Epigenetic mechanisms and factors behind protein diversity

Instructions for protein production are not stored in DNA

The cell is able to use DNA very efficiently. By reading the same DNA sequence, a cell can produce thousands of different proteins without altering DNA. The best known DNA sequence from which a cell can produce up to 32,000 different proteins by alternative splicing is the Dscam sequence of a fruit fly. Such multifunctional utilization of DNA indicates not only the passive nature of DNA as a digital repository of information, but also that DNA doesn't provide instructions for protein production.

The accompanying study states quite unequivocally that alternative splicing, which is thus behind protein diversity, is driven by epigenetic mechanisms and factors.

https://www.cell.com/fulltext/S0092-8674(10)01378-4

Excerpts: "These insights suggest that epigenetic regulation determines not only what parts of the genome are expressed but also how they are spliced."

"A major recent discovery is that chromatin structure and epigenetic histone modifications act as key regulators of alternative splicing."

"Consistently, inhibition of histone deacetylation, DNA methylation, H3K9 methylation, and downregulation of heterochromatin protein 1α (HP1α) abolishes the siRNA-mediated effect on exon E33 splicing, suggesting a role of these modifications in alternative splicing regulation."

 

"These observations point to a role for epigenetic modifications in the regulation of alternative splicing, and this regulation may involve the modulation of RNA Pol II elongation rate."

"An advantage of such a histone-based alternative splicing regulatory system is that it would provide an epigenetic memory for splicing decisions that could be passed on during proliferation of a cell population and could be modified during differentiation without the requirement to establish a new set of alternative splicing rules at each step of differentiation. Obviously, an epigenetic alternative splicing memory would still require the proper expression of splicing factors, a process that itself may be controlled by epigenetic mechanisms. Regardless of mechanisms, it appears that epigenetic regulation is not limited to controlling what regions of the genome are expressed, but also how they are spliced."

Neofunctionalization as evidence for evolution now debunked

Neofunctionalization is based on epigenetic reprogramming

During last two decades, so called neofunctionalization was thought to be an evolutionary process by which a cell generates random gene duplications and these duplications are mutated and in this way, organisms could produce new functions or even structures. Very often neofunctionalization has been a strong argument for evolution believers. Today modern science proves these claims wrong.

https://advances.sciencemag.org/content/5/7/eaaw7006

"Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals."

"Together, this indicates that like H3K27 modification, there is an intense period of DNA methylation reprogramming in the gonad at intermediate stages of sex change. Such distinct sex-specific expression of DNA methyltransferase genes and other epigenetic modifiers was also recently observed in gonadal transcriptomes of other sex-changing fishes and may be important for sexual plasticity."

"Transcriptomic and methylome analyses across sex change in the iconic bluehead wrasse have identified the triggers of socially induced sex change and enactors of gonadal metamorphosis. Our results suggest that the environmental stimulus is exerted via stress, that the subsequent steps involve repression of aromatase, and that distinctive epigenetic reprogramming is associated with reengineering ovaries into testes. Importantly, this does not occur by direct transdifferentiation but involves an intermediate state with altered epigenetic machinery expression that is reminiscent of mammalian naïve pluripotent stem cells and PGCs."

"Gene neofunctionalization following duplication allows for diversification of a standard genetic network and may be one factor contributing to the sexual plasticity that is characteristic of fishes."
 

"The use of neofunctionalized paralogs in sex change was not restricted to hormonal and signaling pathways; we also found duplicated epigenetic machinery in bluehead wrasses that exhibited female- or male-specific expression. Global DNA methylation was remodeled, as expression of female-specific DNMTs was replaced with male-specific expression. The peak in TET expression seen at this time indicates remodeling of DNA methylation that is typical of mammalian PGCs and both naïve and classically grown pluripotent stem cells. The same appeared to be true for histone-modifying machinery; the PRC2 complex is associated with differentiation in mammals and showed high expression in cells belonging to committed sexual phenotypes but was deactivated in the gonads of transitional fish. Likewise, dynamic expression of histone demethylases, acetyltransferases, and variant histones further suggest active chromatin modification during gonadal sex change."

Summary: 

• Stress factors, such as diet type or sex ratios trigger epigenetic modifications.
• Gene duplications in these adaptive processes are based on epigenetic mechanisms and factors.
• The cell is able to modify a novel gene in order to achieve adaptational purposes.
• Organismal change is based on complex epigenetic mechanisms and especially epigenetic reprogramming.
• In this process DNA is just passive information and it has no control over cellular processes.

