Functional and Evolutionary Insights Into Human Brain Development Through Global Transcriptome Analysis

By Matthew B. Johnson, Y. Kawasawa, Christopher E. Mason, Ž. Krsnik, G. Coppola, D. Bogdanović, Daniel H. Geschwind, Shrikant M. Mane, Matthew W. State, N. Šestan. Neuron, 2009

606 citations recorded by the source corpus.

SUMMARY Our understanding of the evolution, formation, and pathological disruption of human brain circuits is impeded by a lack of comprehensive data on the developing brain transcriptome. Thus, we have undertaken whole-genome, exon-level expression analysis of thirteen regions from left and right sides of the mid-fetal human brain, finding 76% of genes to be expressed, and 44% of these to be differentially regulated. These data reveal a large number of specific gene expression and alternative splicing patterns, as well as co-expression networks, associated with distinct regions and neurodevelopmental processes. Of particular relevance to cognitive specializations, we have characterized the transcriptional landscapes of prefrontal cortex and perisylvian speech and language areas, which exhibit a population-level global expression symmetry. Finally, we show that differentially expressed genes are more frequently associated with human-specific evolution of putative cis-regulatory elements. Altogether, these data provide a wealth of novel biological insights into the complex transcriptional and molecular underpinnings of human brain development and evolution.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c7d7692570dfdc4e88ff5903a30578c6f4252d7d

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Citations in the corpus

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex (2014, background): “Multiple splicing isoforms of Ncam1 have been reported previously (Owens et al., 1987; Krushel et al., 1998).”
Development and Evolution of the Human Neocortex (2011, positive): “Global transcriptome analysis of the developing human brain has successfully identified and categorized expression patterns, alternative splicing, and differential regulation of genes in major brain regions (Johnson et al., 2009).”
Evolution of the neocortex: Perspective from developmental biology (2009, neutral): “A recent study examined 13 brain regions from both cerebral hemispheres of the fetal human brai”
Integrative functional genomic analysis of human brain development and neuropsychiatric risks (2018, background): “For example, although we observed differences in the expression of genes associated with these processes (10) across the NCX (fig.”
A practical guide to linking brain-wide gene expression and neuroimaging data (2018, background): “The further advancement of developmental atlases of gene expression (Johnson et al., 2009; Colantuoni et al., 2011; Kang et al., 2011; Fertuzinhos et al., 2014; Bakken et al., 2016) will help to shed light on these dynamic processes.”
Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology (2011, neutral): “These data suggest that typical regional differences, many of which are observed during fetal development 10 , are attenuated in frontal and temporal lobe in autism brain, pointing to abnormal developmental patterning as a potential pathophsyiological driver in ASD.”
Large-Scale Gradients in Human Cortical Organization. (2018, neutral): “While differential gene expression is most pronounced during prenatal development [39] and between subcortical structures [40], substantial spatial variation has also been described within the adult human cerebral cortex [40–43].”
The Cellular and Molecular Landscapes of the Developing Human Central Nervous System (2016, positive): “…products with species-biased expression pattern in the developing human neocortex (Charrier et al., 2012; Florio et al., 2015; Han et al., 2013; Johnson et al., 2009, 2015; Kang et al., 2011; Kwan et al., 2012; Lui et al., 2014; Miller et al., 2014; Pollard et al., 2006; Pollen et al., 2014).”
Spatiotemporal transcriptome of the human brain (2011, background): “Previous transcriptome studies of the developing human brain have used relatively small numbers of samples and predominantly focused on only a few regions or developmental time point”
Cell type– and brain region–resolved mouse brain proteome (2015, neutral): “Q4 7,898 2 (174) 4 (21) 6 (8) 11 (3) 368 117 28 Q3 Q2 Q1 Microglia total”
Temporal dynamics and genetic control of transcription in the human prefrontal cortex (2011, background): “Others have focused on the transcriptome in human fetal brain tissu”