Molecular features driving cellular complexity of human brain evolution – Nature.com

Posted: July 26, 2023 at 1:29 am

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107116 (1975).

Article ADS CAS PubMed Google Scholar

Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601617 (2012).

Article CAS PubMed PubMed Central Google Scholar

Liu, X. et al. Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques. Genome Res. 22, 611622 (2012).

Article CAS PubMed PubMed Central Google Scholar

Sousa, A. M. M. et al. Molecular and cellular reorganization of neural circuits in the human lineage. Science 358, 10271032 (2017).

Article ADS CAS PubMed PubMed Central Google Scholar

Zhu, Y. et al. Spatiotemporal transcriptomic divergence across human and macaque brain development. Science https://doi.org/10.1126/science.aat8077 (2018).

Hodge, R. D. et al. Conserved cell types with divergent features in human versus mouse cortex. Nature 573, 6168 (2019).

Article ADS CAS PubMed PubMed Central Google Scholar

Bakken, T. E. et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598, 111119 (2021).

Article ADS CAS PubMed PubMed Central Google Scholar

Miller, D. J. et al. Prolonged myelination in human neocortical evolution. Proc. Natl Acad. Sci. USA 109, 1648016485 (2012).

Article ADS CAS PubMed PubMed Central Google Scholar

Jakel, S. et al. Altered human oligodendrocyte heterogeneity in multiple sclerosis. Nature 566, 543547 (2019).

Article ADS CAS PubMed PubMed Central Google Scholar

Jeong, H. et al. Evolution of DNA methylation in the human brain. Nat. Commun. 12, 2021 (2021).

Article ADS CAS PubMed PubMed Central Google Scholar

Khrameeva, E. et al. Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains. Genome Res. 30, 776789 (2020).

Article CAS PubMed PubMed Central Google Scholar

Kozlenkov, A. et al. Evolution of regulatory signatures in primate cortical neurons at cell-type resolution. Proc. Natl Acad. Sci. USA 117, 2842228432 (2020).

Article ADS CAS PubMed PubMed Central Google Scholar

Krienen, F. M. et al. Innovations present in the primate interneuron repertoire. Nature 586, 262269 (2020).

Article ADS CAS PubMed PubMed Central Google Scholar

Ma, S. et al. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science https://doi.org/10.1126/science.abo7257 (2022).

Mendizabal, I. et al. Comparative methylome analyses identify epigenetic regulatory loci of human brain evolution. Mol. Biol. Evol. 33, 29472959 (2016).

Article CAS PubMed PubMed Central Google Scholar

Li, W., Mai, X. & Liu, C. The default mode network and social understanding of others: what do brain connectivity studies tell us. Front. Hum. Neurosci. 8, 74 (2014).

Article CAS PubMed PubMed Central Google Scholar

Wang, D. et al. Altered functional connectivity of the cingulate subregions in schizophrenia. Transl. Psychiatry 5, e575 (2015).

Article CAS PubMed PubMed Central Google Scholar

Berto, S. et al. Accelerated evolution of oligodendrocytes in the human brain. Proc. Natl Acad. Sci. USA 116, 2433424342 (2019).

Article ADS CAS PubMed PubMed Central Google Scholar

Franjic, D. et al. Transcriptomic taxonomy and neurogenic trajectories of adult human, macaque, and pig hippocampal and entorhinal cells. Neuron 110, 452469 (2022).

Article CAS PubMed Google Scholar

Brown, T. L. & Verden, D. R. Cytoskeletal regulation of oligodendrocyte differentiation and myelination. J. Neurosci. 37, 77977799 (2017).

Article CAS PubMed PubMed Central Google Scholar

Caglayan, E., Liu, Y. & Konopka, G. Neuronal ambient RNA contamination causes misinterpreted and masked cell types in brain single-nuclei datasets. Neuron https://doi.org/10.1016/j.neuron.2022.09.010 (2022).

Lake, B. B. et al. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. Nat. Biotechnol. 36, 7080 (2018).

Article CAS PubMed Google Scholar

Velmeshev, D. et al. Single-cell genomics identifies cell type-specific molecular changes in autism. Science 364, 685689 (2019).

Article ADS CAS PubMed PubMed Central Google Scholar

Fumagalli, M. et al. The ubiquitin ligase Mdm2 controls oligodendrocyte maturation by intertwining mTOR with G protein-coupled receptor kinase 2 in the regulation of GPR17 receptor desensitization. Glia 63, 23272339 (2015).

Article PubMed Google Scholar

den Hoed, J., Devaraju, K. & Fisher, S. E. Molecular networks of the FOXP2 transcription factor in the brain. EMBO Rep. 22, e52803 (2021).

Article Google Scholar

Konopka, G. et al. Human-specific transcriptional regulation of CNS development genes by FOXP2. Nature 462, 213217 (2009).

