From cytoskeletal dynamics to organ asymmetry: a non-linear, regulative pathway underlies left-right patterningVersion 1 Released on 09 May 2016 under Creative Commons Attribution 4.0 International License
- Department of Biology, School of Arts and Sciences - Tufts University
- Allen Discovery Center at Tufts University *. Unregistered author (unverified)
Consistent left-right asymmetry is a fundamental aspect of the bodyplan across phyla, and errors of laterality form an important class of human birth defects. Its molecular underpinning was first discovered as a sequential pathway of left- and right-sided gene expression that controlled positioning of the heart and visceral organs. Recent data have revised this picture in two important ways. First, the physical origin of chirality has been identified; cytoskeletal dynamics underlie the asymmetry of single cell behavior and of patterning of the left-right axis. Second, the pathway is not linear: early disruptions that alter the normal sidedness of upstream asymmetric genes do not necessarily induce defects in the laterality of the downstream genes or in organ situs. Thus, the LR pathway is a unique example of two fascinating aspects of biology: the interplay of physics and genetics in establishing large-scale anatomy, and regulative (shape-homeostatic) pathways that correct errors of patterning over time. Here, we review aspects of asymmetry from its intracellular, cytoplasmic origins to the recently-uncovered ability of the LR control circuitry to achieve correct gene expression and morphology despite reversals of key “determinant” genes. We provide novel functional data, in Xenopus laevis, on conserved elements of the cytoskeleton that drive asymmetry, and repair of downstream gene expression anomalies over developmental time. LR patterning can thus serve as a paradigm of how subcellular physics and gene expression cooperate to achieve developmental robustness of a body axis.
Most vertebrates (and many invertebrates) have bilaterally-symmetric external bodyplans. Yet these same animals exhibit consistent asymmetries in the position or anatomy of internal organs such as heart, viscera, and brain . Defects in LR asymmetry are an important class of human birth defects, including heterotaxia (the lack of concordance between internal organs, allowing each organ to individually ‘decide’ on its placement on the left or right side of the body), single organ inversions such as dextrocardia (the reversal in position and morphology of the heart), and isomerisms (symmetry of the LR axis, leading to either duplication or complete loss of unpaired organs such as the spleen). Patients with complete reversal of asymmetry (situs inversus) have fewer health consequences than these other conditions because heterotaxia and isomerisms often involve inappropriate connections between the heart, lungs and other visceral organs [2–6]. Interestingly, consistent laterality affects not only the asymmetric organs, but also the manifestation of numerous diseases and conditions affecting paired (seemingly symmetrical) organs, such as hip dysplasia, limb defects, and eye development [7–11]. This includes location and incidence of tumors [12–17], immune responses [18,19], and innervation of sensory organs such as eyes .
LR asymmetry is a unique puzzle in development , in complex organisms and even in colonies of simpler ones . The embryonic anterior-posterior (AP) axis probably exists in order to place sense organs at the end of the animal that encounters novel environments first (oriented with the main axis of motion). The dorso-ventral (DV) axis can be set by gravity or sperm entry point. However, once those two orthogonal axes are set, the alignment of the LR axis is fixed; in order to distinguish L from R, symmetry has to be broken. Crucially, it is not merely a question of making L different from R, but doing it so that the LR axis is consistently oriented with respect to the AP and DV axes. The former process results in fluctuating asymmetry (an indicator of stress via the difficulty of keeping the two halves of the body precisely coordinated during growth); the latter is true biased asymmetry of anatomical structures. This is a difficult problem, as our universe does not macroscopically distinguish left from right [23,24]. This problem was noted long ago, by workers studying chiral biochemistry and its implications for development [25–27], clinical observations of mirror-imaging in anatomical features of human twins , unidirectional coiling of snail shells , and functional handedness in neural lateralization . Since then, consistent LR asymmetry has been identified not only in anatomical structures from somites  to hair whorls [32–36] to deer antlers , but also in functional features such as immune response [38–40] and cancer [41,42,17,43]. Thus, the mechanisms of LR patterning are not only of fundamental interest in developmental biology, but are central to many interesting questions of physiology and evolution.