Highly optimized and polyfunctional DNA code doesn't tolerate mutations

Random mutations never result in any kind of evolution

https://www.worldscientific.com/doi/epdf/10.1142/9789814508728_0006

Excerpts: "There is growing evidence that much of the DNA in higher genomes is poly-functional, with the same nucleotide contributing to more than one type of code. Such poly-functional DNA should logically be multiply-constrained in terms of the probability of sequence improvement via random mutation. We describe a model of this relationship, which relates the degree of poly-functionality and the degree of constraint on mutational improvement. We show that: a) the probability of beneficial mutation is inversely related to the degree that a sequence is already optimized for a given code; b) the probability of beneficial mutation drastically diminishes as the number of overlapping codes increases. The growing evidence for a high degree of optimization in biological systems, and the growing evidence for multiple levels of poly-functionality within DNA, both suggest that mutations that are unambiguously beneficial must be especially rare. The theoretical scarcity of beneficial mutations is compounded by the fact that most of the beneficial mutations that do arise should confer extremely small increments of improvement in terms of total biological function. This makes such mutations invisible to natural selection. Beneficial mutations that are below a population's selection threshold are effectively neutral in terms of selection, and so should be entirely unproductive from an evolutionary perspective. We conclude that beneficial mutations that are unambiguous (not deleterious at any level), and useful (subject to natural selection), should be extremely rare."

"To further test the effect of multiple constraints on the appearance of beneficial mutations, we constructed a simple poly-constrained artificial system based on English crossword puzzles. Crossword puzzles, for our purpose, are simply collections of words with overlapping, shared letters among some of the words. Figure 6 [the picture below] contains an illustration of such puzzles. We are most familiar with two- dimensional crossword puzzles, where up to two words may share a single letter, but crossword puzzles can be extended to many dimensions. An L-dimensional crossword puzzle is here defined as a collection of words, such that up to L words may share a single, overlapping letter, for one or more letters in the puzzle. Each overlap forms a constraint on our puzzle, which limits the possible letters that are allowed in a given position. Increasing the number of words that share a single letter increases the number of constraints on that particular letter, and limits the number of values that letter position may take."

Crossword puzzles are familiar poly-constrained systems. Intersecting words create constraints on overlapping letters, such as the E of FILE in the first puzzle. Although a viable, functional mutation may change FILE to FILL, this would simultaneously change INTOLERANT to the non-functional INTOLLRANT, a non-word. As we increase the number of dimensions, the number of overlapping words can increase as well, further preventing beneficial changes.

My comment: DNA reading mechanisms are able to read DNA from different locations and in both directions (3' and 5'). Words being read often overlap with each other and very often words are palindromes. Especially human genome is so perfectly organized and optimized that it doesn't tolerate random mistakes. This is why there are no fully beneficial mutations in human genome. Instead, the number of harmful genetic errors will soon exceed 2 million at population level. Evolution never happened. Don't be deceived.

Identical genes but non-identical phenotypes

DNA doesn't determine phenotype or organismal traits

1. At cellular level

https://medcraveonline.com/MOJCSR/epigenetic-regulation-mechanisms-in-stem-cell-differentiation.html
 

Excerpt: "Stem cells give rise to almost 200 different cell types that are present in a mammalian organism. In spite of the fact that these distinct cell types have different functions and morphologies, they descend from a common ancestor cell and essentially share the same DNA. The underlying cause for the rise of specific cell types is not genetic differences; it is mostly due to how the genetic information is interpreted. The epigenome, which consists of several degrees of regulatory mechanisms, dictates the gene expression profile of a certain type of cell. Eukaryotic DNA is packaged into chromatin, folded and compacted which in turn affects its functionality as certain regions of DNA will not be accessible whereas some other regions will be easier to access for effect or proteins and modifiers to bind. The chromatin dynamics are modulated by several machineries including but not limited to histone PTMs and their variants, DNA methylation and RNA interference, which have crucial roles in regulating stem cell differentiation, cell fate determination and lineage specification."

2. At tissue level

https://www.colorado.edu/today/2020/07/07/how-does-stem-cell-know-what-become-study-shows-rna-plays-key-role

Excerpts: "Look deep inside our cells, and you’ll find that each has an identical genome –a complete set of genes that provides the instructions for our cells’ form and function.

But if each blueprint is identical, why does an eye cell look and act differently than a skin cell or brain cell? How does a stem cell – the raw material with which our organ and tissue cells are made – know what to become?
 

“All genes are not expressed all the time in all cells. Instead, each tissue type has its own epigenetic program that determines which genes get turned on or off at any moment,” said co-senior author Thomas Cech, a Nobel laureate and distinguished professor of biochemistry. “We determined in great detail that RNA is a master regulator of this epigenetic silencing and that in the absence of RNA, this system cannot work. It is critical for life.”"

