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Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

ABSTRACT: Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

PROVIDER: PRJNA1284906 | ENA |

REPOSITORIES: ENA

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Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

Project description:Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders

| PRJNA1284900 | ENA

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Convergent DNA Methylation Abnormalities at Bivalent Chromatin in Human Growth Disorders [CUT&RUN]

Project description:Overgrowth with Intellectual Disability (OGID) is characterized by generalized overgrowth, including a head circumference and/or height ≥ 2 standard deviations (s.d.) above the mean, accompanied by mild to moderate intellectual disability. Sotos Syndrome, the most common form of OGID, results from loss-of-function (LoF) mutations in NSD1, which encodes a histone methyltransferase. Another major OGID subtype, Tatton-Brown-Rahman syndrome, is caused by LoF mutations in DNMT3A, encoding a de novo DNA methyltransferase. In contrast, gain-of-function (GoF) mutations in DNMT3A cause Heyn-Sproul-Jackson syndrome, characterized by growth restriction and microcephaly. We hypothesize that NSD1 LoF and DNMT3A LoF mutations share a convergent DNA methylation signature that is distinct from the pattern seen in DNMT3A GoF mutations. To test this, we generated human embryonic stem cell lines carrying these growth syndrome-associated mutations in NSD1 and DNMT3A, profiled their DNA methylation patterns using the Illumina EPIC array, and analyzed both shared and unique methylation phenotypes.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders

Project description:Pintacuda G*, Hsu YH*, Tsafou K, Li KW, Martín JM, Riseman J, Biagini JC, Ching JKT, Mena D, Gonzalez-Lozano MA, Egri SB, Jaffe J, Smit AB, Fornelos N, Eggan KC, Lage K. Protein interaction studies in human induced neurons indicate convergent biology underlying autism spectrum disorders. Cell Genomics (2023). [DOI: https://doi.org/10.1016/j.xgen.2022.100250] Autism spectrum disorders (ASD) have been linked to genes with enriched expression in the brain, but it is unclear how these genes converge into cell-type-specific networks. We built a protein-protein interaction network for 13 ASD-associated genes in human excitatory neurons derived from induced pluripotent stem cells (iPSCs). The network contains newly reported interactions and is enriched for genetic and transcriptional perturbations observed in individuals with ASDs. We leveraged the network data to show that the ASD-linked brain-specific isoform of ANK2 is important for its interactions with synaptic proteins and to characterize a PTEN-AKAP8L interaction that influences neuronal growth. The IGF2BP1-3 complex emerged as a convergent point in the network that may regulate a transcriptional circuit of ASD-associated genes. Our findings showcase cell-type-specific interactomes as a framework to complement genetic and transcriptomic data, and illustrate how both individual and convergent interactions can lead to biological insights into ASDs.

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