Early mechanistic work in this field identified a set of chemical agents that was able to perturb (randomize) asymmetry in animal models [44–48]. The first molecular explanations for the asymmetry of body organs came from studies in the chick , with the identification of asymmetrically-expressed genes, such as the left-sided Sonic hedgehog (Shh) and Nodal, the inductive and repressive relationships among these genes, and functional studies showing that aberrant expression of any of these was sufficient to randomize the situs of the heart, gut, and other viscera [50,51]. These data not only helped explain organ laterality in normal development but also provided a mechanistic explanation for laterality disturbances long known to occur in conjoined twins . The central component of the LR pathway was the left-sided cassette formed by Shh inducing expression of Nodal inducing expression of Lefty inducing expression of Pitx2 [53–55].
The conserved molecular pathway in Xenopus, chick, mouse, and zebrafish as described in early work on LR asymmetry [56,57] has since been extended considerably, as described in Figure 1 and reviewed in [58,59], by loss- and gain-of-function approaches in a range of species that reveal the functional connections among LR patterning proteins. New players include Activin, Follistatin, Derrière, Coco, Mad3, BMP, Noggin4, and Fgf8 [60–65,53,66–70]. Recently, other downstream factors have been increasingly demonstrated in unilateral function during LR determination, such as calcium signaling and retinoic acid [71–79]. Together, this body of work reveals a progressive cascade of left- and right-specific activities that involve powerful signaling pathways. These signaling molecules then provide distinct signals to organ primordia on either side of the midline, resulting in asymmetric organogenesis.
Physics upstream and downstream of transcriptional networks
Regardless of the completeness of a transcriptional pathway or network model, one has to explain why the first asymmetric gene becomes expressed on one side but not the other. It is a fundamental limitation of transcriptional regulatory networks that they do not in themselves constrain geometry — no gene regulatory network (GRN) can generate consistently chiral output (distinguish left from right). Thus, upstream of any such regulatory cascade must lie some piece of physics which is able to break symmetry and reliably orient subsequent events with respect to the other two axes [80,81].
Interestingly, this is not strictly a multicellular phenomenon, in a number of systems, from bacteria to ciliates to human somatic cells in vitro, single cells exhibit consistent chirality in their movements and behaviors [25,82–95], both as individual cells and as collectives [92,96]. For example, outgrowth of neurites is predominantly clockwise [84,85,97,90]. The asymmetric growth and migration of various cell types on micropatterned surfaces has demonstrated the role of actomyosin networks in the generation and maintenance of consistent chirality of migration, cell shape, and tissue morphogenesis [82,91]. Thus, metazoan organisms face the problem of amplifying subcellular chirality into tissue-wide asymmetry across a midline, but do not need to reinvent the symmetry-breaking and orientation steps, as these appear to be ancient and ubiquitous.
One candidate for a chiral element of physics upstream of asymmetric gene expression is ciliary flow at neurulation [72,98,99]; this model however faces numerous problems which have been detailed elsewhere [100–104]. Recent functional data revealed conserved mechanisms in a range of organisms from plants to mammals, that establish asymmetry without a ciliated structure, or long before it forms; indeed, many phyla including some vertebrates determine their LR axis very early after fertilization [105–115]. Even mouse embryos are known to exhibit molecular and functional asymmetries (e.g., components such as cofilin, which is also asymmetric in cleavage-stage frog embryos) as early as the cleavage stages [107,116,117].
While ciliary flow may impinge on downstream transcriptional events in those species where it exists (not pig  or chick [118,119] for example), it cannot be the origin of asymmetry in most phyla. From data in a range of model species, it is clear that numerous aspects of development, including maternal protein localization [120,121,111,122], Wnt signaling , and small signaling molecules  are already consistently asymmetric long before cilia appear: most animal embryos can tell their Left from their Right at very early stages. Thus, the search for the origin of asymmetry has been extended far upstream of neurulation [124,47].
