Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

Abstract Accessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43 and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. A more complete set of UMRs and ACRs can be identified when chromatin data is aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are 6-12 fold enriched within regions between genomes. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only ∼5% being polymorphic between genotypes. However, the majority (71%) of UMRs that are shared between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.

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Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

10.1101/2021.03.10.434810 ◽

2021 ◽

Author(s):

Jaclyn M Noshay ◽

Zhikai Liang ◽

Peng Zhou ◽

Peter A Crisp ◽

Alexandre P Marand ◽

...

Keyword(s):

Dna Methylation ◽

Sequence Variation ◽

Reference Genome ◽

De Novo ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Genome Context ◽

Genomic Regions ◽

Genome Assemblies ◽

Accessible Chromatin

AbstractAccessible chromatin and unmethylated DNA are associated with many genes and cis-regulatory elements. Attempts to understand natural variation for accessible chromatin regions (ACRs) and unmethylated regions (UMRs) often rely upon alignments to a single reference genome. This limits the ability to assess regions that are absent in the reference genome assembly and monitor how nearby structural variants influence variation in chromatin state. In this study, de novo genome assemblies for four maize inbreds (B73, Mo17, Oh43 and W22) are utilized to assess chromatin accessibility and DNA methylation patterns in a pan-genome context. The number of UMRs and ACRs that can be identified is more accurate when chromatin data is aligned to the matched genome rather than a single reference genome. While there are UMRs and ACRs present within genomic regions that are not shared between genotypes, these features are substantially enriched within shared regions, as determined by chromosomal alignments. Characterization of UMRs present within shared genomic regions reveals that most UMRs maintain the unmethylated state in other genotypes with only a small number being polymorphic between genotypes. However, the majority of UMRs between genotypes only exhibit partial overlaps suggesting that the boundaries between methylated and unmethylated DNA are dynamic. This instability is not solely due to sequence variation as these partially overlapping UMRs are frequently found within genomic regions that lack sequence variation. The ability to compare chromatin properties among individuals with structural variation enables pan-epigenome analyses to study the sources of variation for accessible chromatin and unmethylated DNA.Article summaryRegions of the genome that have accessible chromatin or unmethylated DNA are often associated with cis-regulatory elements. We assessed chromatin accessibility and DNA methylation in four structurally diverse maize genomes. There are accessible or unmethylated regions within the non-shared portions of the genomes but these features are depleted within these regions. Evaluating the dynamics of methylation and accessibility between genotypes reveals conservation of features, albeit with variable boundaries suggesting some instability of the precise edges of unmethylated regions.

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ATAC-Seq Identifies Chromatin Landscapes Linked to the Regulation of Oxidative Stress in the Human Fungal Pathogen Candida albicans

Journal of Fungi ◽

10.3390/jof6030182 ◽

2020 ◽

Vol 6 (3) ◽

pp. 182

Author(s):

Sabrina Jenull ◽

Michael Tscherner ◽

Theresia Mair ◽

Karl Kuchler

Keyword(s):

Oxidative Stress ◽

Gene Expression ◽

Candida Albicans ◽

Stress Responses ◽

De Novo ◽

Fungal Infections ◽

Chromatin Accessibility ◽

Robust Detection ◽

Genomic Regions ◽

Accessible Chromatin

Human fungal pathogens often encounter fungicidal stress upon host invasion, but they can swiftly adapt by transcriptional reprogramming that enables pathogen survival. Fungal immune evasion is tightly connected to chromatin regulation. Hence, fungal chromatin modifiers pose alternative treatment options to combat fungal infections. Here, we present an assay for transposase-accessible chromatin using sequencing (ATAC-seq) protocol adapted for the opportunistic pathogen Candida albicans to gain further insight into the interplay of chromatin accessibility and gene expression mounted during fungal adaptation to oxidative stress. The ATAC-seq workflow not only facilitates the robust detection of genomic regions with accessible chromatin but also allows for the precise modeling of nucleosome positions in C. albicans. Importantly, the data reveal genes with altered chromatin accessibility in upstream regulatory regions, which correlate with transcriptional regulation during oxidative stress. Interestingly, many genes show increased chromatin accessibility without change in gene expression upon stress exposure. Such chromatin signatures could predict yet unknown regulatory factors under highly dynamic transcriptional control. Additionally, de novo motif analysis in genomic regions with increased chromatin accessibility upon H2O2 treatment shows significant enrichment for Cap1 binding sites, a major factor of oxidative stress responses in C. albicans. Taken together, the ATAC-seq workflow enables the identification of chromatin signatures and highlights the dynamics of regulatory mechanisms mediating environmental adaptation of C. albicans.

