Hindbrain Segmentation Research Articles

Automatic assessment of DWI-ASPECTS for acute ischemic stroke based on deep learning.

Alberta Stroke Program Early Computed Tomography Score (ASPECTS) is a standardized semi-quantitative method for early ischemic changes in acute ischemic stroke. However, ASPECTS is still affected by expert experience and inconsistent results between readers in clinical. This study aims to propose an automatic ASPECTS scoring model based on diffusion-weighted imaging (DWI) mode to help clinicians make accurate treatment plans. Eighty-two patients with stroke were included in the study. First, we designed a new deep learning network for segmenting ASPECTS scoring brain regions. The network is improved based on U-net, which integrates multiple modules. Second, we proposed using hybrid classifiers to classify brain regions. For brain regions with larger areas, we used brain grayscale comparison algorithm to train machine learning classifiers, while using hybrid feature training for brain regions with smaller areas. The average DICE coefficient of the segmented hindbrain area can reach 0.864. With the proposed hybrid classifier, our method performs significantly on both region-level ASPECTS and dichotomous ASPECTS. The sensitivity and accuracy on the test set are 95.51% and 93.43%, respectively. For dichotomous ASPECTS, the intraclass correlation coefficient (ICC) between our automated ASPECTS score and the expert reading was 0.87. This study proposed an automated model for ASPECTS scoring of patients with acute ischemic stroke based on DWI images. Experimental results show that the method of segmentation first and then classification is feasible. Our method has the potential to assist physicians in the Alberta Stroke Program with early CT scoring and clinical stroke diagnosis.

Sea lamprey enlightens the origin of the coupling of retinoic acid signaling to vertebrate hindbrain segmentation

Retinoic acid (RA) is involved in antero-posterior patterning of the chordate body axis and, in jawed vertebrates, has been shown to play a major role at multiple levels of the gene regulatory network (GRN) regulating hindbrain segmentation. Knowing when and how RA became coupled to the core hindbrain GRN is important for understanding how ancient signaling pathways and patterning genes can evolve and generate diversity. Hence, we investigated the link between RA signaling and hindbrain segmentation in the sea lamprey Petromyzon marinus, an important jawless vertebrate model providing clues to decipher ancestral vertebrate features. Combining genomics, gene expression, and functional analyses of major components involved in RA synthesis (Aldh1as) and degradation (Cyp26s), we demonstrate that RA signaling is coupled to hindbrain segmentation in lamprey. Thus, the link between RA signaling and hindbrain segmentation is a pan vertebrate feature of the hindbrain and likely evolved at the base of vertebrates.

Exposure to Tetrabutylammonium Bromide Impairs Cranial Neural Crest Specification, Neurogenic Program, and Brain Morphogenesis.

Tetrabutylammonium bromide (TBAB) is a widely used industrial reagent and is commonly found in our aquatic ecosystem as an industrial byproduct. In humans, the ingestion of TBAB causes severe neurological impairments and disorders such as vertigo, hallucinations, and delirium. Yet, the extent of environmental risk and TBAB toxicity to human health is poorly understood. In this study, we aim to determine the developmental toxicity of TBAB using zebrafish embryos as a model and provide novel insights into the mechanism of action of such chemicals on neurodevelopment and the overall embryonic program. Our results show that exposure to TBAB results in impaired development of the brain, inner ear, and pharyngeal skeletal elements in the zebrafish embryo. TBAB treatment resulted in aberrations in the specification of the neural crest precursors, hindbrain segmentation, and otic neurogenesis. TBAB treatment also induced a surge in apoptosis in the head, tail, and trunk regions of the developing embryo. Long-term TBAB exposure resulted in cardiac edema and craniofacial defects. Further, in silico molecular docking analysis indicated that TBAB binds to AMPA receptors and modulates neural developmental genes such as olfactomedin and acetylcholinesterase in the embryonic brain. To summarize, our study highlights the novel effects of TBAB on embryonic brain formation and segmentation, ear morphogenesis, and craniofacial skeletal development.