3. At body plan level

https://ussromantics.com/2020/01/03/epigenetics-and-imprinting-2-identical-genes-and-non-identical-phenotypes/

Excerpt: "it’s obvious that genetics isn’t the whole story of our inheritance and development because it doesn’t begin to explain how, from one fertilised egg – the union of, or pairing of, two sets of chromosomes – we get, via divisions upon divisions upon divisions, a complex being with brain cells, blood cells, skin cells, liver cells and so forth, all with identical DNA. It also doesn’t explain how a maggot becomes a fly with the same set of genes (or a caterpillar becomes a butterfly, to be a little more uplifting). These transformations, which maintain genetic inheritance while involving massive change, must be instigated and shaped by something over and above genetics but intimately related to it – hence epigenetics. Other examples include whether a crocodile hatchling will turn out male or female – determined epigenetically via the temperature during development, rather than genetically via the Y chromosome in mammals.
 

So, to add to the description I gave last time, the histone proteins that the DNA wraps itself round come in batches or clusters of eight. The DNA wraps around one cluster, then another, and so on with millions of these histone clusters (which have much-studied ‘tails’ sticking out of them). And I should also remind myself that our DNA comes in a four-letter code strung together, out of which is constructed 3 billion or so letters."

My comment: With the same set of DNA there could be a huge number of different phenotypes or outcomes. DNA doesn't determine phenotype or organismal traits or characteristics. It's all epigenetics. DNA does nothing without epigenetic programming. In other words, without epigenetic information profiles the DNA is just passive information.

The theory of evolution needs urgent rethinking

Textbooks give false information about assumed evolution

This is a typical example of a textbook or a web page providing information about organismal change. According to this site, rapid changes in beak size and shape within Darwin's finches is due to evolution and natural selection. These are the key points represented at the site:

• Darwin observed the Galapagos finches had a graded series of beak sizes and shapes and predicted these species were modified from one original mainland species.
• Darwin called differences among species natural selection, which is caused by the inheritance of traits, competition between individuals, and the variation of traits.
• Offspring with inherited characteristics that allow them to best compete will survive and have more offspring than those individuals with variations that are less able to compete.
• Large-billed finches feed more efficiently on large, hard seeds, whereas smaller billed finches feed more efficiently on small, soft seeds.
• When small, soft seeds become rare, large-billed finches will survive better, and there will be more larger-billed birds in the following generation; when large, hard seeds become rare, the opposite will occur.

Key terms are explained in this way:

• natural selection: a process in which individual organisms or phenotypes that possess favorable traits are more likely to survive and reproduce
• evolution: the change in the genetic composition of a population over successive generations
  

Sounds familiar? The evolutionary concept sounds so simple that even a child could understand the basics. But let's have a deeper look at these doctrines. Why are they giving false information?

Claim 1. Darwin observed the Galapagos finches had a graded series of beak sizes and shapes and predicted these species were modified from one original mainland species.

This might be the case. Pretty possible.

Claim 2. Darwin called differences among species natural selection, which is caused by the inheritance of traits, competition between individuals, and the variation of traits.

This is false information. According to modern science, differences among species are caused by epigenetic regulation and inheritable epigenetic memory.

Claim 3. Offspring with inherited characteristics that allow them to best compete will survive and have more offspring than those individuals with variations that are less able to compete.

This is also false information. According to latest research, so called survival of the fittest is due to inheritable epigenetic memory. Organisms have coded mechanisms by which they are able to adapt to changing environment, changing food type etc. Changes occur rapidly and they are inherited to the offspring across multiple generations.

 

Claim 4. Offspring with inherited characteristics that allow them to best compete will survive and have more offspring than those individuals with variations that are less able to compete.

This is partly false information. Offspring with inherited characteristics are adapted in different way than offspring with less inherited characteristics. However, both groups have potential to survive if proper food is available.

Claim 5. Large-billed finches feed more efficiently on large, hard seeds, whereas smaller billed finches feed more efficiently on small, soft seeds.

This is the most pseudoscientific claim. Darwin thought that beak size and shape changes randomly and that birds with certain beak size and shape are forced to select their food type. Modern science has revealed that food type affects organisms epigenomes causing intentional changes to phenotype, in this case to the beak size and shape. In other words, if a bird starts eating seeds, the offspring will have stronger and larger beaks. This is how epigenetic regulation works. No randomness. No natural selection. No random mutations.

