Thursday, October 31, 2024
No menu items!
HomeNatureMolecular programs guiding arealization of descending cortical pathways

Molecular programs guiding arealization of descending cortical pathways

  • Kita, T. & Kita, H. The subthalamic nucleus is one of multiple innervation sites for long-range corticofugal axons: a single-axon tracing study in the rat. J. Neurosci. 32, 5990–5999 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Peng, H. et al. Morphological diversity of single neurons in molecularly defined cell types. Nature 598, 174–181 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yao, Z. et al. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell 184, 3222–3241 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Groh, A. et al. Cell-type specific properties of pyramidal neurons in neocortex underlying a layout that is modifiable depending on the cortical area. Cereb. Cortex 20, 826–836 (2010).

    Article 
    PubMed 

    Google Scholar
     

  • Kim, E. J., Juavinett, A. L., Kyubwa, E. M., Jacobs, M. W. & Callaway, E. M. Three types of cortical layer 5 neurons that differ in brain-wide connectivity and function. Neuron 88, 1253–1267 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Baker, A. et al. Specialized subpopulations of deep-layer pyramidal neurons in the neocortex: bridging cellular properties to functional consequences. J. Neurosci. 38, 5441–5455 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Economo, M. N. et al. Distinct descending motor cortex pathways and their roles in movement. Nature 563, 79–84 (2018).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Tasic, B. et al. Shared and distinct transcriptomic cell types across neocortical areas. Nature 563, 72–78 (2018).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lemon, R. N. The cortical “upper motoneuron” in health and disease. Brain Sci. https://doi.org/10.3390/brainsci11050619 (2021).

  • Zou, Y. Targeting axon guidance cues for neural circuit repair after spinal cord injury. J. Cereb. Blood Flow Metab. 41, 197–205 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jin, J. et al. Dominant heterogeneity of upper and lower motor neuron degeneration to motor manifestation of involved region in amyotrophic lateral sclerosis. Sci. Rep. 9, 20059 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marques, C., Burg, T., Scekic-Zahirovic, J., Fischer, M. & Rouaux, C. Upper and lower motor neuron degenerations are somatotopically related and temporally ordered in the Sod1 mouse model of amyotrophic lateral sclerosis. Brain Sci. https://doi.org/10.3390/brainsci11030369 (2021).

  • Arlotta, P. et al. Neuronal subtype-specific genes that control corticospinal motor neuron development in vivo. Neuron 45, 207–221 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kaiser, J. et al. Molecular specification of cortico-brainstem versus corticospinal projection neurons in development. Preprint at bioRxiv https://doi.org/10.1101/2022.05.31.494253 (2022).

  • O’Leary, D. D. & Terashima, T. Cortical axons branch to multiple subcortical targets by interstitial axon budding: implications for target recognition and “waiting periods”. Neuron 1, 901–910 (1988).

    Article 
    PubMed 

    Google Scholar
     

  • Stanfield, B. B., O’Leary, D. D. & Fricks, C. Selective collateral elimination in early postnatal development restricts cortical distribution of rat pyramidal tract neurones. Nature 298, 371–373 (1982).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Blanquie, O. et al. Electrical activity controls area-specific expression of neuronal apoptosis in the mouse developing cerebral cortex. eLife 6, e27696 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kamiyama, T. et al. Corticospinal tract development and spinal cord innervation differ between cervical and lumbar targets. J. Neurosci. 35, 1181–1191 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Luo, L. & O’Leary, D. D. Axon retraction and degeneration in development and disease. Annu. Rev. Neurosci. 28, 127–156 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Polleux, F., Dehay, C., Goffinet, A. & Kennedy, H. Pre- and post-mitotic events contribute to the progressive acquisition of area-specific connectional fate in the neocortex. Cereb. Cortex 11, 1027–1039 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kebschull, J. M. et al. High-throughput mapping of single-neuron projections by sequencing of barcoded RNA. Neuron 91, 975–987 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pouchelon, G. et al. Modality-specific thalamocortical inputs instruct the identity of postsynaptic L4 neurons. Nature 511, 471–474 (2014).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Lodato, S. et al. Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons. Nat. Neurosci. 17, 1046–1054 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Leamey, C. A. et al. Differential gene expression between sensory neocortical areas: potential roles for Ten_m3 and Bcl6 in patterning visual and somatosensory pathways. Cereb. Cortex 18, 53–66 (2008).

