scholarly journals Characterizing protein-DNA binding event subtypes in ChIP-exo data

2018 ◽  
Author(s):  
Naomi Yamada ◽  
William K.M. Lai ◽  
Nina Farrell ◽  
B. Franklin Pugh ◽  
Shaun Mahony
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Regulatory Protein ◽  
Distribution Patterns ◽  
Dna Interaction ◽  
Binding Modes ◽  
Dna Motifs ◽  
Multiple Protein ◽  
Binding Event ◽  
Dna Crosslinking

AbstractMotivationRegulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5’ → 3’ exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes.ResultsTo systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes.AvailabilityChExMix is available from https://github.com/seqcode/[email protected]

scholarly journals Characterizing protein–DNA binding event subtypes in ChIP-exo data

2018 ◽  
Vol 35 (6) ◽  
pp. 903-913 ◽  
Author(s):  
Naomi Yamada ◽  
William K M Lai ◽  
Nina Farrell ◽  
B Franklin Pugh ◽  
Shaun Mahony
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Regulatory Protein ◽  
Dna Interaction ◽  
Supplementary Information ◽  
Binding Modes ◽  
Dna Motifs ◽  
Multiple Protein ◽  
Binding Event ◽  
Dna Crosslinking

Abstract Motivation Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein–protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein–DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein–DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5′ → 3′ exonuclease digestion. Since different regulatory complexes will result in different protein–DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein–DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes. Results To systematically detect multiple protein–DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes. Availability and implementation ChExMix is available from https://github.com/seqcode/chexmix. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Mechanism of NanR gene repression and allosteric induction of bacterial sialic acid metabolism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher R. Horne ◽  
Hariprasad Venugopal ◽  
Santosh Panjikar ◽  
David M. Wood ◽  
Amy Henrickson ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Dna Binding ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Environmental Changes ◽  
Dna Interaction ◽  
Protein Protein Interactions ◽  
Nutrient Source ◽  
Cryo Electron Microscopy ◽  
Close Proximity

AbstractBacteria respond to environmental changes by inducing transcription of some genes and repressing others. Sialic acids, which coat human cell surfaces, are a nutrient source for pathogenic and commensal bacteria. The Escherichia coli GntR-type transcriptional repressor, NanR, regulates sialic acid metabolism, but the mechanism is unclear. Here, we demonstrate that three NanR dimers bind a (GGTATA)3-repeat operator cooperatively and with high affinity. Single-particle cryo-electron microscopy structures reveal the DNA-binding domain is reorganized to engage DNA, while three dimers assemble in close proximity across the (GGTATA)3-repeat operator. Such an interaction allows cooperative protein-protein interactions between NanR dimers via their N-terminal extensions. The effector, N-acetylneuraminate, binds NanR and attenuates the NanR-DNA interaction. The crystal structure of NanR in complex with N-acetylneuraminate reveals a domain rearrangement upon N-acetylneuraminate binding to lock NanR in a conformation that weakens DNA binding. Our data provide a molecular basis for the regulation of bacterial sialic acid metabolism.

scholarly journals Separate physiological roles of specific and non-specific DNA binding of HU protein in Escherichia coli

2021 ◽  
Author(s):  
Sankar Adhya ◽  
Subhash Verma
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Protein Interactions ◽  
Specific Binding ◽  
Bacterial Genome ◽  
Dna Structure ◽  
Binding Modes ◽  
Chromosomal Dna

Conserved in bacteria, the histone-like protein HU is crucial for genome organization and expression of many genes. It binds DNA regardless of the sequence and exhibits two binding affinities in vitro, low-affinity to any B-DNA (non-specific) and high-affinity to DNA with distortions like kinks and cruciforms (structure-specific), but the physiological relevance of the two binding modes needed further investigation. We validated and defined the three conserved lysine residues, K3, K18, and K83, in Escherichia coli HU as critical amino acid residues for both non-specific and structure-specific binding and the conserved proline residue P63 additionally for only the structure-specific binding. By mutating these residues in vivo, we showed that two DNA binding modes of HU play separate physiological roles. The DNA structure-specific binding, occurring at specific sites in the E. coli genome, promotes higher-order DNA structure formation, regulating the expression of many genes, including those involved in chromosome maintenance and segregation. The non-specific binding participates in numerous associations of HU with the chromosomal DNA, dictating chromosome structure and organization. Our findings underscore the importance of DNA structure in transcription regulation and promiscuous DNA-protein interactions in a dynamic organization of a bacterial genome.