Claim 6. When small, soft seeds become rare, large-billed finches will survive better, and there will be more larger-billed birds in the following generation; when large, hard seeds become rare, the opposite will occur.

This is also based on mechanisms. Organisms are able to regulate the number of offspring along to how much food is available.

Key terms are to be corrected:

Natural selection: An imaginary force that has no true impact on organismal change and biodiversity. Mostly it's just bad or good luck.

Evolution: Organismal change occurs due to epigenetic regulation of pre-existing coded information. No genetic mutations have been associated with beak size or shape within Darwin's finches. Epigenetic regulation results in subtle genetic errors. Gradually this leads to genetic decay, degradation, degeneration and genetic entropy. Evolution never happened.

Epigenetics explains the differences between humans and Neanderthals

Neanderthals were humans. Human evolution is a joke.

https://www.natureworldnews.com/articles/6672/20140419/gene-expression-maps-show-why-humans-neanderthals-look-different.htm

Excerpt: "A new study uses epigenetics to explain the differences between modern humans and Neanderthals.

Epigenetics refers to external modification of DNA. Research has shown that these changes are important in shaping key biological functions.

The study, conducted by a team of Israeli, Spanish and German researchers, was based on maps of gene expression of humans and our ancient cousins, the Neanderthals and the Denisovans.

The research explains why despite being 99.84 percent identical genetically, the Neanderthals looked quite different from humans, nbcnews.com reports.

According to the researchers, the answer lies in a process that controls gene expression called DNA methylation. In this process, a methyl group attaches to a gene and prevents normal genetic activity.

"We wanted to know if we could say anything about how genes were active or regulated in our closest evolutionary relatives," computational biologist Liran Carmel and stem cell biologist Eran Meshorer, at the Hebrew University of Jerusalem, told Nature. "This may be very relevant to explaining some of the known phenotypic differences between us."

Researchers created methylation maps that revealed several regions with different genetic activity, especially in those associated with body shape and neurological diseases such as autism and schizophrenia. However, the maps aren't complete as the research was based on DNA obtained from a few bones.

 

In the study, researchers created methylation maps by measuring the levels of decayed products of unmethylated cytosines and cyctones. Researchers then compared these methylation maps with similar maps of modern humans, according to a news report by Phys.org.

Carmel and colleagues found some 2000 different regions where gene expression was on in humans, but off in Neanderthals or Denisovans or vice versa, nbc.news reported.

The team found significant changes in methylation in some regions such as HoxD cluster, which has earlier been linked with changes in physical appearance. The alterations in HoxD cluster might explain why Neanderthals were short and stout.

Also, researchers found that methylated regions linked with neurological disorders such as autism and schizophrenia were present in modern humans, but not our primitive cousins.
The study is published in the journal Science."

My comment: There is no reason to conclude that Neanderthals were our evolutionary ancestors. They were just humans just like us. They looked different to us, they were short, brutish and stout but these differences are explained by epigenetic control of gene expression. Genetically, at DNA level, they were at least 99.84 % similar to us, probably even closer because methylated cytosines are prone to turn into thymines rapidly after death. The theory of evolution is maintained by stories and fairytales and this research reveals truth about Neanderthals. They were humans. Don't be deceived.

Human mutation rate is way too high for evolution to occur

A few years ago the Junk-DNA theory rescued the evolutionary theory - Today: THERE IS NO JUNK-DNA!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/

Excerpt: "For the human population to maintain a constant size from generation to generation, an increase in fertility must compensate for the reduction in the mean fitness of the population caused, among others, by deleterious mutations. The required increase in fertility due to this mutational load depends on the number of sites in the genome that are functional, the mutation rate, and the fraction of deleterious mutations among all mutations in functional regions. These dependencies and the fact that there exists a maximum tolerable replacement level fertility can be used to put an upper limit on the fraction of the human genome that can be functional. Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%."

https://www.livemint.com/Science/OyB7ydFTcUZOpcXcVmBlpK/Scientists-say-75-of-human-gene-is-junk-DNA.html

Excerpt: "Researchers from the University of Houston in the US found that the functional portion of the human genome probably falls between 10% and 15%, with an upper limit of 25%."

https://futurism.com/new-study-shows-that-only-about-25-of-our-dna-is-functional

Excerpt: "Graur found that even if the rate of deleterious mutation was very low, birth rates would need to be unrealistically high to sustain the population if 80 percent of the genome were functional. As reported by The University of Houston:

"For 80 percent of the human genome to be functional, each couple in the world would have to beget on average 15 children and all but two would have to die or fail to reproduce…If we use the upper bound for the deleterious mutation rate (2 × 10−8 mutations per nucleotide per generation), then … the number of children that each couple would have to have to maintain a constant population size would exceed the number of stars in the visible universe by ten orders of magnitude."

 https://sites.google.com/site/georgiatiptonbzb210assessment/genetic-load

Excerpt: "For humans, the mutation rate is predicted to be approximately 70-150 mutations per generation, much higher than the limit that was proposed earlier. 