One interesting class of models links asymmetry to chromatid segregation [125–128] – a proposal that needs to be tested in the available model systems, as it offers the possibility of linking asymmetry to the fundamental dynamics of DNA. This model has been linked to data on birth defects and epithelial morphogenesis in humans and mice . As in Xenopus, the mouse model has also revealed that $\alpha$-tubulin organization is critical for asymmetry, via studies of the protein Mahogunin [130,105,111,112,131].
A remarkably prescient prediction was made by a paper published before all of the molecular work on the LR pathway , in which Brown and Wolpert hypothesized a chiral element that initiates biased transport inside the early embryonic blastomeres. More recent work in several models have confirmed early hypotheses while elaborating on these ideas [133,134], showing that the cytoskeleton is centrally involved in generating the original asymmetric cues that break and orient symmetry. A number of model species such as C. elegans [135,74,136–138] and snails [139–142] were known to use cytoskeletal dynamics to determine chiral cell behavior and subsequent LR patterning. However recent data in these models, together with mammalian cells and Drosophila [143,144], have revealed many of the key details.
The intriguing structure of centrioles , including their anti-clockwise rotation , and the role of microtubules in generating asymmetry in neutrophils [147,93], plants , and frog  and C. elegans embryos [149,150], lends evidence to the theory that the centrosome could be a symmetry-breaking, chiral structure [100,151]. Evidence for intrinsic chirality, and not interactions with the substrate, were provided by the counter-clockwise rotation exhibited in zebrafish melanophores . A particularly illustrative case of spontaneous intracellular chiral cytoskeletal organization again illustrates the role of actomyosin networks in the ability of $\alpha$-actinin to spontaneously arrange directionally, or reverse the directionality if the protein is grossly overexpressed .
Studies in Drosophila have demonstrated the effect of intrinsic cellular chirality on embryonic laterality [143,152–160]. Unconventional myosins, such as Myosin1d, have a clear role in affecting the asymmetry of the gut and genitalia in Drosophila [158,159] and this asymmetry is due to a direct effect on the actin filaments in epithelia . Actin motility on Myo1c occurs in counterclockwise direction ; myosin V is a left-handed spiral motor toward the plus end of actin , while myosin II is right-handed spiral motor . Moreover, the effect of these unconventional myosins on organismal asymmetry is linked to their effect on intrinsic cellular chirality , and individual cells can contribute to mechanical differences in generating chirality at the tissue level [153,160], a finding also demonstrated in Caenorhabditis elegans [113,134].
Our own work in Xenopus has demonstrated a number of key features that point to the importance of the cytoskeleton at multiple points in laterality. Firstly, fundamental cytoskeletal proteins such as tubulins and myosins are functionally important for normal embryonic laterality at the very earliest points of embryonic development, immediately post-fertilization [111,112]. The cytoskeleton appears to be required for the normal early localization of asymmetric components such as ion channels [121,111,122], a mechanism widely conserved to many somatic cell types [164,165]. Secondly, the conservation of phenotypes obtained from mutations in cytoskeletal and cytoskeleton-associated proteins exhibited in frog, compared to those of plants [111,112], snails , and Drosophila , demonstrate the need for physical signals upstream of gene regulatory networks (GRNs): for example, the organ-specific effects of myosins on Drosophila laterality were replicated in frog , transcending the differences in molecular LR pathways between vertebrates and invertebrates and raising the question of how the cytoskeleton generates chirality. Finally, the apparent disconnect between the asymmetric expression of Nodal and subsequent organ situs observed in mouse  and replicated in frog  highlight a conserved role for the cytoskeleton not only in laterality, but in the ability to correct earlier defects in laterality between the point of expression of markers of laterality and the positioning of visceral organs.
