presentation on epigenomics , and technologies in epigenomics
- 1. CENTRE FOR BIOINFORMATICS PRESENTATION TOPIC- CONCEPT OF EPIGENOMICS SUBMITTED TO - DR. AJIT KUMAR SUBMITTED BY- YANSHIKA ROLLNO- 2318 MSC.BIOINFORMATICS (2ND SEM)
- 2. CONTENT… INTRODUCTION TO EPIGENOMICS MECHANISM TECHNOLOGIES IN EPIGENOMICS NEXT GENERATION SEQUENCING MICROARRAY BASED APPROACHES BIOINFORMATICS TOOL APPLICATIONS OF EPIGENOMICS FUTURE CHALLANGES
- 3. Epigenomics Epigenomics is a field of study that explores the complete set of epigenetic modifications across the entire genome of an organism. Epigenetics refers to changes in gene expression or cellular phenotype that occur without alterations in the underlying DNA sequence. Epigenetic modifications can include DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA
- 4. Epigenetics change is a regular and natural occurrence but can also be influenced by several factors including age, the environment / lifestyle, and disease state. Epigenetics modifications can manifest as commonly as the manner in which cells terminally differentiate to end up as skin cells and liver cells. Epigenetics change can have more damaging effects that can result in diseases like cancer .
- 6. DNA Methylation DNA methylation works by adding a chemical group to DNA. Typically, this group is added to specific places on the DNA, where it blocks the proteins that attach to DNA to “read” the gene. This chemical group can be removed through a process called demethylation. Typically, methylation turns genes “off” and demethylation turns genes “on
- 7. Histone modification DNA wraps around proteins called histones. When histones are tightly packed together, proteins that ‘read’ the gene cannot access the DNA as easily, so the gene is turned “off.” When histones are loosely packed, more DNA is exposed or not wrapped around a histone and can be accessed by proteins that ‘read’ the gene, so the gene is turned “on.” Chemical groups can be added or removed from histones to make the histones more tightly or loosely packed, turning genes “off” or “on.”
- 8. Non-coding RNA Your DNA is used as instructions for making coding and non-coding RNA. Coding RNA is used to make proteins. Non-coding RNA helps control gene expression by attaching to coding RNA, along with certain proteins, to break down the coding RNA so that it cannot be used to make proteins. Non- coding RNA may also recruit proteins to modify histones to turn genes “on” or “off.”
- 9. Technologies in Epigenomics •Next-generation sequencing (NGS) technologies •Microarray-based approaches •Bioinformatics tools for epigenomic data analysis
- 10. Next-generation sequencing (NGS) technologies Next-generation sequencing (NGS) technologies represent a revolutionary advancement in genomic research and have significantly transformed the field of molecular biology. NGS enables rapid and cost-effective sequencing of DNA or RNA molecules, allowing researchers to decipher entire genomes, transcriptomes, and epigenomes with unprecedented speed and accuracy.
- 11. 1. Library Preparation: The process begins with the extraction of DNA or RNA from the sample of interest, such as a tissue biopsy or cultured cells. The extracted nucleic acids undergo fragmentation into smaller fragments, typically ranging from a few hundred to several thousand base pairs in length. Adapters containing short DNA sequences are ligated to the ends of the fragmented nucleic acids. These adapters serve as priming sites for subsequent amplification and sequencing reactions.
- 13. 2. Sequencing: Following library preparation, the fragmented DNA or RNA molecules are loaded onto a sequencing platform. NGS platforms utilize various sequencing-by-synthesis methods, such as Illumina sequencing, Ion Torrent sequencing, or Oxford Nanopore sequencing. During sequencing-by-synthesis, nucleotide bases are sequentially added to the growing DNA strand, and the incorporation of each base is detected and recorded in real-time. Fluorescently labeled nucleotides (in Illumina sequencing) or ion- sensitive semiconductor detectors (in Ion Torrent sequencing) are used to identify the incorporated bases. As the sequencing reaction progresses, millions of DNA fragments are simultaneously sequenced in parallel.
- 15. 3. Data Analysis: The raw sequencing data generated by NGS platforms consist of short DNA sequences (reads) corresponding to the original DNA or RNA fragments. Bioinformatics tools and algorithms are employed to process, align, and assemble the sequencing reads into longer contiguous sequences (contigs) or complete genomes. Additionally, NGS data analysis involves identifying genetic variants, quantifying gene expression levels, mapping epigenetic modifications, and conducting various downstream analyses.
- 17. Microarray-based approaches Microarray-based approaches are powerful tools used in genomics and molecular biology to simultaneously analyze the expression levels of thousands to millions of genes or genetic variants in a sample. These approaches involve the fabrication of microarrays, also known as gene chips or DNA chips, which consist of microscopic spots of DNA or RNA probes immobilized on a solid surface, such as a glass slide or silicon wafer.
- 18. 1. Probe Design and Array Fabrication •DNA or RNA probes, which are short sequences of nucleic acids complementary to specific target genes or transcripts, are designed and synthesized. •The probes are then arrayed onto the surface of a solid support, such as a glass slide, in a spatially defined manner, forming a microarray. •Each spot on the microarray contains thousands to millions of copies of a single probe sequence.
