an expanding scope of applications. Personalized medicine and precision oncology are expected to be major growth areas. Moreover, the rise of epigenome editing tools and novel biomarkers will drive innovation in diagnostics and therapeutics.

Conclusion

The epigenetics market represents a dynamic and rapidly evolving field with immense potential to transform healthcare and research. As we continue to uncover the intricacies of the epigenome, the applications of this science will expand, offering solutions to some of the most challenging medical and scientific problems.

For stakeholders, the key to success lies in leveraging technological advancements, fostering collaborations, and addressing ethical challenges. With sustained investment and innovation, epigenetics is poised to become a cornerstone of modern medicine.

[sunaleisocial]

Scientists identify mechanism behind drug resistance in malaria parasite

New Post has been published on https://sunalei.org/news/scientists-identify-mechanism-behind-drug-resistance-in-malaria-parasite/

Scientists identify mechanism behind drug resistance in malaria parasite

Researchers from the Singapore-MIT Alliance for Research and Technology (SMART), in collaboration with MIT, Columbia University Irving Medical Center, and Nanyang Technological University in Singapore (NTU Singapore), have discovered a new link between malaria parasites’ ability to develop resistance to the antimalarial artemisinin (ART) through a cellular process called transfer ribonucleic acid (tRNA) modification. 

This process allows cells to respond rapidly to stress by altering RNA molecules within a cell. As such, this breakthrough discovery advances the understanding of how malaria parasites respond to drug-induced stress and develop resistance, and paves the way for the development of new drugs to combat resistance.

Malaria is a mosquito-borne disease that afflicted 249 million people and caused 608,000 deaths globally in 2022. ART-based combination therapies, which combine ART derivatives with a partner drug, are first-line treatments for patients with uncomplicated malaria. The ART compound helps to reduce the number of parasites during the first three days of treatment, while the partner drug eliminates the remaining parasites. However, Plasmodium falciparum (P. falciparum), the deadliest species of Plasmodium that causes malaria in humans, is developing partial resistance to ART that is widespread across Southeast Asia and has now been detected in Africa.

In a paper titled “tRNA modification reprogramming contributes to artemisinin resistance in Plasmodium falciparum”, published in the journal Nature Microbiology, researchers from SMART’s Antimicrobial Resistance (AMR) interdisciplinary research group documented their discovery: A change in a single tRNA, a small RNA molecule that is involved in translating genetic information from RNA to protein, provides the malaria parasite with the ability to overcome drug stress. The study describes how tRNA modification can alter the parasite’s response to ART and help it survive ART-induced stress by changing its protein expression profile, making the parasite more resistant to the drug. ART partial resistance causes a delay in the eradication of malaria parasites following treatment with ART-based combination therapies, making these therapies less effective and susceptible to treatment failure.

“Our research, the first of its kind, shows how tRNA modification directly influences the parasite’s resistance to ART, highlighting the potential impact of RNA modifications on both disease and health. While RNA modifications have been around for decades, their role in regulating cellular processes is an emerging field. Our findings highlight the importance of RNA modifications for the research community and the broader significance of tRNA modifications in regulating gene expression,” says Peter Dedon, co-lead principal investigator at SMART AMR, the Underwood-Prescott Professor of Biological Engineering at MIT, and one of the authors of the paper.  

“Malaria’s growing drug resistance to artemisinin, the current last-line antimalarial drug, is a global crisis that demands new strategies and therapeutics. The mechanisms behind this resistance are complex and multifaceted, but our study reveals a critical link. We found that the parasite’s ability to survive a lethal dose of artemisinin is linked to the downregulation of a specific tRNA modification. This discovery paves the way for new strategies to combat this growing global threat,” adds Jennifer L. Small-Saunders, assistant professor of medicine in the Division of Infectious Diseases at CUIMC and first author of the paper.

The researchers investigated the role of epitranscriptomics — the study of RNA modifications within a cell — in influencing drug resistance in malaria by leveraging the advanced technology and techniques for epitranscriptomic analysis developed at SMART. This involves isolating the RNA of interest, tRNA, and using mass spectrometry to identify the different modifications present. They isolated and compared the drug-sensitive and drug-resistant malaria parasites, some of which were treated with ART and others left untreated as controls. The analysis revealed changes in the tRNA modifications of drug-resistant parasites, and these modifications were linked to the increased or decreased translation of specific genes in the parasites. The altered translation process was found to be the underlying mechanism for the observed increase in drug resistance. This discovery also expands our understanding of how microbes and cancer cells exploit the normal function of RNA modifications to thwart the toxic effects of drugs and other therapeutics.

