The central term of genetics— “the gene”—can no longer be defined in simple terms

Reasons why it's difficult to define a gene and why DNA is just a passive information library

http://www.genetics.org/content/205/4/1353

Summary:

• The hypothesis of “one gene—one mRNA—one polypeptide” as a general description of the gene and how it works started to expire, however, when it was realized that a single gene could produce more than one mRNA, and that one gene can be a part of several transcription units. This one-to-several relationship of genes to mRNAs occurs by means of complex promoters and/or alternative splicing of the primary transcript.
  
• Multiple transcription initiation sites, i.e., alternative promoters, have been found in all kingdoms of organisms, and they have been classified into six classes (Schibler and Sierra 1987). All of them can produce transcripts that do not obey the rule of one-to-one correspondence between the gene and the transcription unit, since transcription can be initiated at different promoters. The result is that a single gene can produce more than one kind of transcript (Schibler and Sierra 1987).
  
• The discovery of alternative splicing as a way of producing different transcripts from one gene had a more complex history. In the late 1970s it was discovered, first in animal viruses and then in eukaryotes, that genes have a split structure. That is, genes are interrupted by introns (see review by Portin 1993). Split genes produce one pre-mRNA molecule, from which the introns are removed during the maturation of the mRNA by pre-mRNA splicing. Depending on the gene, the splicing pattern can be invariant (“constitutive”) or variable (“alternative”). In constitutive splicing, all the exons present in a transcript are incorporated into one mature mRNA through invariant ligation of consecutive exons, yielding a single kind of mRNA from the gene. In alternative splicing, nonconsecutive exons are joined by the processing of some, but not all, transcripts from a gene. In other words, individual exons can be excluded from the mature mRNA in some transcripts, but they can be included in others (Leff et al. 1986; Black 2003). Alternative splicing is a regulated process, being tissue-specific and developmental-stage-specific. Nevertheless, the colinearity of the gene and the mRNA is preserved, since the order of the exons in the gene is not changed.
   
  
• In addition to alternative splicing, two other phenomena are now known that contradict a basic tenet of the neoclassical gene concept, namely that amino-acid sequences of proteins, and consequently their functions, are always derivable from the DNA of the corresponding gene. These are the phenomena of RNA editing (reviewed by Brennickle et al. 1999; Witzany 2011) and of gene sharing originally found by J. Piatigorsky (reviewed in Piatigorsky 2007). The term RNA editing describes post-transcriptional molecular processes in which the structure of an RNA molecule is altered. Though a rare event, it has been observed to occur in eukaryotes, their viruses, archaea and prokaryotes, and involves several kinds of base modifications in RNA molecules. RNA editing in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted by the genomic DNA sequence (Brennickle et.al. 1999). The concept of gene sharing describes the fact that different cells contain identically sequenced polypeptides, derived from the same gene, but so differently configured in different cellular contexts that they perform wildly different functions. This phenomenon, facetiously called “protein moonlighting,” means that a gene may acquire and maintain a second function without gene duplication, and without loss of the primary function. Such genes are under two or more entirely different selective constraints (Piatigorsky and Wistow 1989).
  
   

Severe cracks in the concept of the gene

Matters changed, however, when the sequencing projects revealed still more bizarre phenomena:
These new findings have shown that there are multiple possible relationships between DNA sequences and the molecular products they specify. The net result has been the realization that the basic concept of the gene as some form of generic, universal “unit of heredity” is too simple, and correspondingly, that, a new definition or concept of “the gene” is needed (Keller 2000; Falk 2009; Portin 2009). Several observations have been crucial to this re-evaluation, and one of us has reviewed these relatively recently (Portin 2009). They are worth summarizing here:

1. In eukaryotic organisms, there are few if any absolute boundaries to transcription, making it impossible to establish simple general relationships between primary transcripts and the ultimate products of those transcripts.
   
