What Brings Our Genome Alive?

Throughout most of the twentieth century, genes were viewed as the “agents” responsible for an organism’s development, activity, and evolution. Their agency was said to lie in their ability to “regulate”, “organize”, “coordinate”, and “control” physiological processes. DNA, the bearer of these genes, became the “Book of Life” — the essential maker of organisms and driver of evolution. And this view remains stubbornly entrenched today, despite many changes in our understanding. A leading behavioral geneticist has recently written a book entitled, Blueprint: How DNA Makes Us Who We Are.

Nevertheless, the idea that genes are the decisive “first causes” of life — and, more generally, that molecules at the “bottom” ultimately explain everything that happens at larger scales — has come in for a great deal of criticism in recent years. This criticism, as we will see, is fully justified. But the issues can be subtle, as is suggested by an apparent paradox. Philosopher of biology Lenny Moss, who wrote the valuable book, What Genes Can’t Do, has remarked:

Where molecular biology once taught us that life is more about the interplay of molecules than we might have previously imagined, molecular biology is now beginning to reveal the extent to which macromolecules [such as DNA], with their surprisingly flexible and adaptive complex behavior, turn out to be more life-like than we had previously imagined (Moss 2012).

In a similar vein, I myself wrote a decade ago:

Having plunged headlong toward the micro and molecular in their drive to reduce the living to the inanimate, biologists now find unapologetic life staring back at them from every chromatogram, every electron micrograph, every gene expression profile. Things do not become simpler, less organic, less animate. The explanatory task at the bottom is essentially the same as what we faced higher up (Talbott 2010).

But if all this is true, what are we to make of Harvard geneticist Richard Lewontin’s declaration, itself hardly disputable, that

DNA is a dead molecule, among the most nonreactive, chemically inert molecules in the living world. That is why it can be recovered in good enough shape to determine its sequence from mummies, from mastodons frozen tens of thousands of years ago, and even, under the right circumstances, from twenty-million-year-old fossil plants … DNA has no power to reproduce itself. Rather it is produced out of elementary materials by a complex cellular machinery of proteins. While it is often said that DNA produces proteins, in fact proteins (enzymes) produce DNA … Not only is DNA incapable of making copies of itself, aided or unaided, but it is incapable of “making” anything else (Lewontin 1992).

Many astute observers have echoed Lewontin’s remarks, and I have never seen anyone question them, including those who remain enamored of the “Book of Life”. So which is it? When we peer at DNA, do we see a dead molecule or the secret of life? As it happens, there is a simple answer: if we are looking at a molecule conceived in the usual way as a bit of mindless, inherently inert stuff, then, according to our own conceptions, we see only dead stuff. But if we observe the molecule as a system of forces and energies capable of participating and being caught up in the creative life of the whole cell and organism, then we can hardly help recognizing — and perhaps even reverencing — the living performance unfolding before our eyes.

Saying this is one thing; making it both meaningful and profound is quite another — and that is one task of the present book. So let us begin.

Obviously it must be possible, however difficult to conceive. The first thing to realize is that chromosomes do not consist of naked DNA. Their actual substance, an intricately woven and ever-changing structure of DNA, RNA, and protein, is referred to as chromatin. (See Box 3.1 for some basic terminology.) Histone proteins, several of which can bind together in the form of a complex histone core particle, are the single most prominent, non-DNA constituents of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one. The core particle with its DNA wrapping is referred to as a nucleosome (about which you can read much more in Chapter 14), and between 75 and 90 percent of our DNA is wrapped up in nucleosomes. This is one way the cell packs its DNA into a surprisingly small volume.

But how is all this material organized so as to serve the infinitely complex requirements of a flatworm, bumblebee, shark, or human? Biologists have spent a good number of years trying to visualize the functional organization of chromosomes in the cell nucleus, and, while the task is far from finished, a lot of progress has been made.

Two important efforts to map the spatial arrangement of chromosomes were published in 2009 and 2014.¹ The researchers performed detailed analyses that yielded the schematic representations in the two figures below. The first of these studies showed that chromosomes are roughly organized into several functional compartments, represented by the different colors of the spherical globule in Figure 3.1. (The image depicts only the chromosomes, not the contents of the larger nucleus.) Any given chromosome simultaneously participates in multiple compartments, as indicated by the different colors of the linear (unfolded) chromosome shown at the top of the figure. You can, then, readily imagine the tortuous pathways of the intermingling chromosomes — the “twenty-four miles of string in a tennis ball” — constituting the overall globule.

