Finlay, B. L. & Darlington, R. B. Linked regularities in the development and evolution of mammalian brains. Science 268, 1578–1584 (1995).
Barton, R. A. & Harvey, P. H. Mosaic evolution of brain structure in mammals. Nature 405, 1055–1058 (2000).
Krubitzer, L. & Kaas, J. The evolution of the neocortex in mammals: how is phenotypic diversity generated? Curr. Opin. Neurobiol. 15, 444–453 (2005).
Passingham, R. E. & Wise, S. P. The Neurobiology of the Prefrontal Cortex: Anatomy, Evolution, and the Origin of Insight (Oxford Univ. Press, 2015).
Elston, G. N. et al. Specializations of the granular prefrontal cortex of primates: implications for cognitive processing. Anat. Rec. A Discov. Mol. Cell. Evol. Biol. 288, 26–35 (2006).
Semendeferi, K. et al. Spatial organization of neurons in the frontal pole sets humans apart from great apes. Cereb. Cortex 21, 1485–1497 (2011).
Kwan, K. Y. et al. Species-dependent posttranscriptional regulation of NOS1 by FMRP in the developing cerebral cortex. Cell 149, 899–911 (2012).
Gabi, M. et al. No relative expansion of the number of prefrontal neurons in primate and human evolution. Proc. Natl Acad. Sci. USA 113, 9617–9622 (2016).
Caceres, M. et al. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl Acad. Sci. USA 100, 13030–13035 (2003).
Khaitovich, P. et al. Regional patterns of gene expression in human and chimpanzee brains. Genome Res. 14, 1462–1473 (2004).
Uddin, M. et al. Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc. Natl Acad. Sci. USA 101, 2957–2962 (2004).
Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012).
Bauernfeind, A. L. et al. Evolutionary divergence of gene and protein expression in the brains of humans and chimpanzees. Genome Biol. Evol. 7, 2276–2288 (2015).
Sousa, A. M. M. et al. Molecular and cellular reorganization of neural circuits in the human lineage. Science 358, 1027–1032 (2017).
Zhu, Y. et al. Spatiotemporal transcriptomic divergence across human and macaque brain development. Science 362, eaat8077 (2018).
Pollen, A. A. et al. Establishing cerebral organoids as models of human-specific brain evolution. Cell 176, 743–756 (2019).
Kanton, S. et al. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature 574, 418–422 (2019).
Johnson, M. B. et al. Functional and evolutionary insights into human brain development through global transcriptome analysis. Neuron 62, 494–509 (2009).
Pletikos, M. et al. Temporal specification and bilaterality of human neocortical topographic gene expression. Neuron 81, 321–332 (2014).
Li, M. et al. Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362, eaat7615 (2018).
Urade, Y. et al. Precerebellin is a cerebellum-specific protein with similarity to the globular domain of complement C1q B chain. Proc. Natl Acad. Sci. USA 88, 1069–1073 (1991).
Hirai, H. et al. Cbln1 is essential for synaptic integrity and plasticity in the cerebellum. Nat. Neurosci. 8, 1534–1541 (2005).
Uemura, T. et al. Trans-synaptic interaction of GluRδ2 and neurexin through Cbln1 mediates synapse formation in the cerebellum. Cell 141, 1068–1079 (2010).
Matsuda, K. et al. Cbln1 is a ligand for an orphan glutamate receptor δ2, a bidirectional synapse organizer. Science 328, 363–368 (2010).
Yasumura, M. et al. Glutamate receptor delta1 induces preferentially inhibitory presynaptic differentiation of cortical neurons by interacting with neurexins through cerebellin precursor protein subtypes. J. Neurochem. 121, 705–716 (2012).
Wei, P. et al. The Cbln family of proteins interact with multiple signaling pathways. J. Neurochem. 121, 717–729 (2012).
Seigneur, E. & Sudhof, T. C. Genetic ablation of all cerebellins reveals synapse organizer functions in multiple regions throughout the brain. J. Neurosci. 38, 4774–4790 (2018).
Elston, G. N. Pyramidal cells of the frontal lobe: all the more spinous to think with. J. Neurosci. 20, RC95 (2000).
Jacobs, B. et al. Regional dendritic and spine variation in human cerebral cortex: a quantitative golgi study. Cereb. Cortex 11, 558–571 (2001).
Bianchi, S. et al. Synaptogenesis and development of pyramidal neuron dendritic morphology in the chimpanzee neocortex resembles humans. Proc. Natl Acad. Sci. USA 110, 10395–10401 (2013).
Molliver, M. E. et al. The development of synapses in cerebral cortex of the human fetus. Brain Res. 50, 403–407 (1973).
Voigt, T. et al. Synaptophysin immunohistochemistry reveals inside-out pattern of early synaptogenesis in ferret cerebral cortex. J. Comp. Neurol. 330, 48–64 (1993).