- 19. 2. Sample Preparation and Hybridization •Total RNA or cDNA synthesized from RNA samples is labeled with fluorescent dyes (e.g., Cy3 and Cy5) or other detectable markers. •The labeled RNA or cDNA samples are hybridized to the microarray, allowing them to anneal to their complementary probes on the array. •During hybridization, the degree of binding between the labeled sample molecules and the immobilized probes is influenced by factors such as sequence complementarity, temperature, and stringency conditions.
- 20. 3. Detection and Data Analysis: 3. Detection and Data Analysis: •Following hybridization, the microarray is scanned using a fluorescence scanner or other detection system to visualize the bound fluorescent molecules. •The fluorescence intensity at each spot on the microarray corresponds to the abundance of the corresponding gene or transcript in the sample. •Data analysis software is used to process and analyze the raw microarray data, including background subtraction, normalization, and statistical analysis.
- 21. Bioinformatics tools for epigenomic data analysis Bioinformatics tools play a crucial role in analyzing epigenomic data, allowing researchers to extract meaningful insights from large-scale datasets generated by techniques such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), DNA methylation profiling, and chromatin accessibility assays. These tools encompass a wide range of software packages, algorithms, and databases designed to process, visualize, and interpret epigenomic data.
- 22. Epigenome Browser Tools: Visualization tools like the UCSC Genome Browser, IGV (Integrative Genomics Viewer), and WashU Epigenome Browser allow researchers to explore and visualize epigenomic datasets in the context of genomic annotations and other genomic features. Epigenomics Databases: Databases such as ENCODE, Roadmap Epigenomics, and the NIH Epigenomics Data Resource (EDR) provide comprehensive repositories of epigenomic data from various cell types and tissues, along with associated metadata and analysis tools.
- 23. Applications of Epigenomics •Implications in disease research (cancer, neurological disorders, etc.) •Personalized medicine and therapeutic interventions •Environmental and lifestyle factors influencing epigenetic regulation
- 24. Cancer Epigenetic alterations are common in cancer and can contribute to tumor initiation, progression, and metastasis. DNA methylation changes, histone modifications, and dysregulation of non-coding RNAs are frequently observed in cancer cells.
- 25. NEUROLOGICAL DISORDER Alzheimer's Disease: A progressive neurodegenerative disorder characterized by cognitive decline, memory loss, and changes in behavior. Alzheimer's disease is the most common cause of dementia in older adults
- 26. Migraine: A neurological disorder characterized by recurrent episodes of severe headaches, often accompanied by sensory disturbances, such as visual disturbances (aura), nausea, and sensitivity to light and sound
- 27. Personalized medicine and therapeutic interventions Genomic Medicine: Pharmacogenomics, a subset of genomic medicine, focuses on how genetic variations influence drug metabolism, efficacy, and toxicity. By identifying genetic markers predictive of drug response, healthcare providers can optimize medication selection and dosing for each patient. Gene Therapy and Gene Editing: Gene therapy and gene editing technologies offer the potential to correct or modify disease- causing genetic mutations at the molecular level.
- 28. Environmental Influence on the Epigenome The environmental influence on the epigenome refers to how external factors, such as lifestyle, diet, stress, toxins, and other environmental exposures, can modify gene expression patterns without altering the underlying DNA sequence.
- 30. 1. Chemical Exposures: Various chemicals found in the environment, including pollutants, pesticides, heavy metals, and certain medications, can alter epigenetic marks. For example, exposure to pollutants like bisphenol A (BPA) or polycyclic aromatic hydrocarbons (PAHs), potentially contributing to adverse health outcomes such as cancer or neurological disorders. 2. Diet and Nutrition: Dietary components can influence epigenetic mechanisms through various means. For instance, folate, vitamins, and other micronutrients are involved in one-carbon metabolism, which plays a critical role in DNA methylation.
- 31. Stress: Chronic stress can trigger physiological responses in the body, including the release of stress hormones like cortisol. These hormones can impact epigenetic regulation by influencing DNA methylation, histone modifications, and the expression of non-coding RNAs. Physical Activity: Exercise and physical activity have been shown to induce epigenetic modifications, particularly in skeletal muscle and adipose tissue. Regular exercise can alter DNA methylation patterns and histone modifications in genes related to metabolism, inflammation, and oxidative stress.
- 32. Challenges and Future Directions Epigenomic research faces several technical challenges that impact data quality, reproducibility, and interpretation. Some of the key technical challenges in epigenomic research include: Sample Heterogeneity: Epigenomic studies often involve the analysis of complex biological samples composed of multiple cell types. Heterogeneity within samples can confound data interpretation, as epigenetic profiles may vary across cell types. Techniques for isolating specific cell populations or single-cell epigenomic methods are needed to accurately characterize cell-type- specific epigenetic signatures.
- 33. Low Input and Limited Sample Availability: Epigenomic assays typically require small amounts of starting material, particularly for rare or precious samples, such as clinical biopsies or patient-derived tissues. Developing robust protocols and optimized workflows for low-input samples is essential for obtaining reliable epigenomic data from limited material.