Epigenomics - Science topic

Hello Danica Rena

The genetic factors known to be involved in breast cancer risk comprise about 30 genes. These include the high-penetrance early-onset breast cancer genes, BRCA1 and BRCA2, a number of rare cancer syndrome genes, and rare genes with more moderate penetrance.

BRCA1 and BRCA2 genes, are the ones which contain over 1000 mutations. Genetic screening for the spectrum of important mutations in these genes in high-risk families is well established. The BRCA1 ‘breast cancer 1 early-onset’ gene is involved in susceptibility to breast and ovarian cancer at a young age, and tumors can arise through somatic or germline mutations. Impaired or lost BRCA1 function underlies substantial genome instability including increase in the number of mutations, DNA breakage and chromatid exchanges, increased sensitivity to DNA damage, and defects in cell-cycle checkpoint functions. The role of BRCA1 in the DNA damage response is that of ‘caretaker’ or ‘master regulator’ in the genome.

BRCA2 gene is a crucial element in the DNA repair process which, if impaired through mutation, can lead to chromosome instability and cancer. It is known to mediate recombinational DNA repair by promoting assembly of RAD51 onto single-stranded DNA. Mutations in the BRCA2 gene may disrupt this mechanism and impair repair of DNA breaks.

Germline mutations in the TP53 gene cause Li–Fraumeni syndrome, a phenotype which includes early-onset breast cancer, but these mutations are far rarer.

There are a number of syndromes that include breast cancer as a component of the disease phenotype. Rare to uncommon mutations in the PTEN and STK11 genes cause Cowden and Peutz–Jeghers syndromes, respectively, and both are associated with considerably increased breast cancer risk. The E-cadherin gene (CDH1) encodes a cellular adhesion protein and is a powerful tumor suppressor of breast cancer. It is particularly implicated in invasive lobular breast carcinomas. RAD51C is another gene involved in the recombinational repair of double-stranded DNA breaks. Rare germline mutations have been shown to confer increased risks of breast and ovarian cancer.

Epigenetics refers to changes in gene expression without changes in the DNA sequence. These include alterations in DNA methylation, histone post-translational modifications, recruitment of chromatin remodeling factors, and expression of micro (miR) and long (lncR) non-coding RNA.

Most of the breast cancer cases are sporadic, and are not related to germline mutations in genes such as the tumor suppressor gene, and usually occur later in life. Epigenetic modifications caused by environmental pollutants, foods, and drinking water are sources of xenobiotics including agonists of the AHR (PAH, dioxin, phthalates, PCB), BPA, and arsenic may contribute epigenetically by dysregulating tumor suppressor gene leading to breast cancer. These epigenetic modifications such as CpG methylation may be conserved through cycles of cell division and transmitted to cell progenies. The accumulation of epigenetic changes in tumor suppressor gene may contribute to the “cancer epigenome” in the same individual or subsequent generations even after removal of the stimuli.

A typical example is BRCA-1 whose repression through CpG methylation in sporadic breast tumors confers a “BRCAness” tumor phenotype similar to that generally seen in BRCA-1 mutation carriers. In mutation carriers (like BRCA-1), epigenetic silencing of the wild-type allele may contribute to loss of heterozygosity and breast tumor development.

Steps to lower the risk of getting breast cancer.

Genetic counseling and testing can be done to look for inherited mutations in the BRCA1 and BRCA2 genes (or less commonly in genes such as PTEN, TP53, or others mentioned above). This might be an option for some women who have been diagnosed with breast cancer, as well as for certain women with factors that put them at higher risk for breast cancer, such as a strong family history.

If one has a higher than usual risk of developing breast cancer, one could use the approach called "chemoprevention”. These are drugs that may help prevent breast cancer. For breast cancer, use of hormone-blocking drugs help to reduce cancer risk. When there is a BRCA1 or BRCA2 genetic mutation present, which substantially increases the risk of breast cancer, preventive removal of breasts may be considered.

Best.

Democracy is of course the best system of government and the best elective form. As I have argued, democracy is also a form of behavior. When political institutions perform democratically, when political actors also behave democratically, then the citizenry has strong incentives to behave in the same way. But for democracy to be effectively a form of behavior, people need to learn to live in a democracy. In this, in addition to political institutions, the values of democracy are very important.

He left the link of a text in which he developed this idea. See particularly the Introduction.