Article ADS CAS PubMed PubMed Central Google Scholar

Doan, R. N. et al. Mutations in human accelerated regions disrupt cognition and social behavior. Cell 167, 341354 (2016).

Article CAS PubMed PubMed Central Google Scholar

Franchini, L. F. & Pollard, K. S. Human evolution: the non-coding revolution. BMC Biol. 15, 89 (2017).

Article PubMed PubMed Central Google Scholar

Capra, J. A., Erwin, G. D., McKinsey, G., Rubenstein, J. L. & Pollard, K. S. Many human accelerated regions are developmental enhancers. Philos. Trans. R. Soc. Lond. B 368, 20130025 (2013).

Article Google Scholar

Girskis, K. M. et al. Rewiring of human neurodevelopmental gene regulatory programs by human accelerated regions. Neuron https://doi.org/10.1016/j.neuron.2021.08.005 (2021).

Wagnon, J. L. et al. CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function. PLoS Genet. 8, e1003067 (2012).

Article CAS PubMed PubMed Central Google Scholar

Lundgaard, I. et al. Neuregulin and BDNF induce a switch to NMDA receptor-dependent myelination by oligodendrocytes. PLoS Biol. 11, e1001743 (2013).

Article PubMed PubMed Central Google Scholar

Prufer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 4349 (2014).

Article ADS PubMed Google Scholar

Arora, V. et al. Increased Grik4 gene dosage causes imbalanced circuit output and human disease-related behaviors. Cell Rep. 23, 38273838 (2018).

Article CAS PubMed Google Scholar

Kim, T. K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182187 (2010).

Article ADS CAS PubMed PubMed Central Google Scholar

Yap, E. L. & Greenberg, M. E. Activity-regulated transcription: bridging the gap between neural activity and behavior. Neuron 100, 330348 (2018).

Article CAS PubMed PubMed Central Google Scholar

Berto, S. et al. Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat. Neurosci. 24, 554564 (2021).

Article CAS PubMed PubMed Central Google Scholar

Ducker, G. S. & Rabinowitz, J. D. One-carbon metabolism in health and disease. Cell Metab. 25, 2742 (2017).

Article CAS PubMed Google Scholar

Yeung, M. S. et al. Dynamics of oligodendrocyte generation and myelination in the human brain. Cell 159, 766774 (2014).

Article CAS PubMed Google Scholar

Marques, S. et al. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 352, 13261329 (2016).

Article ADS CAS PubMed PubMed Central Google Scholar

Buchanan, J. et al. Oligodendrocyte precursor cells ingest axons in the mouse neocortex. Proc. Natl Acad. Sci. USA 119, e2202580119 (2022).

Article CAS PubMed PubMed Central Google Scholar

Jorstad, N. L. et al. Comparative transcriptomics reveals human-specific cortical features. Preprint at bioRxiv https://doi.org/10.1101/2022.09.19.508480 (2022).

Berg, M. et al. FastCAR: Fast Correction for Ambient RNA to facilitate differential gene expression analysis in single-cell RNA-sequencing datasets. Preprint at bioRxiv https://doi.org/10.1101/2022.07.19.500594 (2022).

McLean, C. Y. et al. Human-specific loss of regulatory DNA and the evolution of human-specific traits. Nature 471, 216219 (2011).

Article ADS CAS PubMed PubMed Central Google Scholar

Hickey, S. L., Berto, S. & Konopka, G. Chromatin decondensation by FOXP2 promotes human neuron maturation and expression of neurodevelopmental disease genes. Cell Rep. 27, 16991711 (2019).

Article CAS PubMed PubMed Central Google Scholar

Yang, C. C. et al. Discovering chromatin motifs using FAIRE sequencing and the human diploid genome. BMC Genomics 14, 310 (2013).

Article CAS PubMed PubMed Central Google Scholar

Ataman, B. et al. Evolution of osteocrin as an activity-regulated factor in the primate brain. Nature 539, 242247 (2016).

Article ADS PubMed PubMed Central Google Scholar

Pruunsild, P., Bengtson, C. P. & Bading, H. Networks of cultured iPSC-derived neurons reveal the human synaptic activity-regulated adaptive gene program. Cell Rep. 18, 122135 (2017).

Article CAS PubMed PubMed Central Google Scholar

Qiu, J. et al. Evidence for evolutionary divergence of activity-dependent gene expression in developing neurons. Elife https://doi.org/10.7554/eLife.20337 (2016).

Hrvatin, S. et al. Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex. Nat. Neurosci. 21, 120129 (2018).

Article CAS PubMed Google Scholar

Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).

Article ADS CAS PubMed PubMed Central Google Scholar

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 20782079 (2009).

Article PubMed PubMed Central Google Scholar

Zhao, H. et al. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics 30, 10061007 (2014).

Article PubMed Google Scholar

Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923930 (2014).

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Molecular features driving cellular complexity of human brain evolution - Nature.com

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