Concentration dependent chromatin states induced by the bicoid morphogen gradient

In Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset of its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations. This may be a common property of developmental transcription factors that must gain early access to their target enhancers while the chromatin state of the genome is being remodeled during large-scale transitions in the gene regulatory landscape.

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Concentration Dependent Chromatin States Induced by the Bicoid Morphogen Gradient

10.1101/133348 ◽

2017 ◽

Cited By ~ 3

Author(s):

Colleen E. Hannon ◽

Shelby A. Blythe ◽

Eric F. Wieschaus

Keyword(s):

Target Genes ◽

Positional Information ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Genome Wide ◽

Low Concentrations ◽

High Concentrations ◽

Accessible Chromatin ◽

Anterior Posterior

ABSTRACTIn Drosophila, graded expression of the maternal transcription factor Bicoid (Bcd) provides positional information to activate target genes at different positions along the anterior-posterior axis. We have measured the genome-wide binding profile of Bcd using ChIP-seq in embryos expressing single, uniform levels of Bcd protein, and grouped Bcd-bound targets into four classes based on occupancy at different concentrations. By measuring the biochemical affinity of target enhancers in these classes in vitro and genome-wide chromatin accessibility by ATAC-seq, we found that the occupancy of target sequences by Bcd is not primarily determined by Bcd binding sites, but by chromatin context. Bcd drives an open chromatin state at a subset its targets. Our data support a model where Bcd influences chromatin structure to gain access to concentration-sensitive targets at high concentrations, while concentration-insensitive targets are found in more accessible chromatin and are bound at low concentrations.

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Runx1 Shapes the Chromatin Landscape Via a Cascade of Direct and Indirect Targets

10.1101/2020.09.25.313767 ◽

2020 ◽

Author(s):

Matthew R. Hass ◽

Daniel Brisette ◽

Sreeja Parameswaran ◽

Mario Pujato ◽

Omer Donmez ◽

...

Keyword(s):

Transcription Factor ◽

Large Scale ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Genome Wide ◽

Related Transcription Factor ◽

Indirect Consequence ◽

Genome Scale ◽

Upregulated Genes ◽

Transcription Factor 1

AbstractRunt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion of Runx1 in an embryonic kidney-derived cell (mK4) results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci are enriched for Runx sites, remain bound by Runx2, but lose chromatin accessibility and expression in Runx1 knockout cells. Unexpectedly, regions near upregulated genes are depleted of Runx sites and are instead enriched for Zeb transcription factor binding sites. Re-expressing Zeb2 in Runx1 knockout cells restores suppression. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that genome-scale derepression is an indirect consequence of losing Runx1-dependent Zeb expression.

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Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets

PLoS Genetics ◽

10.1371/journal.pgen.1009574 ◽

2021 ◽

Vol 17 (6) ◽

pp. e1009574

Author(s):

Matthew R. Hass ◽

Daniel Brissette ◽

Sreeja Parameswaran ◽

Mario Pujato ◽

Omer Donmez ◽

...

Keyword(s):

Transcription Factor ◽

Large Scale ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Metanephric Mesenchyme ◽

Genome Wide ◽

Related Transcription Factor ◽

Subsequent Activation ◽

Genome Scale ◽

Upregulated Genes

Runt-related transcription factor 1 (Runx1) can act as both an activator and a repressor. Here we show that CRISPR-mediated deletion of Runx1 in mouse metanephric mesenchyme-derived mK4 cells results in large-scale genome-wide changes to chromatin accessibility and gene expression. Open chromatin regions near down-regulated loci enriched for Runx sites in mK4 cells lose chromatin accessibility in Runx1 knockout cells, despite remaining Runx2-bound. Unexpectedly, regions near upregulated genes are depleted of Runx sites and are instead enriched for Zeb transcription factor binding sites. Re-expressing Zeb2 in Runx1 knockout cells restores suppression, and CRISPR mediated deletion of Zeb1 and Zeb2 phenocopies the gained expression and chromatin accessibility changes seen in Runx1KO due in part to subsequent activation of factors like Grhl2. These data confirm that Runx1 activity is uniquely needed to maintain open chromatin at many loci, and demonstrate that Zeb proteins are required and sufficient to maintain Runx1-dependent genome-scale repression.