The different compartments are distinguished by the kinds of genes residing in them and by the chromatin proteins, the modifications of those proteins, and the vast number of associated molecules in the nucleus that influence how those genes will be expressed and even what sort of products they will yield. In addition, researchers are widely agreed that the entire aggregate is more or less partitioned into two broader compartments, referred to as the “A” and “B” compartments. “A” tends to contain more active genes and to consist of more open chromatin, while “B” contains less active genes and more condensed chromatin.

The picture is always dynamic. Chromosomes move. Or, rather, they are brought into motion. Particular genes — which is to say, particular parts of chromosomes — can be shifted from one compartment to another, and the associations they form with other chromosomal regions — whether on the same or different chromosomes — can be decisive for the regulation of gene expression. One way to picture a part of this dynamism is shown in Figure 3.2.

Of the two widely separated loci thus brought together, one may be near a gene while the other is near regulatory elements necessary for that gene to be expressed. Their coming together (or not) is therefore part of how genes come to be expressed (or not). And, likewise, the reconfiguration of such loops may be critical for the altered expression of genes as the cellular and organismal context changes.

But it’s not just the contact at the base of a loop that matters. Each loop as a whole forms its own domain, within which interactions typically occur more frequently than between more widely separated loci. And this organization of chromosomes into functional regions takes place at different scales, which have not at all been fully explored as yet. For example, researchers have identified “topologically associated domains” (TADs) dividing any given chromosome into regions of, say, one or two million “letters”. Interactions within such domains are more frequent than between domains. But there are no absolute rules in such matters. Sometimes the fraternizing bits of DNA are separated on their chromosome by tens of millions of “letters”, or reside on entirely different chromosomes.

We have so far hardly done more than hint at the true dynamism that enlivens our genetic heritage. The general picture of complex, three-dimensional organization has certainly galvanized molecular biologists. John Rinn, director of the Rinn Lab at Harvard, has said of the nuclear space and its chromosomal drama, “It’s genomic origami … It’s the shape that you fold [the genome] into that matters” (quoted in Zimmer 2015). According to the 2014 paper cited above, “A loop that turns a gene on in one cell type might disappear in another. A domain may move from subcompartment to subcompartment as its flavor changes. No two cell types [have their chromosomes] folded alike. Folding drives function.”⁴ And Suhas Rao, the paper’s lead author and a researcher at Baylor College of Medicine’s Center for Genome Architecture, remarked:

A loop is the fundamental fold in the cell’s toolbox. We found that the formation and dissolution of DNA loops inside the nucleus enables different cells to create an almost endless array of distinct three-dimensional folds and, in so doing, accomplish an extraordinary variety of functions (quoted in Physorg 2014).

Every overall configuration (involving many factors we have not yet considered) represents a unique balance between constrained and liberated expression of our total complement of 21,000 genes.⁵ Moreover, new features of chromosome spatial and dynamic organization continue to be elucidated on a regular basis, and there appears to be no limit to the variety and scale of these features.

Think about all this dynamic form and movement for a while, and you may find yourself asking, along with me: What possible mechanism could ensure the coherence of all this movement and gesturing in relation to all the requirements of the trillions of cells in your or my body, or the tissues and organs into which those cells are organized, as we go about our endlessly varying activities under endlessly varying conditions?

The DNA double helix can likewise be loosened by twisting, along with formation of coils, and it can also be tightened and coiled. In fact, it happens that both effects result wherever the enzymes transcribing DNA into RNA are at work. And this twisting in one direction or another in turn either encourages or discourages the expression of nearby genes.⁷

In other words, there are transient chromosome domains established by the twisting forces (torsion) that are communicated more or less freely (and not only by transcribing enzymes) along bounded segments of the chromosome. The loci within such a region share a common torsion, and this can attract a common set of regulatory proteins that read the changes as “suggestions” about activating or repressing nearby genes (Lavelle 2009; Kouzine et al. 2008). The torsion also tends to correlate with the level of compaction of the chromatin fiber, which in turn correlates with many other aspects of gene regulation.

Picture the situation concretely. Every bodily activity or condition presents its own requirements for gene expression. Whether you are running or sleeping, starving or feasting, rousing yourself to action or calming down, suffering a flesh wound or recovering from pneumonia — in all cases the body and many of its different cells have specific, almost incomprehensibly complex and changing requirements for differential expression of thousands of genes. And one thing (among countless others) bearing on this differential expression in all its fine detail is the coiling and uncoiling of chromosomes.