Downstream of the chiral physics within cells lie physiological mechanisms that amplify subcellular chiralities into true LR asymmetries across cell fields. One such system is the diffusion-based LALI (local activation, long range inhibition) system described in mouse [166,167]. Another is the chiral bioelectric gradient that redistributes intracellular morphogens such as maternal serotonin [120,168–171,110,172,78,173]. This process is most well-understood in frog embryos, but has also been observed and functionally implicated in amphioxus , sea urchin [168,175,176], C. elegans [177–179], zebrafish [120,180,181], and recently humans [182,183]. Indeed very recent analysis of the differences between blastomeres in the very earliest stages of embryo development, identified distinct metabolites in L vs. R cells in the 8-cell embryo using mass spectrometry . The majority of these metabolites themselves have roles in functional regulation of ion transport [184–192], suggesting possible feedback loops in electrophysiology that could be important amplifying mechanisms for initially subtle LR asymmetry. Both of these systems impinge upon a key asymmetric gene – NODAL [193,62], and lie upstream of a cascade of asymmetric gene interactions. However, much as it needs a physical process to anchor consistent asymmetry upstream, genetic pathways likewise need to control physical forces in order to actually implement asymmetric morphogenesis.
GRNs feed into specific proteins that harness physical forces such as tension and adhesion to control asymmetric bending and growth of internal organs . Mechanical forces are critical for the rotation and looping of internal organs ([195,196], see reviews for the heart in chick [197–200]). In the development of Xenopus gut morphology, a rightward torsion results in concave and convex topologies for cells on the left and right sides of the lateral plate mesoderm respectively, and cells on the right elongate twice as much as cells on the left, although proliferation rates remain the same . Similarly, in Drosophila, asymmetries arising from planar cell polarity in gut looping through the activity of myosin1d were able to generate differences in tension, with greater tension on the left side of the cell driving leftward rotation . In heart looping, a similar role for actin and myosin in driving dextral looping has been exhibited in zebrafish  and chick . Recently computational modeling has supported evidence suggesting that differential growth supplies the forces that cause the heart tube to bend ventrally, while cytoskeletal movements can drive rightward torsion . The maintenance of symmetry could also be due to differences in the composition of the extracellular matrix (ECM) as observed in perturbations of ECM composition in frog and chick embryos [204,48].
Developmental regeneration: robustness of the LR pathway
Bracketed upstream and downstream by interaction with physical forces, the middle of the LR patterning process consists of a pathway made up of sequentially interacting left- and right-sided gene products (Fig. 1). The implication of this kind of induction/repression model is that if something goes wrong upstream — if a particular gene is expressed on the wrong side for example — then the downstream elements will likewise be incorrect. For example, in the early work on LR determining genes in chick, it was shown that if the left-sided Shh gene was misexpressed on the right side, right-sided expression of the normally left-sided gene Nodal followed, and organs were subsequently randomized.
Importantly however, development in many species is highly regulative: early errors (e.g., splitting embryos in half ) can become subsequently corrected. While many perturbations overcome this basic shape homeostasis property (resulting in birth defects), it is nevertheless true that embryos are highly robust because of the ability to remodel after some kinds of deviations from the normal sequence of events. One example is the derivation of largely normal frog faces from early embryos with severely malformed facial structures, which self-correct over time . The mechanisms of robustness and shape homeostasis are poorly understood at the mechanistic level, although they are now increasing objects of interest in molecular developmental biology [207–209] and regenerative medicine [210–212].
Self-correction capabilities in the LR pathway are a novel, molecularly-tractable example of regenerative repair. It is a uniquely-accessible context in which to study the regulatory mechanisms that recognize and reverse abnormal patterning states. Here, we identify new aspects of the cytoskeletal machinery that lie upstream of the LR asymmetry patterning pathway and investigate their robustness. We quantitatively analyze published data as well as our new functional studies to reveal remarkable flexibility in the GRN that belies a simple linear pathway to reveal remarkable pattern robustness.
Results: endogenous repairing of induced left-right defects
The canonical description of the left-right patterning pathway in vertebrates, regardless of the proposed point of symmetry breaking, follows the linear track of leftward activation of Nodal, downstream activation of Lefty and Pitx2, and thence to the correct placement of visceral organs. However, we have observed in our recent studies of the determination of laterality in Xenopus, many anomalies and exceptions to this neat pipeline.
