Introduction to epigenetics

welcome to our course titled introduction to epigenetics the materials for this first lesson will provide you with the general introduction to epigenetics or above genetics an important research area for molecular biology and important for analysis of molecular data types left chip seek my sole physique and specialized RNA see we hope to make these lessons informative for beginners and advanced users by touching on some important concepts maybe without going into much detail where possible as a quick guide we will introduce important biological and analytical concepts related to the types of data used to analyze epigenetic variation we will also introduce several commonly used tools for epigenetic data analysis more in-depth study will be provided in subsequent lectures and reference materials included in the discussed projects and methods historically the word epigenetics was used to describe events that could not be explained by genetic principles Konrad Waddington that lived between 1905 and 1975 who is given credit for coining the term defined epigenetics as the branch of biology which studies the causal interaction between genes and their products which bring the phenotype into being his understanding of potential epigenetic changes are shown in these figures from his publication on the topic as opposed to his predecessors Waddington understood the limitations of possible epigenetic changes and related the landscape of this potential as a link between genes and the environment over the years numerous biological phenomena some considered bizarre and inexplicable have been lumped into the category of epigenetics these include seemingly unrelated processes such as para mutation in maize position effect variation in the fruit fly Drosophila and imprinting of specific paternal or maternal loss AI in mammals although mysteries abound the field is uncovering common molecular mech underlying epigenetic phenomena that affect human health or understanding of disease and the fascinating and heritable traits that are not recorded in the DNA today we understand epigenetics as the study of mechanisms that cause changes in gene expression but that are not changes in the DNA sequence these mechanisms include DNA methylation histone modification activity of non-coding RNA such as micro RNAs and the effect of non-coding repeating regions in the DNA code before we go into the specifics of epigenetic variation or regulation let's discuss the structure of DNA and how it is organized in eukaryotic cells as you remember the foundational understanding about phenotypes is that DNA codes for genes those genes are transcribed into RNA which are then translated into proteins however these processes appear to be regulated by a variety of mechanisms that are not directly recorded in the actual code of DNA in fact individuals and members of different species can have similar DNA like twins or many conserved genes like humans and monkeys but significant phenotypic variation can be easily observed that is the result of epigenetic changes that are either established and passed through generations or acquired and lost throughout the organisms lifetime the eukaryotic cell has a nucleus that contains tightly packaged DNA folded into structures that we all know as chromosomes these are packaged together by the way of chromatin protein complexes that the DNA is wrapped around on these images you can see how the DNA string has more bumps or beads these visible beads are called histones when these beads were originally discovered scientists first confused them with genes until eventually it was proven that the string-like structures actually contained the genetic code histones can be either grouped together forming lumps of DNA or as we can see in the picture on the right relaxed and spread out the changes in the way DNA is packaged is used for cell division when whole chromosomes need to be moved around or to regulate what code is more or less accessible for transcription the regulation of DNA compactness is regulated in several ways one of these is DNA methylation site design which is one of the amino acids can be modified by a methyl group ch3 attached by a specialized protein called DNA methyl transferase in the first minutes of life when we are composed of a single cell and this epigenetic information has been wiped clean in the fertilized egg the methyl groups have been removed and even and every gene is like all the others through the process of cell differentiation DNA methyl transferases add methyl groups to genes shutting off some in activating others when a cell divides the epigenetic information must be transmitted to each of the new cells a different DNA methyl transferase dnmt1 adds the proper methyl groups to these DNA strands as it is replicated the information is propagated in a tricky way methyl groups almost always added to site design bases with these sequences CG and GC notice that both strands have a cytosine so in a methylated region of DNA both strands will have a methyl group when the DNA is replicated each of the new DNA double helix E's will have one old strand complete with methyl groups and one strand which is not methylated so dnmt1 just needs to look for CG base steps where only one strand has a methyl group the basic repeating unit of chromatin is the nucleosome in which hundred and forty-six base pairs of DNA wraps around an octamer of core histones consisting of pairs of h3 h4 h2a and h2b in terminal tails of histones protrude out of the nucleosome and are subject to a variety of post translational modifications such as acids elation