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OCHROdb: a comprehensive, quality checked database of open chromatin regions from sequencing data

10.1101/484840 ◽

2018 ◽

Cited By ~ 1

Author(s):

Parisa Shooshtari ◽

Samantha Feng ◽

Viswateja Nelakuditi ◽

Justin Foong ◽

Michael Brudno ◽

...

Keyword(s):

Gene Regulation ◽

Large Scale ◽

Target Genes ◽

Cell Types ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Sequencing Data ◽

Genomic Regions ◽

Multiple Samples ◽

Regulatory Sites

ABSTRACTInternational consortia, including ENCODE, Roadmap Epigenomics, Genomics of Gene Regulation and Blueprint Epigenome have made large-scale datasets of open chromatin regions publicly available. While these datasets are extremely useful for studying mechanisms of gene regulation in disease and cell development, they only identify open chromatin regions in individual samples. A uniform comparison of accessibility of the same regulatory sites across multiple samples is necessary to correlate open chromatin accessibility and expression of target genes across matched cell types. Additionally, although replicate samples are available for majority of cell types, a comprehensive replication-based quality checking of individual regulatory sites is still lacking. We have integrated 828 DNase-I hypersensitive sequencing samples, which we have uniformly processed and then clustered their regulatory regions across all samples. We checked the quality of open-chromatin regions using our replication test. This has resulted in a comprehensive, quality-checked database of Open CHROmatin (OCHROdb) regions for 194 unique human cell types and cell lines which can serve as a reference for gene regulatory studies involving open chromatin. We have made this resource publicly available: users can download the whole database, or query it for their genomic regions of interest and visualize the results in an interactive genome browser.

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The LEAFY floral regulator displays pioneer transcription factor properties

10.1101/2021.01.07.425699 ◽

2021 ◽

Author(s):

Xuelei Lai ◽

Romain Blanc-Mathieu ◽

Loic GrandVuillemin ◽

Ying Huang ◽

Arnaud Stigliani ◽

...

Keyword(s):

Gene Expression ◽

Target Genes ◽

Chromatin Accessibility ◽

Nucleosomal Dna ◽

Genome Wide ◽

Pioneer Transcription Factor ◽

Floral Gene ◽

Expression Program

Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and often highly methylated. Subsequently, they are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that LFY binds a subset of regions occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes, APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launch the floral gene expression program.

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Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression

Journal of Developmental Biology ◽

10.3390/jdb9010006 ◽

2021 ◽

Vol 9 (1) ◽

pp. 6

Author(s):

Narendra Pratap Singh ◽

Bony De Kumar ◽

Ariel Paulson ◽

Mark E. Parrish ◽

Carrie Scott ◽

...

Keyword(s):

Dna Binding ◽

Target Genes ◽

Embryonic Stem ◽

Binding Motif ◽

Binding Assays ◽

Histone Marks ◽

Genome Wide ◽

Hox Cofactors

Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif HB1RE (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel HB1RE motif contributes to HOXB1 function in part through a repressive role in gene expression.

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Genome-wide effects of chromatin on vitamin D signaling

Journal of Molecular Endocrinology ◽

10.1530/jme-19-0246 ◽

2020 ◽

Vol 64 (4) ◽

pp. R45-R56 ◽

Cited By ~ 3

Author(s):

Andrea Hanel ◽

Henna-Riikka Malmberg ◽

Carsten Carlberg

Keyword(s):

Vitamin D ◽

Binding Sites ◽

Target Genes ◽

Chromatin Accessibility ◽

Transcription Start Sites ◽

Dihydroxyvitamin D ◽

Genome Wide ◽

Spatio Temporal ◽

Vitamin D Signaling ◽

The Impact

Molecular endocrinology of vitamin D is based on the activation of the transcription factor vitamin D receptor (VDR) by the vitamin D metabolite 1α,25-dihydroxyvitamin D3. This nuclear vitamin D-sensing process causes epigenome-wide effects, such as changes in chromatin accessibility as well as in the contact of VDR and its supporting pioneer factors with thousands of genomic binding sites, referred to as vitamin D response elements. VDR binding enhancer regions loop to transcription start sites of hundreds of vitamin D target genes resulting in changes of their expression. Thus, vitamin D signaling is based on epigenome- and transcriptome-wide shifts in VDR-expressing tissues. Monocytes are the most responsive cell type of the immune system and serve as a paradigm for uncovering the chromatin model of vitamin D signaling. In this review, an alternative approach for selecting vitamin D target genes is presented, which are most relevant for understanding the impact of vitamin D endocrinology on innate immunity. Different scenarios of the regulation of primary upregulated vitamin D target genes are presented, in which vitamin D-driven super-enhancers comprise a cluster of persistent (constant) and/or inducible (transient) VDR-binding sites. In conclusion, the spatio-temporal VDR binding in the context of chromatin is most critical for the regulation of vitamin D target genes.

