Gene Modification Quotes

It seems right now that all I’ve ever done in my life is making my way here to you.’ I could see that Rosie could not place the line from The Bridges of Madison County that had produced such a powerful emotional reaction on the plane. She looked confused. ‘Don, what are you…what have you done to yourself?’ ‘I’ve made some changes.’ ‘Big changes.’ ‘Whatever behavioural modifications you require from me are a trivial price to pay for having you as my partner.’ Rosie made a downwards movement with her hand, which I could not interpret. Then she looked around the room and I followed her eyes. Everyone was watching. Nick had stopped partway to our table. I realised that in my intensity I had raised my voice. I didn’t care. ‘You are the world’s most perfect woman. All other women are irrelevant. Permanently. No Botox or implants will be required. ‘I need a minute to think,’ she said. I automatically started the timer on my watch. Suddenly Rosie started laughing. I looked at her, understandably puzzled at this outburst in the middle of a critical life decision. ‘The watch,’ she said. ‘I say “I need a minute” and you start timing. Don is not dead. 'Don, you don’t feel love, do you?’ said Rosie. ‘You can’t really love me.’ ‘Gene diagnosed love.’ I knew now that he had been wrong. I had watched thirteen romantic movies and felt nothing. That was not strictly true. I had felt suspense, curiosity and amusement. But I had not for one moment felt engaged in the love between the protagonists. I had cried no tears for Meg Ryan or Meryl Streep or Deborah Kerr or Vivien Leigh or Julia Roberts. I could not lie about so important a matter. ‘According to your definition, no.’ Rosie looked extremely unhappy. The evening had turned into a disaster. 'I thought my behaviour would make you happy, and instead it’s made you sad.’ ‘I’m upset because you can’t love me. Okay?’ This was worse! She wanted me to love her. And I was incapable. Gene and Claudia offered me a lift home, but I did not want to continue the conversation. I started walking, then accelerated to a jog. It made sense to get home before it rained. It also made sense to exercise hard and put the restaurant behind me as quickly as possible. The new shoes were workable, but the coat and tie were uncomfortable even on a cold night. I pulled off the jacket, the item that had made me temporarily acceptable in a world to which I did not belong, and threw it in a rubbish bin. The tie followed. On an impulse I retrieved the Daphne from the jacket and carried it in my hand for the remainder of the journey. There was rain in the air and my face was wet as I reached the safety of my apartment.

An arcane microbial defense, devised by microbes, discovered by yogurt engineers, and reprogrammed by RNA biologists, has created a trapdoor to the transformative technology that geneticists had sought so longingly for decades: a method to achieve directed, efficient, and sequence-specific modification of the human genome.

the conclusion I wish to draw is not really disputable. If host behaviour or physiology is a parasite adaptation, there must be (have been) parasite genes ‘for’ modifying the host, and the host modifications are therefore part of the phenotypic expression of those parasite genes. The extended phenotype reaches out of the body in whose cells the genes lie, reaches out to the living tissues of other organisms.

The next step in the process of making modern farming more efficient and profitable was genetic modification. In bioengineered plants, lectins are artificially inserted. Scientists selectively add foreign genes into a plant’s basic genome to command the plant to manufacture specific lectins that enhance the plant’s ability to resist insects and other pests. This is one form of genetically modified organisms (GMO).

The drive to change the genome of a human embryo has turned into an intercontinental arms race. As of this writing, four other groups in China are reportedly working on introducing permanent mutations in human embryos. By the time this book is published, I would not be surprised if the first successful targeted genome modification of a human embryo had been achieved in a laboratory. The first "post-genomic" human might be on his or her way to being born.

Morgan had discovered an important modification to Mendel's laws. Genes did not travel separately; instead, they moved in packs. Packets of information were themselves packaged-into chromosomes, and ultimately in cells. But the discovery had a more important consequence: conceptually, Morgan had not just linked genes; he had linked two disciplines-cell biology and genetics. The gene was not a "purely theoretical unit." It was a material thing that lived in a particular location, and a particular form, within a cell.

The word epigenetics literally means “above the gene.” It refers to the control of genes not from within the DNA itself but from messages coming from outside the cell—in other words, from the environment. These signals cause a methyl group (one carbon atom attached to three hydrogen atoms) to attach to a specific spot on a gene, and this process (called DNA methylation) is one of the main processes that turns the gene off or on. (Two other processes, covalent histone modification and noncoding RNA, also turn genes on and off,

Genetic atomism is dead. Hereditary stability and hereditary change are both based, not on a mosaic of genes, but on the action of the gene-complex 'as a whole'. But this face-saving expression-which is now coming into increased use-is empty, like so many other holistic formulations, unless we interpolate between the gene-complex as a whole, and the individual gene, a hierarchy of genetic sub-assemblies-self-regulating holons of heredity, which control the development of organs, and also control their possible evolutionary modifications, by canalising the effects of random mutations. A hierarchy with its built-in, self-regulatory safeguards is a stable affair. It cannot be pulled in here, pulled out there, like Patou belabouring his model. It is capable of variation and change, but only in co-ordinated ways and only in limited directions.

