With increasing amounts of data being collected in various fields of neuroscience, there is a growing need for robust techniques for the analysis of this information. This thesis focuses on the evaluation and development of quantitative frameworks for the analysis and classification of neuronal data from a variety of contexts. Firstly, I investigate methods for analysing spontaneous neuronal network activity recorded on microelectrode arrays (MEAs). I perform an unbiased evaluation of the existing techniques for detecting ‘bursts’ of neuronal activity in these types of recordings, and provide recommendations for the robust analysis of bursting activity in a range of contexts using both existing and adapted burst detection methods. These techniques are then used to analyse bursting activity in novel recordings of human induced pluripotent stem cell-derived neuronal networks. Results from this review of burst analysis methods are then used to inform the development of a framework for characterising the activity of neuronal networks recorded on MEAs, using properties of bursting as well as other common features of spontaneous activity. Using this framework, I examine the ontogeny of spontaneous network activity in in vitro neuronal networks from various brain regions, recorded on both single and multi-well MEAs. I also develop a framework for classifying these recordings according to their network type, based on quantitative features of their activity patterns. Next, I take a multi-view approach to classifying neuronal cell types using both the morphological and electrophysiological features of cells. I show that a number of multi-view clustering algorithms can more reliably differentiate between neuronal cell types in two existing data sets, compared to single-view clustering techniques applied to either the morphological or electrophysiological ‘view’ of the data, or a concatenation of the two views. To close, I examine the properties of the cell types identified by these methods.

Our ability to learn relies on the potential of neuronal networks to change through experience. The primary visual cortex (V1) has become a popular system for studying how experience shapes cortical neuronal networks. Experience-dependent plasticity in V1 has been extensively studied in young animals, revealing that experiences in early postnatal life substantially shape neuronal activity in the developing cortex. In contrast, less is known about how experiences modify the representation of visual stimuli in the adult brain. In addition, adult experience-dependent plasticity remains largely unexplored in neurodevelopmental disorders. To address this issue, we established a two-photon calcium imaging set-up, suitable for chronic imaging of neuronal activity in awake-behaving mice. We implemented protocols for the reliable expression of genetically encoded calcium indicators (GCaMP6), for the implantation of a chronic cranial window and for the analysis of chronic calcium imaging data. This approach enables us to monitor the activity of hundreds of neurons across days, and up to 4-5 weeks. We used this technique to determine whether the daily exposure to high-contrast gratings would induce experience-dependent changes in V1 neuronal activity. We monitored the activity of putative excitatory neurons and of three non-overlapping populations of inhibitory interneurons in layer 2/3 of adult mice freely running on a cylindrical treadmill. We compared the results obtained from mice that were exposed daily to either a high-contrast grating or to a grey screen and characterized their neuronal response properties. Our results did not reveal significant differences in neuronal properties between these two groups, suggesting a lack of stimulus-specific plasticity in our experimental conditions. However, we did observe and characterize, in both groups, a wide range of activity changes in individual cells over time. We finally applied the same method to investigate impairments in experience-dependent plasticity in a mouse model of intellectual disability (ID), caused by synaptic GTPase-activating protein (SynGAP) haploinsufficiency. SynGAP haploinsufficiency is a common de novo genetic cause of non-syndromic ID and is considered a Type1 risk for autism spectrum disorders. While the impact of Syngap gene mutations has been thoroughly studied at the molecular and cellular levels, neuronal network deficits in vivo remain largely unexplored. In this study, we compared in vivo neuronal activity before and after monocular deprivation in adult mutant mice and littermate controls. These results revealed differences in baseline network activity between both experimental groups. These impairments in cortical neuronal network activity may underlie sensory and cognitive deficits in patients with Syngap gene mutations.