If this were the case, scientists have calculated that only 1% of functional data was possible, far less than the 80% prediction given by the ENCODE Project.

After further scientific study was undertaken, however, it was suggested that humans may actually be able to withstand more than 1 deleterious mutation per generation. It was thought that they may, in fact be able to withstand between 2 and 10. Using this information, it is estimated that 10% of the human genome would then exhibit an organism-level function, leaving 90% to be classified as junk DNA."

https://www.nature.com/news/2009/090827/full/news.2009.864.html

Excerpt: "Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome."

Modern science reveals that the junk-DNA theory is just wishful thinking

https://www.futurity.org/junk-dna-1728712/

https://www.researchgate.net/publication/269187480_Non-coding_RNAs_Biological_functions_and_applications?fbclid=IwAR2RYi1Zw99F_-87r8sj0Q3z1FqHJQ19dCBHZUwDbSx2jaV4GPsBLO4ThRY

"In addition, there has been an explosion of research addressing possible functional roles for the other 98% of the human genome that does not encode proteins. In fact, >90% of the human genome is likely to be transcribed yielding a complex network of overlapping transcripts that include tens of thousands of long RNAs with little or no protein forming capacity; they are collectively called non-coding RNA."

https://www.myscience.org/news/2021/the_cause_of_genetic_diseases_can_also_be_found_in_gene_deserts-2021-unibas

"The study in the scientific journal Nature shows that a single genetic change in the "junk DNA" long thought to be useless can have serious consequences."

My comment: Every scientist realizes the truth about high mutation rate (mutational load, genetic load) within humans and other organisms, too. The junk-DNA theory was developed in order to the problem of mutational load to be solved. Today, serious scientists admit that there is no junk-DNA in cells of organisms. But the high harmful mutational load remains. Conclusions are obvious: Evolution never happened. Don't get lost, my friends.

Epigenetic on/off switching by cytosine methylation

Methylated cytosines (C) outside CpG islands control gene expression

https://www.sciencedaily.com/releases/2021/04/210416131923.htm

Excerpt: "Based on previous work by a group in Italy, the researchers were confident that CRISPRoff would be able to silence specific genes, but they suspected that some 30 percent of human genes would be unresponsive to the new tool.

DNA consists of four genetic letters -- A, C, G, T -- but, in general, only Cs next to Gs can be methylated. To complicate matters, scientists have long believed that methylation could only silence genes at sites in the genome where CG sequences are highly concentrated, regions known as "CpG islands."

Since nearly a third of human genes lack CpG islands, the researchers assumed methylation wouldn't switch these genes off. But their CRISPRoff experiments upended this epigenetic dogma.

"What was thought before this work was that the 30 percent of genes that do not have CpG islands were not controlled by DNA methylation," said Gilbert. "But our work clearly shows that you don't require a CpG island to turn genes off by methylation. That, to me, was a major surprise."

Epigenetic Inheritance Enhances CRISPRoff's Therapeutic Potential

Easy-to-use epigenetic editors like CRISPRoff have tremendous therapeutic potential, in large part because, like the genome, the epigenome can be inherited.

When CRISPRoff silences a gene, not only does the gene remain off in the treated cell, it also stays off in the descendants of the cell as it divides, for as many as 450 generations.

To the researchers' surprise, this held true even in maturing stem cells. Though the transition from stem cell to differentiated adult cell involves a significant rewiring of the epigenome, the methylation marks deposited by CRISPRoff were faithfully inherited in a significant fraction of cells that made this transition.

These findings suggest that CRISPRoff would only need to be administered once to have lasting therapeutic effects, making it a promising approach for treating rare genetic disorders -- including Marfan syndrome, which affects connective tissue, Job's syndrome, an immune system disorder, and certain forms of cancer -- that are caused by the activity of a single damaged copy of a gene."

My comment: Old dogmas are upended again. This discovery emphasizes the role of epigenetic mechanisms and factors in DNA transcription and minimizes the role of the DNA in these cellular processes. This research also confirms that epigenetic changes might be very robust and long standing, even over 450 generations. DNA methylation patterns affect both transcription and alternative splicing procedures so it's one of the most significant factors influencing organismal adaptation and even speciation. However, changes in methylation patterns never result in any kind of evolution. Don't get lost, my friends.