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Methylation profiling of the chimpanzee CNTNAP2 gene in brain using high-resolution tiling arrays.

ABSTRACT: Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the chimpanzee genome, encompassing 2.5 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire chimpanzee CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp. Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays.

ORGANISM(S): Pan troglodytes

PROVIDER: GSE52949 | GEO | 2014/02/20

SECONDARY ACCESSION(S): PRJNA230522

REPOSITORIES: GEO

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Methylation profiling of the chimpanzee CNTNAP2 gene in brain using high-resolution tiling arrays.

Project description:Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the chimpanzee genome, encompassing 2.5 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire chimpanzee CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp. Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays. MeDIP-based CNTNAP2 methylation profiling

2014-02-20 | E-GEOD-52949 | biostudies-arrayexpress

Methylation profiling of the human CNTNAP2 gene in brain using high-resolution tiling arrays.

Project description:Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the human genome, encompassing 2.3 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire human CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp. Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays. MeDIP-based CNTNAP2 methylation profiling

2014-02-20 | E-GEOD-52948 | biostudies-arrayexpress

Methylation profiling of the human CNTNAP2 gene in brain using high-resolution tiling arrays.

Project description:Accelerated brain development is a unique feature of the human species. Not only the size but also morphology, in particular the connections between frontal cortex and basal ganglia distinguish the human brain from great apes and other primates. Recent findings suggest that structural features which may be important for language acquisition are influenced by FOXP2, key regulator of CNTNAP2. CNTNAP2 is one of the largest genes in the human genome, encompassing 2.3 Mb. It encodes a neurexin with essential roles in the vertebrate nervous system. The aim of our study was to compare the methylation patterns of CNTNAP2 in human and chimpanzee brains, assuming that epigenetic regulation is essential for brain development and human language abilities. To this end, we designed a NimbleGen tiling array covering the entire human CNTNAP2 gene plus 0.1 Mb up- and downstream flanking sequence with an average resolution of 13 bp. Methylated DNA ImmunoPreciptation (MeDIP) was used to enrich cytosine-methylated DNA fragments for downstream analysis with high-resolution tiling arrays.

2014-02-20 | GSE52948 | GEO

Cntnap2 KO mouse mPFC proteome for ASD

Project description:Autism Spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder where patients have impaired social behavior and communication, and restricted interests. Although various studies have been carried out to unveil the mechanisms associated with ASD, its pathophysiology is still poorly understood. Genetic variants on CNTNAP2 have been found and considered representative ASD genetic risk factors, and disruption of Cntnap2 causes ASD phenotypes in mice. Here, we performed an integrative multi-omics analysis by combining quantitative proteometabolomics data of Cntnap2 knockout (KO) mice with multi-omics data from ASD patients and forebrain organoids to elucidate Cntnap2-dependent molecular networks of ASD. First, we found Cntnap2-associated molecular signatures and cellular processes by conducting mass spectrometry-based proteometabolomic analysis of the medial prefrontal cortex of the Cntnap2 KO mouse model. Then, we narrowed these identified processes into bona fide ASD molecular processes by incorporating multi-omics data of ASD patients' prefrontal cortex. Further, we mapped cell-type-specific ASD networks by reanalyzing single-cell RNA-seq data of forebrain organoids derived from patients with CNTNAP2 mutation. Finally, we constructed a Cntnap2-associated ASD network model consisting of mitochondrial dysfunction, axonal impairment, and synaptic activity. Our results may shed light on understanding of the Cntnap2-dependent molecular networks of ASD.

2023-03-11 | PXD031656 | Pride

Pan troglodytes

Project description:Methylation profiling of the chimpanzee CNTNAP2 gene in brain using high-resolution tiling arrays.

| PRJNA230522 | ENA

Developmental Deficits of MGE-derived Interneurons in the Cntnap2 Knockout Mouse Model of Autism Spectrum Disorder