   Hence, the structural boundaries of the gene as the unit of transcription are often far from clear, as documented particularly well in mammals (reviewed by Carninci 2006). In reality, whole chromosomes, if not the whole genome, seem to be continuums of transcription (Gingeras 2007). Furthermore, the genome is full of overlapping transcripts, thus making it impossible to draw 1:1:1 relationship between specific DNA sequences, transcripts and functions (Pearson 2006). Indeed, convincing evidence indicates that the human genome is comprehensively transcribed from both DNA strands, so that the majority of its bases can be found in primary transcripts that compendiously overlap one another (The FANTOM Consortium and RIKEN Genome Exploration Group 2005; The ENCODE Project Consortium 2007; 2012). Both protein coding and noncoding transcripts may be derived from either or both DNA strands, and they may be overlapping and interlaced. Furthermore, different transcripts often include the same coding sequences (Mattick 2005). The functional significance of these overlaps is still largely unclear, but there is an increasing number of examples in which both transcripts are known to have protein-coding exons from one position in the genome combined with exons from another part of the genome hundreds of thousands of nucleotides away (Kapranov et al. 2007). This was wholly unanticipated when the 1960s definition of the gene was formulated.
   
   
2. Exons of different genes can be members of more than one transcript.
   Gene fusion, at the level of transcripts, is a reality, and is completely at odds with the “one gene—one mRNA—one protein” hypothesis. And this is not a rare phenomenon. It has been estimated that at least 4–5% of the tandem gene pairs in the human genome can be transcribed into a single RNA sequence, called chimeric transcripts, encoding a putative chimeric protein (Parra et al. 2006).
   
   
3. Comparably, in the organelles of microbial eukaryotes, many examples of “encrypted” genes are known: genes are often in pieces that can be found as separate segments around the genome.
   Hence, in addition to the fusion of two adjacent genes at the level of transcription, different building blocks of a given mRNA molecule can often be located, as modules, on different chromosomes (reviewed in Landweber 2007). Some evidence indicates that, even in multicellular eukaryotes, protein-coding transcripts are derived from different nonhomologous chromosomes (reviewed in Claverie 2005).
   
   
4. In contradiction to the neoclassical definition of a gene, which posits that the hereditary information resides solely in DNA sequences, there is increasing evidence that the functional status of some genes can be inherited from one generation of individuals to the next, a phenomenon known as transgenerational epigenetic inheritance (Holliday 1987; Gerhart and Kirschner 2007; Jablonka and Raz 2009).
   
   
5. Finally, in addition to protein coding genes, there are many RNA-encoding genes that produce diverse RNA molecules that are not translated to proteins.

My comment: Defining a gene seems to be very complex. This points to Intelligent Design and Creation. 

Same DNA, different eye colors

Researchers obtained fruit fly lines having the same DNA sequence but different eye colors

https://phys.org/news/2017-04-mechanism-epigenetic-inheritance.html

Excerpt: "Giacomo Cavalli's team at the Institute of Human Genetics (University of Montpellier / CNRS), in collaboration with the French National Institute for Agricultural Research (INRA), has demonstrated the existence of transgenerational epigenetic inheritance (TEI) among Drosophila fruit flies. By temporarily modifying the function of Polycomb Group (PcG) proteins—which play an essential role in development—the researchers obtained fruit fly lines having the same DNA sequence but different eye colors. An example of epigenetic inheritance, this color diversity reflects varying degrees of heritable, but reversible, gene repression by PcG proteins. It is observed in both transgenic and wild-type lines and can be modified by environmental conditions such as ambient temperature. The scientists' work is published in Nature Genetics.

Same DNA, different color. Researchers have obtained drosophila epilines—that is, genetically identical lineages with distinct epigenetic characteristics—with white, yellow, and red eyes respectively. They achieved this by transiently disturbing interactions between target genes and PcG proteins, which are complexes involved in the repression of several genes governing development. Cavalli and his team at the Institute of Human Genetics (University of Montpellier / CNRS) are the first to show that regulation of gene position can lead to transgenerational inheritance.

DNA is not the only medium for communicating information necessary for cell function. Cell processes are also determined by the chemical labeling (or marks) and specific spatial organization of our genomes, which are epigenetic characteristics—that is, nongenetic but nonetheless inheritable traits. Epigenetic marks include modifications of histones, the proteins around which DNA is wound. PcG proteins, on the other hand, play a regulatory role by affecting 3-D chromosomal configuration, which establishes certain interactions between genes in the cell nucleus. The position of a gene at any given moment determines whether it is active or repressed.