This was a pilot study we conducted some time ago but was the first in the area at that time: Preliminary indications of the effect of a brief yoga intervention on markers of inflammation and DNA methylation in chronically stressed women | Translational Psychiatry (nature.com)

hi Adriana milena Olarte Aponte

This paper may be helpful.

You can look at these review papers and there you can focus on those studies who had used those cell lines.

Few individual epigenetic regulators were studied using one of these cell lines.

Regards

Saurabh

Dongyun Jiang What do you mean by epigenetic modifications? A good way of starting would be to see if the genes of interest are transcription factors of activators, in which case you can do a literature search for possible histone modifications at that particular locus.

Epigenetic modifications around genes and activators are very dynamic and keep changing depending on cell type and microenvironment, in my opinion your best way is to do a literature search keeping in mind your specific experimental conditions.

Assuming that intergenerational epigenetic effects caused gene silencing/methylation and the body's ability to produce amino acids was impaired. The aim is to enquire datasets and find if there is any pattern in amino acid depletion. For example, glutamine depletion and its effects. Similarly, there may be depletion in other amino acids, causing disturbances in homeostasis.

You have to look into Pubmed, that is best answer. Best my point of view could be different from other person's. You can go into Google scholar and look the citation index of papers, will give you best papers

Amir Hossein Kayvanjoo : Thank you so much for taking the time to repply.

Jan Bińkowski : Thank you for the links, specially the ChAMP. I was learning the sesame library but this champ seems have a lot more.

Thank you

But some of our Indian scientists are good with epigenetics.

Hi Boris.

Did you check the ng-mast or pubmlst for the NG genome?

The male tiger pufferfish showed higher methylation level (66.009%) than in female (65.027%) and the pseudo male showed an increase in methylation level (65.945%) which is close to methylation level in male after low-temperature induction. This phenomenon was also observed in Chinese tongue sole and tilapia.

Not sure if there are any journals without an APC. You can consider Preprint servers including biorxiv, medrxiv, etc.

Hi Kjell Sjoberg

you can to to the dbEM, a database with tools for analyzing data, and also with a list of selected publications in the "information" tab (http://crdd.osdd.net/raghava/dbem/)

all the best

fred

The website can be found here: https://dnamage.genetics.ucla.edu

Look at the 'TUTORIALonlineCalculator.pdf' file on the page to understand how to submit your data as a CSV file and how to interpret the results.

Alternatively, the R code is available. I think it's linked to in the supplementary data of Horvath's original paper, if I remember correctly.

Waters is one of the most popular

thank you, dear Shin Murakami for your sugession

Hello Faezeh Soheiliazad

The probability is less that the cells may be intact.

Usually, freeze drying which removes moisture through sublimation, has been used for long-term storage of food and drugs.

Freeze-drying of cells, is done less frequently due to difficulties to load cells with lyoprotectants. Bacteria and yeast are inherently more resistant towards drying stress and by washing the cells with cryoprotectant before lyophilization helps. Moreover, these cells synthesize lyoprotectants upon exposure to stress and can be freeze-dried, while resuming metabolism upon rehydration.

However, mammalian cells typically do not survive freeze drying. I suppose these cumulus cells won’t be intact for cell counting.

Best.

@Desirée

Please specify from which origin you are going to do RNA sequence? If plant species, you may contact through message .

LinkedIn is also an excellent place to search for new jobs/academic positions :) One of the best ways to get a PhD is to search for other positions as well, such as research assistant or academic assistant. If you are able to show what you are capable of before a PhD position is posted, it is more likely that you can get it (if you have good work ethics and show you are capable of the job).

Good luck!

I suggest you to read this paper

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(there will be some regulation,but it will be very difficult to control. however, you cannot avoid any regulation from the start). Sorry I have taken all this time to answer

Nucleosome remodeling and X-inactivation/X-upregulation are a few other examples that might influence gene expression. I have recently addressed the epigenetic mechanisms involved in the pathogenesis of COVID-19. I'd appreciate your comments.

Dear Paulina Díaz-Garrido thank you for your interesting technical question. please have a look at the following potentially useful links which might help you in your analysis:

1. Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community

This article is freely available as public full text on ResearchGate.

2. Top Ten Ways to Improve Your RNA Isolation

Even today, Darwin has made great contributions to evolution. However, there are many gaps to it, and one of them is epigenetics. It is sustained, but even so, the theory does not get lost, it suports it.

Dear Krushna!