Interplay of Eph-Ephrin Signalling and Cadherin Function in Cell Segregation and Boundary Formation.

The segregation of distinct cell populations to form sharp boundaries is crucial for stabilising tissue organisation, for example during hindbrain segmentation in craniofacial development. Two types of mechanisms have been found to underlie cell segregation: differential adhesion mediated by cadherins, and Eph receptor and ephrin signalling at the heterotypic interface which regulates cell adhesion, cortical tension and repulsion. An interplay occurs between these mechanisms since cadherins have been found to contribute to Eph-ephrin-mediated cell segregation. This may reflect that Eph receptor activation acts through multiple pathways to decrease cadherin-mediated adhesion which can drive cell segregation. However, Eph receptors mainly drive cell segregation through increased heterotypic tension or repulsion. Cadherins contribute to cell segregation by antagonising homotypic tension within each cell population. This suppression of homotypic tension increases the difference with heterotypic tension triggered by Eph receptor activation, and it is this differential tension that drives cell segregation and border sharpening.

Retinoic Acid Signaling in Vertebrate Hindbrain Segmentation: Evolution and Diversification

In metazoans, Hox genes are key drivers of morphogenesis. In chordates, they play important roles in patterning the antero-posterior (A-P) axis. A crucial aspect of their role in axial patterning is their collinear expression, a process thought to be linked to their response to major signaling pathways such as retinoic acid (RA) signaling. The amplification of Hox genes following major events of genome evolution can contribute to morphological diversity. In vertebrates, RA acts as a key regulator of the gene regulatory network (GRN) underlying hindbrain segmentation, which includes Hox genes. This review investigates how the RA signaling machinery has evolved and diversified and discusses its connection to the hindbrain GRN in relation to diversity. Using non-chordate and chordate deuterostome models, we explore aspects of ancient programs of axial patterning in an attempt to retrace the evolution of the vertebrate hindbrain GRN. In addition, we investigate how the RA signaling machinery has evolved in vertebrates and highlight key examples of regulatory diversification that may have influenced the GRN for hindbrain segmentation. Finally, we describe the value of using lamprey as a model for the early-diverged jawless vertebrate group, to investigate the elaboration of A-P patterning mechanisms in the vertebrate lineage.

Segmentation and patterning of the vertebrate hindbrain.

During early development, the hindbrain is sub-divided into rhombomeres that underlie the organisation of neurons and adjacent craniofacial tissues. A gene regulatory network of signals and transcription factors establish and pattern segments with a distinct anteroposterior identity. Initially, the borders of segmental gene expression are imprecise, but then become sharply defined, and specialised boundary cells form. In this Review, we summarise key aspects of the conserved regulatory cascade that underlies the formation of hindbrain segments. We describe how the pattern is sharpened and stabilised through the dynamic regulation of cell identity, acting in parallel with cell segregation. Finally, we discuss evidence that boundary cells have roles in local patterning, and act as a site of neurogenesis within the hindbrain.

Normal human brainstem development in vivo: aquantitative fetal MRI study.