    Article 
    PubMed 

    Google Scholar
     

  • Zhang, M. et al. Molecularly defined and spatially resolved cell atlas of the whole mouse brain. Nature 624, 343–354 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Britanova, O. et al. Satb2 is a postmitotic determinant for upper-layer neuron specification in the neocortex. Neuron 57, 378–392 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Molyneaux, B. J. et al. Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons. J. Neurosci. 29, 12343–12354 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bunt, J. et al. Combined allelic dosage of Nfia and Nfib regulates cortical development. Brain Neurosci. Adv. 1, 2398212817739433 (2017).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Azim, E., Shnider, S. J., Cederquist, G. Y., Sohur, U. S. & Macklis, J. D. Lmo4 and Clim1 progressively delineate cortical projection neuron subtypes during development. Cereb. Cortex 19, i62–i69 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Magrinelli, E. et al. Heterogeneous fates of simultaneously-born neurons in the cortical ventricular zone. Sci. Rep. 12, 6022 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Krontira, A. C. et al. Human cortical neurogenesis is altered via glucocorticoid-mediated regulation of ZBTB16 expression. Neuron 112, 1426–1443 (2024).

  • Su, Z. et al. Dlx1/2-dependent expression of Meis2 promotes neuronal fate determination in the mammalian striatum. Development https://doi.org/10.1242/dev.200035 (2022).

  • Dupacova, N., Antosova, B., Paces, J. & Kozmik, Z. Meis homeobox genes control progenitor competence in the retina. Proc. Natl Acad. Sci. USA 118, e2013136118 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Piper, M. et al. NFIA controls telencephalic progenitor cell differentiation through repression of the Notch effector Hes1. J. Neurosci. 30, 9127–9139 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • das Neves, L. et al. Disruption of the murine nuclear factor I-A gene (Nfia) results in perinatal lethality, hydrocephalus, and agenesis of the corpus callosum. Proc. Natl Acad. Sci. USA 96, 11946–11951 (1999).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kamimoto, K. et al. Dissecting cell identity via network inference and in silico gene perturbation. Nature 614, 742–751 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Santinha, A. J. et al. Transcriptional linkage analysis with in vivo AAV-Perturb-seq. Nature 622, 367–375 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gu, Z. et al. Control of species-dependent cortico-motoneuronal connections underlying manual dexterity. Science 357, 400–404 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • López-Bendito, G. et al. Robo1 and Robo2 cooperate to control the guidance of major axonal tracts in the mammalian forebrain. J. Neurosci. 27, 3395–3407 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ugolini, G. & Kuypers, H. G. J. M. Collaterals of corticospinal and pyramidal fibres to the pontine grey demonstrated by a new application of the fluorescent fibre labelling technique. Brain Res. 365, 211–227 (1986).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Perry, B. A. L. & Mitchell, A. S. Considering the evidence for anterior and laterodorsal thalamic nuclei as higher order relays to cortex. Front. Mol. Neurosci. 12, 167 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Van Horn, S. C. & Sherman, S. M. Differences in projection patterns between large and small corticothalamic terminals. J. Comp. Neurol. 475, 406–415 (2004).

    Article 
    PubMed 

    Google Scholar
     

  • Spead, O. & Poulain, F. E. Trans-axonal signaling in neural circuit wiring. Int. J. Mol. Sci. https://doi.org/10.3390/ijms21145170 (2020).

