Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Vermunt, Marit W.; Tan, Sander; Castelijns, Bas; Geeven, Geert; Reinink, Peter; Bruijn, Ewart de; Kondova, Ivanela; Persengiev, Stephan P.; Bank, Netherlands Brain; Bontrop, Ronald E.; Cuppen, Edwin; Laat, Wouter de; Creyghton, Menno P.

doi:10.1038/nn.4229

Cited by 124 publications

(177 citation statements)

References 64 publications

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“…To investigate regulatory mechanisms associated with gene expression level differences among species, we further reanalyzed published H3K27ac chromatin immunoprecipitation sequencing data (ChIP-seq) collected in eight brain regions of three humans, two chimpanzees, and three rhesus monkeys (Vermunt et al 2016). Six of the eight regions overlapped with brain regions used for the RNA-seq measurements (Fig.…”

Section: Data Descriptionmentioning

confidence: 99%

“…Primary CREs were directly obtained from published data (Vermunt et al 2016) (Gene Expression Omnibus accession no. GSE67978).…”

Section: Cres' H3k27ac Coverage Quantificationmentioning

confidence: 99%

“…Analyses of epigenetic modifications identified promoters and enhancers potentially involved in human corticogenesis (Reilly et al 2015), as well as active human-specific cis-regulatory elements in adult brains (Vermunt et al 2016).…”

mentioning

confidence: 99%

“…We further utilized published epigenome data (Vermunt et al 2016) collected in eight brain regions of humans, chimpanzees, and macaques to assess and compare putative regulatory mechanisms that drive gene expression differences among species.…”

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confidence: 99%

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Human-specific features of spatial gene expression and regulation in eight brain regions

Efimova

et al. 2018

Genome Res.

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Molecular maps of the human brain alone do not inform us of the features unique to humans. Yet, the identification of these features is important for understanding both the evolution and nature of human cognition. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, a gibbon, and macaques. An analysis of spatial transcriptome trajectories across eight brain regions in four primate species revealed 1851 genes showing human-specific transcriptome differences in one or multiple brain regions, in contrast to 240 chimpanzee-specific differences. More than half of these human-specific differences represented elevated expression of genes enriched in neuronal and astrocytic markers in the human hippocampus, whereas the rest were enriched in microglial markers and displayed human-specific expression in several frontal cortical regions and the cerebellum. An analysis of the predicted regulatory interactions driving these differences revealed the role of transcription factors in species-specific transcriptome changes, and epigenetic modifications were linked to spatial expression differences conserved across species.

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Section: Data Descriptionmentioning

confidence: 99%

“…Primary CREs were directly obtained from published data (Vermunt et al 2016) (Gene Expression Omnibus accession no. GSE67978).…”

Section: Cres' H3k27ac Coverage Quantificationmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Human-specific features of spatial gene expression and regulation in eight brain regions

Efimova

et al. 2018

Genome Res.

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“…To explore cis-regulatory elements Vermunt et al analysed H3K27ac ChIP-seq within eight anatomical regions of the brain in human, chimpanzee and rhesus macaque [76]. They identified that the location of the majority of peaks (~93%) had been conserved since the last common ancestor (LCA) of these three species ~25 million years ago (MYA).…”

Section: Sequence Redundancy In Enhancersmentioning

confidence: 99%

Insights in human epigenomic dynamics through comparative primate analysis

Bell

2016

Genomics

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Epigenomic analysis gives a molecular insight into cell-specific genomic activity. It provides a detailed functional plan to dissect an organism, tissue by tissue.Therefore comparative epigenomics may increase understanding of human-acquired traits, by revealing regulatory changes in systems such as the neurological, musculoskeletal, and immunological.Enhancer loci evolve fast by hijacking elements from other tissues or rewiring and amplifying existing units for human-specific function. Promoters by contrast often require a CpG dense genetic infrastructure. Specific interplay occurs between the two, but also a shared modality of function, with coordination from global chromatin-modifying enzymes. Changes in specific transcription factor binding sites also facilitate the local epigenetic state. In the case of CTCF, these may further influence 3-dimensional structure and interaction.How these mechanistic units are modulated between tissue and species enables more comprehensive understanding of human processes and pathology.With this, precise therapeutic targeting of these epigenetic modifications may become possible.

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Tissue Regeneration Enhancer Elements: A Way to Unlock Endogenous Healing Power

Yang

Kang

2018

Developmental Dynamics

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Regenerative capacity is widespread throughout almost all animal phyla. However, the distribution pattern remains incompletely understood. Various examples show that very closely related species display different regenerative capacities. Why and how have diverse regenerative capacities evolved across species? One prevailing thought in the field of regeneration is that most regeneration‐associated factors are evolutionarily conserved, suggesting the existence of an innate tissue regeneration ability in all species. However, its regulation is differentially controlled in distinct species, resulting in heterogeneous regenerative capabilities. In this review, we discuss regeneration‐associated enhancers, the key cis‐regulatory elements controlling gene expression, their underlying molecular mechanisms, and their influence on regenerative capacity. Understanding the regulatory mechanisms of regeneration enhancers can provide fundamental insights into tissue regeneration and further help us develop therapeutic strategies to unlock latent healing powers in humans. Developmental Dynamics 248:34–42, 2019. © 2018 Wiley Periodicals, Inc.

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Epigenomic annotation of gene regulatory alterations during evolution of the primate brain

Cited by 124 publications

References 64 publications

Human-specific features of spatial gene expression and regulation in eight brain regions

Human-specific features of spatial gene expression and regulation in eight brain regions

Insights in human epigenomic dynamics through comparative primate analysis

Tissue Regeneration Enhancer Elements: A Way to Unlock Endogenous Healing Power

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