For example, in studying proteins with roles in early embryonic asymmetries , and in particular cytoskeletal proteins with a conserved role in determining embryonic laterality [105,112], the number of embryos with reversed organs is actually smaller than the number with incorrect Nodal expression (Table 1). This suggests that the pathway from Nodal to organ situs is not as linear as had been assumed: having incorrect Nodal expression does not actually mean that an embryo’s organs will be reversed, despite Nodal’s established role as a determinant or “master regulator” of LR situs.
|Protein||Nodal expression||Reversed Organs||Reference||Degree of repair|
|(R: 10%, Bi: 9%, N: 18%)|
|(R: 9%, Bi: 8%, N: 9%)|
|(R: 7%, Bi: 9%, N: 5%)|
|(R: 12%, Bi: 30%, N: 23%)|
|Protein||Nodal expression||Reversed Organs||Reference||Degree of repair|
|(R: 10%, Bi: 17%, N: 30%)|
|(R: 1%, Bi: 19%, N: 4%)|
|(R: 5%, Bi: 16%, N: 14%)|
|(R: 9%, Bi: 8%, N: 26%)|
|(R: 7%, Bi: 4%, N: 17%)|
|(R: 26%, Bi: 13%, N: 5%)|
|Incorrect Nodal expression||Reversed Organs||Reference||Degree of repair|
|spontaneous cardiac reversals|
Reviewing the literature for evidence of these phenomena, we found some interesting supportive observations. To begin with, there were a number of observations showing various degrees of correction or “fixing” of laterality defects from early to late markers (Table 4).
|Protein||Nodal expression||Reversed Organs||Reference||Degree of repair|
|Cx26 2 of 4-cell:||48%||32%||||33%|
|ventral||(R: 1%, Bi: 1%, N: 46%)|
|Cx43 2 of 4-cell:||32%||22%||||31%|
|ventral||(R: 0%, Bi: 5%, N: 27%)|
|H7 2 of 4-cell:||57%||29%||||49%|
|ventral||(R: 5%, Bi: 14%, N: 38%)|
|(R: 18%,||(R: 4%,||(R: 23%,|
|Bi: 7%,||Bi: 32%,||Bi: 18%,|
|N: 11%)||N: 4%)||N: 6%)|
|(R: 6%,||(R: 2%,|
|Bi: 15%,||Bi: 5%,|
|N: 15%)||N: 9%)|
|Protein||Nodal expression||Reversed Organs||Reference||Degree of repair|
|BVg1 R3 16-cell||88%||89%||||-1%|
|tAR L1 16-cell||“complex”||51%||||Unknown|
|BMP2 L2 16-cell||30%||85/58%||||Unclear|
|BMP2 R2 16-cell||17.5%||0%||||Complete|
|Xwnt-8 L4, BVg1 R1||66%||88%||||-33%|
|Xwnt-8 L4, BVg L1||“not determined”||14%||||Unknown|
|BVg1 L4 16-cell||15%||10%||||33%|
|BVg1 R4 16-cell||75%||52%||||31%|
|Activin A PROTEIN|
|at Stage 20|
|Activin A PROTEIN|
|Left-sided Injection||Not shown||19%||||Unknown|
|at Stage 20|
|(R: 10%,||(R: 3%,|
|Bi: 26%,||Bi: 2%,|
|N: 7%)||N: 9%)|
|(R: 10%,||(R: 2%,|
|Bi: 21%,||Bi: 4%,|
|N: 13%)||N: 10%)|
|(R: 1%,||(R: 0%,||(R: 0%,|
|Bi: 2%,||Bi: 1%,||Bi: 2%,|
|N: 4%)||N: 2%)||N: 2%)|
|(R: 10%,||(R: 0%,||(R: 0%,|
|Bi: 23%,||Bi: 0%,||Bi: 0%,|
|N: 11%)||N: 8%)||N: 4%)|
|(R: 4%,||(R: 3%,||(R: 6%,|
|Bi: 10%,||Bi: 1%,||Bi: 10%,|
|N: 12%)||N: 16%)||N: 7%)|
|(R: 1%,||(R: 4%,||(R: 0%,|
|Bi: 8%,||Bi: 4%,||Bi: 7%,|
|N: 5%)||N: 0%)||N: 7%)|
|(R: 6%,||(R: 10%,||(R: 12%,|
|Bi: 8%,||Bi: 2%,||Bi: 12%,|
|N: 10%)||N: 15%)||N: 10%)|
|(R: 1%,||(R: 1%,||(R: 0%,|
|Bi: 2%,||Bi: 0%,||Bi: 0%,|
|N: 5%)||N: 13%)||N: 0%)|
|(R: 6%,||(R: 0%,||(R: 3%,|
|Bi: 23%,||Bi: 5%,||Bi: 3%,|
|N: 8%)||N: 2%)||N: 3%)|
|(R: 6%,||(R: 0%,||(R: 5%,|