Through temporary disruption of these interactions, the scientists were able to produce Drosophila epilines characterized by different levels of PcG-dependent gene repression or activation. They verified that these epilines were indeed isogenic, or genetically identical, by sequencing the genome of each. Despite their identical DNA, the integrity of epilines—and the unique phenotypic characteristics they program—can be maintained across generations. But this phenomenon is reversible. Crosses between drosophilas with over- or underexpressed genes and others having no such modifications to gene activity "reset" eye color without altering the DNA sequence, thus demonstrating the epigenetic nature of this inheritance.

The researchers then showed that new environmental conditions, such as a different ambient temperature, can affect the expression of epigenetic information over several generations, but they do not erase this information. Such transient effects of environmental factors to which earlier generations were exposed on the expression of characteristics in their progeny illustrate the unique, pliable nature of this epigenetic mechanism. By conducting "microcosm" experiments that recreated natural environmental conditions, the researchers—working with INRA—confirmed that epigenetic inheritance in Drosophila can be maintained in the wild.
 

Giacomo Cavalli's crew has therefore proven the existence of Polycomb-mediated stable transgenerational epigenetic inheritance dependent on 3-D chromosomal structure. Their findings offer new horizons for biomedical science. They suggest that epigenetics could partly solve the mystery of "missing heritability"—that is, the absence of any apparent link between genetic makeup and certain normal hereditary traits and diseases."

My comment: Human eye color is also regarded as polygenic trait which means there's no one certain gene in response of determining eye color. Pigment production and regulation is instead controlled by epigenetic factors and mechanisms.This means that also skin color and hair color variation are regulated by epigenetic factors. Modern science has revealed that human characteristics are not determined by DNA sequences. This is why the theory of evolution is the most serious heresy of our time. Don't get lost.

Epigenetic markers control where and how much protein is made by a gene

Harvard University research: Adverse Early Experiences Can Have Lifelong Consequences

https://developingchild.harvard.edu/science/deep-dives/gene-environment-interaction/?platform=hootsuite

Excerpt: "Science tells us that the interactions between genes and environment shape human development. Despite the misconception that genes are “set in stone,” research shows that early experiences can determine how genes are turned on and off — and even whether some are expressed at all. The healthy development of all organs, including the brain, depends on how much and when certain genes are activated to do certain tasks. The experiences that children have early in life, therefore, play a crucial role in the development of brain architecture. Ensuring that children have appropriate, growth-promoting early experiences is an investment in their ability to become healthy, productive members of society.

Experiences Affect How Genes Are Expressed

Inside the nucleus of each cell in our bodies, we have chromosomes, which contain the code for characteristics that pass to the next generation (My add: characteristics are passed with guidance of non coding RNA molecules). Within these chromosomes, specific segments of genetic code, known as genes, make up long, double-helix strands of DNA.

Children inherit approximately 23,000 genes from their parents (My add: The number of protein coding DNA strands is about 19,600 in human genome), but not every gene does what it was designed to do. Experiences (My add: and several other environmental factors) leave a chemical “signature” on genes that determine whether and how the genes are expressed. Collectively, those signatures are called the epigenome.

The brain is particularly responsive to experiences and environments during early development. External experiences spark signals between neurons, which respond by producing proteins. These gene regulatory proteins head to the nucleus of the neural cell, where they either attract or repel enzymes that can attach them to the genes. Positive experiences, such as exposure to rich learning opportunities, and negative influences, such as malnutrition or environmental toxins, can change the chemistry that encodes genes in brain cells — a change that can be temporary or permanent. This process is called epigenetic modification.

Adverse Early Experiences Can Have Lifelong Consequences

Epigenetic “markers” control where and how much protein is made by a gene, effectively turning the gene “on” or “off.” Such epigenetic modification typically occurs in cells that comprise organ systems, thereby influencing how these structures develop and function. Therefore, experiences that change the epigenome early in life, when the specialized cells of organs such as the brain, heart, or kidneys are first developing, can have a powerful impact on physical and mental health for a lifetime.
 