Please You look at following articles:

https://www.frontiersin.org/articles/10.3389/fonc.2019.00853/full

What you need?

I do remember scientists were very concerned on why epigentics could not be hereditable. I do think it was a very surprising fact, that maybe research "froze". They did say they were going to find the proof. There was some traces or pecularities at the time were offspring do get epigenetics from the parents. Just the peculiarities but apparently it was impossible to reproduce at least some of the epigenome on the next generation. Still, it was very difficult to obtain this label. Maybe suggest recent research the characters of the epigenome may be able to transmit, these traits, the (mechanisms) the methylation, the epigenome but being unique to each individual as there was no evidence that could proof it. It was very difficult to point and say they become from the same parent, and only say these traits were the only thing that made it possible. They did say they were going to keep searching as there was and there is still an air of mystery on epigenome. It only sits on top of the DNA mainly. Maybe even suggest there are other forms of heritable epigenomics and it may not be the epigenomics were are used. (maybe they did find some inheritance of this main epigenome)

Dear Kevin Llinás-Caballero,

In my opinion, it is hard to extract all the histones when you using RIPA or another common lysis buffer to get the whole cell lysates, it is likely dependent on the chromatin status. For example, when you treat the cells with DNA damage reagents,  the chromatin becomes loose and you may get more total histones using RIPA buffer. 

So I recommend you to use an acid extraction method to get the histones.

Good luck

1. Harvest cells and wash twice with ice-cold PBS. PBS can be supplemented with 5mM Sodium Butyrate to

retain levels of histone acetylation.

2. Resuspend cells in Triton Extraction Buffer (TEB: PBS containing 0.5% Triton X 100 (v/v), 2mM

phenylmethylsulfonyl fluoride (PMSF), 0.02% (w/v) NaN3) at a cell density of 107 cells per ml.

3. Lyse cells on ice for 10 minutes with gentle stirring.

4. Centrifuge at 2000rpm for 10 minutes at 4°C. Remove and discard the supernatant.

5. Wash the cells in half the volume of TEB and centrifuge at before.

6. Resuspend the pellet in 0.2N HCl at a cell density of 4x107cells per ml.

7. Acid extract the histones overnight at 4°C.

8. Centrifuge samples at 2000rpm for 10 minutes at 4°C.

9. Removed the supernatant and determine protein content using the Bradford assay.

10. Store aliquots at -20°C.

Do you have any idea what these other co-factors might be? if not ChIP-seq would not really be possible if you don't know the protein of interest for the cofactor. At that point I would think about trying other methods.

firstly, to minimize the platelet contamination from PBMCsw, best way is multiple washing with PBS at low speed for longer time.

And to cryo-preserve buffy coat, you should use 90%FBS+10% DMSO, but if you only going to extract nucleic acid from cells, Using 90% Complete medium (90% RPMI + 10% FBS) with 10% DMSO may also work.

Few people use lower concentration of DMSO as, DMSO hinders in the downstreaming process (DMSO is know inhibitor of PCR). SO, you may use as low as 7% DMSO.

All the best.

Yes, I have experience in the transient expression of Cas proteins in Plants. We use the PVX based expression system. These Cas proteins will work efficiently even when they are not a part of the genome. But KRAB mainly induced de-acetylation and methylation of histone, resulting in reversible gene repression. I suggest if you really want epigenome editing use dCas9-DNMT3A combination.

Using RRBS data as a first approach might be a good idea. Specially if you wish to analyze methylation patterns in promoter regions. Although, WGBS data could give you more information, the amount of data to be analyzed for each sample is much more compared to RRBS data and the coverage of promoter regions using either RRBS or WGBS should be very similar.

Another thing to consider is the amount of datasets found for each approach.

If computing power is not a problem, I will start analyzing whole genome data instead of specific chromosomes.

Yes. Exposure of primary cells to stress (resulting in alterations in DNA) in culture is known to alter their response to a variety of drug treatments. Accordingly, genetic changes have been documented in benign tumors.

Hi!

If you have Geneious software, there are some free tools that finds CpG island in your sequence.

Good luck!

it doesn't matter - first deposit in biorxiv or medrxiv - then you will have a online peer review by scientists around the world on twitter. Then you can decide where to go! COVID-19 has a fast track acceptance rate!