The aim of the studies included in the thesis is to better understand the interplay between neuronal activity-dependent gene regulation and the bioactive vitamin A metabolite all-trans-retinoic acid (RA) during postnatal development, refinement and maintenance of precise neuronal connectivity using the olfactory sensory neuron (OSN) in the olfactory epithelium (OE) of genetically modified mice as a model. We show that: Inhibition of RA receptor (RAR)-mediated transcription in OSNs reduces expression of the olfactory cyclic nucleotide-gated (CNG) ion channel, which is required for odorant receptor (OR)-mediated stimulus transduction. This, results in increased OSN death and errors in precise connectivity. The increased cell death may be a consequence of reduced intrinsic excitability and/or reduced influx of Ca2+ ions while the errors in connectivity may be due to altered OR-dependent expression of axonal guidance proteins, such as Kirrel-2 and Neuropilin-1. Expression of the RA catabolic enzyme Cyp26B1 in OSNs is positively regulated by RAR-mediated transcription as well as sensory stimulation in a CNG channel-dependent manner. This shows that neuronal activity and local vitamin A metabolism are parts of novel regulatory feedback loop controlling precise connectivity and neuronal survival. The feedback loop may be a form of homeostatic plasticity in response to global changes in neuronal activity. BACE1, an enzyme is implicated in Alzheimer´s disease, and Cyp26B1 are inversely regulated by CNG channel-dependent sensory stimulation. Cyp26B1 expression is switched on at birth, forms a topographic expression gradient in OE and inhibits BACE1 expression into an inverse counter gradient. Taken together these results reveal a novel neuronal activity-dependent mechanism by which sensory stimuli can shape spatial gene expression via altered RA bioavailability. Increased Cyp26B1 expression stimulates turnover of OSNs during adult neurogenesis by a non-cell-autonomous mechanism. The gradient of Cyp26B1 expression correlates with spatially-regulated diversification of OSNs into subpopulations that express different subsets of OR genes. Cyp26B1 expression influences spatial OR diversification of OSNs by two different mechanisms. In the ventrolateral OE, Cyp26B1 inhibits OR expression by blocking OSN differentiation at a stage that may be associated with the cell intrinsic mechanism regulating OR gene choice. In the dorsomedial OE the expression frequency of some ORs is unaltered while other increases, presumably as a consequence of neuronal activity-dependent competition. A probable function of graded and activity-dependent Cyp26B1 expression is to form a topographic partitioning of the olfactory sensory map into functional domains, which gradually differ from each other with regard to experience-driven plasticity and neurogenic potential along the dorsomedial-ventrolateral axis of OE.

The objective of the thesis is to get familiar with the method of psychophysiological interactions and its common inplementation. It is explaining the usual methods of removing disruptive signals from the data processed in correlation analysis and presents the possibility of their implementation. In the practical part it is focused on cerating suggested program and its testing on the real data sets.

RNA epigenetics or Epitranscriptomics has emerged as a new field for understanding the post-transcriptional regulation of gene expression by RNA modifications. Among numerous types of RNA modifications, RNA cytosine-5 methylation (5-mrC) is recognized as an important epitranscriptomic mark that modulates mRNA transportation, stability and translation. In chapter 1, we summarize the currently available approaches to detect 5-mrC modification at global, transcriptome-wide and locus-specific levels, and compare the corresponding advantages and disadvantages of the techniques. We further focus on the bioinformatics data analysis of RNA bisulfite sequencing datasets by comparing existing packages with respect to key parameters for alignment and methylation calling and filtering of potentially false positive 5-mrC sites. To investigate the dynamic regulation of 5-mrC modification, as described in chapter 2, we adopt a widely used neuronal activity model, and perform RNA sequencing (RNA-seq) and RNA bisulfite sequencing (RNA BS-seq) to profile gene expression as well as transcriptome-wide 5-mrC modification. We have identified distinct gene expression profiles and differentially methylated 5-mrC sites (DMS) in neurons upon activation, and the genes with DMS sites are enriched with mitochondrial and synaptic functions. Moreover, it reveals a negative correlation between RNA methylation and mRNA expression in mouse cortical neurons during neuronal activity. Thus, these findings identify the dynamic regulation of 5-mrC modification during neuronal activity and reveal a potential link between RNA methylation and mRNA expression. In chapter 3, we investigate the effect of folate, a methyl-donor, on RNA cytosine-5 methylation (5-mrC) modification in adult mouse