The fact that genes are vulnerable to modification in response to toxic stress, nutritional problems, and other negative influences underscores the importance of providing supportive and nurturing experiences for young children in the earliest years, when brain development is most rapid. From a policy perspective, it is in society’s interest to strengthen the foundations of healthy brain architecture in all young children to maximize the return on future investments in education, health, and workforce development."

My comment: Serious scientists in the academic field are realizing what factors control the reading and expressing of DNA. Epigenetic markers control where and how much protein is made by a gene. To be exact, this regulation is mostly done at pre-mRNA --> mRNA level in which the cell is able to modify RNAs in several complex and intelligent ways. But epigenetic markers control also how DNA is read into transcription. This is why DNA is just a passive information library. 

Epigenetics is arguably more important than the field of genetics

Cancer is not a disease based on genetic mutations as has almost universally been touted by the mainstream, but is instead a metabolic disorder

http://www.doctorschierling.com/blog/epigenetics-relationship-to-inflammation-cancer-and-a-myriad-of-other-genetic-diseases?utm_source=dlvr.it&utm_medium=twitter

Excerpt: "One of the reasons I left cancer research, I noticed early on the approach was all wrong. First they were essentially using germ theory - treating cancer as an invader other than self that had to be defeated with external weapons of mass destruction. Obviously an ineffective approach, yet it continues. In many of the trials we conducted the treatments were so toxic that patients died much sooner than they would have with no treatment at all. Then came the gene theory- they were convinced they could isolate just a few genes gone rogue, target them and cure cancer. Still failed. Then they targeted angiogenesis (VEGF inhibitors) proliferation proteins Kinase inhibitors, mTOR inhibitors etc. These drugs would control cancer growth for a period of time but the body is so intelligent that after awhile the cellular machinery adapted and bypassed the inhibition, and became much more virulent. Essentially, they were chasing pathways that could be inhibited to stop growth, but they failed to search for the underlying cause. People do not get' cancer their body has created cancer. Why is the body making these changes on the cellular level? What is the body attempting to protect itself from by making these changes? I believe that allopathic medicine is stuck in an old paradigm based on Newtonian physics and linear cause and effect ---- car mechanic medicine. Until there is a massive paradigm shift based on quantum physics, energy, metabolism, and cellular adaptation in response to environment; allopathic approaches to cancer and other chronic diseases will continue to fall short. I like to ask patients….. if your goldfish was sick what would you do? Most likely you would look at their tank - is it big enough? and their water- is it clean enough? is the pH correct? and their food- too much? too little? wrong kind? Are there other fish in tank? You probably wouldn’t take them immediately to the vet for blood work and an MRI.
( An astounding quote from an individual from a functional medicine group I am in, who left cancer research to become an MD.)

Although we've made some progress since the early days of the Genome Project --- started in 1990, it took 13 years to sequence all 3.3 billion base pairs in human DNA --- it has not proved the be-all-end-all it was, and in many cases, continues to be hyped as. It seems that the next big "genetic" thing is always just around the corner, with CRISPR being the latest. Why is this? Why hasn't genetics proved to be as helpful as many prophesied it would? In a word, epigenetics. Huh? According to a twelve year old study from Environmental Health Perspectives (Epigenetics: The Science of Change), we not only get a working definition of epigenetics, but why, as I've been telling readers for years, it's arguably more important than the field of genetics.

"Understanding cancer would be one long-term goal for the U.S. project, but epigenetics—changes in gene expression heritable from cell to daughter cell without changes in DNA sequence—transcends any one disease. 'It has profound implications in aging, neurological disorders, and child development,' says Peter Jones, another group member and director of the Norris Comprehensive Cancer Center at the University of Southern California. Jones and his colleagues argue that the importance of epigenetics in human disease, together with the maturing of technologies for mapping epigenetic changes, make a human epigenome project both critical and feasible. Epigenetics, says cancer biologist Jean-Pierre Issa of The University of Texas M.D. Anderson Cancer Center, could prove more important than genetics for understanding environmental causes of disease. 'Cancer, atherosclerosis, Alzheimer’s disease are all acquired diseases where the environment very likely plays an important role,' he points out. 'And there’s much more potential for the epigenome to be affected … than the genome itself. It’s just more fluid and more easy to be the culprit.'"

