Intra- and Interspecific Variation in Primate Gene Expression Patterns

Enard, Wolfgang; Khaitovich, Philipp; Klose, Joachim; Zöllner, Sebastian; Heissig, Florian; Giavalisco, Patrick; Nieselt, Kay; Muchmore, Elaine A.; Varki, Ajit; Ravid, Rivka; Doxiadis, Gaby M.; Bontrop, Ronald E.; Pääbo, Svante

doi:10.1126/science.1068996

Cited by 779 publications

(661 citation statements)

References 10 publications

Supporting

Mentioning

611

Contrasting

Unclassified

Order By: Relevance

“…An alternate, albeit related, explanation would be that regions with low genetic variance have greater functional constraints on their determinants of cortical thickness, such that genetic mutations influencing these regions will typically be eliminated quickly from the population through purifying selection. Comparative genomic experiments have shown that a subset of neurally-expressed genes have evolved more rapidly in humans than in other primates [Chimpanzee Sequencing and Analysis Consortium, 2005;Dorus et al, 2004;Khaitovich et al, 2005]; both gene expression changes and protein sequence modification have accelerated in humans relative to nonhuman primates [Caceres et al, 2003;Enard et al, 2002;Gu and Gu, 2003;Hsieh et al, 2003;Uddin et al, 2004]. The findings of increased genetic variance in evolutionarily recent structures may represent a remnant of these rapid neurogenetic changes that accompanied our divergence from other primates.…”

Section: Discussionmentioning

confidence: 99%

Differences in genetic and environmental influences on the human cerebral cortex associated with development during childhood and adolescence

Lenroot

Schmitt

Ordaz

et al. 2007

Human Brain Mapping

308

260

View full text Add to dashboard Cite

In this report, we present the first regional quantitative analysis of age-related differences in the heritability of cortical thickness using anatomic MRI with a large pediatric sample of twins, twin siblings, and singletons (n 5 600, mean age 11.1 years, range 5-19). Regions of primary sensory and motor cortex, which develop earlier, both phylogenetically and ontologically, show relatively greater genetic effects earlier in childhood. Later developing regions within the dorsal prefrontal cortex and temporal lobes conversely show increasingly prominent genetic effects with maturation. The observation that regions associated with complex cognitive processes such as language, tool use, and executive function are more heritable in adolescents than children is consistent with previous studies showing that IQ becomes increasingly heritable with maturity(Plomin et al. [1997]: Psychol Sci 8:442-447). These results suggest that both the specific cortical region and the age of the population should be taken into account when using cortical thickness as an intermediate phenotype to link genes, environment, and behavior. Hum Brain Mapp 30: [163][164][165][166][167][168][169][170][171][172][173][174] 2009. V V C 2007 Wiley-Liss, Inc.

show abstract

Section: Discussionmentioning

confidence: 99%

Differences in genetic and environmental influences on the human cerebral cortex associated with development during childhood and adolescence

Lenroot

Schmitt

Ordaz

et al. 2007

Human Brain Mapping

308

260

View full text Add to dashboard Cite

show abstract

“…By now it is wellrecognized that cis-regulatory change is a key process in evolution for the origin of distinct phenotypes in eukaryotes (Enard et al, 2002). In bacteria, the importance of gene-expression as a governing factor for evolution, habitat adaptation and diversification is recognized as well (c.f.…”

Section: Introductionmentioning

confidence: 99%

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

et al. 2014

View full text Add to dashboard Cite

Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.

show abstract

“…The aim has been to characterize general trends in the evolution of gene expression rather than to identify specific genes of interest. To date, conclusions about the selection pressures acting on gene expression have been conflicting 2,3,6,[11][12][13] .These studies have all relied on data collected from arrays using gene probes that were designed on the basis of human sequences only. However, sequence mismatches affect hybridization intensity and can therefore bias estimates of gene expression differences between species 14 .…”

mentioning

confidence: 99%

Expression profiling in primates reveals a rapid evolution of human transcription factors

Gilad

Oshlack

Smyth

et al. 2006

Nature

285

253

View full text Add to dashboard Cite

Although it has been hypothesized for thirty years that many human adaptations are likely to be due to changes in gene regulation 1 , almost nothing is known about the modes of natural selection acting on regulation in primates. Here we identify a set of genes for which expression is evolving under natural selection. We use a new multi-species complementary DNA array to compare steady-state messenger RNA levels in liver tissues within and between humans, chimpanzees, orangutans and rhesus macaques. Using estimates from a linear mixed model, we identify a set of genes for which expression levels have remained constant across the entire phylogeny (,70 million years), and are therefore likely to be under stabilizing selection. Among the top candidates are five genes with expression levels that have previously been shown to be altered in liver carcinoma. We also find a number of genes with similar expression levels among non-human primates but significantly elevated or reduced expression in the human lineage, features that point to the action of directional selection. Among the gene set with a human-specific increase in expression, there is an excess of transcription factors; the same is not true for genes with increased expression in chimpanzee.A number of recent studies have used DNA microarrays to compare patterns of gene expression between closely related species 2-9 . Within primates, the focus has been primarily on human-chimpanzee comparisons, estimating gene expression profiles for a number of tissues, including liver, brain and heart 2,6,7,10 . The aim has been to characterize general trends in the evolution of gene expression rather than to identify specific genes of interest. To date, conclusions about the selection pressures acting on gene expression have been conflicting 2,3,6,[11][12][13] .These studies have all relied on data collected from arrays using gene probes that were designed on the basis of human sequences only. However, sequence mismatches affect hybridization intensity and can therefore bias estimates of gene expression differences between species 14 . This limitation of single-species arrays is especially problematic when the goal is to study how expression changes over evolutionary time. To make comparisons between more distantly related primate species, we generated a multi-species cDNA array that allows comparison of gene expression between species without the confounding effects of sequence divergence 14 . This cDNA array contains probes for 1,056 orthologous genes from four species (see Supplementary Methods) 14 .We used this array to compare gene expression profiles in the livers of humans, chimpanzees (Pan troglodytes), orangutans (Pongo pygmaeus) and rhesus macaques (Macaca mulatta), the phylogeny of which represents approximately 70 million years (Myr) of evolution. By assigning expression changes in the liver to particular lineages, we were able to identify the first set of genes for which regulation seems to be under lineage-specific selection pressures. In order to measure gene...

show abstract

Intra- and Interspecific Variation in Primate Gene Expression Patterns

Cited by 779 publications

References 10 publications

Differences in genetic and environmental influences on the human cerebral cortex associated with development during childhood and adolescence

Differences in genetic and environmental influences on the human cerebral cortex associated with development during childhood and adolescence

Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification

Expression profiling in primates reveals a rapid evolution of human transcription factors

Contact Info

Product

Resources

About