With so much concerted movement going on (including the looping we heard about earlier) how does the cell keep all those “twenty four miles of string in the tennis ball” from getting hopelessly tangled? We do at least know some of the players addressing the problem. For example, there are complex protein enzymes called topoisomerases, which the cell employs to help manage the spatial organization of chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of individual genes or regions of the chromosome and prevent a hopeless mass of knots.

Some topoisomerases cut just one strand of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. This alters the supercoiling of the DNA. Other topoisomerases can undo knots by cutting both strands, passing a loop of the chromosome through the gap thus created, and then sealing the gap again.

Imagine trying this with miles of string wrapped around millions of minuscule beads compacted into a few cubic inches of space, with the string all the while looping and squirming like a nest of snakes in order to bring all the right loci together so as to achieve the tasks of the moment. (And how are these tasks “known”?) I don’t think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts have been made to analyze the local forces and “mechanisms” at play in isolated reactions.

Or again, DNA is said to “breathe” in rhythmical movements as it tightens and relaxes its embrace of the histone core particles mentioned earlier. And again, it breathes in a different sort of rhythm as the two strands of the double helix alternately separate and reunite at particular loci. And yet again, there are many profoundly significant structural novelties to which DNA lends itself, beyond the double helix. All this and much more is the cell’s way of evoking the genetic performance that it needs — a performance that expresses the cell’s own life and that of the organism as a whole.⁸

And so, when researchers refer to the “choreography” of the cell nucleus and the “dance” of chromosomes, as they sometimes do, their language is closer to being literal than many have imagined. If the organism is to survive, chromosomal movements must be well-shaped responses to sensitively discerned needs — all in harmony with innumerable dance partners, and all resulting in every gene being expressed or not according to the meaning of the larger drama. We can hardly help asking: If such choreography is how the organism lives and performs at the molecular level, what does this mean for the nature of molecular biological explanation?

Yes, the use of terms such as “dance” and “choreography” in molecular biology is rather distinctive. Some might call it eccentric. But this particular eccentricity has for some time now been creeping into the conventional technical literature. We have already heard of “genomic origami”, an idea that has almost become a cliché. And we have also been told: “The statement, ‘genomes exist in space and time in the cell nucleus’ is a trivial one, but one that has long been ignored in our studies of gene function” — this according to two leaders of the current work: Job Dekker, head of a bioinformatics lab studying the spatial organization of genomes at the University of Massachusetts Medical School, and Tom Misteli, a research director at the National Cancer Institute. Recent investigations, they say, have taught us that “gene expression is not merely controlled by the information contained in the DNA sequence”, but also by the “higher-order organization of chromosomes” and “long-range interactions in the context of nuclear architecture” (Dekker and Misteli 2015).

This last remark may startle some readers into the sudden realization that in all the foregoing there has been no discussion of the famed DNA sequence — the supposedly precise logical content of the “coded genetic program” that “makes us who we are”. Why is that?

It looks very much as if the chromosome, along with everything else in the cell, is itself a manifestation of life, not a logic or mechanism explaining life. This performance cannot be captured with an abstract code. Gene regulation is defined less by static elements of logic than by the quality and force of its various gestures. Brought into movement by its surroundings, the chromosome becomes an expression of a larger context of living activity.

The fixation upon an abstract, neatly identifiable informational sequence has served well the compulsion among biologists to find precise, unambiguous, logically clean, and satisfyingly deterministic causal explanations. Nevertheless, what’s been happening in rapidly intensifying fashion over the past couple of decades, has been a forced retreat from explanations of this sort. To cite a few key words and phrases from the contemporary literature: everything turns out to be mind-numbingly complex, which means, in part, that context makes all the difference. We are forced to try to understand how regulatory networks, intricate feedback loops, and the frequent difficulty of distinguishing causes from effects bear upon our biological understanding. Ultimately, we seem to be driven toward systems biology, an easily degraded term that many seem to prefer over the embarrassment (and richer meaning) of holistic biology.

What is not generally realized, however, is that this retreat from simplistic “causal mechanisms” suggests a movement toward a kind of explanation biologists have not yet come to terms with. It is, after all, one thing to explain, say, how a topoisomerase enzyme “mechanistically” passes one double-stranded section of DNA through another, and quite a different thing to ask how this activity — which could be carried out in countless different patterns — is made to harmonize with everything else going on at the molecular level in order to produce an overall, directed, coherent outcome for the cell as a whole. How might we make sense of the vast coordination of trillions of molecular events in the interest of a larger picture that is subject to continual change, as when a cell initiates the transition leading toward cell division?