Hi,

A nice platform to explore public datasets such as TCGA, ENCODE, ROADMAP, GEO, and IHEC is the WashU Epigenome Browser, where you can access a broad range of transcription and epigenetic datasets, ranging from RNA-seq to WGBS, ChIP-seq, among others. Wash U harbors different datasets for hg19 and hg38 genomes, therefore I suggest that you explore both options.

I hope you find it useful.

Regards,

link: http://epigenomegateway.wustl.edu/browser/

I will also recommend following the recently published article in Nature journal.

Hi

I agree with Lenin Yong 's comment above, i.e. Quicker the better for extracting DNA

BW

Stephen

Md Saidur Rahman Thank you, I will try it. I 'm working on methylation like you. I have used the protocol in PMID: 23916795 with some modifications. But now I have problem in some patients although sperm count was good but the extracted DNA had very low concentration and quality.

Hi Wilfried,

My point is just that most part of the time it's cheaper to do 850K ($250-$350 per sample) than designing a more targeted approach unless you have thousands of samples. So I think it's worth to look at that option if the CpGs you are looking at are covered in 850K. it's easier, faster and cheaper.

but we can also help design the targeted by BSAS or Pyro if you want.

Geoffrey

If you are interested in a particular gene, UCSC genome browser HAIB Methyl RRBS Track (ENCODE at UCSC Downloads Subtracks⇓ Description⇓ Contact⇓ HAIB Methyl RRBS Track Settings) is a good place, too.

Dear Ho Nguyen Tuong,

you can download the manifest of the HumanMethylation450 BeadChip directly from the Illumina Homepage (https://support.illumina.com/downloads/infinium_humanmethylation450_product_files.html). This manifest includes all information about the CpG sites, like the corresponding gene, and the chromosomal position.

As I have never worked with QDMR I cannot tell you if this tool is useful for this purpose. Usually, I use the ChAMP pipeline in R to analyse Illumina BeadChip data (https://www.bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html).

Greetings,

Julie Krainer

I have a rough idea now but I still need help: I recently learned that a lot of cell lines are primary cells transformed by virus, such as the abelson virus transformed pre-B cell line. The beauty of this cell line is that when you add a tyrosine kinase inhibitor STI571, cell cycle will be arrested and cells start to differentiate (i.e. rearrange their light chains). I was wondering if there are any other cell lines with same properties?

Thank you everyone

Yes it´s and I try ton found the right place of hope to our cancer patients about precissioin medicine. Thanks

Nitesh Kumar Sharma thank you very much...

Dear Abhijeet Singh thank you for your answer but actually I had tried to explain why I want to learn. I am researching on cancer drug resistance and this resistance can be due to epigenetics changes in cell. Hence, these topics are relatively close to each other as to me. I have written all them down because I thought maybe there could be specific tools or databases which I do not know about these. Wish you good work!

Environmental impact on speed breeding has not yet studied but the environmental influence on plant aspect like morphological changes and nutrient changes have been studied so for.

Regards

Dear Umut Erdogdu , ,

Thank you for your suggestions. It is very helpful.

Best regards.

Hello Jessica,

If you are talking about DNA methylation - it its really stable and can be profiled from minute amount of DNA. However, in plants some methylation might be more prone to changes under stress - such as those induced during sample collection. Maybe for seagrass you can keep the samples in good condition up until genomic DAN extraction. You idea was to cast them into a gel and then process with molecular analyses? maybe you can snap freeze the samples like this for long term storage?

I hope this helps a little.

Cheers,

Antoine.

I am not an immunologist, but I believe they would inherit the effector phenotype if differentiation is truly an epigenetic phenomenon.

Parham has given a correct answer, SNP is not an epigenetic modification, it's a genetic modification, it's a mutation. But SNP could be an excellent marker to correlate different levels of allele expression and allele structure. Even though the SNP could not be directly responsible of this variation in expression level, it can be linked to other mutations on the same allele sequence so giving the opportunity to establish the causal relation.

I can only think that the standards were having problem.

Answer of the question

Cancer is name of the a kind phenotype not genotype

https://science.sciencemag.org/content/364/6444/eaaw0726

This is a broad technical question involving various mechanistic steps. It is currently established that epigenetic marks (involving methylation and acetylation of the histone and the DNA) make a huge contribution in the genome (within the nucleasome) and sometimes (not all time) become inherited.

To this question, mutation in the sequence of the bases is one alteration that ensued which is transferable to subsequent generation.