ABSTRACTObjectivesTo characterize spatiotemporal growth differences of prenatal brainstem substructures and cerebellum, using linear biometry and planimetry on fetal magnetic resonance imaging (MRI).MethodsIn this retrospective study, we included fetuses with normal brain and a precise midsagittal T2‐weighted brain MRI sequence obtained between May 2003 and April 2019. The cross‐sectional area, rostrocaudal diameter and anteroposterior diameter of the midbrain, pons (basis pontis and pontine tegmentum), medulla oblongata and cerebellar vermis, as well as the transverse cerebellar diameter, were quantified by a single observer. The diameters were also assessed by a second observer to test inter‐rater variability.ResultsWe included 161 fetuses with normal brain and a precise midsagittal MRI sequence, examined at a mean ± SD gestational age of 25.7 ± 5.4 (range, 14 + 0 to 39 + 2) weeks. All substructures of the fetal brainstem and the cerebellum could be measured consistently (mean ± SD interobserver intraclass correlation coefficient, 0.933 ± 0.065). We provide reference data for diameters and areas of the brainstem and cerebellum in the second and third trimesters. There was a significant quadratic relationship between vermian area and gestational age, and all other measured parameters showed a significant linear growth pattern within the observed period (P < 0.001). A significant change in the relative proportions of the brainstem substructures occurred between the beginning of the second trimester and the end of the third trimester, with an increase in the area of the pons (P < 0.001) and a decrease in that of the midbrain (P < 0.001), relative to the total brainstem area.ConclusionsThe substructures of the fetal brainstem follow a distinct spatiotemporal growth pattern, characterized by a relative increase in the pons and decrease in the midbrain, between 15 and 40 weeks of gestation. Caution is needed when interpreting fetal brainstem appearance during the early second trimester, as the brainstem proportions differ significantly from the adult morphology. The reference data provided herein should help to increase diagnostic accuracy in detecting disorders of defective hindbrain segmentation. © 2020 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

The Role of Noradrenergic and Glutamatergic Signaling in Noradrenergic Neurons in Respiratory Control

Central noradrenergic (NA) neurons are a critical component of the brainstem respiratory network that maintains blood CO2 and O2 levels through respiratory chemoreflexes. NA dysfunction is implicated in numerous developmental respiratory disorders such as the fatal Sudden Infant Death Syndrome (SIDS), Rett Syndrome, and Congenital Central Hypoventilation Syndrome (CCHS), in which abnormal chemosensory function is implicated. However, which NA neurons modulate respiratory chemoreflexes and the underlying mechanisms are still not fully understood. Previous studies in our lab utilizing intersectional chemogenetic (hM4D and hM3D DREADD mediated) inhibition and excitation identified multiple rhombomere (transient genetically-defined hindbrain segments arising during early development) specific NA populations that play a role in the adult hypercapnic chemoreflex. NA neurons are typically thought to communicate with synaptic partners through noradrenaline as their primary neurotransmitter. However, the excitatory neurotransmitter, glutamate, is also expressed in subpopulations of NA neurons including those derived from rhombomeres playing a role in the hypercapnic reflex. Prior studies have implicated NA derived glutamatergic signaling in respiratory control. Thus, we seek to determine the relative roles of noradrenergic and glutamatergic signaling in rhombomeric NA populations that are involved in adult respiratory chemoreflexes. To determine the requirement of noradrenergic signaling in the hypercapnic reflex, we aim to conditionally ablate noradrenergic signaling in rhombomeric NA sub-populations by crossing rhombomere specific Credrivers with the THflox/flox(tyrosine hydroxylase) allele to remove dopamine and downstream (nor) adrenaline production in targeted neurons. We also aim to determine if the glutamate producing NA neurons represented a larger functional cohort in breathing control. We therefore used our intersectional strategy to target and chemogenetically activate (hM3D) or inhibite (hM4De) glutamate co-expressing NA neurons (defined by partially overlapping Vglut2Cre; DBHFLPo activity) which are expected to comprise a super-set of rhombomere specific NA neurons that play a role in respiratory chemoreflexes. Whole-body barometric plethysmography was used to measure the respiratory function of the mice under room air (21%O2,79%N2) and hypercapnia (21%O2, 74%N2, 5% CO2). Our preliminary data suggests that removing noradrenergic signaling in a key rhombomeric NA subpopulation does not inhibit the hypercapnic reflex while DREADD mediated inhibition does reduce the hypercapnic reflex. Acute inhibition of glutamate-expressing NA neurons shows a reduction in the hypercapnic ventilatory reflex while acute activation of these same neurons shows a significantly enhanced reflex. Altogether, these preliminary data suggest that glutamate production may delineate a functionally specific NA subpopulation in the hypercapnic reflex and offers additional clues to the respective roles of noradrenaline and glutamatergic signaling in the noradrenergic system.

