Questions tagged [epigenetics]

Mechanisms for inheriting phenotype outside of the genomic DNA sequence.

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Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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Role of epigenetics in evolution and transmission of defects caused by drugs

In a documentary, they were saying that epigenetics changes caused by the environment in an individual can be transferred to the following generations. I have some questions on that: How many ...
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How can we determine which chromosome came from which parent?

In this article there is a graph (figure 1) describing different levels of methylation in the maternal and paternal chromosomes after karyogamy. How can the researchers identify which chromosome ...
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Tree-pest coevolution

Many trees first reproduce decades after germination. Many pests of trees reproduce in under a year. It would seem that the pests have an advantage in the evolutionary arms-race, as they can evolve ...
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Can untargeted metabolomics detect epigenomic changes such as methylation?

My main focus is transcriptomics analysis and very recently I have also started working on metabolomics. From my transcriptomic data it looks like there is a gene/protein that could potentially ...
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Has lamarckism been discredited? [duplicate]

Lamarckism is a pre-darwinian theory according to which an organism's traits acquired to adapt to the environment are passed onto its offspring. A couple of years ago, I attended an event with Richard ...
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DNA methylation and the validity of the definition of epigenetics

I am currently studying a textbook that presents the following definition of epigenetics: Epigenetics is defined as heritable changes in gene expression without changes in the DNA sequence. The ...
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Fully understanding the Horvath clock and other epigenetic clocks?

My goal is to deeply understand both biological and quantitative theories that underly the Horvath clock and other epigenetic clocks and especially their limitations. I would love to know references ...
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Can epigenetics have positive impact on the genes are development?

I know that epigenetics have capacity to affect and degrade the genes thereby inducing problems/illness/degradation in body functions. Can they also make better genes or have positive impact on ...
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Single-cell ATAC seq arrays

As part of a data analysis project, I encountered two kinds of single-cell assays for transposase-accessible chromatin using sequencing (single-cell ATAC seq) methods. The first uses combinatorial ...
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Studying the epigenetic variability, can I use SNPs?

So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed ...
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what causes epigenetic dysregulation in cancer?

Do mutations in regulatory gene sequences lead to changes in epigenetic alterations in cancer, and if so which ones? I know abnormal hypermethylation of GCP islands occurs in promoters of tumour ...
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Are epigenetic modifications the most stable mechanisms for cell differentiation?

Wondering what the general take is on what are the molecular mechanisms that are mostly responsible for cell type differentiation stability; ie, for a cell's identity to actually become 'locked in' ...
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Is it possible to change the DNA of all the cells of an adult human [closed]

The process of making and transferring changes is pretty straightforward relatively speaking in an embroyo. You change the DNA of one cell and all the cells now inherit this change. But let's say ...
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Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that?

Is there natural biological processes in which the full (full reprogramming into pluripotent state) or partial (partial reprogramming, stopped before point-of-no-return, preserving the functional ...
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Techniques of molecular medicine/biology for aesthetic medicine?

Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but ...
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why nucleosome spacing is longer in heterochromatin than euchromatin

Heterochromatin is defined as tightly packed form of DNA. But some experiments show that the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are longer ...
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Do epigenetics determine the proteins a cell produces and therefore it's function?

I'm having trouble understanding what epigenetics is in a simple sense. How I imagine it is that if we had 2 twins with identical DNA and we let them live we will see that they'll develop differently....
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Is there any example of genetic mechanism of delayed onset toxic effects?

We know that exposure to many toxic chemicals during embryonic development may show toxic effects later in life. It is called Developmental Origins of Health and Disease (DOHAD). Most of the ...
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Semantics Question: epigenetic mark on a person's DNA?

In an article on biomarkers of child abuse, the author referred to an "epigenetic mark on a person's DNA". It's a popular science article, so the language may reflect a combination of the journalist's ...
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Can supplements affect DNA? (Could 10,000% Methylcobalamin affect MTHFR genotype)

Originally titled "Could B12 supplementation affect dna test results for B12 need?" - B12 just seems like a good example question to frame the more general question of "Can supplements affect DNA?" I ...
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What is the relationship between induction of cell differentiation and DNA methylation status?

This may sound like a broad question to ask, but I am working on interpreting a review article for my epigenetics course and I'm having trouble reconciling two seemingly contradictory things this ...
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epigenetic vs. environmental factors

I'm trying to understand the difference between epigenetic and environmental factors. For example, if gene A increases the risk of lung cancer by 50% and smoking increases the risk by another 75% when ...
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How can epigenetic changes be erased if they are inherited?

I’m a little bit confused about DNA methlyation reprogramming and about the nature of an epigenetic phenomenon. According to Wikipedia: After fertilization the paternal and maternal genomes are ...
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What kind of code is neural code? [closed]

It's rather clear and commonsensical what the genetic code is, how it is inscribed (as a sequence of nucleotides in the DNA), what it means, and most of all: how it is decoded and works. It's less ...
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“50% of the variance in antisocial phenotypes is the result of genetic factors” means what?

How can i understand the following sentence: Overall, the conclusions reached by these studies have been highly consistent in showing that approximately 50% of the variance in antisocial phenotypes ...
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How do cells become differentiated using epigenetics despite having the same genome?

