ArticlePLoS genetics2013
The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 38 citations in OpenAlex.
- MER57E3 transposable elements regulate gene expression in a human cell model of neural development.Genome biology · 2026Article
- Article
- Transposons contribute to the acquisition of cell type-specific cis-elements in the brain.Communications biology · 2023Article
- T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data.Mobile DNA · 2022Article
- Transcriptional network orchestrating regional patterning of cortical progenitors.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Review
- Neurobiological functions of transcriptional enhancers.Nature neuroscience · 2020Review
- Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1.Scientific reports · 2018Article
- Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences.Molecular biology and evolution · 2017Article
- CisMapper: predicting regulatory interactions from transcription factor ChIP-seq data.Nucleic acids research · 2017Article
- Searching for convergent pathways in autism spectrum disorders: insights from human brain transcriptome studies.Cellular and molecular life sciences : CMLS · 2016Review
- TBR1 regulates autism risk genes in the developing neocortex.Genome research · 2016Article
- Transcriptional and epigenetic mechanisms of early cortical development: An examination of how Pax6 coordinates cortical development.The Journal of comparative neurology · 2016Review
- Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.Molecular psychiatry · 2016Article
- Changes in the enhancer landscape during early placental development uncover a trophoblast invasion gene-enhancer network.Placenta · 2016Article
- Coexpression networks identify brain region-specific enhancer RNAs in the human brain.Nature neuroscience · 2015Article
- A family of transposable elements co-opted into developmental enhancers in the mouse neocortex.Nature communications · 2015Article
- From trans to cis: transcriptional regulatory networks in neocortical development.Trends in genetics : TIG · 2015Review
- DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.Epigenetics & chromatin · 2015Article
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Genetic studies have identified a core set of transcription factors and target genes that control the development of the neocortex, the region of the human brain responsible for higher cognition. The specific regulatory interactions between these factors, many key upstream and downstream genes, and the enhancers that mediate all these interactions remain mostly uncharacterized. We perform p300 ChIP-seq to identify over 6,600 candidate enhancers active in the dorsal cerebral wall of embryonic day 14.5 (E14.5) mice. Over 95% of the peaks we measure are conserved to human. Eight of ten (80%) candidates tested using mouse transgenesis drive activity in restricted laminar patterns within the neocortex. GREAT based computational analysis reveals highly significant correlation with genes expressed at E14.5 in key areas for neocortex development, and allows the grouping of enhancers by known biological functions and pathways for further studies. We find that multiple genes are flanked by dozens of candidate enhancers each, including well-known key neocortical genes as well as suspected and novel genes. Nearly a quarter of our candidate enhancers are conserved well beyond mammals. Human and zebrafish regions orthologous to our candidate enhancers are shown to most often function in other aspects of central nervous system development. Finally, we find strong evidence that specific interspersed repeat families have contributed potentially key developmental enhancers via co-option. Our analysis expands the methodologies available for extracting the richness of information found in genome-wide functional maps.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.