The Neurogenic Fate of the Hindbrain Boundaries Relies on Notch-Dependent Asymmetric Cell Divisions

The generation of cell diversity in the central nervous system occurs during embryogenesis and requires a precise balance between cell proliferation, commitment to specific fates, and further neuronal differentiation. The cellular and molecular mechanisms regulating this balance in the embryonic brain are still poorly understood. Here we study how the neurogenic capacity in the embryonic hindbrain is spatiotemporally allocated, and how the fate and the growth of the hindbrain boundary cells are regulated. By generating a CRISPR-based knock-in zebrafish transgenic line to specifically label the hindbrain boundaries, we unveiled that boundary cells undergo a functional transition to become neurogenic during hindbrain segmentation concurrently as they maintain the progenitor cell pool. Boundary cells engaged in neurogenesis coinciding with the onset of Notch signaling, which triggered their asymmetrical cell division. Our findings reveal that distinct neurogenic phases take place during hindbrain growth and suggest that boundary cells contribute to refine the final number, identity, and proportion of neurons in the brain.

The Role of Noradrenergic and Glutamatergic Signaling in Noradrenergic Neurons in Respiratory Control

Central noradrenergic (NA) neurons are a critical component of the brainstem respiratory network that maintains blood CO2 and O2 levels through respiratory chemoreflexes. NA dysfunction is implicated in numerous developmental respiratory disorders such as the fatal Sudden Infant Death Syndrome (SIDS), Rett Syndrome, and Congenital Central Hypoventilation Syndrome (CCHS), in which abnormal chemosensory function is implicated. However, which NA neurons modulate respiratory chemoreflexes and the underlying mechanisms are still not fully understood. Previous studies in our lab utilizing intersectional chemogenetic (hM4D and hM3D DREADD mediated) inhibition and excitation identified multiple rhombomere (transient genetically‐defined hindbrain segments arising during early development) specific NA populations that play a role in the adult hypercapnic chemoreflex. NA neurons are typically thought to communicate with synaptic partners through noradrenaline and adrenaline as their primary neurotransmitter. However, the excitatory neurotransmitter, glutamate, is also expressed in subpopulations of NA neurons including rhombomeric NA neurons playing a role in the hypercapnic reflex. Prior studies have implicated NA derived glutamatergic signaling in respiratory control. Thus, we seek to determine the relative roles of noradrenergic and glutamatergic signaling in rhombomeric NA populations that are involved in adult respiratory chemoreflexes. To determine the requirement of noradrenergic signaling in the hypercapnic reflex, we aim to conditionally ablate noradrenergic signaling in rhombomeric NA sub‐populations by crossing rhombomere specific Credrivers with the THflox/flox(tyrosine hydroxylase) allele to remove dopamine and downstream (nor) adrenaline production in targeted neurons. We also aim to determine if the glutamate producing NA neurons represent a larger functional cohort in breathing control. We therefore used our intersectional strategy to target and chemogenetically activate (hM3D) or inhibite (hM4De) glutamate co‐expressing NA neurons (defined by partially overlapping Vglut2Cre; DBHFLPo activity) which are expected to comprise a super‐set of rhombomere specific NA neurons that play a role in respiratory chemoreflexes. Whole‐body barometric plethysmography was used to measure the respiratory function of the mice under room air (21%O2, 79%N2) and hypercapnia (21%O2, 74%N2, 5% CO2). Our preliminary data suggests that removing noradrenergic signaling in a key rhombomeric NA subpopulation does not inhibit the hypercapnic reflex while DREADD mediated inhibition does reduce the hypercapnic reflex. Acute inhibition of glutamate‐expressing NA neurons shows a reduction in the hypercapnic ventilatory reflex while acute activation of these same neurons shows a significantly enhanced reflex. Altogether, these preliminary data suggest that glutamate production may delineate a functionally specific NA subpopulation in the hypercapnic reflex and offers additional clues to the respective roles of noradrenaline and glutamatergic signaling in the noradrenergic system.Support or Funding InformationR01HL153505

A single cell transcriptome atlas of the developing zebrafish hindbrain.