neural stem cells (NSCs). Compared to the control, NSCs cultured in folate deficiency or supplementation condition have shown no changes in mRNA expression, but significant changes in mRNA translation efficiency. RNA bisulfite sequencing of both total and polysome poly(A) RNA samples shows distinct 5-mrC profiles in NSCs treated with different concentrations of folic acid. It also shows consistent hypermethylation in polysome mRNAs than that in total mRNAs. This study presents the comprehensive influence of folate deficiency and supplementation on RNA cytosine-5 methylation and mRNA translation. / Doctor of Philosophy / RNA epigenetics, a collection of RNA modifications, has recently emerged as an exciting, new field for understanding post-transcriptional regulation of gene expression. RNA cytosine-5 methylation (5-mrC) is one of the most well-known RNA modifications that modulates mRNA export, stability and translation. In the first chapter, we summarize the currently available methods for the measurement of 5-mrC modification. We highlight one of the techniques, RNA bisulfite sequencing (RNA BS-seq) and focus on the bioinformatics data analysis of RNA BS-seq datasets. We have compared several existing tools in regard of the key parameters in data analysis. In the second chapter, we adopt a widely used neuronal activity model to study the dynamic regulation of RNA cytosine-5 methylation (5-mrC). We perform RNA-seq and RNA BS-seq in neurons in response to stimulation. We have identified numerous differentially expressed genes and differentially methylated 5-mrC sites in activated neurons and find that these DMS-related genes are associated with mitochondrial and synaptic functions. Furthermore, we identify a negative correlation between RNA methylation and mRNA expression, indicating a potential role of 5-mrC modification in the regulation of mRNA expression. In the third chapter, we investigate the influence of a nutrient supplement, folic acid, on 5-mrC modification in adult mouse neural stem cells. Compared to the control, NSCs cultured in folate deficiency or supplementation condition have shown no changes in mRNA expression, but significant changes in mRNA translation efficiency. We perform RNA bisulfite sequencing of both total poly(A) RNA samples and polysome poly(A) RNA samples. We identify distinct 5-mrC profiles in NSCs treated with different concentrations of folic acid. It shows consistent hypermethylation in polysome mRNAs than that in total mRNAs. This study presents the comprehensive influence of folate deficiency and supplementation on RNA cytosine-5 methylation and mRNA translation.

Low intensity and low frequency ultrasound has been shown to modulate ion channel currents, membrane capacitive currents, and as a result, neuronal activity. Ultrasound has been used as a non-invasive way to modulate neuronal activity in vivo using mice as well as human subjects. Ultrasound with acoustic frequency as low as 0.35 MHz can be focussed on a region as small as 2 mm with reversible effects and no increase in temperature. In this study, two ultrasound transducers with different resonant frequency have been used to excite neuronal cultures. The resulting changes in the network properties such as synchronised network burst frequency, density, clustering and path length have been analysed. The study shows that ultrasound stimulation at acoustic frequency 450 kHz (ISPPA =11.3 mW/cm2) significantly modulates the above mentioned parameters and causes deviations from small world network properties of the control network.

Le temps est une dimension universelle traitée par les systèmes sensoriels, qui est essentielle pour attribuer un sens à des stimuli comme la parole ou la musique pour l'audition. Cependant, les mécanismes requis pour le traitement temporel restent en grande part méconnus. Dans cette thèse, nous avons examiné un type de mécanisme faisant sans doute partie intégrante de tout traitement temporel : la formation de nouvelles traces mnésiques pour l’information temporelle. Nous avons étudié principalement la modalité auditive, mais aussi d'autres modalités sensorielles, comme le toucher, la vision, et la stimulation électrique directe du système auditif périphérique avec un implant cochléaire. Toutes les expériences ont utilisé un nouveau paradigme expérimental, adapté de précédentes études conçues pour étudier la mémoire auditive (Agus, Thorpe, & Pressnitzer, 2010). Au lieu d'utiliser du bruit comme stimulus, nous avons utilisé des séquences d’intervalles de temps irréguliers délimités par de brèves impulsions d'énergie, adaptées à la modalité étudiée. Dans une première série d'expériences, nous avons étudié la modalité auditive chez des auditeurs normo-entendants, en utilisant des trains de clics audio comme stimuli. Nous avons démontré, pour la première fois, un apprentissage rapide de sons contenant uniquement des informations temporelles. Dans une seconde série d'expériences, nous avons appliqué le même paradigme à trois modalités sensorielles (audition, toucher et vision), en utilisant des clics