scholarly journals Zelda potentiates transcription factor binding to zygotic enhancers by increasing local chromatin accessibility during early Drosophila melanogaster embryogenesis

2018 ◽  
Author(s):  
Xiao-Yong Li ◽  
Michael B. Eisen
Keyword(s):  
Transcription Factor ◽  
Structural Changes ◽  
Temporal Dynamics ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Additional Function ◽  
Factor Binding ◽  
Early Embryos ◽  
Chromatin Structural ◽  
Pioneer Factor

AbstractThe maternally deposited transcription factor Zelda binds to and is required for the activation of a large number of genes in early Drosophila development, and has been suggested to act as a pioneer factor. In this study, we investigated the temporal dynamics of Zelda binding along with the maternal patterning factors Dorsal and Caudal during early embryogenesis. We found in regions bound by Zelda and either Dorsal or Caudal, Zelda binding was detected, and reached maximum levels, earlier than Caudal and Dorsal, providing support of its role as a pioneer factor. We found that Dorsal and Caudal binding correlated strongly with Zelda binding at mitotic cycle 12, suggesting that Zelda is important for early binding by these factors and early onset of their target gene expression. At the same time, we show that among Dorsal target enhancers, the dorsal and ventral ectoderm enhancers are much more strongly associated with Zelda than mesoderm enhancers, revealing an additional function of Zelda in coordinating spatial activity of enhancers. We have also investigated the role of Zelda on chromatin structure. We found that in early embryos, before Dorsal and Caudal are bound at significant levels, Zelda binding is associated with histone acetylation and local histone depletion. These chromatin associated changes accompanied with increased local chromatin accessibility were also detected around Zelda peaks in coding sequences that do not appear to play a role in subsequent transcription factor binding. These findings suggest that Zelda binding itself can lead to chromatin structural changes. Finally, we found that Zelda motifs, both bound and unbound, tend to be associated with positioned nucleosomes, which we suggest may be important for the regulatory specificity of enhancers.

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

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.

scholarly journals Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

2010 ◽  
Vol 21 (3) ◽  
pp. 447-455 ◽  
Author(s):  
R. Pique-Regi ◽  
J. F. Degner ◽  
A. A. Pai ◽  
D. J. Gaffney ◽  
Y. Gilad ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Dna Sequence ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Factor Binding

Defined Structural Changes Occur in a Nucleosome upon Amt1 Transcription Factor Binding

2004 ◽  
Vol 342 (5) ◽  
pp. 1391-1402 ◽  
Author(s):  
Cindy L. White ◽  
Karolin Luger
Keyword(s):  
Transcription Factor ◽  
Structural Changes ◽  
Transcription Factor Binding ◽  
Factor Binding

scholarly journals Assessing the model transferability for prediction of transcription factor binding sites based on chromatin accessibility

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Sheng Liu ◽  
Cristina Zibetti ◽  
Jun Wan ◽  
Guohua Wang ◽  
Seth Blackshaw ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Factor Binding ◽  
Model Transferability

scholarly journals Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Lianggang Huang ◽  
Xuejie Li ◽  
Liangbo Dong ◽  
Bin Wang ◽  
Li Pan
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Filamentous Fungi ◽  
Binding Sites ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Culture Conditions ◽  
Factor Binding ◽  
Tn5 Transposase

Abstract Background The identification of open chromatin regions and transcription factor binding sites (TFBs) is an important step in understanding the regulation of gene expression in diverse species. ATAC-seq is a technique used for such purpose by providing high-resolution measurements of chromatin accessibility revealed through integration of Tn5 transposase. However, the existence of cell walls in filamentous fungi and associated difficulty in purifying nuclei have precluded the routine application of this technique, leading to a lack of experimentally determined and computationally inferred data on the identity of genome-wide cis-regulatory elements (CREs) and TFBs. In this study, we constructed an ATAC-seq platform suitable for filamentous fungi and generated ATAC-seq libraries of Aspergillus niger and Aspergillus oryzae grown under a variety of conditions. Results We applied the ATAC-seq assay for filamentous fungi to delineate the syntenic orthologue and differentially changed chromatin accessibility regions among different Aspergillus species, during different culture conditions, and among specific TF-deleted strains. The syntenic orthologues of accessible regions were responsible for the conservative functions across Aspergillus species, while regions differentially changed between culture conditions and TFs mutants drove differential gene expression programs. Importantly, we suggest criteria to determine TFBs through the analysis of unbalanced cleavage of distinct TF-bound DNA strands by Tn5 transposase. Based on this criterion, we constructed data libraries of the in vivo genomic footprint of A. niger under distinct conditions, and generated a database of novel transcription factor binding motifs through comparison of footprints in TF-deleted strains. Furthermore, we validated the novel TFBs in vivo through an artificial synthetic minimal promoter system. Conclusions We characterized the chromatin accessibility regions of filamentous fungi species, and identified a complete TFBs map by ATAC-seq, which provides valuable data for future analyses of transcriptional regulation in filamentous fungi.