Rakic, P. et al. Concurrent overproduction of synapses in diverse regions of the primate cerebral cortex. Science 232, 232–235 (1986).
Shibata, M. et al. Regulation of prefrontal patterning and connectivity by retinoic acid. Nature https://doi.org/10.1038/s41586-021-03953-x (2021).
Kang, H. J. et al. Spatiotemporal transcriptome of the human brain. Nature 478, 483–489 (2011).
Lambert, N. et al. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS ONE 6, e17753 (2011).
Miller, J. A. et al. Transcriptional landscape of the prenatal human brain. Nature 508, 199–206 (2014).
ENCODE Project Consortium et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Chiang, M. Y. et al. An essential role for retinoid receptors RARβ and RXRγ in long-term potentiation and depression. Neuron 21, 1353–1361 (1998).
Krezel, W. et al. Impaired locomotion and dopamine signaling in retinoid receptor mutant mice. Science 279, 863–867 (1998).
Kwan, K. Y. et al. SOX5 postmitotically regulates migration, postmigratory differentiation, and projections of subplate and deep-layer neocortical neurons. Proc. Natl Acad. Sci. USA 105, 16021–16026 (2008).
Shim, S. et al. Cis-regulatory control of corticospinal system development and evolution. Nature 486, 74–79 (2012).
Clarke, R. A. & Eapen, V. Balance within the neurexin trans-synaptic connexus stabilizes behavioral control. Front. Hum. Neurosci. 8, 52 (2014).
State, M. W. & Sestan, N. The emerging biology of autism spectrum disorders. Science 337, 1301–1303 (2012).
Sudhof, T. C. Synaptic neurexin complexes: a molecular code for the logic of neural circuits. Cell 171, 745–769 (2017).
Willsey, A. J. et al. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 997–1007 (2013).
Gulsuner, S. et al. Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell 154, 518–529 (2013).
Lewis, D. A. & Mirnics, K. Transcriptome alterations in schizophrenia: disturbing the functional architecture of the dorsolateral prefrontal cortex. Prog. Brain Res. 158, 141–152 (2006).
Dy, P., Han, Y. & Lefebvre, V. Generation of mice harboring a Sox5 conditional null allele. Genesis 46, 294–299 (2008).
Mathelier, A. et al. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 44, D110–D115 (2016).
Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).
Shim, S. et al. Regulation of EphA8 gene expression by TALE homeobox transcription factors during development of the mesencephalon. Mol. Cell. Biol. 27, 1614–1630 (2007).
Wang, H. et al. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153, 910–918 (2013).
Liu, P. et al. A highly efficient recombineering-based method for generating conditional knockout mutations. Genome Res. 13, 476–484 (2003).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Wilkinson, D. G. & Nieto, M. A. Detection of messenger RNA by in situ hybridization to tissue sections and whole mounts. Methods Enzymol. 225, 361–373 (1993).
Hunt, C. A. et al. PSD-95 is associated with the postsynaptic density and not with the presynaptic membrane at forebrain synapses. J. Neurosci. 16, 1380–1388 (1996).
Essrich, C. et al. Postsynaptic clustering of major GABAA receptor subtypes requires the γ2 subunit and gephyrin. Nat. Neurosci. 1, 563–571 (1998).
Ippolito, D. M. & Eroglu, C. Quantifying synapses: an immunocytochemistry-based assay to quantify synapse number. J. Vis. Exp. 45, 2270 (2010).
Fiala, J. C. Reconstruct: a free editor for serial section microscopy. J. Microsc. 218, 52–61 (2005).
Risher, W. C. et al. Rapid Golgi analysis method for efficient and unbiased classification of dendritic spines. PLoS ONE 9, e107591 (2014).
Kaur, N. et al. Neural stem cells direct axon guidance via their radial fiber scaffold. Neuron 107, 1197–1211 (2020).
Meijering, E. et al. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 58, 167–176 (2004).
Hinrichs, A. S. et al. The UCSC Genome Browser database: update 2006. Nucleic Acids Res. 34, D590–D598 (2006).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24-26 (2011).
Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).
Rosenbloom, K. R. et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 41, D56–D63 (2013).
Shibata, M. et al. MicroRNA-9 regulates neurogenesis in mouse telencephalon by targeting multiple transcription factors. J. Neurosci. 31, 3407–3422 (2011).
Morozov, Y. M., Ayoub, A. E. & Rakic, P. Translocation of synaptically connected interneurons across the dentate gyrus of the early postnatal rat hippocampus. J. Neurosci. 26, 5017–5027 (2006).
Morozov, Y. M., Mackie, K. & Rakic, P. Cannabinoid type 1 receptor is undetectable in rodent and primate cerebral neural stem cells but participates in radial neuronal migration. Int. J. Mol. Sci. 21, 1–19 (2020).
Thompson, C. L. et al. A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. Neuron 83, 309–323 (2014).