ABSTRACTSegmentation of the vertebrate hindbrain leads to the formation of rhombomeres, each with a distinct anteroposterior identity. Specialised boundary cells form at segment borders that act as a source or regulator of neuronal differentiation. In zebrafish, there is spatial patterning of neurogenesis in which non-neurogenic zones form at boundaries and segment centres, in part mediated by Fgf20 signalling. To further understand the control of neurogenesis, we have carried out single cell RNA sequencing of the zebrafish hindbrain at three different stages of patterning. Analyses of the data reveal known and novel markers of distinct hindbrain segments, of cell types along the dorsoventral axis, and of the transition of progenitors to neuronal differentiation. We find major shifts in the transcriptome of progenitors and of differentiating cells between the different stages analysed. Supervised clustering with markers of boundary cells and segment centres, together with RNA-seq analysis of Fgf-regulated genes, has revealed new candidate regulators of cell differentiation in the hindbrain. These data provide a valuable resource for functional investigations of the patterning of neurogenesis and the transition of progenitors to neuronal differentiation.

A Hox gene regulatory network for hindbrain segmentation.

In vertebrates, the hindbrain serves as a highly conserved complex coordination center for regulating many fundamental activities of the central nervous system, such as respiratory rhythms, sleep patterns and equilibrium, and it also plays an important role in craniofacial development. The basic ground plan that underlies the diverse functions of the hindbrain and its neural crest derivatives is established and patterned by a process of segmentation. Through a dynamic series of signaling and regulatory interactions the developing hindbrain is transiently compartmentalized into a set of seven segmental units, termed rhombomeres. The nested expression of the Hox family of transcription factors is tightly coupled to the process of segmentation and provides a molecular code for specifying the unique regional properties of the hindbrain and its neural crest derived craniofacial structures. The high degree of similarity in hindbrain architecture between diverse vertebrates has enabled cross-species regulatory analysis. This has facilitated the experimental assembly of the signaling and regulatory interactions, which underlie the process of segmentation, into a Hox-dependent gene regulatory network (GRN) model. This hindbrain GRN is a key regulatory feature of head patterning, conserved to the base of vertebrate evolution. This regulatory framework also serves as a basis for comparing and contrasting GRNs that govern cranial neural crest formation and axial patterning and provide insight into regulatory mechanisms associated with the evolution of novel vertebrate traits. The purpose of this review is to discuss the majorfeatures of the GRN for hindbrain segmentation and its relationship to the broader functional role of the hindbrain in patterning head development.

Inter-rhombomeric interactions reveal roles for fibroblast growth factors signaling in segmental regulation of EphA4 expression.

The basic ground plan of vertebrate hindbrain is established through a process of segmentation, which generates eight transient lineage-restricted cellular compartments called rhombomeres (r). The segments adopt distinct individual identities in response to axial patterning signals. It is unclear whether signaling between rhombomeres plays a conserved role in regulating segmental patterning during hindbrain development. Using tissue manipulations of rhombomeres in chicken embryos, we have uncovered roles for r2 and r4 in regulating the expression of EphA4 in r3 and r5. Perturbations of signaling pathways reveal that these regulatory inputs from r2 and r4 into EphA4 expression are mediated independent of inputs from Krox20 through cues involving fibroblast growth factor (FGF) signaling. These interactions are stage dependent and are set up in embryos with <10 somites. We show that r2 and r4 function as temporally dynamic signaling centers in the early patterning of adjacent hindbrain segments and this activity is dependent upon the FGF pathway. These results reveal that inter-rhombomeric signaling is a conserved feature of the regulatory networks that control the specification of individual rhombomere identities in vertebrate hindbrain segmentation. However, the timing of when restricted domains of FGF signaling are coupled to formation of r4 may vary between the species.