Wang’s reference to whatever is “desirable or undesirable for the final outcome” is what we must ultimately reckon with. That is, the context to which the topoisomerase molecule must conform is, in the end, the activity of the whole organism, with its requirements for specific gene expression in every part of the body. Put simply, the molecule must meaningfully participate in everything — organism and environment — without fixed limit. This points to the need for a kind of explanation biologists in general seem unwilling to acknowledge. For it would, indeed, upset the entire world of conventional biological thought, based as that thought is on local, analyzable, physical cause and effect. “Desirable” and “undesirable” are not physical categories.¹⁰

Yes, we have every reason to believe that whatever happens, happens lawfully. But this still leaves us with the question, “How does our understanding of the overall coherence of cellular and organismal processes relate to the lawfulness we unfailingly observe whenever we isolate particular interactions and analyze them in physical and chemical terms?” That lawfulness continues the same throughout all cellular activity of the most diverse sorts, and it does not seem to have any obvious provisions for explaining the unique, ever-varying principles of coordination and coherence governing biological entities ranging from cells to organs to whole organisms within their environments.

Notes

1. See Lieberman-Aiden 2009 and Rao 2014.

2. Figure 3.1 credit: Miriam Huntley, Rob Scharein, and Erez Lieberman-Aiden. Linear chromosome at top of figure: Ed Yong (CC BY-SA 3.0).

3. Figure 3.2 credit: from Rao et al. 2014.

4. The quote comes from the author’s video abstract of their paper in Cell. See Rao 2014.

5. Toward the end of the Human Genome Project in 2000, according to a report in Nature, “geneticists were running a sweepstake on how many genes humans have, and wagers ranged from tens of thousands to hundreds of thousands. Almost two decades later, scientists armed with real data still can’t agree on the number”. Current estimates tend to run between 19,000 and 22,000, but recent criticisms “underscore just how difficult it is to identify new genes, or even to define what a gene is” (Willyard 2018).

6. Lavelle 2009. Nucleoproteins are proteins bound up with DNA or RNA.

7. To get more specific about it, think of it this way. If, taking a double-stranded rope in hand, you insert a pencil between the strands and force it in one direction along the rope, you will find the strands winding ever more tightly ahead of the pencil’s motion and unwinding behind. An RNA polymerase, which must separate the two strands of DNA as it transcribes a gene, can in the right circumstances have an effect rather like the pencil: it will cause what is called “negative supercoiling” (loosening of the double helix spiral) behind itself, and “positive supercoiling” ahead. And if, say, negative supercoiling has already occurred in the region being transcribed, the polymerase will find it much easier to separate the two strands and do its work. So in this way the variations in coiling along the length of a chromosome either encourage or discourage the transcription of particular genes.

8. To get a rough sense merely for the number of significant variations in DNA double helix conformation and the kind of effect they can have, here is a statement enumerating such variations and their bearing on a single regulatory feature, namely, the position of certain nucleosomes (which themselves play a key role in regulation of gene expression). There is no need to understand the different technical terms in order to get a feel for the complexity of the sculptural details of any particular stretch of DNA, and the kind of role these details can play in relation to gene expression.

Variant –1 nucleosomes exhibited a preference for sequences with altered features such as propeller twist, opening, electrostatic potential, minor groove width, rise, stagger, helix twist, and shear and roll. Variant –1 nucleosomes that shifted downstream in KDM5B-depleted ES cells preferred sequences with increased propeller twist, opening, electrostatic potential, stagger, minor groove width, rise, and buckle, while –1 variant nucleosomes that shifted upstream preferred sequences with decreased propeller twist, opening, electrostatic potential, stagger, minor groove width, rise, and buckle … Combined, these findings suggest that DNA shape predicts sequence preferences of canonical nucleosomes and variant nucleosomes. These results also suggest that histone DNA binding patterns such as bending or electrostatic interactions may be influenced by posttranslational modifications such as H3K4 methylation (Kurup, Campeanu and Kidder 2019).

9. Figure 3.3 credit: Both images are in the public domain via the Creative Commons.

10. It is remarkable to watch the eagerness with which biologists pull the evolutionary wool over their own eyes. We are told that “desirable” and “undersirable” really refer to whether a trait is or is not conducive to an organism’s survival. And survivability is explained purely as a play of physically lawful activities. Ask yourself: how does this line of thought make more explicable what we have just heard about the activity of topoisomerases in the cell. To say that natural selection must somehow create and preserve mechanisms that perform the physically inexplicable does nothing to remove the problem of physical inexplicability. (For more, see Part 2, “Extending the Organism’s Story: Toward an Evolutionary Narrative”.)

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Steve Talbott :: What Brings Our Genome Alive?