|Bi: 9%,||Bi: 12%,||Bi: 5%,|
|N: 10%)||N: 10%)||N: 29%)|
|(R: 8%,||(R: 25%,||(R: 17%,|
|Bi: 17%,||Bi: 15%,||Bi: 9%,|
|N: 19%)||N: 10%)||N: 22%)|
Overexpression of Nodal and effects on laterality
The data above shows that when very early LR patterning steps are perturbed, and Nodal expression is incorrect, there can be a subsequent correction of this information downstream to lead to a lower number of tadpoles with reversed organs. However, we wanted to test whether direct misexpression of Nodal led to a clear mispatterning of laterality markers, and a reversal of organ situs, or whether misexpression of Nodal could also be corrected or tolerated by the developing embryo. What happens if Nodal is directly randomized, by forced misexpression of Nodal protein on the right side, or by overexpression of Nodal in general? A number of studies have already looked at the effect of Nodal overexpression in Xenopus, using both the injection of plasmid DNA [220,221] and mRNA  (summarized in Table 10).
|Treatment||Pitx2 expression||Reversed Organs||Reference|
|Xnr1 plasmids into 1 of 4 - left||9%|||
|Xnr1 plasmids into 1 of 4 - right||86%|||
|50 pg Xnr1 into LPM dorsal blastomeres,||85%|||
|DR injections xnr1 20pg pXEX||61%|||
|DR injections xnr1 100pg pXEX||71%|||
|DR injections xnr1 20pg pCSKAX||76%|||
|DR injections xnr1 100pg pCSKA||68%|||
|DL injections xnr1 20pg pXEX||20%|||
|DL injections xnr1 100pg pXEX||25%|||
|DL injections xnr1 20pg pCSKA||33%|||
|DL injections xnr1 100pgpCSKA||50%|||
|Lefty expression||Pitx2 expression||Reversed Organs||Degree of Repair|
|(R: 27%, Bi: 32%, N: 2%)||(R: 20%, Bi: 40%, N: 1%)|
|Organ placement||Left-sided||Right-sided||Both sides|
Gene-regulatory cascades form an important part of the middle phases of LR patterning , but important elements of physics and physiology lie upstream, in determining the sidedness of the first asymmetric transcription, and downstream, in implementing laterality cues toward asymmetric morpogenesis. Early events feed into different parts of the LR cascade, such as overexpression of Wnt8 and of the C314D mutant of mahogunin which is unable to ubiquitylate -tubulin. Indeed, some aspects of tissue morphogenesis may be intrinsic, using cell-level chirality to implement asymmetric looping directly, as may occur in Drosophila  and zebrafish .
While many organisms establish large-scale asymmetries, it is interesting that chirality is fundamental to individual cells – an ancient evolutionary feature that metazoans exploit for macroscopic anatomical purposes. Aside from highlighting the propagation of properties across orders of magnitude of scale, laterality sheds light on the relationship between genome and fundamentally epigenetic factors. In single-cell ciliates, Beisson and Sonneborn demonstrated that reversal of a ciliary row in the cell cortex is propagated to offspring. Their function is also reversed, and cells eventually starve because food particles are swept into the wrong direction; their normal genome is powerless to rescue them [223–226].
