Project description:High order chromatin structure and DNA methylation are implicated in multiple development processes and diseases. Despite the recent developments of methods studying high order chromatin interactions, how DNA methylation is associated with high order chromatin structure is not clear. Currently, it is believed that the insulator protein CTCF binding is blocked by DNA methylation, occurring in its core binding site. Thus the disruption of CTCF binding will result in the ectopic assessment of enhancer in the isolated neighborhood. However, not all CTCF bears CpG sites in its core binding site and no integrated analysis has been applied to discover the relationship between DNA methylation and high order chromatin structure utilizing the DNA methylome data. Here we found the lowly methylated DNA methylation canyon are interacting with each other specifically in CD34+ CD38- hematopoietic stem and progenitor cells (HSPC) but not its differentiated progenitors. The DNA methylation canyon interactions are enriched for H3K27me3 mark and represent a different category of interactions other than looped domain mediated by CTCF extrusion mechanism. We also found these canyons are contributing to the active HOX gene expression acting as scaffolds for gene expression rather enhancers. Disruption of canyon interaction with CTCF deletion and whole canyon deletion result in a great compromise of self-renewal ability of HSPC and the decrease of expression of active HOXA/B gene.
Project description:The inverse correlation between DNA methylation and steady state mRNA levels is imperfect; a large number of genes, which are unmethylated in the promoter region, are silenced. We show here that either pharmacological inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR) or knockdown with shRNA dramatically expands the number of transcription initiation positions in the genome including many unmethylated promoters. Induction of unmethylated promoters in response to inhibition of DNMT1 is a result of activation by demethylation of methylated upstream regulators such as the transcription factor HNF4A. Our results imply that the landscape of genes that are regulated by DNA methylation is more wide-ranging than genes silenced by methylation of their own cis regulatory sequences. We propose a hierarchical model of transcriptional control by DNA methylation whereby regulation of unmethylated promoters is dependent on the methylation state of trans upstream regulators.
Project description:The inverse correlation between DNA methylation and steady state mRNA levels is imperfect; a large number of genes, which are unmethylated in the promoter region, are silenced. We show here that either pharmacological inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR) or knockdown with shRNA dramatically expands the number of transcription initiation positions in the genome including many unmethylated promoters. Induction of unmethylated promoters in response to inhibition of DNMT1 is a result of activation by demethylation of methylated upstream regulators such as the transcription factor HNF4A. Our results imply that the landscape of genes that are regulated by DNA methylation is more wide-ranging than genes silenced by methylation of their own cis regulatory sequences. We propose a hierarchical model of transcriptional control by DNA methylation whereby regulation of unmethylated promoters is dependent on the methylation state of trans upstream regulators.
Project description:The inverse correlation between DNA methylation and steady state mRNA levels is imperfect; a large number of genes, which are unmethylated in the promoter region, are silenced. We show here that either pharmacological inhibition of DNA methyltransferase (DNMT1) with 5-aza-2'-deoxycytidine (5-azaCdR) or knockdown with shRNA dramatically expands the number of transcription initiation positions in the genome including many unmethylated promoters. Induction of unmethylated promoters in response to inhibition of DNMT1 is a result of activation by demethylation of methylated upstream regulators such as the transcription factor HNF4A. Our results imply that the landscape of genes that are regulated by DNA methylation is more wide-ranging than genes silenced by methylation of their own cis regulatory sequences. We propose a hierarchical model of transcriptional control by DNA methylation whereby regulation of unmethylated promoters is dependent on the methylation state of trans upstream regulators.
Project description:In this study, we investigated the dynamics during differentiation of the in vivo binding sites of ZBTB2, a putative reader for unmethylated DNA. We performed DNA pull-downs followed by mass spectrometry, using a genomic sequence containing either unmethylated or methylated CpGs, to study the influence of DNA methylation on ZBTB2 binding. Additionally, we performed interaction proteomics to identify ZBTB2 interaction partners. We found that ZBTB2 recruits a zinc finger module of three proteins to unmethylated DNA.
Project description:This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health.
Project description:Precise identification of causal variants within credible intervals of eQTL associations is needed to identify regulatory GWAS variants. We show that CROPseq, namely multiplex CRISPR-Cas9 genome editing combined with single cell RNAseq, is a viable strategy for fine mapping regulatory SNPs. Mutations were induced nearby 67 SNPs in three genes, two of which, rs2251039 and rs17523802, significantly altered CISD1 and PARK7 expression, respectively, and overlap with chromatin accessibility peaks.
Project description:CpG-islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 possesses an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. Absence of SAMD1 impairs ES cell differentiation processes, leading to mis-regulation of key biological pathways. Together, our work establishes SAMD1 as a novel chromatin regulator acting at unmethylated CGIs.