A note of caution: epigenetics is also on the verge of transforming into a dangerous idea. Epigenetic modifications of genes can potentially superpose historical and environmental information on cells and genomes—but this capacity is speculative, limited, idiosyncratic, and unpredictable: a parent with an experience of starvation produces children with obesity and overnourishment, while a father with the experience of tuberculosis, say, does not produce a child with an altered response to tuberculosis. Most epigenetic “memories” are the consequence of ancient evolutionary pathways, and cannot be confused with our longing to affix desirable legacies on our children. As with genetics in the early twentieth century, epigenetics is now being used to justify junk science and enforce stifling definitions of normalcy. Diets, exposures, memories, and therapies that purport to alter heredity are eerily reminiscent of Lysenko’s attempt to “reeducate” wheat using shock therapy. Mothers are being asked to minimize anxiety during their pregnancy—lest they taint all their children, and their children, with traumatized mitochondria. Lamarck is being rehabilitated into the new Mendel. These glib notions about epigenetics should invite skepticism. Environmental information can certainly be etched on the genome. But most of these imprints are recorded as “genetic memories” in the cells and genomes of individual organisms—not carried forward across generations. A man who loses a leg in an accident bears the imprint of that accident in his cells, wounds, and scars—but does not bear children with shortened legs. Nor has the uprooted life of my family seem to have burdened me, or my children, with any wrenching sense of estrangement. Despite Menelaus’s admonitions, the blood of our fathers is lost in us—and so, fortunately, are their foibles and sins. It is an arrangement that we should celebrate more than rue. Genomes and epigenomes exist to record and transmit likeness, legacy, memory, and history across cells and generations. Mutations, the reassortment of genes, and the erasure of memories counterbalance these forces, enabling unlikeness, variation, monstrosity, genius, and reinvention—and the refulgent possibility of new beginnings, generation upon generation.

What holds cells in this teetering position? In 2006, a group headed by Eric Lander at the Broad Institute in Boston, found at least part of the answer. A key set of genes in ES cells, the pluripotent cells we have come to know so well, were found to have a really strange histone modification pattern. These were genes that were very important for controlling if an ES cell stayed pluripotent, or differentiated. Histone H3K4 was methylated at these genes, which normally is associated with switching on gene expression. H3K27 was also methylated. This is normally associated with switching off gene expression. So, which modification would turn out to be stronger? Would the genes be switched on or off? The answer turned out to be both. Or neither, depending on which way we look at it. These genes were in a state called ‘poised’. Given the slightest encouragement – a change in culture conditions that pushed cells towards differentiation for example – one or other of these methylations was lost. The gene was fully switched on, or strongly repressed, depending on the epigenetic modification

There is increasing evidence that at least some of the targeting of epigenetic modifications can be explained by interactions with long ncRNAs. Jeannie Lee and her colleagues have recently investigated long ncRNAs that bind to a complex of proteins. The complex is called PRC2 and it generates repressive modifications on histones. PRC2 contains a number of proteins, and the one that interacts with the long ncRNAs is probably EZH2. The researchers found that the PRC2 complex bound to literally thousands of different long ncRNA molecules in embryonic stem cells from mice13. These long ncRNAs may act as bait. They can stay tethered to the specific region of the genome where they are produced, and then attract repressive enzymes to shut off gene expression. This happens because the repressive enzyme complexes contain proteins like EZH2 that are capable of binding to RNA.

The Air ncRNA gave scientists important insights into how these long ncRNAs repress gene expression. The ncRNA remained localised to a specific region in the cluster of imprinted genes, and acted as a magnet for an epigenetic enzyme called G9a. G9a puts a repressive mark on the histone H3 proteins in the nucleosomes deposited on this region of DNA. This histone modification creates a repressive chromatin environment, which switches off the genes.

