2013
DOI: 10.1371/journal.pgen.1003433
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Coordinated Cell Type–Specific Epigenetic Remodeling in Prefrontal Cortex Begins before Birth and Continues into Early Adulthood

Abstract: Development of prefrontal and other higher-order association cortices is associated with widespread changes in the cortical transcriptome, particularly during the transitions from prenatal to postnatal development, and from early infancy to later stages of childhood and early adulthood. However, the timing and longitudinal trajectories of neuronal gene expression programs during these periods remain unclear in part because of confounding effects of concomitantly occurring shifts in neuron-to-glia ratios. Here,… Show more

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Cited by 66 publications
(67 citation statements)
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“…Brain eSNPs were generated by using genotype and gene expression profiles from 8 datasets (Colantuoni et al, 2011; Gibbs et al, 2010; Zhang, 2013) (Table S1). The brain CRE annotation map was generated based on chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments of histone modifications (Cheung et al, 2010; Maurano et al, 2012; Shulha et al, 2013; Shulha et al, 2012; Zhu et al, 2013) (Table S2, S3). We integrated data from specific sets of histone methylation and acetylation markings and DNase I hypersensitive sites (DHS) to define five types of CREs: active promoter, active enhancer, poised promoter, repressed enhancer and open chromatin regions.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…Brain eSNPs were generated by using genotype and gene expression profiles from 8 datasets (Colantuoni et al, 2011; Gibbs et al, 2010; Zhang, 2013) (Table S1). The brain CRE annotation map was generated based on chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments of histone modifications (Cheung et al, 2010; Maurano et al, 2012; Shulha et al, 2013; Shulha et al, 2012; Zhu et al, 2013) (Table S2, S3). We integrated data from specific sets of histone methylation and acetylation markings and DNase I hypersensitive sites (DHS) to define five types of CREs: active promoter, active enhancer, poised promoter, repressed enhancer and open chromatin regions.…”
Section: Resultsmentioning
confidence: 99%
“…ChIP-seq and DHS data generated as part of the ENCODE (Maurano et al, 2012) and REMC (Zhu et al, 2013) projects for human brain/neuron (Table S2), T - helper cells, liver, skin and adipose tissue were downloaded from the NCBI repository (http://www.ncbi.nlm.nih.gov/geo/roadmap/epigenomics/). Additional data for the dorsolateral prefrontal cortex after fluorescence-activated cell sorting (FACS) were generated as described previously (Cheung et al, 2010; Shulha et al, 2013; Shulha et al, 2012) (Table S3). …”
Section: Methodsmentioning
confidence: 99%
“…Third, the techniques we used in this study do not allow us to draw any conclusions regarding cytosine methylation verses hydroxymethylation, subregion specificity (for example CA1 vs. dentate), or cell-type specificity (i.e. glia vs. neurons), though increasing evidence suggests these are important considerations to keep in mind when interpreting methylation data (Brown, Weaver, Meaney, & Szyf, 2008; Huang et al, 2010; Jin, Kadam, & Pfeifer, 2010; Lister et al, 2013; Roth, et al, 2011; Shulha, Cheung, Guo, Akbarian, & Weng, 2013). We also acknowledge here with the large number of BSP measurements and tests on these data, the expected number of false rejections is increased above 5%.…”
Section: Discussionmentioning
confidence: 99%
“…A few studies have surveyed epigenetic marks in the brain following cell sorting to separate neurons from non-neurons; as might be predicted, very different patterns of age-related epigenetic changes are seen in neuronal versus non-neuronal cells (e.g. [74,75]). This is a relatively crude division, however.…”
Section: (D) Accounting For Cellular Heterogeneitymentioning
confidence: 99%