scholarly journals HDAC inhibitor Givinostat targets DNA-binding of human CGGBP1

2020 ◽  
Author(s):  
Manthan Patel ◽  
Divyesh Patel ◽  
Subhamoy Datta ◽  
Umashankar Singh
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Histone Deacetylases ◽  
Antineoplastic Agent ◽  
Dna Binding Protein ◽  
Dna Interaction ◽  
Cancer Cell Proliferation ◽  
Screening Assay ◽  
Chemical Inhibitors ◽  
Simple Screening

ABSTRACTThe antineoplastic agent Givinostat inhibits histone deacetylases. We present here our finding that the DNA-binding of human CGGBP1 is also inhibited by Givinostat. CGGBP1, a DNA-binding protein, is required for cancer cell proliferation. In our quest to exploit the potential anti-proliferative effects of CGGBP1 inhibition, we have developed a simple screening assay to identify chemical inhibitors of DNA-protein interactions. We have applied this screen for human CGGBP1 on a library of 1685 compounds and found that Givinostat is a direct inhibitor of CGGBP1-DNA interaction. The mechanism of action of Givinostat should thus extend beyond HDACs to include the inhibition of the myriad functions of CGGBP1 that depend on its binding to the DNA.

scholarly journals Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP type c-di-GMP phosphodiesterases

2021 ◽  
Author(s):  
Michael Y. Galperin ◽  
Shan-Ho Chou
Keyword(s):  
Protein Interactions ◽  
Regulatory Protein ◽  
Second Messenger ◽  
Distribution Patterns ◽  
Distribution Functions ◽  
Amino Acid Residues ◽  
Sequence Motifs ◽  
Protein Protein Interactions ◽  
Conserved Sequence ◽  
Common Domain

The HD-GYP domain, named after two of its conserved sequence motifs, was first described in 1999 as a specialized version of the widespread HD phosphohydrolase domain that had additional highly conserved amino acid residues. Domain associations of HD-GYP indicated its involvement in bacterial signal transduction and distribution patterns of this domain suggested that it could serve as a hydrolase of the bacterial second messenger c-di-GMP, in addition to or instead of the EAL domain. Subsequent studies confirmed the ability of various HD-GYP domains to hydrolyze c-di-GMP to linear pGpG and/or GMP. Certain HD-GYP-containing proteins hydrolyze another second messenger, cGAMP, and some HD-GYP domains participate in regulatory protein-protein interactions. The recently solved structures of HD-GYP domains from four distinct organisms clarified the mechanisms of c-di-GMP binding and metal-assisted hydrolysis. However, the HD-GYP domain is poorly represented in public domain databases, which causes certain confusion about its phylogenic distribution, functions, and domain architectures. Here, we present a refined sequence model for the HD-GYP domain and describe the roles of its most conserved residues in metal and/or substrate binding. We also calculate the numbers of HD-GYPs encoded in various genomes and list the most common domain combinations involving HD-GYP, such as the RpfG (REC-HD-GYP), Bd1817 (DUF3391-HD-GYP), and PmGH (GAF-HD-GYP) protein families. We also provide the descriptions of six HD-GYP-associated domains, including four novel integral membrane sensor domains. This work is expected to stimulate studies of diverse HD-GYP-containing proteins, their N-terminal sensor domains, and the signals to which they respond.

A new visible-light-driven photoelectrochemical biosensor for probing DNA–protein interactions

2015 ◽  
Vol 51 (39) ◽  
pp. 8381-8384 ◽  
Author(s):  
Zheng-Yuan Ma ◽  
Yi-Fan Ruan ◽  
Nan Zhang ◽  
Wei-Wei Zhao ◽  
Jing-Juan Xu ◽  
...  
Keyword(s):  
Dna Binding ◽  
Visible Light ◽  
Protein Interactions ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Dna Interaction ◽  
Visible Light Driven ◽  
Photoelectrochemical Biosensor ◽  
Dna Protein Interactions

A novel photoelectrochemical approach was achieved for the detection of a DNA binding protein via the protein–DNA interaction.