Yap/Taz-TEAD activity links mechanical cues to progenitor cell behavior during zebrafish hindbrain segmentation.

Cells perceive their microenvironment through chemical and physical cues. However, how the mechanical signals are interpreted during embryonic tissue deformation to result in specific cell behaviors is largely unknown. The Yap/Taz family of transcriptional co-activators has emerged as an important regulator of tissue growth and regeneration, responding to physical cues from the extracellular matrix, and to cell shape and actomyosin cytoskeletal changes. In this study, we demonstrate the role of Yap/Taz-TEAD activity as a sensor of mechanical signals in the regulation of the progenitor behavior of boundary cells during zebrafish hindbrain compartmentalization. Monitoring of in vivo Yap/Taz activity during hindbrain segmentation indicated that boundary cells responded to mechanical cues in a cell-autonomous manner through Yap/Taz-TEAD activity. Cell-lineage analysis revealed that Yap/Taz-TEAD boundary cells decreased their proliferative activity when Yap/Taz-TEAD activity ceased, which preceded changes in their cell fate from proliferating progenitors to differentiated neurons. Functional experiments demonstrated the pivotal role of Yap/Taz-TEAD signaling in maintaining progenitor features in the hindbrain boundary cell population.

An atlas of anterior hox gene expression in the embryonic sea lamprey head: Hox-code evolution in vertebrates

In the hindbrain and the adjacent cranial neural crest (NC) cells of jawed vertebrates (gnathostomes), nested and segmentally-restricted domains of Hox gene expression provide a combinatorial Hox-code for specifying regional properties during head development. Extant jawless vertebrates, such as the sea lamprey (Petromyzon marinus), can provide insights into the evolution and diversification of this Hox-code in vertebrates. There is evidence for gnathostome-like spatial patterns of Hox expression in lamprey; however, the expression domains of the majority of lamprey hox genes from paralogy groups (PG) 1-4 are yet to be characterized, so it is unknown whether they are coupled to hindbrain segments (rhombomeres) and NC. In this study, we systematically describe the spatiotemporal expression of all 14 sea lamprey hox genes from PG1-PG4 in the developing hindbrain and pharynx to investigate the extent to which their expression conforms to the archetypal gnathostome hindbrain and pharyngeal hox-codes. We find many similarities in Hox expression between lamprey and gnathostome species, particularly in rhombomeric domains during hindbrain segmentation and in the cranial neural crest, enabling inference of aspects of Hox expression in the ancestral vertebrate embryonic head. These data are consistent with the idea that a Hox regulatory network underlying hindbrain segmentation is a pan vertebrate trait. We also reveal differences in hindbrain domains at later stages, as well as expression in the endostyle and in pharyngeal arch (PA) 1 mesoderm. Our analysis suggests that many Hox expression domains that are observed in extant gnathostomes were present in ancestral vertebrates but have been partitioned differently across Hox clusters in gnathostome and cyclostome lineages after duplication.

Towards a ‘Green Allopathy’: Biomedicalization and the Naturopathic Medicine Profession in Ontario, Canada

Different classes of primary afferents from semicircular canal and otolith organs project to the vestibular nuclei, but do not follow a topographic representation as seen for other sense organs. Second-order vestibular neurons give rise to different pathways that serve gaze and body stabilization during active and passive head motion or self-motion perception and spatial orientation. These projections originate in specific genetically determined hindbrain segments and are defined by their motor or premotor targets, an organization that appears to be preserved throughout vertebrate evolution.

Neuron-specific Mafb knockout causes growth retardation accompanied by an impaired growth hormone/insulin-like growth factor I axis.