“At SMART AMR, we’re at the forefront of exploring epitranscriptomics in infectious diseases and antimicrobial resistance. Epitranscriptomics is an emerging field in malaria research and plays a crucial role in how malaria parasites develop and respond to stress. This discovery reveals how drug-resistant parasites exploit epitranscriptomic stress response mechanisms for survival, which is particularly important for understanding parasite biology,” says Peter Preiser, co-lead principal investigator at SMART AMR, professor of molecular genetics and cell biology at NTU Singapore, and another author of the paper.

The research sets the foundation for the development of better tools to study RNA modifications and their role in resistance while simultaneously opening new avenues for drug development. RNA-modifying enzymes, especially those linked to resistance, are currently understudied, and they are attractive targets for the development of new and more effective drugs and therapies. By hindering the parasite’s ability to manipulate these modifications, drug resistance can be prevented from arising. Researchers at SMART AMR are actively pursuing the discovery and development of small molecule and biological therapeutics that target RNA modifications in viruses, bacteria, parasites, and cancer.

The research is carried out by SMART and supported by the National Research Foundation Singapore under its Campus for Research Excellence And Technological Enterprise program.

[rnomics]

Enhanced ac4C detection in #RNA via chemical reduction and cDNA synthesis with modified dNTPs [Method]

The functional analysis of epitranscriptomic modifications in RNA is constrained by a lack of methods that accurately capture their locations and levels. We previously demonstrated that the RNA modification N4-acetylcytidine (ac4C) can be mapped at base-resolution through sodium borohydride reduction to tetrahydroacetylcytidine (tetrahydro-ac4C), followed by cDNA synthesis to misincorporate adenosine opposite reduced ac4C sites, culminating in C:T mismatches at acetylated cytidines (RedaC:T). However, this process is relatively inefficient, resulting in less than 20% C:T mismatches at a fully modified ac4C site in 18S rRNA. Considering that ac4C locations in other substrates including mRNA are unlikely to reach full penetrance, this method is not ideal for comprehensive mapping. Here, we introduce "RetraC:T" (reduction to tetrahydro-ac4C and reverse transcription with amino-dATP to induce C:T mismatches) as a method with enhanced ability to detect ac4C in cellular RNA. In brief, RNA is reduced through NaBH4 or the closely related reagent sodium cyanoborohydride (NaCNBH3) followed by cDNA synthesis in the presence of a modified DNA nucleotide, 2-amino-dATP, that preferentially binds to tetrahydro-ac4C. Incorporation of the modified dNTP substantially improved C:T mismatch rates, reaching stoichiometric detection of ac4C in 18S rRNA. Importantly, 2-amino-dATP did not result in truncated cDNA products nor increase mismatches at other locations. Thus, modified dNTPs are introduced as a new addition to the toolbox for detecting ac4C at base resolution. http://rnajournal.cshlp.org/cgi/content/short/rna.079863.123v1?rss=1&utm_source=dlvr.it&utm_medium=tumblr

[didanawisgi]

Abstract

The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of “viral factories” by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.

[tumimmtxpapers]

Recent Advances in RNA m6A Modification in Solid Tumors and Tumor Immunity

An analogous field to epigenetics is referred to as epitranscriptomics, which focuses on the study of post-transcriptional chemical modifications in RNA. RNA molecules, including mRNA, tRNA, rRNA, and other non-coding RNA molecules, can be edited with numerous modifications. The most prevalent modification in eukaryotic mRNA is N6-methyladenosine (m⁶A), which is a reversible modification found in over 7000 human genes. Recent technological advances have accelerated the characterization of these... http://dlvr.it/T0MYFV

[jobrxiv]

Postdoc in RNA biology and Epitranscriptomics University of Copenhagen The Sandelin group is looking to recruit a talented postdoctoral researcher for a project on how chemical modifications on RNA impact RNA fate See the full job description on jobRxiv: https://jobrxiv.org/job/university-of-copenhagen-27778-postdoc-in-rna-biology-and-epitranscriptomics/?feed_id=65208 #ScienceJobs #hiring #research Copenhagen #Denmark #PostdoctoralFellow

[healthcaremarketanalysis]

Exploring the Epigenetics Market: Trends, Growth, and Future Prospects

The epigenetics market is gaining significant momentum in the life sciences and healthcare sectors. This field, which studies heritable changes in gene expression without altering the DNA sequence, is instrumental in understanding complex biological processes and diseases. From drug discovery to personalized medicine, epigenetics offers transformative potential, making it a crucial area of research and development.

In this blog, we’ll delve into the key trends, market dynamics, applications, and growth drivers shaping the epigenetics market.

Understanding Epigenetics

Epigenetics refers to modifications on DNA or associated proteins that regulate gene activity without changing the underlying sequence. These modifications include:

DNA Methylation – The addition of methyl groups to DNA, often silencing gene expression.

Histone Modification – Changes in proteins around which DNA is wrapped, affecting gene accessibility.