In this model, there is a vicious cycle of events that results in the generation of a more and more repressed state. One of the predictions from this model is that repressive histone modifications attract DNA methyltransferases, which deposit DNA methylation near those histones. This methylation in turn attracts more repressive histone modifying enzymes, creating a self-perpetuating cycle that leads to an increasingly hostile region for gene expression. Experimental data suggest that in many cases this model seems to be right. Repressive histone modifications can act as the bait to attract DNA methylation to the promoter of a tumour suppressor gene. A key example of this is an epigenetic enzyme we met in the previous chapter, called EZH2. The EZH2 protein adds methyl groups to the lysine amino acid at position 27 on histone H3. This amino acid is known as H3K27. K is the single letter code for lysine (L is the code for a different amino acid called leucine).

It’s abundantly clear that these events do happen, and quite frequently, but often it’s been difficult to identify exactly how a tumour suppressor has mutated. In the last fifteen years, we’ve started to realise that there is another way that a tumour suppressor gene can become inactivated. The gene may be silenced epigenetically. If the DNA at the promoter becomes excessively methylated or the histones are covered in repressive modifications, the tumour suppressor will be switched off. The gene has been inactivated without changing the underlying blueprint.

In our model, treatment with 5-azacytidine will drive down the DNA methylation for as long as the patients take the drug. Unfortunately, many cancer drugs have serious side-effects and the DNMT inhibitors are no exception. The side effects may eventually become such a problem that the patient has to stop taking the drug. However, the patient’s cancer cells probably still have histone modifications at the tumour suppressor genes. Once the patient stops taking 5-azacytidine, these histone modifications almost certainly start to attract the DNMT enzymes all over again, re-initiating stable repression of gene expression.

Part of this may involve the small percentage of histones that are present in the sperm genome. Many of these are located at the imprinting control regions, and may protect these regions from reprogramming when the sperm and the egg fuse25. Histone modifications also play a role in establishing ‘new’ imprints during gamete production. It seems to be important that the imprinting control regions lose any histone modifications that are associated with switching genes on. Only then can the permanent DNA methylation be added26. It’s this permanent DNA methylation that marks a gene with a repressive imprint.

There’s an amazing family of genes, called HOX genes. When they’re mutated in fruit flies (Drosophila melanogaster) the results are incredible phenotypes, such as legs growing out of the head14. There’s a long ncRNA known as HOTAIR, which regulates a region of genes called the HOX-D cluster. Just like the long ncRNAs investigated by Jeannie Lee, HOTAIR binds the PRC2 complex and creates a chromatin region which is marked with repressive histone modifications. But HOTAIR is not transcribed from the HOX-D position on chromosome 12. Instead it is encoded at a different cluster of genes called HOX-C on chromosome 215. No-one knows how or why HOTAIR binds at the HOX-D position. There’s a related mystery around the best studied of all long ncRNAs, Xist. Xist ncRNA spreads out along almost the entire inactive X chromosome but we really don’t know how. Chromosomes don’t normally become smothered with RNA molecules. There’s no obvious reason why Xist RNA should be able to bind like this, but we know it’s nothing to do with the sequence of the chromosome. The experiments described in the last chapter, where Xist could inactivate an entire autosome as long as it contained an X inactivation centre, showed that Xist just keeps on travelling once it’s on a chromosome. Scientists are basically still completely baffled about these fundamental characteristics of this best-studied of all ncRNAs.

Reprogramming is what John Gurdon demonstrated in his ground-breaking work when he transferred the nuclei from adult toads into toad eggs. It’s what happened when Keith Campbell and Ian Wilmut cloned Dolly the Sheep by putting the nucleus from a mammary gland cell into an egg. It’s what Yamanaka achieved when he treated somatic cells with four key genes, all of which code for proteins highly expressed naturally during this reprogramming phase. The egg is a wonderful thing, honed through hundreds of millions of years of evolution to be extraordinarily effective at generating vast quantities of epigenetic change, across billions of base-pairs. None of the artificial means of reprogramming cells comes close to the natural process in terms of speed or efficiency. But the egg probably doesn’t quite do everything unaided. At the very least, the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily. The sperm epigenome is primed to be reprogrammed6. Unfortunately, these priming chromatin modifications (and many other features of the sperm nucleus), are missing if an adult nucleus is reprogrammed by transferring it into a fertilised egg. That’s also true when an adult nucleus is reprogrammed by treating it with the four Yamanaka factors to create iPS cells. In both these circumstances, it’s a real challenge to completely reset the epigenome of the adult nucleus. It’s just too big a task. This is probably why so many cloned animals have abnormalities and shortened lifespans. The defects that are seen in these cloned animals are another demonstration that if early epigenetic modifications go wrong, they may stay wrong for life. The abnormal epigenetic modification patterns result in permanently inappropriate gene expression, and long-term ill-health.