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ATF3 drives senescence by reconstructing accessible chromatin profiles

10.1101/2020.08.13.249458 ◽

2020 ◽

Author(s):

Chao Zhang ◽

Xuebin Zhang ◽

Yiting Guan ◽

Xiaoke Huang ◽

Lijun Zhang ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transcription Factors ◽

Regulatory Mechanism ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Dynamic Landscape ◽

Intergenic Regions ◽

Senescence Program ◽

Accessible Chromatin

AbstractChromatin architecture and gene expression profile undergo tremendous reestablishment during senescence. However, the regulatory mechanism between chromatin reconstruction and gene expression in senescence remain elusive. The chromatin accessibility is an excellent perspective to reveal the latent regulatory elements. Thus, we depicted the landscapes of chromatin accessibility and gene expression during HUVECs senescence. We found that chromatin accessibilities are re-distributed during senescence. The senescence related increased accessible regions (IARs) and the decreased accessible regions (DARs) are mainly distributed in distal intergenic regions. The DARs are correlated with the function declines caused by senescence, whereas the IARs are involved in the regulation for senescence program. Moreover, the heterochromatin contributes most of IARs in senescent cells. We identified that the AP-1 transcription factors, especially ATF3 is responsible for driving chromatin accessibility reconstruction in IARs. In particular, DNA methylation is negatively correlated with chromatin accessibility during senescence. AP-1 motifs with low DNA methylation may improve their binding affinity in IARs and further opens the chromatin nearby. Our results described a dynamic landscape of chromatin accessibility whose remodeling contributes to the senescence program. And we identified a cellular senescence regulator, AP-1, which promotes senescence through organizing the accessibility profile in IARs.

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FGF signalling regulates enhancer activation during ear progenitor induction

10.1101/595058 ◽

2019 ◽

Author(s):

Monica Tambalo ◽

Maryam Anwar ◽

Mohi Ahmed ◽

Andrea Streit

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

De Novo ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Fibroblast Growth ◽

Active Chromatin ◽

Histone Acetyl Transferase ◽

Fgf Signalling ◽

Genomic Regions

ABSTRACTThe fibroblast growth factor pathway is essential for inner ear induction in many vertebrates, however how it regulates the chromatin landscape to coordinate the activation of otic genes remains unclear. Here we show that FGF exposure of sensory progenitors leads to rapid deposition of active chromatin marks H3K27ac near hundreds of FGF-responsive, otic-epibranchial progenitor (OEP) genes, while H3K27ac is depleted in the vicinity of non-otic genes. Genomic regions that gain H3K27ac act as cis-regulatory elements controlling OEP gene expression in time and space and define a unique transcription factor signature likely to control their activity. Finally, we provide evidence that in response to FGF signalling the transcription factor dimer AP1 recruits the histone acetyl transferase p300 to OEP enhancers and that de novo acetylation is required for subsequent expression of OEP genes. Thus, during ear induction FGF signalling modifies the chromatin landscape to promote enhancer activation and chromatin accessibility.

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Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development

10.1101/2021.03.05.434138 ◽

2021 ◽

Author(s):

Andrew Clugston ◽

Andrew Bodnar ◽

Débora Malta Cerqueira ◽

Yu Leng Phua ◽

Alyssa Lawler ◽

...

Keyword(s):

Progenitor Cells ◽

Kidney Development ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Microrna Expression ◽

Genome Wide ◽

Extracellular Matrix Interactions ◽

Genomic Regions ◽

Nephron Progenitor ◽

Accessible Chromatin

AbstractMammalian nephrons originate from a population of nephron progenitor cells (NPCs), and it is known that NPCs’ transcriptomes change throughout nephrogenesis during healthy kidney development. To characterize chromatin accessibility and microRNA (miRNA) expression throughout this process, we collected NPCs from mouse kidneys at embryonic day 14.5 (E14.5) and postnatal day zero (P0) and assayed cells for transposase-accessible chromatin and small RNA expression. We observe 46,374 genomic regions of accessible chromatin, with 2,103 showing significant changes in accessibility between E14.5 and P0. In addition, we detect 1,104 known microRNAs, with 114 showing significant changes in expression. Genome-wide, changes in DNA accessibility and microRNA expression highlight biological processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways such as Notch. Furthermore, our data identify novel candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in NPC differentiation; we also associate expression-changing microRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements. Overall, our data characterize NPCs during kidney development and point out new candidate regulatory elements for genes and microRNA with key roles in nephrogenesis.