Non-Coding RNAs – Molecules that influence gene expression post-transcriptionally.

Epigenetic mechanisms are reversible, making them attractive therapeutic targets for diseases like cancer, neurodegenerative disorders, and autoimmune conditions.

Market Overview

Market Size and Growth

The global epigenetics market was valued at approximately $1.4 billion in 2023 and is projected to grow at a CAGR of 15-18% over the next decade. This growth is driven by increasing research in gene therapy, rising cancer prevalence, and advancements in epigenetic technologies.

Key Market Segments

The market can be categorized into the following:

Products:

Reagents

Kits

Instruments (e.g., sequencers, microarrays)

Software

Applications:

Oncology

Developmental Biology

Metabolic Disorders

Neurology

End Users:

Academic Research Institutions

Pharmaceutical and Biotechnology Companies

Contract Research Organizations (CROs)

Drivers of Market Growth

1. Rising Prevalence of Cancer

Cancer is a leading application area for epigenetic research. Abnormal epigenetic modifications are closely linked to tumorigenesis. Epigenetic therapies, such as DNA methylation inhibitors and histone deacetylase (HDAC) inhibitors, are showing promising results in cancer treatment.

2. Advances in Epigenomics Technologies

The development of high-throughput sequencing and microarray platforms has made it possible to study epigenetic changes on a genome-wide scale. Tools like CRISPR-based epigenome editing are expanding research possibilities.

3. Increasing Focus on Personalized Medicine

Epigenetics plays a critical role in tailoring therapies based on individual genetic and epigenetic profiles. This approach is gaining traction, especially in oncology and chronic disease management.

4. Government and Private Funding

Governments worldwide are investing heavily in genomics and epigenetics research. For instance, the National Institutes of Health (NIH) in the U.S. allocates substantial grants for epigenetics projects. Private investments and collaborations are also fueling market growth.

Challenges in the Epigenetics Market

1. High Costs of Research and Equipment

Epigenetic research requires advanced instruments and reagents, which can be cost-prohibitive for smaller organizations.

2. Complexity of Epigenetic Mechanisms

The dynamic and reversible nature of epigenetic changes makes it challenging to pinpoint causal relationships between modifications and diseases.

3. Regulatory and Ethical Issues

Using epigenetic data in personalized medicine raises concerns about data privacy and ethical implications.

Emerging Trends in the Epigenetics Market

1. Integration of AI and Big Data

Artificial Intelligence (AI) and machine learning algorithms are being used to analyze complex epigenomic datasets, accelerating discoveries.

2. Focus on Epitranscriptomics

This subfield studies modifications in RNA rather than DNA, opening new avenues for understanding gene regulation.

3. Development of Epigenetic Biomarkers

Biomarkers are being developed for early diagnosis, prognosis, and treatment monitoring in diseases like cancer, Alzheimer’s, and diabetes.

4. Expansion of Non-Oncology Applications

While oncology dominates the market, epigenetics is increasingly applied in neurodegenerative diseases, cardiovascular disorders, and metabolic syndromes.

Competitive Landscape

Key players in the epigenetics market include:

Illumina, Inc. – Leading in sequencing technologies.

Thermo Fisher Scientific, Inc. – Offering comprehensive epigenetics solutions.

Abcam plc – Specializing in antibodies and kits for epigenetic research.

Qiagen – Providing tools for epigenomic studies.

Merck KGaA – Known for its advanced reagents and inhibitors.

Collaborations, acquisitions, and product launches are common strategies adopted by these players to strengthen their market position.

Applications of Epigenetics

1. Cancer Research and Therapy

Epigenetic drugs are used to reprogram cancer cells, making them more susceptible to traditional therapies.

2. Developmental Biology

Epigenetics helps unravel how environmental factors influence gene expression during development.

3. Neurology

Research in conditions like Alzheimer’s and Parkinson’s diseases focuses on epigenetic mechanisms underlying neuronal dysfunction.

4. Agriculture and Veterinary Science

Epigenetic studies in plants and animals aim to enhance productivity and disease resistance.

Future Prospects

The future of the epigenetics market is promising, with continued advancements in technology and an expanding scope of applications. Personalized medicine and precision oncology are expected to be major growth areas. Moreover, the rise of epigenome editing tools and novel biomarkers will drive innovation in diagnostics and therapeutics.

Conclusion

The epigenetics market represents a dynamic and rapidly evolving field with immense potential to transform healthcare and research. As we continue to uncover the intricacies of the epigenome, the applications of this science will expand, offering solutions to some of the most challenging medical and scientific problems.

For stakeholders, the key to success lies in leveraging technological advancements, fostering collaborations, and addressing ethical challenges. With sustained investment and innovation, epigenetics is poised to become a cornerstone of modern medicine.