How is epigenetics used in the differentiation of cells and is this the only thing that is used? I've seen that transcription factors play a role but are these simply proteins that initially write the ...
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DNA methylation in different positions

I'm trying to understand how does DNA methylation and histone methylation status of promoters differs given their position in a gene? Does position affect whether they are repressive or activating?
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Is protein production doubled if you have homozygous dominant genes as opposed to heterozygous genes?

At school we were taught in quite simplistic terms. We were told that there is a dominant and recessive type of every gene and that if the dominant gene was present, the protein is produced and if it ...
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Is there any biological basis for the emphasis on the value of the firstborn son?

Is the firstborn son biologically different in any way from the sons that follow? Perhaps his epigenome is different? I have heard that a man's testosterone levels decrease when he becomes a father --...
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Have researchers discovered how epigenetic information is passed down during cell division?

For example, how are histone code patterns passed down? This question was asked a few years ago in this thread: How are epigenetic marks transmitted during cell division? However, it has been a few ...
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On parents' similarity

I don't know if this is a real claim, I live in Mexico City and most of the people I know are more similar to their father than to their mother? Why is that? Are the x and y cromosomes somehow related ...
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Is there any technique can quickly expand one set of cell chromosomes?

Assume a cell type is very scarce while isolated out and hard to expand in vitro, and I wanna have more of its chromosomes, is there any technique , in vivo or in vitro or ex vitro, any would count, ...
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How does CpG island methylation lead to gene silencing?

I see often the blanket statement that CpG island methylation can lead to gene silencing. However, I have been unable to find a straightforward explanation of the mechanism by this. Is it a purely ...
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Can epigenetic structures carry a trait?

Can epigenetic structures cause a trait to manifest in a person if the trait is not already in the DNA? In all my readings I have yet to find a definitive statement that it is impossible.
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can genetic material actually provide a physical description of appearance?

A bodies genetic material provides the blueprint for your appearance. Your predisposition to be tall, freckled, blue eyed and blonde are encoded from birth. However, external and environmental ...
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Can a gene-expression or epigenetic 'user-history' be found in the body?

(EDITED - a lot of what I am saying is implicit and simplified. I'm not looking to recreate the numerous textbooks and scientific papers on how DNA works). As far as I can understand it, an ...
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Spermatogenesis in humans - timing of phases and chromatin modifications

I'm interested in the timing of events during human spermatogenesis, ideally with some references I can build off of. Specifically, I am trying to pin down the number of days for: Spermatogenesis, ...
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Are enhancers and silencers considered as epigenetic modifications?

Are enhancers and silencers considered as epigenetic modifications? I am confused as it seems like enhancers and silencers are sequences on the DNA and how they work is through binding with proteins, ...
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Is post-transcriptional regulation of gene expression an epigenetic process?

Is post-transcriptional regulation of gene expression (for example regulation by microRNAs) a type of epigenetic gene expression regulation? I think we can categorize it as epigenetic since the DNA ...
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How to confirm pure-breeding parents

I was reading Genetic Analysis (Sanders, Bowman) and saw the following figure summarizing the 1909 work of Herman Nilsson-Ehle in describing the genetic control of kernel color in wheat: How did ...
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Allele-specific bisulfite sequencing

When evaluating methylation status at various CpG sites after sequencing, how much consideration should one give to random single base pair insertions and deletions. Suppose there is a CA dinucleotide;...
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Can the restless leg syndrome may have been caused due to natural selection? [closed]

Disclaimer: I don't know how much restless the leg has to be, in order to be considered a syndrome. RLS runs not only in my family but also several people in the locality. My hypothesis is that RLS ...
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Does the bending of a tree's trunk in the wind stimulate and strengthen root growth?

Recently Southern California experienced extreme wind velocities and afterwards the news reported over 300 trees had fallen in San Diego County. I had either heard or read somewhere that the action of ...
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Are epigenetic changes involved in evolution?

Evolution leads to phenotypic changes through changes in DNA such as mutations. Mutations are transmitted to offspring. Cumulative mutational changes across many generations may cause evolution and ...
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Difference between micro RNA and short-interfering RNA and CRISPR Cas 9 system?

I read this article https://www.quantamagazine.org/20150206-crispr-dna-editor-bacteria/ and am slightly puzzled as to why the CRISPR/Cas 9 system is seen as being so revolutionary. It seems like the ...
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Do findings on promoter methylation of the serotonin transporter gene and amygdala activity contradict the established view of serotonergic function?

In this article http://www.nature.com/neuro/journal/v17/n9/full/nn.3778.html it states that Increased promoter methylation of the serotonin transporter gene predicted increased threat related ...
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Prader-Willi Syndrome and Angelman Syndrome?

On the website http://www.whatisepigenetics.com/fundamentals/2/ it states that the imprint disorders Prader-Willi syndrome and Angelman syndrome, display an abnormal phenotype as a result of the ...
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How does one predict the methylation pattern?

Suppose, we have a double stranded DNA like 5' AGCTAGGAGAGACCAGGTTCC 3' 3' TCGATCCTCTCTGGTCCAAGG 5' Where would the methylated cytosine be? Is there any randomness?
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Function and Mechanism of Height Genes

I have an inquiry regarding the exact function of height genes. To my knowledge, although they are heavily regulated by epigenetic factors, height genes can have either an "on" or an "off" allele, ...