audio, des impulsions de mouvement au bout des doigts, et des flashs de lumière pour délimiter les intervalles de temps dans les différences modalités. Nous avons observé des formes qualitativement similaires d'apprentissage perceptif pour les trois modalités, avec un apprentissage rapide dans tous les cas, ainsi qu'un transfert d'apprentissage au toucher ou à la vision pour des séquences initialement apprises de façon auditive. Dans une troisième série d'expériences, nous avons testé des malentendants stimulés électriquement par leur implant cochléaire avec des séquences d'impulsions irrégulières. Nous avons trouvé des indications d’une plasticité préservée pour l'apprentissage rapide des informations temporelles chez ces auditeurs. Enfin, nous présentons des résultats préliminaires en utilisant une nouvelle technique susceptible de révéler certains des mécanismes neuronaux sous-jacents à l'apprentissage perceptuel rapide. Nous avons mesuré la dilatation pupillaire pendant que les auditeurs effectuaient la tâche de mémoire auditive et observé des changements systématiques de la taille de la pupille avec l'apprentissage. En conclusion, la thèse montre une capacité remarquable des systèmes perceptifs à apprendre des séquences temporelles complexes lorsqu'elles apparaissent plusieurs fois dans l'environnement, et suggère de nouvelles méthodes expérimentales pour étudier plus avant les mécanismes neuronaux sous-jacents. / Time is a universal feature of all information processed by sensory systems, and temporal patterning is often essential for attributing meaning to external stimuli such as speech or music in audition. However, many of the mechanisms needed for temporal processing are still unclear. In this thesis, we investigated one type of mechanism arguably integral to any kind of temporal processing: the formation of novel memories for temporal patterns. We studied mainly the auditory modality, but also other sensory modalities such touch, vision, and electric hearing with a cochlear implant. All experiments used a novel experimental paradigm, adapted from a previous study designed to explore auditory memory of random noise (Agus, Thorpe, & Pressnitzer, 2010). Instead of using noise as the complex stimulus to learn, we used irregular time patterns made of random time intervals delineated by modality-adapted brief energy pulses. In a first series of experiments, we investigated the auditory modality in normal hearing listeners, using click trains as stimuli. We demonstrated for the first time a rapid learning of stimuli containing solely temporal cues. In a second series of experiments, we applied the same paradigm to multiple sensory modalities (audition, touch, and vision), using audio clicks, motion pulses to the fingertips, and light to delineate time intervals. We found a qualitatively similar forms of perceptual learning for all three modalities, with rapid learning in all cases, as well as a transfer of learning to touch or vision for patterns learnt initially learnt in audition. In a third series of experiments, we tested hearing impaired listeners stimulated through their cochlear implant with sequences of electrical pulses. We found evidence for preserved plasticity for the rapid learning of time patterns in those listeners. Finally, we present preliminary data using a novel technique for studying the underlying neural mechanisms of rapid perceptual learning. We measured pupil dilation while listeners performed the memory task and observed systematic changes in pupil size with perceptual learning. In conclusion, the thesis shows a remarkable ability of perceptual systems to learn complex time patterns as they re-occur in the environment, and suggests new experimental methods to further study the underlying neural mechanisms.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19270号 / 医博第4034号 / 新制||医||1011(附属図書館) / 32272 / 京都大学大学院医学研究科医学専攻 / (主査)教授 髙橋 良輔, 教授 渡邉 大, 教授 富樫 かおり / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Tesi realitzada a l'Equip de Neurociència de Sistemes - IDIBAPS / Since the discovery of the place cells in 1971 by John O’Keefe and colleagues an extensive work over the hippocampus has been developed as the mammal model of spatial navigation. Place cells are rodents’ hippocampal neurons whose firing is associated to certain locations of the environment. A majority of studies have focused on how the place fields (the area where the firing of a neuron is restricted) are generated in relation to the static cues of the environment (O'Keefe and Conway, 1978; Muller et al., 1987; Gothard et al., 1996). The present work assessed a similar question but regarding the dynamic cues surrounding the subject, and with the hypothesis that the hippocampus is also representing the position of other moving objects. In order to demonstrate if that was the case, we developed a behavioural protocol in which rats learnt to discriminate the movements of a robot in order to obtain reward, an Operant Position Discrimination Task (OPDT). Once the protocol was validated, the subjects were chronically implanted