All this reprogramming of the genome in normal early development changes the epigenome of the gametes and creates the new epigenome of the zygote. This ensures that the gene expression patterns of eggs and sperm are replaced by the gene expression patterns of the zygote and the subsequent developmental stages. But this reprogramming also has another effect. Cells can accumulate inappropriate or abnormal epigenetic modifications at various genes. These disrupt normal gene expression and can even contribute to disease, as we shall see later in this book. The reprogramming of the egg and the sperm prevent them from passing on from parent to offspring any inappropriate epigenetic modifications they have accumulated. Not so much wiping the slate clean, more like re-installing the operating system.

Even though these individuals had seemed perfectly healthy at birth, something that had happened during their development in the womb affected them for decades afterwards. And it wasn’t just the fact that something had happened that mattered, it was when it happened. Events that take place in the first three months of development, a stage when the foetus is really very small, can affect an individual for the rest of their life. This is completely consistent with the model of developmental programming, and the epigenetic basis to this. In the early stages of pregnancy, where different cell types are developing, epigenetic proteins are probably vital for stabilising gene expression patterns. But remember that our cells contain thousands of genes, spread over billions of base-pairs, and we have hundreds of epigenetic proteins. Even in normal development there are likely to be slight variations in the expression of some of these proteins, and the precise effects that they have at specific chromosomal regions. A little bit more DNA methylation here, a little bit less there. The epigenetic machinery reinforces and then maintains particular patterns of modifications, thus creating the levels of gene expression. Consequently, these initial small fluctuations in histone and DNA modifications may eventually become ‘set’ and get transmitted to daughter cells, or be maintained in long-lived cells such as neurons, that can last for decades. Because the epigenome gets ‘stuck’, so too may the patterns of gene expression in certain chromosomal regions. In the short term the consequences of this may be relatively minor. But over decades all these mild abnormalities in gene expression, resulting from a slightly inappropriate set of chromatin modifications, may lead to a gradually increasing functional impairment. Clinically, we don’t recognise this until it passes some invisible threshold and the patient begins to show symptoms.

Here’s the sequence of epigenetic events in very early development: The male and female pronuclei (from the sperm and the egg respectively) are carrying epigenetic modifications; The epigenetic modifications get taken off (in the immediate post-fertilisation zygote); New epigenetic modifications get put on (as the cells begin to specialise). This is a bit of a simplification. It’s certainly true that researchers can detect huge swathes of DNA demethylation during stage 2 from this list. However, it’s actually more complicated than this, particularly in respect of histone modifications. Whilst some histone modifications are being removed, others are becoming established. At the same time as the repressive DNA methylation is removed, certain histone marks which repress gene expression are also erased. Other histone modifications which increase gene expression may take their place. It’s therefore too naïve to refer to the epigenetic changes as just being about putting on or taking off epigenetic modifications. In reality, the epigenome is being reprogrammed.

April 2015, China announced its use of a new technology known as CRISPR (Clustered Regularly Interspersed Palindromic Repeats), used for the purpose of simplified gene editing. This new genetic modification technology is fast, simple to use, and inexpensive. A recent Chinese biotech start-up named Amino has brought this technology to everyone in a kit that retails for just under seven hundred dollars. Yes, for less than a good smartphone,

The ‘epi’ in epigenetics is derived from Greek and means at, on, to, upon, over or beside. The DNA in our cells is not some pure, unadulterated molecule. Small chemical groups can be added at specific regions of DNA. Our DNA is also smothered in special proteins. These proteins can themselves be covered with additional small chemicals. None of these molecular amendments changes the underlying genetic code. But adding these chemical groups to the DNA, or to the associated proteins, or removing them, changes the expression of nearby genes. These changes in gene expression alter the functions of cells, and the very nature of the cells themselves. Sometimes, if these patterns of chemical modifications are put on or taken off at a critical period in development, the pattern can be set for the rest of our lives,

be able to repair.  But they’re doing it more smoothly.  As if by design.  That’s what was so astonishing when we saw it before.  But the bacterium is different.  These are replicating even faster.  It’s as if once the DNA was infused into the genes of the bacteria, something happened.” “I don’t know if the Chinese changed something during their extraction process, even inadvertently.  But if they did, it could explain the difference in cellular function.  In fact, even if it wasn’t something during extraction, just the transfer from one life form to another could be enough to trigger a modification.  Or a mutation.  Even a single base pair

McGill researcher Moshe Szyf compared the epigenetic profiles of hundreds of children born into the extreme ends of social privilege in the United Kingdom and measured the effects of child abuse on both groups. Differences in social class were associated with distinctly different epigenetic profiles, but abused children in both groups had in common specific modifications in seventy-three genes. In

There is compelling evidence to argue that cells can sense and respond to the stiffness of their ECM and that they transmit these cues to the nucleus to alter their shape and modify their chromatin accessibility either directly or indirectly by modulating cellular metabolism. What has yet to be determined is whether these tension-induced changes in chromatin modification and chromosomal localization are accompanied by specific differences in gene expression and whether altering the metabolic state of the cell could modify these phenotypes. Moreover, whether similar effect occur in fibrotic, stiffened tumor tissues and if this influences gene expression to drive a tumor-like behavior in the cells and tissue remain unclear.