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Interplay between Histone and DNA Methylation Seen through Comparative Methylomes in Rare Mendelian Disorders

International Journal of Molecular Sciences ◽

10.3390/ijms22073735 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3735

Author(s):

Guillaume Velasco ◽

Damien Ulveling ◽

Sophie Rondeau ◽

Pauline Marzin ◽

Motoko Unoki ◽

...

Keyword(s):

Dna Methylation ◽

Catalytic Domain ◽

De Novo ◽

Mutation Screening ◽

Histone H3 ◽

Regulatory Elements ◽

Germline Mutations ◽

Dna Methyltransferases ◽

Mendelian Disorders ◽

Epigenetic Machinery

DNA methylation (DNAme) profiling is used to establish specific biomarkers to improve the diagnosis of patients with inherited neurodevelopmental disorders and to guide mutation screening. In the specific case of mendelian disorders of the epigenetic machinery, it also provides the basis to infer mechanistic aspects with regard to DNAme determinants and interplay between histone and DNAme that apply to humans. Here, we present comparative methylomes from patients with mutations in the de novo DNA methyltransferases DNMT3A and DNMT3B, in their catalytic domain or their N-terminal parts involved in reading histone methylation, or in histone H3 lysine (K) methylases NSD1 or SETD2 (H3 K36) or KMT2D/MLL2 (H3 K4). We provide disease-specific DNAme signatures and document the distinct consequences of mutations in enzymes with very similar or intertwined functions, including at repeated sequences and imprinted loci. We found that KMT2D and SETD2 germline mutations have little impact on DNAme profiles. In contrast, the overlapping DNAme alterations downstream of NSD1 or DNMT3 mutations underlines functional links, more specifically between NSD1 and DNMT3B at heterochromatin regions or DNMT3A at regulatory elements. Together, these data indicate certain discrepancy with the mechanisms described in animal models or the existence of redundant or complementary functions unforeseen in humans.

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Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

Genetics ◽

10.1093/genetics/iyaa003 ◽

2020 ◽

Vol 217 (1) ◽

Author(s):

Jaclyn M Noshay ◽

Alexandre P Marand ◽

Sarah N Anderson ◽

Peng Zhou ◽

Maria Katherine Mejia Guerra ◽

...

Keyword(s):

Transposable Elements ◽

Allelic Variation ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Transcriptional Responses ◽

Maize Genotypes ◽

Show Evidence ◽

Regulatory Potential ◽

Dna Regulatory Elements ◽

Accessible Chromatin

Abstract Transposable elements (TEs) have the potential to create regulatory variation both through the disruption of existing DNA regulatory elements and through the creation of novel DNA regulatory elements. In a species with a large genome, such as maize, many TEs interspersed with genes create opportunities for significant allelic variation due to TE presence/absence polymorphisms among individuals. We used information on putative regulatory elements in combination with knowledge about TE polymorphisms in maize to identify TE insertions that interrupt existing accessible chromatin regions (ACRs) in B73 as well as examples of polymorphic TEs that contain ACRs among four inbred lines of maize including B73, Mo17, W22, and PH207. The TE insertions in three other assembled maize genomes (Mo17, W22, or PH207) that interrupt ACRs that are present in the B73 genome can trigger changes to the chromatin, suggesting the potential for both genetic and epigenetic influences of these insertions. Nearly 20% of the ACRs located over 2 kb from the nearest gene are located within an annotated TE. These are regions of unmethylated DNA that show evidence for functional importance similar to ACRs that are not present within TEs. Using a large panel of maize genotypes, we tested if there is an association between the presence of TE insertions that interrupt, or carry, an ACR and the expression of nearby genes. While most TE polymorphisms are not associated with expression for nearby genes, the TEs that carry ACRs exhibit enrichment for being associated with higher expression of nearby genes, suggesting that these TEs may contribute novel regulatory elements. These analyses highlight the potential for a subset of TEs to rewire transcriptional responses in eukaryotic genomes.