Your reply is very basic and general C K Gomathy , i already come across attached article. We need deeper knowledge with some practical guide especially with epigenetics. Image analysis using deep learning is relatively easy compare to epignetic data and epigenetic data more complecated. We are loooking for easy autoencoders and decoders for interpreting results at gene level.

This article will help you to conduct epigenetic analysis in a clinical nutrition

from a randomized controlled trial. Good luck!!

You may find useful these references:

However, epigenetic remodelling is not something you can manipulate at will, it depends on the cell developmental state, the tissue type, the environmental conditions, and the hormonal stimuli present.

My advice is look for available regeneration protocols for close relatives of the species you want to regenerate and test how these work on your case.

Most trees, including conifers, have extremely large genomes with high duplication and tend to have a large number of transposable elements of various classes. It may be hard to promote plant embryogenesis from callus, and sometimes direct organogenesis is more effective.

An example:

Thank you.

@ Hasna Mohaus

Please take a look at this useful RG link.

Thanks!

Children are a life passage for parents .Parent observe the children in very close & loving action which may establish a bond between children & parents with the schooling age parents observe the life behavior of his children in their school response among their school friends .

It is this environment which help the children to go ahead to independently with the study & other behavior in the family ,friends & society .

Some years back I have expressed a similar views in the line of our present question which I submit herewith for your kind perusal

With our arrival of any children with their first cry they listen to the sound of her mother with her loving smile .It is after certain period the child can get & observe the environment of the family including his caste,creed .& religion . It is the responsibility of the parents to observation of his nature his childish behavior & his likely interest in his observation & also in his movement .

With this initial stage of observation for his child parents can convenient change the attitude & the behavior of the child with there are observing in the action of child . With this the parent should teach his initial good behavior & see that he may not play any mischief or rough behavior of his childhood friend .

If the child follows the practice in his school days he can certainly become a good behavior boy both with the family or among his friend circle or even his class room also .

This is my personal opinion

There's a nice update to RnBeads (2.0) that was just published. Knowledge of R programming is a must, but otherwise very straightforward. Please message me if you have specific questions!

The paper:

We have not tested the interaction mentioned aboveز

This is a wide subject but I think that those sites will give you a good start.

Matthias R. Schaefer

Thank you Matthias, it is very helpful!

In my opinion, owing to the vastness of the genetic and epigenetic alterations in cancer the only way forward is to get rid of the mutated cells. Genome editing of immune cells could help achieve this but I don't think we will ever be able to revert the actual cancer cells back to their former 'healthy' state.

Cancer cells have inherent misregulation of gene networks/programs. Though one cannot exclude the possibility of mutations in the Ecad gene body that may affect transcript or protein levels/trafficking/function, I would most readily believe that epigenetic regulation is the most common cause of Ecad suppression. Further, at the epigenetic level it is likely more complex than promoter methylation and involves other cis regulatory modules.

I think the answer is no. There is sufficient variation in the genome such that each individual has unique identifiers, whereas the epigenome varies even within an individual depending on the origin of the cells used for analyses..

Hi Prasanna,

you should have a look in the implication of genetics in this disease and therefore the repartition of disease genes among populations. there are a lot of papers and reviews, just read this one: http://www.jcancer.org/v10p0643.htm. but it's sure that environmental factors as microbiome and foods have real impacts on gene behavior ( ).

fred

Hello, Quorum sensing of bacteria is the regulation of gene expression in response to fluctuations in cell-population density. Quorum sensing bacteria produce and release chemical signal molecules called autoinducers that increase in concentration as a function of cell density. The detection of a minimal threshold stimulatory concentration of an autoinducer leads to an alteration in gene expression. But each of cell is individual organism.

Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Epigenetic changes are inheritable changes in gene expression that do not result from changes in the DNA sequence. Eukaryotic gene expression begins with control of access to the DNA.

Epi Info software

Dear David, I think that epigenetics could play a role. There are quite a number of studies that at least suggest the possibility. For example, see Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17046-9. doi: 10.1073/pnas.0806560105. Epub 2008 Oct 27. Annu Rev Public Health. 2011;32:237-62. doi: 10.1146/annurev-publhealth-031210-101230. BMJ Open. 2016 Nov 23;6(11):e011768. doi: 10.1136/bmjopen-2016-011768. Although these studies deal with malnutrition in early development and its effects on health later in life, it is a good possibility that different environmental factors could affect different aspects later in life.