Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

Babbitt, Courtney C.; Fédrigo, Olivier; Pfefferle, Adam D.; Boyle, Alan P.; Horvath, Julie E.; Furey, Terrence S.; Wray, Gregory A.

doi:10.1093/gbe/evq002

Cited by 96 publications

(102 citation statements)

References 80 publications

(168 reference statements)

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“…Consistent with this, previous studies have identified a large number of genes differentially expressed among primates [7][8][9][10][11][12][13][14][15][16], and in a few cases, have also found that the inter-species changes in gene expression level might explain differences in complex phenotypes between primates [17][18][19][20][21][22]. However, we still know little about the underling regulatory mechanisms leading to the differences in gene expression levels across species.…”

Section: Introductionsupporting

confidence: 54%

Epigenetic modifications are associated with inter-species gene expression variation in primates

et al. 2014

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Section: Introductionsupporting

confidence: 54%

Epigenetic modifications are associated with inter-species gene expression variation in primates

et al. 2014

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“…(b) Evidence for changes in energy transport In brain tissues, there is a consistent pattern of changes in expression of genes critical to aerobic energy metabolism [67,69,71,91]. This includes categories such as oxidative phosphorylation, electron transport and other nuclearencoded genes that function in the mitochondria.…”

Section: Evidence From the Evolution Of Gene Expression Between Humanmentioning

confidence: 99%

Genomic signatures of diet-related shifts during human origins

et al. 2010

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There are numerous anthropological analyses concerning the importance of diet during human evolution. Diet is thought to have had a profound influence on the human phenotype, and dietary differences have been hypothesized to contribute to the dramatic morphological changes seen in modern humans as compared with non-human primates. Here, we attempt to integrate the results of new genomic studies within this well-developed anthropological context. We then review the current evidence for adaptation related to diet, both at the level of sequence changes and gene expression. Finally, we propose some ways in which new technologies can help identify specific genomic adaptations that have resulted in metabolic and morphological differences between humans and non-human primates.

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“…corticocortical connectivity | human transcriptome | association cortex | supragranular | brain evolution P atterns of gene expression in the cerebral cortex are generally conserved across species, reflecting strong constraints in the development and evolution of cortical architecture (1)(2)(3)(4)(5)(6). Previous work examining transcriptional variation in nonhuman primates and rodents indicate that molecular similarities between cortical regions in the adult brain are best explained by spatial proximity (7,8).…”

mentioning

confidence: 99%

Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

Krienen

Yeo

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

214

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The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.corticocortical connectivity | human transcriptome | association cortex | supragranular | brain evolution P atterns of gene expression in the cerebral cortex are generally conserved across species, reflecting strong constraints in the development and evolution of cortical architecture (1-6). Previous work examining transcriptional variation in nonhuman primates and rodents indicate that molecular similarities between cortical regions in the adult brain are best explained by spatial proximity (7, 8). Molecular variation often takes the form of graded expression along a principal axis, in many cases appearing as rostrocaudal gradients across the cortex (8). The strong tendency for transcriptional variation to follow spatial proximity in the adult cortex likely reflects both functional gradients, as well as their developmental origins in terms of physical and temporal adjacency during neurogenesis of cells destined for neighboring locations in the cortex (at least for cells derived from the ventricular proliferative pool) (7).Spatial proximity likely captures the major features governing how molecular profiles vary across the cortex in all species, including humans. However, the expansion of the cerebral cortex in primates...

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Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

Cited by 96 publications

References 80 publications

Epigenetic modifications are associated with inter-species gene expression variation in primates

Epigenetic modifications are associated with inter-species gene expression variation in primates

Genomic signatures of diet-related shifts during human origins

Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

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