with tetrodes in the CA1 region of the hippocampus. In this way the activity of single hippocampal cells could be isolated off-line and the LFP of the area stored during the recordings. Using this method, the relationship between the firing of the cells and the field activity with the spatial parameters of the robot could be evaluated. The results showed a modulation by the dynamic cue of the theta oscillation. While the locomotor activity of the subjects is directly related to the power of theta in natural conditions (Vanderwolf, 1969), during the movement of the robot such relationship was disrupted and the band power between 4-12 Hz showed a trough at this time. The analysis of the single cells’ activity showed neurons locked to several spatial features of the dynamic cue. First, the position of the rat and the robot where analysed by information content parameters. Skaggs Index and Positional information (Markus et al., 1994; Olypher et al., 2003) showed neurons locked to the position of the subject as expected in CA1 and also other neurons locked to the positions of the robot. Second, moving from the spatial analysis to the temporal one, we found responses to the movement of the robot like OFF/ON variations of the basal activity of the neurons. Such changes in the firing patterns where quantified by the Mutual Information index (Nelken and Chechik, 2007) demonstrating that a large fraction of the neurons have a significant differential pattern of activity during the movement of the robot towards one side or the other. The use of the same index, MI, for the evaluation of the static or dynamic condition of the robot, also resulted in a set of neurons spiking with significant disparity during such epochs. In conclusion, the present work has demonstrated the existence of neural correlates locked to a dynamic cue in the hippocampus. Both the field activity at the theta range, LFP between 4 and 12 Hz, and the activity of the hippocampal neurons were found to reflect and/or encode the spatial features of a dynamic cue. The present work has in this way enlarged the limited evidence present in the prior literature about the role of the hippocampus in the tracking and localization of dynamic cues with the use of a behavioural protocol where both the spatial and temporal dynamics could be assessed. / La correcta localización y seguimiento de las pistas dinámicas que se encuentran en el ambiente es una tarea crucial para el individuo. Comportamientos fundamentales como la caza, el apareamiento o el escape necesitan una correcta identificación de la posición de presas, congéneres y depredadores para su correcta realización. El sistema cerebral encargado de localizar al propio sujeto en el ambiente se sabe que se encuentra en la formación hipocampal después de que diversos estudios hayan demostrado la necesidad del mismo para una correcta orientación (Morris et al., 1982) y, aún más importante, tras el descubrimiento en roedores de neuronas que disparan únicamente en espacios restringidos del entorno, las células de lugar (O'Keefe and Dostrovsky, 1971). Si bien se conoce que estos procesos están fundados en una correcta representación de la posición de las pistas estáticas del ambiente (O'Keefe and Conway, 1978; Muller et al., 1987; Gothard et al., 1996), que sirven de referencia para la propia localización, poco se sabe acerca de cómo se integra la información relativa a los objetos y/o sujetos móviles que se encuentran en el mismo ambiente. Este trabajo tiene como objetivo principal intentar responder a esta pregunta, es decir, ¿en qué modo el hipocampo procesa la información relativa a las pistas dinámicas? Para el desarrollo del estudio, primero, se diseñó una tarea comportamental que asegurara el hecho de que la pista dinámica resultase relevante para los sujetos de forma que los mismos prestaran atención a sus movimientos. Con este fin elegimos utilizar un robot cuyos desplazamientos pueden ser finamente controlados y asociar una recompensa a determinados patrones de navegación del robot. Después de probar con diferentes tareas de discriminación se llegó a una configuración (Operant Position Discrimination Task, OPDT) que permitía a los animales seguir los movimientos del robot desde un espacio separado en el cual recibían la recompensa en caso de discernir correctamente los desplazamientos de la pista. Una vez validada la tarea comportamental, a los sujetos que alcanzaron altas tasas de rendimiento se les implantaron tetrodos en la zona CA1 del hipocampo, lugar en el que se encuentran las células de lugar más estables. Una vez hecho el implante se procedió a registrar la actividad cerebral durante la ejecución de la tarea. Por una parte se aislaron los potenciales de acción pertenecientes a neuronas únicas y el potencial de campo de la zona, LFP. Respecto a la actividad de campo, LFP, se observó una disminución significativa de la potencia en la banda theta, 4-12 Hz, relacionada generalmente con la actividad locomotora del sujeto (Vanderwolf, 1969) durante el movimiento del robot. Durante el resto del registro la relación