scholarly journals HDAC inhibitor Givinostat targets DNA-binding of human CGGBP1

2020 ◽  
Author(s):  
Manthan Patel ◽  
Divyesh Patel ◽  
Subhamoy Datta ◽  
Umashankar Singh
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Histone Deacetylases ◽  
Antineoplastic Agent ◽  
Dna Binding Protein ◽  
Dna Interaction ◽  
Cancer Cell Proliferation ◽  
Screening Assay ◽  
Chemical Inhibitors ◽  
Simple Screening

Abstract The antineoplastic agent Givinostat inhibits histone deacetylases. We present here our finding that the DNA-binding of human CGGBP1 is also inhibited by Givinostat. CGGBP1, a DNA-binding protein, is required for cancer cell proliferation. In our quest to exploit the potential anti-proliferative effects of CGGBP1 inhibition, we have developed a simple screening assay to identify chemical inhibitors of DNA-protein interactions. We have applied this screen for human CGGBP1 on a library of 1685 compounds and found that Givinostat is a direct inhibitor of CGGBP1-DNA interaction. The mechanism of action of Givinostat should thus extend beyond HDACs to include the inhibition of the myriad functions of CGGBP1 that depend on its binding to the DNA.

scholarly journals A biophysical approach to predicting protein-DNA binding energetics

2014 ◽  
Author(s):  
George Locke ◽  
Alexandre V Morozov
Keyword(s):  
Dna Binding ◽  
High Throughput ◽  
Graphical Representation ◽  
Dna Interaction ◽  
Order Effects ◽  
Binding Modes ◽  
Parameter Uncertainties ◽  
Control Of Gene Expression ◽  
Biophysical Approach

Sequence-specific interactions between proteins and DNA play a central role in DNA replication, repair, recombination, and control of gene expression. These interactions can be studied in vitro using microfluidics, protein-binding microarrays (PBMs), and other high-throughput techniques. Here we develop a biophysical approach to predicting protein-DNA binding specificities from high-throughput in vitro data. Our algorithm, called BindSter, accommodates multiple protein species competing for access to DNA and alternative binding modes of the same protein, while rigorously taking into account all sterically allowed configurations of DNA-bound particles. BindSter can be used with a hierarchy of protein-DNA interaction models of increasing complexity. We observe that the quality of BindSter predictions does not change significantly as some of the energy parameters vary over a sizable range. To take this degeneracy into account, we have developed a graphical representation of parameter uncertainties, called IntervalLogo. We find that our simplest model, in which each nucleotide in the binding site is treated independently, performs better than previous biophysical approaches. The extensions of this model, in which contributions of longer words are also considered, result in further improvements, underscoring the importance of higher-order effects in protein-DNA energetics. In contrast, we find little evidence for multiple binding modes for the transcription factors (TFs) in our dataset. Furthermore, there is limited consistency in predictions for the same TF utilizing microfluidics and PBM experimental platforms.

scholarly journals HDAC inhibitor Givinostat targets DNA-binding of human CGGBP1

2020 ◽  
Author(s):  
Manthan Patel ◽  
Divyesh Patel ◽  
Subhamoy Datta ◽  
Umashankar Singh
Keyword(s):  
Dna Binding ◽  
Protein Interactions ◽  
Histone Deacetylases ◽  
Antineoplastic Agent ◽  
Dna Binding Protein ◽  
Dna Interaction ◽  
Cancer Cell Proliferation ◽  
Screening Assay ◽  
Chemical Inhibitors ◽  
Simple Screening

Abstract The antineoplastic agent Givinostat inhibits histone deacetylases. We present here our finding that the DNA-binding of human CGGBP1 is also inhibited by Givinostat. CGGBP1, a DNA-binding protein, is required for cancer cell proliferation. In our quest to exploit the potential anti-proliferative effects of CGGBP1 inhibition, we have developed a simple screening assay to identify chemical inhibitors of DNA-protein interactions. We have applied this screen for human CGGBP1 on a library of 1685 compounds and found that Givinostat is a direct inhibitor of CGGBP1-DNA interaction. The mechanism of action of Givinostat should thus extend beyond HDACs to include the inhibition of the myriad functions of CGGBP1 that depend on its binding to the DNA.

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