  • Itoh, Y., Sahni, V., Shnider, S. J., McKee, H. & Macklis, J. D. Inter-axonal molecular crosstalk via Lumican proteoglycan sculpts murine cervical corticospinal innervation by distinct subpopulations. Cell Rep. 42, 112182 (2023).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stanfield, B. B. & O’Leary, D. D. The transient corticospinal projection from the occipital cortex during the postnatal development of the rat. J. Comp. Neurol. 238, 236–248 (1985).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Holt, C. E., Martin, K. C. & Schuman, E. M. Local translation in neurons: visualization and function. Nat. Struct. Mol. Biol. 26, 557–566 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Poulopoulos, A. et al. Subcellular transcriptomes and proteomes of developing axon projections in the cerebral cortex. Nature 565, 356–360 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, Y. et al. Ryk-mediated Wnt repulsion regulates posterior-directed growth of corticospinal tract. Nat. Neurosci. 8, 1151–1159 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Sahni, V., Itoh, Y., Shnider, S. J. & Macklis, J. D. Crim1 and Kelch-like 14 exert complementary dual-directional developmental control over segmentally specific corticospinal axon projection targeting. Cell Rep. https://doi.org/10.1016/j.celrep.2021.109842 (2021).

  • Sahni, V. et al. Corticospinal neuron subpopulation-specific developmental genes prospectively indicate mature segmentally specific axon projection targeting. Cell Rep. 37, 109843 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Riccomagno, M. M. & Kolodkin, A. L. Sculpting neural circuits by axon and dendrite pruning. Annu. Rev. Cell Dev. Biol. 31, 779–805 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benison, A. M., Rector, D. M. & Barth, D. S. Hemispheric mapping of secondary somatosensory cortex in the rat. J. Neurophysiol. 97, 200–207 (2007).

  • Jacomy, M., Venturini, T., Heymann, S. & Bastian, M. ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software. PLoS ONE 9, e98679 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Platt, R. J. et al. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell 159, 440–455 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chung, K. & Deisseroth, K. CLARITY for mapping the nervous system. Nat. Methods 10, 508–513 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Voigt, F. F. et al. The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nat. Methods 16, 1105–1108 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Goubran, M. et al. Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Nat. Commun. 10, 5504 (2019).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Morgens, D. W. et al. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat. Commun. 8, 15178 (2017).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bareyre, F. M., Kerschensteiner, M., Misgeld, T. & Sanes, J. R. Transgenic labeling of the corticospinal tract for monitoring axonal responses to spinal cord injury. Nat. Med. 11, 1355–1360 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Klingler, E. et al. Temporal controls over inter-areal cortical projection neuron fate diversity. Nature 599, 453–457 (2021).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Gu, Z., Eils, R. & Schlesner, M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics 32, 2847–2849 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ero, C., Gewaltig, M. O., Keller, D. & Markram, H. A cell atlas for the mouse brain. Front. Neuroinform. 12, 84 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • McGinnis, C. S., Murrow, L. M. & Gartner, Z. J. DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors. Cell Syst. 8, 329–337 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Telley, L. et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science 364, eaav2522 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Prados, J. Bundle Methods for Regularized Risk Minimization Package. R package version 4.4 (2018).

  • Teo, C. H., Vishwanathan, S. V. N., Smola, A. & Le, Q. V. Bundle methods for regularized risk minimization. J. Mach. Learn. Res. 11, 311–365 (2010).

    MathSciNet 

    Google Scholar
     

  • Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoffman, G. E. & Schadt, E. E. variancePartition: interpreting drivers of variation in complex gene expression studies. BMC Bioinform. 17, 483 (2016).

    Article 

    Google Scholar
     

  • Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16, 278 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, T. et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb.) 2, 100141 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • Hill, A. J. et al. On the design of CRISPR-based single-cell molecular screens. Nat. Methods 15, 271–274 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Robinson, M. D., McCarthy, D. J. & Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139–140 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Yao, Z. et al. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex. Nature 598, 103–110 (2021).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, L. et al. BRICseq bridges brain-wide interregional connectivity to neural activity and gene expression in single animals. Cell 182, 177–188 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bankhead, P. et al. QuPath: open source software for digital pathology image analysis. Sci. Rep. 7, 16878 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cribari-Neto, F. & Zeileis, A. Beta regression in R. J. Stat. Softw. 34, 1–24 (2010).

    Article 

    Google Scholar
     

  • Hothorn, T., Bretz, F. & Westfall, P. Simultaneous inference in general parametric models. Biom. J. 50, 346–363 (2008).

    Article 
    MathSciNet 
    PubMed 

    Google Scholar
     

  • RELATED ARTICLES

    Most Popular

    Recent Comments