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

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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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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Detecting differential transcription factor activity from ATAC-seq data

10.1101/315622 ◽

2018 ◽

Cited By ~ 2

Author(s):

Ignacio J. Tripodi ◽

Mary A. Allen ◽

Robin D. Dowell

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Chromatin Accessibility ◽

Open Chromatin ◽

Nucleotide Polymorphisms ◽

Transcription Factor Activity ◽

Factor Activity ◽

Genome Wide ◽

Recognition Motifs ◽

Differential Transcription

AbstractTranscription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TF are altered by a perturbation is simple, quick to implement and can be used when biological samples are limited. In the future, we envision this method could be applied to determining which TFs show altered activity in response to a wide variety of drugs and diseases.

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Concentration dependent chromatin states induced by the bicoid morphogen gradient

eLife ◽

10.7554/elife.28275 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 35

Author(s):

Colleen E Hannon ◽

Shelby A Blythe ◽

Eric F Wieschaus

Keyword(s):

Large Scale ◽

Common Property ◽

Target Genes ◽

Positional Information ◽

Chromatin Accessibility ◽

Chromatin State ◽

Open Chromatin ◽

Genome Wide ◽

High Concentrations

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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Integrating transcription factor abundance with chromatin accessibility in human erythroid lineage commitment

10.1101/2021.03.23.436609 ◽

2021 ◽

Author(s):

Reema Baskar ◽

Amy F Chen ◽

Patricia M.B. Favaro ◽

Warren Reynolds ◽

Fabian Muller ◽

...

Keyword(s):

Transcription Factor ◽

Chromatin Accessibility ◽

Erythroid Cell ◽

Open Chromatin ◽

Protein Abundance ◽

Intracellular Protein ◽

Simultaneous Quantification ◽

Genome Wide ◽

Transcription Factor Motif ◽

Factor Abundance

We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance. By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.

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High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

Nature Communications ◽

10.1038/s41467-021-23213-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Sarah E. Pierce ◽

Jeffrey M. Granja ◽

William J. Greenleaf

Keyword(s):

Transcription Factor ◽

Single Cell ◽

Cancer Cells ◽

High Throughput ◽

Regulatory Networks ◽

Temporal Dynamics ◽

Chromatin Accessibility ◽

Regulatory Regions ◽

Factor Binding ◽

Genome Wide

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

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Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

Genome Biology ◽

10.1186/s13059-021-02325-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tejaswi Iyyanki ◽

Baozhen Zhang ◽

Qixuan Wang ◽

Ye Hou ◽

Qiushi Jin ◽

...

Keyword(s):

Bladder Cancer ◽

Transcription Factor ◽

Cancer Cell ◽

Genome Structure ◽

Transcription Factor Binding ◽

Specific Gene ◽

Open Chromatin ◽

Factor Binding ◽

3D Genome ◽

Genome Wide

Abstract Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown. Result We determine the genome-wide transcriptome, enhancer landscape, and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration. Conclusion In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

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Genome‐wide reduction in chromatin accessibility and unique transcription factor footprints in endothelial cells and fibroblasts in scleroderma skin

Arthritis & Rheumatology ◽

10.1002/art.41694 ◽

2021 ◽

Author(s):

Pei‐Suen Tsou ◽

Pamela J. Palisoc ◽

Mustafa Ali ◽

Dinesh Khanna ◽

Amr H Sawalha

Keyword(s):

Endothelial Cells ◽

Transcription Factor ◽

Chromatin Accessibility ◽

Genome Wide

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Genome-Wide identification of doublesex and Mab-3-Related transcription factor (DMRT) genes in nile tilapia (oreochromis niloticus)

Biotechnology Reports ◽

10.1016/j.btre.2019.e00398 ◽

2019 ◽

Vol 24 ◽

pp. e00398 ◽

Cited By ~ 1

Author(s):

Imran zafar ◽

Mohd Ashraf Rather ◽

Bhushan C. Dhandare

Keyword(s):

Transcription Factor ◽

Oreochromis Niloticus ◽

Nile Tilapia ◽

Genome Wide ◽

Nile Tilapia Oreochromis Niloticus ◽

Related Transcription Factor

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Histone deacetylase 3 preferentially binds and collaborates with the transcription factor RUNX1 to repress AML1–ETO–dependent transcription in t(8;21) AML

Journal of Biological Chemistry ◽

10.1074/jbc.ra119.010707 ◽

2020 ◽

Vol 295 (13) ◽

pp. 4212-4223 ◽

Cited By ~ 1

Author(s):

Chun Guo ◽

Jian Li ◽

Nickolas Steinauer ◽

Madeline Wong ◽

Brent Wu ◽

...

Keyword(s):

Transcription Factor ◽

Fusion Protein ◽

Histone Deacetylase ◽

Transcriptional Activation ◽

Target Genes ◽

Chromosomal Translocation ◽

Histone Deacetylase 3 ◽

Genome Wide ◽

Related Transcription Factor ◽

Almost All

In up to 15% of acute myeloid leukemias (AMLs), a recurring chromosomal translocation, termed t(8;21), generates the AML1–eight–twenty-one (ETO) leukemia fusion protein, which contains the DNA-binding domain of Runt-related transcription factor 1 (RUNX1) and almost all of ETO. RUNX1 and the AML1–ETO fusion protein are coexpressed in t(8;21) AML cells and antagonize each other's gene-regulatory functions. AML1–ETO represses transcription of RUNX1 target genes by competitively displacing RUNX1 and recruiting corepressors such as histone deacetylase 3 (HDAC3). Recent studies have shown that AML1–ETO and RUNX1 co-occupy the binding sites of AML1–ETO–activated genes. How this joined binding allows RUNX1 to antagonize AML1–ETO–mediated transcriptional activation is unclear. Here we show that RUNX1 functions as a bona fide repressor of transcription activated by AML1–ETO. Mechanistically, we show that RUNX1 is a component of the HDAC3 corepressor complex and that HDAC3 preferentially binds to RUNX1 rather than to AML1–ETO in t(8;21) AML cells. Studying the regulation of interleukin-8 (IL8), a newly identified AML1–ETO–activated gene, we demonstrate that RUNX1 and HDAC3 collaboratively repress AML1–ETO–dependent transcription, a finding further supported by results of genome-wide analyses of AML1–ETO–activated genes. These and other results from the genome-wide studies also have important implications for the mechanistic understanding of gene-specific coactivator and corepressor functions across the AML1–ETO/RUNX1 cistrome.

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