entre velocidad y potencia de theta se mantuvo y sólo en el periodo de discriminación del movimiento del robot esta relación se vio alterada con un mínimo de potencia observado en diferentes sujetos y registros. La actividad de las neuronas se analizó en función de los parámetros espaciales y dinámicos de la rata y el robot. Mirando la especificidad espacial del disparo de las neuronas a través de los parámetros Skaggs Index y Positional information (Markus et al., 1994; Olypher et al., 2003) se encontraron células significativamente ligadas en su actividad a la posición del sujeto o del robot. La actividad de las neuronas también se analizó de forma temporal, tomando como referencia el inicio de los estímulos, es decir el movimiento del robot hacia un lado u otro. Utilizando como índice la Mutual Information (Nelken and Chechik, 2007) se encontró que una larga proporción de las neuronas tienen respuestas diferenciales durante el movimiento del robot hacia uno de los lados. A su vez, el mismo análisis, pero en esta ocasión comparando los periodos en los que la pista se encuentra inmóvil con los que está en movimiento, determinó que otra fracción de las neuronas tiene patrones de disparo diferenciales según sea la condición dinámica de la pista. El conjunto de los resultados obtenidos indica claramente que el hipocampo se encuentra involucrado activamente en la localización y el seguimiento de las pistas dinámicas, siendo esto reflejado tanto en la actividad de sus neuronas como en la actividad de campo global. Los parámetros espaciales de la pista que resultaron modulados durante la tarea fueron su posición, la dirección de su movimiento y el hecho en sí de permanecer inmóvil o en desplazamiento.

Le néocortex est une région du cerveau qui traite toutes les entrées sensorielles et créé des réponses comportementales. Il est subdivisé en zones fonctionnelles, chacune ayant une cytoarchitecture, un motif d’expression génique et un profil de connectivité spécifiques. L'organisation en zones est pré-modelée par des gènes organisateurs, et ensuite affinée par l’activité sensorielle. Dans cette étude, j'ai étudié d'abord si ce pré-modelage est établi dans les progéniteurs et/ou les cellules post-mitotiques, et si l'activité neuronale spontanée est nécessaire pour l’établissement de la connectivité correcte entre néocortex et thalamus, station relais principale des données sensorielles. Avec l'aide d'une série de souris transgéniques, j’ai montré que la fonction du gène organisateur COUP-TFI est suffisante et nécessaire pour organiser l'identité sensorielle dans les cellules post-mitotiques, et que COUP-TFI régule l'activité intrinsèque des neurones corticaux, influençant la bonne intégration des entrées thalamiques dans le cortex somatosensoriel. J’ai montré que COUP-TFI contrôle directement l'expression du gène Egr1, qui dépend fortement de l'activité neuronale. COUP-TFI et Egr1 agissent sur l'acquisition de la morphologie des cellules étoilées dans les neurones de la couche 4, cibles principales des axones thalamiques et trait typique des zones somatosensoriels primaires. En conclusion, ce travail montre que le pré-modelage cortical dépend primordialement d’un programme génétique établi dans les cellules post-mitotiques et que l'activité intrinsèque et les propriétés génétiques agissent ensemble pour façonner l'organisation des premiers circuits dans le néocortex. / The neocortex is a region of the brain that processes all sensory inputs creating appropriate behavioral responses. It is subdivided into functional areas, each with a specific cytoarchitecture, gene expression pattern and connectivity profile. The organization into areas is pre-patterned by the action of areal patterning genes, and subsequently refined by sensory evoked activity. In this study, I have first investigated whether early areal patterning is committed in progenitor and/or post-mitotic cells, and then assessed whether spontaneous neuronal activity is required in establishing correct connectivity between the neocortex and the thalamus, the principal relay station of peripheral sensory inputs. With the help of a series of transgenic mice, my work showed that the function of the areal patterning gene COUP-TFI is sufficient and necessary to organize sensory identity in post-mitotic cells, and that COUP-TFI regulates intrinsic activity properties of cortical neurons, and thus proper integration of thalamic inputs into the somatosensory cortex. In particular, I found that COUP-TFI directly controls the expression of the immediate early gene Egr1, which expression levels strongly depend on neuronal activity. Both COUP-TFI and Egr1 act on the acquisition of the stellate cell morphology of layer 4 neurons, the main targets of thalamic axons and a typical trait of primary somatosensory areas. In conclusion, this work demonstrates that cortical area patterning primordially depends on a genetic program established in post-mitotic cells and that intrinsic genetic and activity properties act together to shape the organization of early circuits in the neocortex.