The original picture of the LR cascade made use of a midline barrier which separated distinct Left- and Right-sided programs of repression and induction . This was subsequently revised by the finding that the L and R sides needed to communicate long-range via gap junction-mediated physiological signals for proper expression of early asymmetric genes [186,228], but the importance of establishing a robust midline was clear [229–233]; indeed, the LR axis cannot be oriented without a midline that sets the axis of symmetry. While some animals are thought to establish the midline later than others, and the LR axis is often viewed as being defined after and with respect to the AP and DV axes, cleavage patterns and the prevalence of strictly bilateral gynandropmorphs resulting from very early cleavage events reveal that from insects to man [234–236], separating the L and R sides is one of the first things most embryos do . Once the midline separates L and R compartments and they establish their unique identities, the standard model holds that cascades of genes become expressed sequentially, in a functional pathway that should propagate errors as genes inappropriately expressed on one side exert their effects and turn on/off downstream genes counter to their normal restricted unilateral patterns.
Most importantly, we have found, in both our new data and data from published experiments in Xenopus, discrepancies between the incidence of incorrect expression of early laterality markers and that of abnormal positioning of organs; these examples reveal the ability of embryos to correct defects in LR patterning over time (Figure 2). For example, early misexpression of unconventional myosin proteins (Table 2) and the mahogunin protein which targets $\alpha$-tubulin for degradation (Tables 8,9) strongly disrupt the normal laterality of Nodal expression but have no effect on the positioning of organs in those embryos.
In the case of low-frequency vibrations that induce LR patterning defects in early embryos, it appears that the early (cleavage) stages are crucial for enabling downstream repair mechanisms post-Nodal. Vandenberg et al. found that the level of Nodal expression randomization was constant and high despite the stage at which treatment began (as long as treatment occurred prior to blastula stage), but in all cases the percentage of resulting tadpoles with mispatterned organs was lower (, summarized in Figure 3A). This underscores the potential divergence between organ endpoints and marker expression in experiments with different timing conditions, and suggests that future studies cannot simply use gene expression readouts but must score organs as well to get a true picture of the effects of specific perturbations on the LR pathway. These data suggest that the earliest events (from 1-cell to st. 6) are important to enabling whatever mechanisms allow organs to form correctly despite abnormal Nodal laterality, as the ability to repair organ positioning increases progressively with treatments that start at later cleavage stages.
Interestingly, grouping the experimental results on normalization of downstream steps by the type of early perturbation (Figure 3B, Supplementary Table 1) suggests that the degree of laterality repair capability varies depending on the type of perturbation (the LR pathway target that was perturbed to generate the Nodal randomization). Perturbations of motor proteins, and the early cytoskeleton, within the first cell division, is tolerable to a certain degree as it largely becomes normalized by the time of organogenesis; but manipulations of ion flows are apparently not possible to recover from. It should also be noted that in most cases within the serotonergic group, Lefty appeared to be bypassed (Table 7). These data suggest that further study into the different degree of pathway repair downstream of targeting different types of components of LR patterning may shed greater light on the mechanism, and robustness, of LR patterning and the normalization of downstream targets despite randomized prior steps.
The data also reveal non-linearity of the pathway as some elements can be bypassed: interfering with early serotonin and monoamine oxidase signaling results in organ-level LR defects despite the correct expression of Lefty (Table 7). A dynamical systems view of these repair pathways, as a network rather than a linear pathway with “necessary and sufficient” master regulators, is necessary, as has already been noticed in the field of cancer and the search for driver genes [241–246]. The future is likely to involve not only molecular-genetic picture of these repair pathways, but a cybernetic, systems-control view of the information processed by these closed-loop, shape-homeostatic capabilities of embryogenesis [247–251]. It thus becomes clear that checking immediate downstream consequences of gene misexpression is not sufficient for functional analyses; a subtler strategy targeting further upstream of a gene of interest, which gives the embryo more time to recognize errors, is required to form a full picture of regulatory networks and “necessary and sufficient” claims for an explanation of what gene product determines expression of some other gene product.