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dnAQET: a framework to compute a consolidated metric for benchmarking quality of de novo assemblies

BMC Genomics ◽

10.1186/s12864-019-6070-x ◽

2019 ◽

Vol 20 (1) ◽

Author(s):

Gokhan Yavas ◽

Huixiao Hong ◽

Wenming Xiao

Keyword(s):

Quality Assessment ◽

Genome Assembly ◽

Reference Genome ◽

De Novo ◽

Quality Score ◽

De Novo Genome Assembly ◽

Genome Assemblies ◽

Reference Genomes ◽

Better Than

Abstract Background Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome research. Although many quality metrics have been proposed and software tools for calculating those metrics have been developed, the existing tools do not produce a unified measure to reflect the overall quality of an assembly. Results To address this issue, we developed the de novo Assembly Quality Evaluation Tool (dnAQET) that generates a unified metric for benchmarking the quality assessment of assemblies. Our framework first calculates individual quality scores for the scaffolds/contigs of an assembly by aligning them to a reference genome. Next, it computes a quality score for the assembly using its overall reference genome coverage, the quality score distribution of its scaffolds and the redundancy identified in it. Using synthetic assemblies randomly generated from the latest human genome build, various builds of the reference genomes for five organisms and six de novo assemblies for sample NA24385, we tested dnAQET to assess its capability for benchmarking quality evaluation of genome assemblies. For synthetic data, our quality score increased with decreasing number of misassemblies and redundancy and increasing average contig length and coverage, as expected. For genome builds, dnAQET quality score calculated for a more recent reference genome was better than the score for an older version. To compare with some of the most frequently used measures, 13 other quality measures were calculated. The quality score from dnAQET was found to be better than all other measures in terms of consistency with the known quality of the reference genomes, indicating that dnAQET is reliable for benchmarking quality assessment of de novo genome assemblies. Conclusions The dnAQET is a scalable framework designed to evaluate a de novo genome assembly based on the aggregated quality of its scaffolds (or contigs). Our results demonstrated that dnAQET quality score is reliable for benchmarking quality assessment of genome assemblies. The dnQAET can help researchers to identify the most suitable assembly tools and to select high quality assemblies generated.

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Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer

10.1101/2021.05.21.445142 ◽

2021 ◽

Author(s):

Jean S Fain ◽

Axelle Loriot ◽

Anna Diacofotaki ◽

Aurelie Van Tongelen ◽

Charles De Smet

Keyword(s):

Dna Methylation ◽

Dna Methyltransferase ◽

De Novo ◽

Tumor Development ◽

Epigenetic Mark ◽

Dna Hypomethylation ◽

Dna Hypermethylation ◽

Bioinformatics Analyses ◽

Genomic Regions ◽

Methylation Patterns

DNA methylation is an epigenetic mark associated with gene repression. It is now well established that tumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) of methylation marks in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark known to be deposited during progression of the transcription machinery and to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of increased DNA methylation in the MAGEA6/GABRA3 locus. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo- and hypermethylation. In several of these loci, DNA hypermethylation affected tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.

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Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer

Scientific Reports ◽

10.1038/s41598-021-96844-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jean S. Fain ◽

Axelle Loriot ◽

Anna Diacofotaki ◽

Aurélie Van Tongelen ◽

Charles De Smet

Keyword(s):

Dna Methylation ◽

Dna Methyltransferase ◽

De Novo ◽

Tumor Development ◽

Transcriptional Elongation ◽

Dna Hypomethylation ◽

Dna Hypermethylation ◽

Bioinformatics Analyses ◽

Genomic Regions ◽

Methylation Patterns

AbstractTumor development involves alterations in DNA methylation patterns, which include both gains (hypermethylation) and losses (hypomethylation) in different genomic regions. The mechanisms underlying these two opposite, yet co-existing, alterations in tumors remain unclear. While studying the human MAGEA6/GABRA3 gene locus, we observed that DNA hypomethylation in tumor cells can lead to the activation of a long transcript (CT-GABRA3) that overlaps downstream promoters (GABRQ and GABRA3) and triggers their hypermethylation. Overlapped promoters displayed increases in H3K36me3, a histone mark deposited during transcriptional elongation and known to stimulate de novo DNA methylation. Consistent with such a processive mechanism, increases in H3K36me3 and DNA methylation were observed over the entire region covered by the CT-GABRA3 overlapping transcript. Importantly, experimental induction of CT-GABRA3 by depletion of DNMT1 DNA methyltransferase, resulted in a similar pattern of regional DNA hypermethylation. Bioinformatics analyses in lung cancer datasets identified other genomic loci displaying this process of coupled DNA hypo/hypermethylation, and some of these included tumor suppressor genes, e.g. RERG and PTPRO. Together, our work reveals that focal DNA hypomethylation in tumors can indirectly contribute to hypermethylation of nearby promoters through activation of overlapping transcription, and establishes therefore an unsuspected connection between these two opposite epigenetic alterations.

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