Allow me to explain EPIGENETICS in a nutshell. Although people carry genes for any number of diseases, said diseases are not expressed unless the genes are acted on by their environment. In other words these genes must be 'turned on' by certain chemical messengers or they don't create the disease processes mentioned above. What's more, because of epigenetics we are learning that at least to some degree, the sins of the fathers (or mothers) can be passed on to their offspring. Did you follow that? Some of these epigenetic traits are actually heritable.
This month's issue of Oncotarget published a study (Inborn-Like Errors of Metabolism are Determinants of Breast Cancer Risk, Clinical Response and Survival: A Study of Human Biochemical Individuality) by a team of 35 researchers from 17 institutions throughout the U.S., Brazil and Europe. Over 1,200 patients were involved. The gist of the study? Cancer occurs because cancer cells make and use energy differently than normal cells. Challenging decades of genomic research, this team determined cancer not to be a disease based on genetic mutations as has almost universally been touted by the mainstream, but is instead a metabolic disorder just as diabetes is a metabolic disorder. Lead author, oncologist, hematologist, internist, and Professor of Pharmacology at Cal State Irvine, Dr. Robert Nagourney, put it this way.

"This suggests that cancer is not a genetic disease arising solely from mutations as we have all been taught, but instead a metabolic condition that develops under the stress of cellular nutrient deprivation. Cells that cannot generate enough energy due to lack of oxygen, sugars or proteins, common to many cancers, use altered metabolic pathways to ensure their survival. Unfortunately these cancer cells' success comes at the expense of the host patient."

Achieving an accuracy rate of detecting cancer in over 95% of the cases, the researchers ran both healthy controls and patients with various sorts of CANCER, including BREAST CANCER, through a series of blood tests, where the blood levels of over 200 chemicals, sugars, amino acids, proteins, and fats, were measured via mass spectrometry. When the controls were compared to cancer patients, there were striking differences that clearly delineated those with cancer from those without. "The metabolic changes identified are consistent with inborn-like errors of metabolism and define a continuum from normal controls to elevated risk to invasive breast cancer." In other words, whether one carried a certain cancer gene or not, cancer could be detected with extreme accuracy simply by looking very closely at blood work (it could be done with a single drop of blood).

While this was hailed as a scientific breakthrough, I must disagree. It's just that a huge segment of the medical community has been ignoring their own research for the past century. Not only do we know that certain CHEMICAL EXPOSURES epigenetically predispose people to cancer, but we know that excess sugar consumption does as well. It was 1931's Nobel Laureate, DR. OTTO WARBURG, who won because nearly 9 decades ago he was referring to cancer as a metabolic disease ---- a disease that survives, thrives, and spreads, by fermenting sugar."

My comment: Genetic mutations are no causes for cancers, instead they are consequences. DNA reading procedures are done via epigenetic information layers, factors and control. Cellular processes go through the epigenetic regulation before DNA is read. And DNA is read because the cell produces functional RNA-molecules that also control cellular processes. The cell has several clever ways to edit and modify RNA-molecules. This means genetic mutations don't necessarily mean anything for the cell, because they can be edited out during RNA-production.

DNA is just a passive information library and it's not your destiny. The theory of evolution is the most serious heresy of our time. Don't get lost.

Histones control how DNA is read

Histones control both structural and functional aspects of our genetic hardware

https://www.scimex.org/newsfeed/honey-bees-unravel-nature-nurture-mysteries

Excerpt: "They say leaders are born not made, but it seems the opposite is true for queen bees, according to a new study by researchers from The Australian National University (ANU) and Queen Mary University of London.

Larvae turn into queen bees when they are fed a nutritious diet called ‘royal jelly’.