In a sense, pattern homeostasis, such as seen in reparative regeneration widely across the tree of life , could be seen as a primary biological capability. Development is really just an example of regeneration – restoring the whole body from 1 cell (fertilized egg). No wonder that regenerative repair, which can make up for disruption of pattern with flexible corrective processes, also occurs in embryogenesis. While not surprising given regulative development as a whole, it sheds new light on the definition of “master regulator” or “determinant” genes for specific developmental outcomes. While loss- and gain-of-function tests (such as those that had been performed for Nodal in the early years of the study of the LR pathway) may indicate that a certain gene’s expression is a driver of what happens next, it has to be kept in mind that this may not be the whole story. Two things can be readily missed by experiments that are narrowly focused on direct functional change of the gene expression and an immediate readout of direct downstream response genes. First, the downstream consequences could be wiped out by corrective mechanisms, which can limit the validity of “necessary and sufficient” claims for specific gene products with respect to final patterning outcome. Second, the results may be quite different if that gene’s expression is deranged by targeting much earlier steps (giving the organism time to notice the problem and activate robust repair pathways).
These data and analyses suggest a new direction in this field, focused on a systems-level understanding of how distinct molecular steps are multiplexed by the embryo for monitoring, setting, and continuously re-setting the LR identity of its tissues. In the sense that embryogenesis is an example of the more general phenomenon of regeneration (rebuilding the whole body from 1 cell), the LR asymmetry mechanisms may be a window on a much more general and widely-relevant phenomenon than just the patterning of the LR axis. The study of these dynamics could reveal fundamental aspects of how genetics interfaces with physics to implement robust, self-correcting systems. The impact of this would extend beyond development and birth defects, to the understanding of evolution, regenerative medicine, and artificial life.
Materials and Methods
Subcloning was carried out into pCS2+ using standard methods as described previously .
This study was carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and Tufts IACUC protocol #M2014-79. Xenopus embryos were collected and maintained according to standard protocols  in 0.1 x Modified Marc’s Ringers (MMR), pH 7.8, and staged according to .
Capped, synthetic mRNAs were dissolved in water and injected into embryos in 3% Ficoll using standard methods . mRNA injections were made into the animal pole of eggs within 30 minutes post fertilization (mpf) at 14 \textdegree C, or into 1 of 2 cells of Stage 2  embryos (as indicated) using borosilicate glass needles calibrated to deliver a 10 nl injection volume.
Xenopus embryos were analyzed for position (situs) of three organs; the heart, stomach and gallbladder  at Stage 45 . Heterotaxic embryos were defined as having a reversal in one or more organs. Only embryos with normal dorsoanterior development and clear left- or right-sided organs were scored. A $\chi^2$ test was used to compare absolute counts of heterotaxic embryos.
In situ hybridization
Whole mount in situ hybridization was optimized using standard protocols [253,254] with probes against Xnr1 (the Xenopus Nodal) , Lefty  and Pitx2  generated in vitro from linearized template using DIG labeling mix (Roche). A $\chi^2$ test was used to compare absolute counts of embryos with correct (expression on the left lateral plate mesoderm) versus incorrect (absent, bilateral or right-sided) marker expression.
We thank Joan Lemire and Jean-Francois Paré for cloning assistance and helpful comments on the manuscript, and other members of the Levin lab and the LR asymmetry and regeneration communities for many helpful discussions. We gratefully acknowledge support of the Templeton World Charity Foundation TWCF0089/AB55, sub award from Physical Science Oncology Center supported by Award Number U54CA143876 from the National Cancer Institute, and the Paul G. Allen Family Foundation.
- Supplementary Table 1: Experimental evidence for fixing grouped according to functional targets.
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