Mammalian postnatal growth is regulated primarily by the growth hormone (GH)/insulin-like growth factor I (IGF-I) axis. MafB is a basic leucine zipper (bZip) transcription factor that has pleiotropic functions. Although MafB plays a critical role in fetal brain development, such as in guidance for hindbrain segmentation, its postnatal role in neurons remains to be elucidated. To investigate this, we used neuron-specific Mafb conditional knockout (cKO) mice. In addition to an approximately 50% neonatal viability, the Mafb cKO mice exhibited growth retardation without apparent signs of low energy intake. Notably, serum IGF-I levels of these mice in the postnatal stage were lower than those of control mice. They seemed to have a neuroendocrine dysregulation, as shown by the upregulation of serum GH levels in the resting state and an inconsistent secretory response of GH upon administration of growth hormone-releasing hormone. These findings reveal that neuronal MafB plays an important role in postnatal development regulated by the GH/IGF-I axis.

Features of the structure, development, and activity of the zebrafish noradrenergic system explored in new CRISPR transgenic lines.

The noradrenergic (NA) system of vertebrates is implicated in learning, memory, arousal, and neuroinflammatory responses, but is difficult to access experimentally. Small and optically transparent, larval zebrafish offer the prospect of exploration of NA structure and function in an intact animal. We made multiple transgenic zebrafish lines using the CRISPR/Cas9 system to insert fluorescent reporters upstream of slc6a2, the norepinephrine transporter gene. These lines faithfully express reporters in NA cell populations, including the locus coeruleus (LC), which contains only about 14 total neurons. We used the lines in combination with two-photon microscopy to explore the structure and projections of the NA system in the context of the columnar organization of cell types in the zebrafish hindbrain. We found robust alignment of NA projections with glutamatergic neurotransmitter stripes in some hindbrain segments, suggesting orderly relations to neuronal cell types early in life. We also quantified neurite density in the rostral spinal cord in individual larvae with as much as 100% difference in the number of LC neurons, and found no correlation between neuronal number in the LC and projection density in the rostral spinal cord. Finally, using light sheet microscopy, we performed bilateral calcium imaging of the entire LC. We found that large-amplitude calcium responses were evident in all LC neurons and showed bilateral synchrony, whereas small-amplitude events were more likely to show interhemispheric asynchrony, supporting the potential for targeted LC neuromodulation. Our observations and new transgenic lines set the stage for a deeper understanding of the NA system.

Cooperation, cis-interactions, versatility and evolutionary plasticity of multiple cis-acting elements underlie krox20 hindbrain regulation.

Cis-regulation plays an essential role in the control of gene expression, and is particularly complex and poorly understood for developmental genes, which are subject to multiple levels of modulation. In this study, we performed a global analysis of the cis-acting elements involved in the control of the zebrafish developmental gene krox20. krox20 encodes a transcription factor required for hindbrain segmentation and patterning, a morphogenetic process highly conserved during vertebrate evolution. Chromatin accessibility analysis reveals a cis-regulatory landscape that includes 6 elements participating in the control of initiation and autoregulatory aspects of krox20 hindbrain expression. Combining transgenic reporter analyses and CRISPR/Cas9-mediated mutagenesis, we assign precise functions to each of these 6 elements and provide a comprehensive view of krox20 cis-regulation. Three important features emerged. First, cooperation between multiple cis-elements plays a major role in the regulation. Cooperation can surprisingly combine synergy and redundancy, and is not restricted to transcriptional enhancer activity (for example, 4 distinct elements cooperate through different modes to maintain autoregulation). Second, several elements are unexpectedly versatile, which allows them to be involved in different aspects of control of gene expression. Third, comparative analysis of the elements and their activities in several vertebrate species reveals that this versatility is underlain by major plasticity across evolution, despite the high conservation of the gene expression pattern. These characteristics are likely to be of broad significance for developmental genes.

Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.