Royal jelly has the capacity to influence the genetic instructions encoded in the honey bee genome, a process called ‘epigenetics’ or ‘above genetics’.

So how does this quirk of nature actually work?

“We hypothesised that royal jelly acts via a special class of proteins called histones that are directly associated with DNA and control both structural and functional aspects of our genetic hardware,” Ryszard Maleszka from the ANU Research School of Biology said.

“These proteins are modified by various chemical tags, which provides them with the needed flexibility to coordinate the expression of all genes and respond to changing extremal conditions.”

Bees are eusocial insects, meaning there’s usually one individual who reproduces (the queen) and the rest of the females in the colony perform a large repertoire of tasks.
 

They all start out with the same genetic blueprint, but differential feeding controls their developmental fate, setting a larva on the path to becoming a queen, or a sterile worker.

The study found big differences in genes involved in certain behaviours and brain development.

“The extent of histone modifications uncovered by this study is remarkable and exceeded our expectations. We were able to identify where the important differences are in the genomes of workers and queen,” Dr Paul Hurd from Queen Mary University said.

“We suspect here might even be specific enhancers in the genome that determine worker phenotype or queen phenotype and it might be possible in the future to manipulate those and see how we can reverse or change the trajectory.”

The workers have a much more enhanced development of the brain and neural-system, which is consistent with their sophisticated adult behaviours such as navigation, communication and long-term memory.

As expected, the queen was found to have more enhanced metabolic processes and reproductive features.

While more research is required to find a more definitive answer on the potential benefits of royal jelly to humans, these findings could change the way we look at our own diets.

“It could help us gain some understanding of what happens to humans or mammals in general when they overeat or change their dietary habits,” Professor Maleszka said."

My comment: DNA is just a passive information library for the cell. DNA is not your destiny. DNA doesn't dictate traits of an organism. DNA has no control over cellular processes. Epigenetic factors and mechanisms have the control.

Transgenerational Epigenetic Inheritance - Epigenetic Marks to Phenotype

Differentiation in Embryonic Cells: Linking Histone Acetylation and DNA Methylation to a Heritable Phenotype

Excerpt: "Although the mechanisms of how histone marks such as acetyl tags are maintained are still to be determined, it has been shown that these acetyl tags can in fact be transmitted through sex gametes and cause a heritable phenotype in the growing embryonic cells. For example in Study 2, acetyl tags were seen at the BDNF promoters in the sperm of the cocaine-sired fathers as well as in the male progeny. Another example is shown below.

In the Study by van der Heijden et al, they used DAPI (to stain the nucleus) and specific antibodies for staining acetylated lysine 8 on histone 4 (in green) to show that after fertilization of egg and sperm, acetyl tags are seen in the zygote that were passed on from the sperm of the fathers. The figure above shows their results, with the sperm pronucleus in panel A and the eventual spreading of the acetyl tags once the nucleus begins to decondense.

These acetyl tags, passed on through sperm, have then been shown to create heritable phenotypes in the resulting progeny. As seen in the second major study highlighted on this site, the acetyl tags were maintained and they increased expression of specific genes. Acetyl tags are also known to be able to shut genes down by recruiting molecular machinery to modify the nucleosome. One such pathway includes the shutting off of the Oct4 pluripotency gene in differentiating embryonic cells, so that reprogramming may be shut down. 

Here acetyl tags recruit G9a (a methyltransferase) and HDACs and allow for the deacetylation and demethylation of the histones. G9a will then methylate K9 of histone 3, which then attracts histone methyl-binding proteins such as HP1. These recruit DNMTs to methylate the DNA, shutting off the gene. Other genes have been shown to be shut down in a similar pathway during early embryonic development."

My comment: This is how transgenerational epigenetic inheritance works. This is why genetically (DNA) identical twins might have different colors of skin, eyes and hair. These histone epigenetic markers are mediated by non coding RNA molecules during early stages of embryonic development. Histone code is a biological database that is able to store most of organisms' traits (phenotype). Any change in organisms is due to epigenetic regulation of existing biological information or gradual but inevitable disappearance of information. That's why there's no mechanism for evolution. Don't get lost.