In the mammalian genome,most CpGs are methylated.However,CpGs within the CpG islands(CGIs)are largely unmethylated,which are important for gene expression regulation.The mechanism underlying the low methylation levels...In the mammalian genome,most CpGs are methylated.However,CpGs within the CpG islands(CGIs)are largely unmethylated,which are important for gene expression regulation.The mechanism underlying the low methylation levels at CGIs remains largely elusive.KDM2 proteins(KDM2A and KDM2B)are H3K36me2 demethylases known to bind specifically at CGIs.Here,we report that depletion of each or both KDM2 proteins,or mutation of all their JmjC domains that harbor the H3K36me2 demethylation activity,leads to an increase in DNA methylation at selective CGIs.The Kdm2a/2b double knockout shows a stronger increase in DNA methylation compared with the single mutant of Kdm2a or Kdm2b,indicating that KDM2A and KDM2B redundantly regulate DNA methylation at CGIs.In addition,the increase of CGI DNA methylation upon mutations of KDM2 proteins is associated with the chromatin environment.Our findings reveal that KDM2A and KDM2B function redundantly in regulating DNA methylation at a subset of CGIs in an H3K36me2 demethylation-dependent manner.展开更多
Intellectual disability(ID)is a condition characterized by cognitive impairment and difficulties in adaptive functioning.In our research,we identified two de novo mutations(c.955C>T and c.732C>A)at the KDM2A loc...Intellectual disability(ID)is a condition characterized by cognitive impairment and difficulties in adaptive functioning.In our research,we identified two de novo mutations(c.955C>T and c.732C>A)at the KDM2A locus in individuals with varying degrees of ID.In addition,by using the Gene4Denovo database,we discovered five additional cases of de novo mutations in KDM2A.The mutations we identified significantly decreased the expression of the KDM2A protein.To investigate the role of KDM2A in neural development,we used both 2D neural stem cell models and 3D cerebral organoids.Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells(NPCs),increases apoptosis,induces premature neuronal differentiation,and affects synapse maturation.Through ChIP-Seq analysis,we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis.In addition,the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes.By integrating ChIP-Seq and RNA-Seq data,we made a significant discovery of the core genes'remarkable enrichment in the MAPK signaling pathway.Importantly,this enrichment was specifically linked to the p38 MAPK pathway.Furthermore,disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID,autism spectrum disorder,and schizophrenia.Overall,our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes,thereby modulating the MAPK signaling pathway and potentially impacting early brain development.展开更多
基金supported by the National Natural Science Foundation of China(32070607)the National Key Research and Development Program of China(2020YFA0804000)the CAS Project for Young Scientists in Basic Research(YSBR-012).
文摘In the mammalian genome,most CpGs are methylated.However,CpGs within the CpG islands(CGIs)are largely unmethylated,which are important for gene expression regulation.The mechanism underlying the low methylation levels at CGIs remains largely elusive.KDM2 proteins(KDM2A and KDM2B)are H3K36me2 demethylases known to bind specifically at CGIs.Here,we report that depletion of each or both KDM2 proteins,or mutation of all their JmjC domains that harbor the H3K36me2 demethylation activity,leads to an increase in DNA methylation at selective CGIs.The Kdm2a/2b double knockout shows a stronger increase in DNA methylation compared with the single mutant of Kdm2a or Kdm2b,indicating that KDM2A and KDM2B redundantly regulate DNA methylation at CGIs.In addition,the increase of CGI DNA methylation upon mutations of KDM2 proteins is associated with the chromatin environment.Our findings reveal that KDM2A and KDM2B function redundantly in regulating DNA methylation at a subset of CGIs in an H3K36me2 demethylation-dependent manner.
基金supported by the National Natural Science Foundation of China(82022024,31970572,and 31871276)the National Key R&D Project of China(2016YFC1306000 and 2017YFC0908701)+3 种基金the Innovation-driven Project of Central South University(2020CX003)The Natural Science Foundation of Hunan Province(2023JJ40793)NIH grants(U01 MH122591,1U01MH116489,and 1R01MH110920)the Postgraduate Scientific Research Innovation Project of Hunan Province(CX20220320).
文摘Intellectual disability(ID)is a condition characterized by cognitive impairment and difficulties in adaptive functioning.In our research,we identified two de novo mutations(c.955C>T and c.732C>A)at the KDM2A locus in individuals with varying degrees of ID.In addition,by using the Gene4Denovo database,we discovered five additional cases of de novo mutations in KDM2A.The mutations we identified significantly decreased the expression of the KDM2A protein.To investigate the role of KDM2A in neural development,we used both 2D neural stem cell models and 3D cerebral organoids.Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells(NPCs),increases apoptosis,induces premature neuronal differentiation,and affects synapse maturation.Through ChIP-Seq analysis,we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis.In addition,the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes.By integrating ChIP-Seq and RNA-Seq data,we made a significant discovery of the core genes'remarkable enrichment in the MAPK signaling pathway.Importantly,this enrichment was specifically linked to the p38 MAPK pathway.Furthermore,disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID,autism spectrum disorder,and schizophrenia.Overall,our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes,thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