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N6-methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription

Science ◽

10.1126/science.aay6018 ◽

2020 ◽

Vol 367 (6477) ◽

pp. 580-586 ◽

Cited By ~ 46

Author(s):

Jun Liu ◽

Xiaoyang Dou ◽

Chuanyuan Chen ◽

Chuan Chen ◽

Chang Liu ◽

...

Keyword(s):

Messenger Rna ◽

Embryonic Stem ◽

Chromatin Accessibility ◽

Chromatin State ◽

Open Chromatin ◽

Dependent Manner ◽

Nuclear Exosome ◽

Regulatory Rnas ◽

Nuclear Degradation ◽

Long Interspersed Element

N6-methyladenosine (m6A) regulates stability and translation of messenger RNA (mRNA) in various biological processes. In this work, we show that knockout of the m6A writer Mettl3 or the nuclear reader Ythdc1 in mouse embryonic stem cells increases chromatin accessibility and activates transcription in an m6A-dependent manner. We found that METTL3 deposits m6A modifications on chromosome-associated regulatory RNAs (carRNAs), including promoter-associated RNAs, enhancer RNAs, and repeat RNAs. YTHDC1 facilitates the decay of a subset of these m6A-modified RNAs, especially elements of the long interspersed element-1 family, through the nuclear exosome targeting–mediated nuclear degradation. Reducing m6A methylation by METTL3 depletion or site-specific m6A demethylation of selected carRNAs elevates the levels of carRNAs and promotes open chromatin state and downstream transcription. Collectively, our results reveal that m6A on carRNAs can globally tune chromatin state and transcription.

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Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci

eLife ◽

10.7554/elife.31977 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 60

Author(s):

Matthias Thurner ◽

Martijn van de Bunt ◽

Jason M Torres ◽

Anubha Mahajan ◽

Vibe Nylander ◽

...

Keyword(s):

Type 2 Diabetes ◽

Pancreatic Islet ◽

Molecular Mechanisms ◽

Association Studies ◽

Human Islets ◽

Chromatin Accessibility ◽

Chromatin State ◽

Open Chromatin ◽

Genome Wide Association Studies

Human genetic studies have emphasised the dominant contribution of pancreatic islet dysfunction to development of Type 2 Diabetes (T2D). However, limited annotation of the islet epigenome has constrained efforts to define the molecular mechanisms mediating the, largely regulatory, signals revealed by Genome-Wide Association Studies (GWAS). We characterised patterns of chromatin accessibility (ATAC-seq, n = 17) and DNA methylation (whole-genome bisulphite sequencing, n = 10) in human islets, generating high-resolution chromatin state maps through integration with established ChIP-seq marks. We found enrichment of GWAS signals for T2D and fasting glucose was concentrated in subsets of islet enhancers characterised by open chromatin and hypomethylation, with the former annotation predominant. At several loci (including CDC123, ADCY5, KLHDC5) the combination of fine-mapping genetic data and chromatin state enrichment maps, supplemented by allelic imbalance in chromatin accessibility pinpointed likely causal variants. The combination of increasingly-precise genetic and islet epigenomic information accelerates definition of causal mechanisms implicated in T2D pathogenesis.

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Genome-Wide Identification and Characterization of Long Non-Coding RNAs in Peanut

Genes ◽

10.3390/genes10070536 ◽

2019 ◽

Vol 10 (7) ◽

pp. 536 ◽

Cited By ~ 2

Author(s):

Xiaobo Zhao ◽

Liming Gan ◽

Caixia Yan ◽

Chunjuan Li ◽

Quanxi Sun ◽

...

Keyword(s):

Large Scale ◽

Target Genes ◽

Sequencing Data ◽

Regulatory Processes ◽

Genome Wide ◽

Non Coding Rnas ◽

Identification And Characterization ◽

Lower Expression ◽

Weighted Correlation

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.

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