Project description:Interneurons are fundamental cells for maintaining the excitation-inhibition balance in the brain in health and disease. While interneurons have been shown to play a key role in the pathophysiology of autism spectrum disorder (ASD) in adult mice, little is known about how their maturation is altered in the developing striatum in ASD. Here, we aimed to track striatal developing interneurons and elucidate the molecular and physiological alterations in the Cntnap2 knockout mouse model. Using Stereo-seq and single-cell RNA sequencing data, we first characterized the pattern of expression of Cntnap2 in the adult brain and at embryonic stages in the medial ganglionic eminence (MGE), a transitory structure producing most cortical and striatal interneurons. We found that Cntnap2 is enriched in the striatum, compared to the cortex, particularly in the developing striatal cholinergic interneurons. We then revealed enhanced MGE-derived cell proliferation, followed by increased cell loss during the canonical window of developmental cell death in the Cntnap2 knockout mice. We uncovered specific cellular and molecular alterations in the developing Lhx6-expressing cholinergic interneurons of the striatum, which impacts interneuron firing properties during the first postnatal week. Overall, our work unveils some of the mechanisms underlying the shift in the developmental trajectory of striatal interneurons which greatly contribute to the ASD pathogenesis.

2023-01-12 | GSE222383 | GEO

Patient-derived hiPSC neurons with heterozygous CNTNAP2 deletions display altered neuronal gene expression and network activity

Project description:We queried the expression of CNTNAP2 in Ngn2-induced neurons from each member of this family trio, hypothesizing that heterozygous intragenic deletions may affect the expression of CNTNAP2.

2017-08-19 | GSE102838 | GEO

Human-specific transcriptional regulation of CNS development genes by FOXP2

Project description:The signaling pathways orchestrating both the evolution and development of language in the human brain remain unknown. To date, the transcription factor FOXP2 is the only gene implicated in Mendelian forms of human speech and language dysfunction1,2. It has been proposed, that the amino acid composition in the human variant of FOXP2 has undergone accelerated evolution, and this change occurred around the time of language emergence in humans3,4. However, this remains controversial, and whether the acquisition of these amino acids in human FOXP2 has any functional consequence in human neurons remains untested. Here, we demonstrate that these two amino acids confer new functionality in terms of differential transcriptional regulation, and extend these observations to in vivo brain, showing that several of the differential FOXP2 targets significantly overlap with genes different between human and chimpanzee brain. We also identify novel relationships among the differentially expressed genes with additional critical regulators of neuronal development. These data provide support for the functional relevance of changes that occur on the human lineage by showing that the two amino acids unique to human FOXP2 can lead to significant differences in gene expression patterns across brain evolution, with direct consequences for human brain development and disease. Since FOXP2 has an important role in the use of language in humans, the identified targets may have a critical function in the development and evolution of language circuitry in humans.

2009-11-12 | GSE18142 | GEO

Early-life stress of Cntnap2 heterozygous mice demonstrates a gene by environment interaction model for developmental brain disorders

Project description:We examined whether adult heterozygous mice (Cntnap2+/-; phenotypically normal) subjected to an early-life stress would have social-related deficits and disruptions in 5-hydroxymethylcytosine (5hmC), similar to the Cntnap2-/-.

2021-12-20 | GSE87032 | GEO

PTPRD and CNTNAP2 as markers of tumor aggressiveness in oligodendrogliomas

Project description:Oligodendrogliomas are typically associated with the most favorable prognosis among diffuse gliomas. However, many of the tumors progress, eventually leading to patient death. To characterize the changes associated with oligodendroglioma recurrence and progression, we analyzed two recurrent oligodendroglioma tumors upon diagnosis and after tumor relapse based on whole-genome and RNA sequencing. Relapsed tumors were diagnosed as glioblastomas with an oligodendroglioma component before the World Health Organization classification update in 2016. Both patients died within 12 months after relapse. One patient carried an inactivating POLE mutation leading to a clearly hypermutated progressed tumor. Strikingly, both relapsed tumors carried focal chromosomal rearrangements in PTPRD and CNTNAP2 genes with associated decreased gene expression. TP53 mutation was also detected in both patients after tumor relapse. In The Cancer Genome Atlas (TCGA) diffuse glioma cohort, PTPRD expression decreased by tumor grade in all diffuse glioma subtypes, while CNTNAP2 expression was associated with diffuse glioma subtypes and with tumor grade in oligodendrogliomas and IDH wild-type astrocytomas. Low expression of the genes was associated with poor overall survival. Our analysis provides information about aggressive oligodendrogliomas with worse prognosis and suggests that PTPRD and CNTNAP2 expression could represent an informative marker for their stratification.

2022-08-24 | GSE196707 | GEO

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