phosphorylation you halation and lysine and arginine methylation a set elation was the first of these modifications to be linked with active transcription and subsequently phosphorylation of histone h3 was found to cooperate with a situation and translational activation some histone methylation events have also been associated with transcription activation and others with gene silencing one important aspect of histones is that they can be changed to alter how much packing the DNA is capable of there are several modifications that affect how well DNA is packaged the basic regulation is done via groups of atoms that are at the ends of histones these can be of several types and will have a positive or a negative charge that either track them together or force them apart the DNA region that is wrapped around the histones can be more or less accessible causing variation in gene expression histone proteins or nucleosomes undergo a host of different post translational modifications including phosphorylation acetylation and methylation which have profound effects on the remodeling of chromatin histone modifications can function either individually or combinatorially to govern such processes as transcription replication DNA repair and apoptosis methyl groups of atoms increased packing an acetal group decreases packing also phosphoryl group can be attached to the histones and cause a decrease in packing these groups of atoms are attached to various types of histones at various locations as the DNA is wrapped around the histones and can be more or less accessible various positions of the DNA are affected these include the promoter region transcription start sites and the introns and exons of genes each one of these elements can have a significant effect on the level of gene expression on alternative splicing as well as other downstream regulation of pathways the size of the region and its location are both important it turns out that different histone modifications are associated with specific widths and profiles of Peaks that can be detected in chip seek data so how can we study comments and changes and histone modification chromatin immunoprecipitation or chip seek uses antibodies designed to bind to specific proteins of interest pío is these can be histones or other complexes attached to the DNA the antibodies bind to proteins thus helping cut out the portions of DNA that we would like to select for sequencing then the antibodies and proteins are removed from DNA and libraries for sequencing are produced the whole process looks the following DNA and protein of interests are selected and antibodies are designed fragmented DNA help select those areas that have proteins attached to them antibodies are then attached to the proteins of interest and those sections are selected then the DNA is released and sequencing libraries are prepared after sequencing we analyze the data for Peaks looking for specific patterns that are associated with different histone modifications and the openness or closeness of DNA the major goal of the chip seek analysis of signal distribution is to detect genome fragments that are enriched with upregulated signals these fragments could be transcription factor binding sites chromatin remodeling or genome transcription events the main algorithmic challenge here is to detect accurately short and long upregulated genome fragments generating a whole genome landscape for the signal probably the most discussed issue in chip seek experiments is the best method to find true peaks in the data a peak is a site where multiple reads have mapped and produced a pileup chip sequencing is most often performed with single and reads and chip fragments are sequenced from their 5 prime ends only this creates two distinct peaks one in each strand with the binding site falling in the middle of these Peaks the distance from the middle of the to the binding site is often referred to as this shift ship si can be used to study histone modifications and the regions that are affected by histone methylation or a situation but the DNA methylation has to be studied using a different method called bisulfate sequencing this method looks for methylated cytosines across the whole Gihon a one of the major challenges in analyzing whole genome bisulfite sequencing data is related to the library preparation step cytosines on both strands of the DNA can be methylated when the strands are separated by sulphate conversion changes the non methylated cytosines to uracil methyl groups protect the methylated cytosine so they are not affected during the subsequent PCR amplification step uracil that appears from by sulphate conversion will be transformed into thymine thus a triple conversion between amino acids occurs at the analytical challenge is to accurately map reads to their original location differentiating between conversions that happened as a result of by sulphate conversion of unmethylated cytosines and thymines that were a part of the original sequence since both strands of the DNA are sequenced their complementarity can be leveraged to address this challenge comparing quality of mapping to the reference genome with potential changes of site assigns to uracil makes the analysis of such data computationally intensive and time-consuming in our next lecture we will discuss non-coding rnas and their role in gene expression regulation and epigenetics

Channel: Pine Biotech

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Keywords: epigenetics, epigenomics, chip-seq, wgbs, chromatin, chromosomes, t-bio, tbioinfo

Id: IAu44BkOaSs

Length: 12min 50sec (770 seconds)

Published: Wed Dec 05 2018