Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
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ABSTRACT:
PROVIDER: PRJNA634104 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11818962_1.fastq.gz | Fastqsanger.gz | |||
| SRR11818962_2.fastq.gz | Fastqsanger.gz | |||
| SRR11818963_1.fastq.gz | Fastqsanger.gz | |||
| SRR11818963_2.fastq.gz | Fastqsanger.gz | |||
| SRR11818964_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
Similar Datasets
Project description:Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
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Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
2021-09-09 | GSE150929 | GEO
Project description:The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions.
2020-08-22 | GSE152046 | GEO
Project description:The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
| S-EPMC7519222 | biostudies-literature
Project description:Cis-regulatory elements control gene expression in time and space
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Project description:Intervals of unmethylated DNA spatially co-segregate in cis and in trans [WGBS]
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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.
2025-07-13 | GSE85376 | GEO
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.
2025-07-13 | GSE85313 | GEO
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.
2025-07-13 | GSE85312 | GEO
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.
2018-01-29 | PXD007099 | Pride