scholarly journals The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

2011 ◽  
Vol 12 (4) ◽  
pp. R34 ◽  
Author(s):  
Xiao-Yong Li ◽  
Sean Thomas ◽  
Peter J Sabo ◽  
Michael B Eisen ◽  
John A Stamatoyannopoulos ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Factor Binding

scholarly journals Chromatin accessibility and transcription factor binding through the perspective of mitosis

Transcription ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 236-240
Author(s):  
Rémi-Xavier Coux ◽  
Nick D.L. Owens ◽  
Pablo Navarro
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Factor Binding

scholarly journals Uncovering divergence in gene expression regulation in the adaptation of yeast to nitrogen scarcity

2021 ◽  
Author(s):  
Carlos A. Villarroel ◽  
Paulo Canessa ◽  
Macarena Bastias ◽  
Francisco A Cubillos
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Gene Expression Regulation ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Expression Regulation ◽  
Factor Binding ◽  
Allele Specific ◽  
The Impact ◽  
Allelic Bias

Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism has been described among natural yeast populations, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq and RNA-seq. We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the Nitrogen Catabolite Repression regulatory pathway and demonstrates a cis x environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility and allelic differences in transcription factor binding in response to low nitrogen culture conditions.

scholarly journals Constructing Gene Regulatory Networks using Epigenetic Data

2020 ◽  
Author(s):  
Abhijeet Rajendra Sonawane ◽  
Dawn L. DeMeo ◽  
John Quackenbush ◽  
Kimberly Glass
Keyword(s):  
Transcription Factor ◽  
Gene Regulatory Networks ◽  
Message Passing ◽  
Regulatory Networks ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Sequence Motif ◽  
Epigenetic Information ◽  
Factor Binding ◽  
Gene Regulatory

AbstractThe biological processes that drive cellular function can be represented by a complex network of interactions between regulators (transcription factors) and their targets (genes). A cell’s epigenetic state plays an important role in mediating these interactions, primarily by influencing chromatin accessibility. However, effectively leveraging epigenetic information when constructing regulatory networks remains a challenge. We developed SPIDER, which incorporates epigenetic information (DNase-Seq) into a message passing framework in order to estimate gene regulatory networks. We validated SPIDER’s predictions using ChlP-Seq data from ENCODE and found that SPIDER networks were more accurate than other publicly available, epigenetically informed regulatory networks as well as networks based on methods that leverage epigenetic data to predict transcription factor binding sites. SPIDER was also able to improve the detection of cell line specific regulatory interactions. Notably, SPIDER can recover ChlP-seq verified transcription factor binding events in the regulatory regions of genes that do not have a corresponding sequence motif. Constructing biologically interpretable, epigenetically informed networks using SPIDER will allow us to better understand gene regulation as well as aid in the identification of cell-specific drivers and biomarkers of cellular phenotypes.

scholarly journals TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence

2019 ◽  
Author(s):  
Ningxin Ouyang ◽  
Alan P. Boyle
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Training Data ◽  
Distinct Advantage ◽  
Factor Binding ◽  
Dna Elements

AbstractTranscription is tightly regulated by cis-regulatory DNA elements where transcription factors can bind. Thus, identification of transcription factor binding sites is key to understanding gene expression and whole regulatory networks within a cell. The standard approaches for transcription factor binding sites (TFBSs) prediction such as position weight matrices (PWMs) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) are widely used but have their drawbacks such as high false positive rates and limited antibody availability, respectively. Several computational footprinting algorithms have been developed to detect TFBSs by investigating chromatin accessibility patterns, but also have their limitations. To improve on these methods, we have developed a footprinting method to predict Transcription factor footpRints in Active Chromatin Elements (TRACE). Trace incorporates DNase-seq data and PWMs within a multivariate Hidden Markov Model (HMM) to detect footprint-like regions with matching motifs. Trace is an unsupervised method that accurately annotates binding sites for specific TFs automatically with no requirement on pre-generated candidate binding sites or ChIP-seq training data. Compared to published footprinting algorithms, TRACE has the best overall performance with the distinct advantage of targeting multiple motifs in a single model.

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