Enhanced Maps of Transcription Factor Binding Sites Improve Regulatory Networks Learned from Accessible Chromatin Data

AbstractThe control of gene expression by transcription factor binding sites frequently determines phenotype. However, it has been difficult to assay the function of single transcription factor binding sites within larger transcription networks. Here, we developed such a method by using deactivated Cas9 to disrupt binding to specific sites on the genome. Since CRISPR guide RNAs are longer than transcription factor binding sites, flanking sequence can be used to target specific sites. Targeting deactivated Cas9 to a specific Oct4 binding site in the Nanog promoter blocked Oct4 binding, reduced Nanog expression, and slowed division. Multiple guide RNAs allows simultaneous inhibition of multiple binding sites and conditionally-destabilized dCas9 allows rapid reversibility. The method is a novel high-throughput approach to systematically interrogate cis-regulatory function within complex regulatory networks.

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

10.1101/801001 ◽

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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Identification of Transcription Factor Binding Sites using ATAC-seq

10.1101/362863 ◽

2018 ◽

Cited By ~ 2

Author(s):

Zhijian Li ◽

Marcel H. Schulz ◽

Martin Zenke ◽

Ivan G. Costa

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Markov Models ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Variable Order ◽

Open Chromatin ◽

Factor Binding ◽

Specific Protocol ◽

Accessible Chromatin

1AbstractTransposase-Accessible Chromatin (ATAC) followed by sequencing (ATAC-seq) is a simple and fast protocol for detection of open chromatin. However, computational footprinting in ATAC-seq, i.e. search for regions with depletion of cleavage events due to transcription factor binding sites, has been poorly explored so far. We propose HINT-ATAC, a footprinting method that addresses ATAC-seq specific protocol artifacts. HINT-ATAC uses a probabilistic framework based on Variable-order Markov models to learn the complex sequence cleavage preferences of the transposase enzyme. Moreover, we observed specific strand specific cleavage patterns around the binding sites of transcription factors, which are determined by local nucleosome architecture. HINT-ATAC explores local nucleosome architecture to significantly outperform competing footprinting methods in predicting transcription factor binding sites by ChIP-seq. HINT-ATAC is an open source software and available online at www.regulatory-genomics.org/hint

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Cross-species analysis of melanoma enhancer logic using deep learning

10.1101/2019.12.21.885715 ◽

2019 ◽

Cited By ~ 2

Author(s):

Liesbeth Minnoye ◽

Ibrahim Ihsan Taskiran ◽

David Mauduit ◽

Maurizio Fazio ◽

Linde Van Aerschot ◽

...

Keyword(s):

Transcription Factor ◽

Melanoma Cell ◽

Gene Regulatory Networks ◽

Binding Sites ◽

Regulatory Networks ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding ◽

Depth Analysis ◽

Gene Regulatory

AbstractGenomic enhancers form the central nodes of gene regulatory networks by harbouring combinations of transcription factor binding sites. Deciphering the combinatorial code by which these binding sites are assembled within enhancers is indispensable to understand their regulatory involvement in establishing a cell’s phenotype, especially within biological systems with dysregulated gene regulatory networks, such as melanoma. In order to unravel the enhancer logic of the two most common melanoma cell states, namely the melanocytic and mesenchymal-like state, we combined comparative epigenomics with machine learning. By profiling chromatin accessibility using ATAC-seq on a cohort of 27 melanoma cell lines across six different species, we demonstrate the conservation of the two main melanoma states and their underlying master regulators. To perform an in-depth analysis of the enhancer architecture, we trained a deep neural network, called DeepMEL, to classify melanoma enhancers not only in the human genome, but also in other species. DeepMEL revealed the presence, organisation and positional specificity of important transcription factor binding sites. Together, this extensive analysis of the melanoma enhancer code allowed us to propose the concept of a core regulatory complex binding to melanocytic enhancers, consisting of SOX10, TFAP2A, MITF and RUNX, and to disentangle their individual roles in regulating enhancer accessibility and activity.

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