Given that the modification is so small, it’s perhaps surprising that it will come up over and over again in this book, and in any discussion of epigenetics. This is because methylation of DNA has profound effects on how genes are expressed, and ultimately on cellular, tissue and whole-body functions.

Genetic modification” refers to several techniques for changing organisms to suit our wants and needs. The technology involves various methods for inserting one or more specific genes directly into a target organism, or selectively altering or silencing a gene that is already there. There are two basic types of gene insertions: transgenic and cisgenic. Cisgenic insertion involves inserting genes from closely related species, ones that could potentially crossbreed with the target species. Transgenic insertion involves genes from distant species—even from different kingdoms of life, such as putting a gene from a bacterium into a plant.

As we have learned, the immune system stimulates inflammation to defend us from pathogens as well as self-inflicted damage caused by physical activity. In short bursts, inflammation is lifesaving, but low levels of inflammation that last for months or years are pernicious because they slowly attack our bodies. Over time, the destructive effects of chronic, simmering inflammation accumulate in cells and tissues from head to toe including neurons in the brain, cartilage in joints, the walls of arteries, and insulin receptors in muscle and fat cells. If oxidation, mitochondrial dysfunction, mutations, glycation, and inflammation were not enough, plenty of other processes also contribute to senescence by damaging and degrading cells. Over time, tiny molecules glue themselves to the DNA in cells. These so-called epigenetic (on top of the genome) modifications can affect which genes are expressed in particular cells.31 Because environmental factors like diet, stress, and exercise partly influence epigenetic modifications, the older we are, the more of them we accumulate.32 Most epigenetic modifications are harmless, but the more you have for a given age, the higher your risk of dying.33 Other forms of senescence include cells losing the ability to recycle damaged proteins,34 inadequately sensing and acquiring nutrients,35 and (less likely) being unable to divide because the little caps (telomeres) that protect the ends of chromosomes from unraveling have become too short.36

The genetic mechanisms that were described here are a collection of exotic mutations: new cis-regulatory elements from transposable elements; novel transcription factor functions; and new miRNAs. It seems that rewiring a gene regulatory network, as required for the evolution a morphological novelty, uses a quite different set of mechanisms than usually associated with adaptive changes that is, changes in enzyme activity and gene expression due to small changes in cis-regulatory elements. This distinction hints at the possibility that the difference between adaptation and innovation is not only conceptual, but that the conceptual difference might be mirrored by a difference in the molecular mechanisms. It is far from clear whether this distinction will hold up, because there are still only a limited number of cases of innovations that are understood at the molecular level. However, one should at not prematurely dismiss this possibility. The possibility of a mechanistic difference beween adaptation and innovation is also interesting because the characteristics of the genetic mechanisms may explain the phenomenology of innovations; innovations tend to be rare and episodic and result in a phenotype that tends to be canalized in its major features. As discussed above, one of the main characteristics of mutations by transposable elements is that they are episodic and specific to certain lineages. Mutations caused by transposable elements are most prevalent after the infection of a genome by a new retrovirus or any other new transposable elements. Similarly, gene duplications also temporarily open a window of evolvability by releasing constraints on gene evolution, and the maintenance of duplicated genes is often associated with body plan innovations. There is also a tendency for maintaining novel genetic elements with the origin of morphological novelties: new genes, new cis-regulatory elements, new miRNAs, and probably many others. Transcription factor protein evolution is likely necessary for the evolution of novel functional specificities, and miRNAs are involved in canalizing phenotypes once they have arisen. Hence, the conceptual uniqueness of innovations (i.e., the origination of novel cell type or of a quasi-independent body part) as compared to adaptation (i.e. the modification of existing body parts and physiological processes) may require a set of mutational mechanisms that can radically rewire gene regulatory networks and stabilize/canalize the phenotypic product of these changes. If further research supports this idea, then the conceptual distinction between adaptation and innovation will be linked to and grounded in the distinctness of the underlying molecular mechanisms.

Incrementalization simplifies problems by partitioning what’s novel (new) from what is already known. Then fast, small bites are tackled one after the other, rather than trying to swallow one large bite. By holding the base of what is known as constant, modifications can be focused on a smaller portion of the larger system.