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Pranzatelli TJF, Michael DG, Chiorini JA. ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference. BMC Genomics 2018; 19:563. [PMID: 30064353 PMCID: PMC6069842 DOI: 10.1186/s12864-018-4943-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/16/2018] [Indexed: 01/07/2023] Open
Abstract
Background Chromatin accessibility profiling assays such as ATAC-seq and DNase1-seq offer the opportunity to rapidly characterize the regulatory state of the genome at a single nucleotide resolution. Optimization of molecular protocols has enabled the molecular biologist to produce next-generation sequencing libraries in several hours, leaving the analysis of sequencing data as the primary obstacle to wide-scale deployment of accessibility profiling assays. To address this obstacle we have developed an optimized and efficient pipeline for the analysis of ATAC-seq and DNase1-seq data. Results We executed a multi-dimensional grid-search on the NIH Biowulf supercomputing cluster to assess the impact of parameter selection on biological reproducibility and ChIP-seq recovery by analyzing 4560 pipeline configurations. Our analysis improved ChIP-seq recovery by 15% for ATAC-seq and 3% for DNase1-seq and determined that PCR duplicate removal improves biological reproducibility by 36% without significant costs in footprinting transcription factors. Our analyses of down sampled reads identified a point of diminishing returns for increased library sequencing depth, with 95% of the ChIP-seq data of a 200 million read footprinting library recovered by 160 million reads. Conclusions We present optimized ATAC-seq and DNase-seq pipelines in both Snakemake and bash formats as well as optimal sequencing depths for ATAC-seq and DNase-seq projects. The optimized ATAC-seq and DNase1-seq analysis pipelines, parameters, and ground-truth ChIP-seq datasets have been made available for deployment and future algorithmic profiling. Electronic supplementary material The online version of this article (10.1186/s12864-018-4943-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J F Pranzatelli
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20816, USA
| | - Drew G Michael
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20816, USA
| | - John A Chiorini
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 10 Center Drive, Bethesda, MD, 20816, USA.
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Nguyen Le Minh P, Velázquez Ruiz C, Vandermeeren S, Abwoyo P, Bervoets I, Charlier D. Differential protein-DNA contacts for activation and repression by ArgP, a LysR-type (LTTR) transcriptional regulator in Escherichia coli. Microbiol Res 2018; 206:141-58. [PMID: 29146251 DOI: 10.1016/j.micres.2017.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/19/2017] [Accepted: 10/20/2017] [Indexed: 11/21/2022]
Abstract
ArgP is a LysR-type transcriptional regulator (LTTR) that operates with two effector molecules, lysine and arginine, to differentially regulate gene expression. Effector-free ArgP stimulates transcription of all investigated regulon members, except argO, whereas lysine abolishes this effect. Activation of argO, encoding an exporter for arginine and canavanine, is strictly dependent on arginine-bound ArgP. Lysine counteracts this effect and even though lysine-bound ArgP stimulates RNA polymerase recruitment at the argO promoter, the complex is non-productive. It is presently unclear what distinguishes argO from other ArgP targets and how binding of arginine and lysine translates in antagonistic effects on promoter activity. Here we generate high resolution contact maps of effector-free and effector-bound ArgP-DNA interactions and identify the sequence 5'-CTTAT as the consensus recognition motif for ArgP binding. argO is the only operator at which ArgP binding overlaps the -35 promoter element and binding of arginine results in a repositioning of the promoter proximal bound ArgP-arg subunits. This effect was mimicked by the generation of a 10bp insertion mutant (ins-10) in the argO operator that renders its activation by ArgP arginine-independent. ArgP-induced DNA bending of the argO operator by approximately 60° was found to be effector independent. An ArgP:DNA binding stoichiometry of 4:1 indicates binding of four ArgP subunits even to DNA constructs that are truncated for one binding subsite (ΔABS). These results provide insight into the molecular mechanisms of ArgP-mediated regulation and a molecular explanation for the unique arginine-dependence of argO activation that distinguishes this particular ArgP target from all others.
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Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D. Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. Mol Cell 2017; 67:411-422.e4. [PMID: 28735898 PMCID: PMC5548954 DOI: 10.1016/j.molcel.2017.06.027] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 05/22/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022]
Abstract
Transcription initiation entails chromatin opening followed by pre-initiation complex formation and RNA polymerase II recruitment. Subsequent polymerase elongation requires additional signals, resulting in increased residence time downstream of the start site, a phenomenon referred to as pausing. Here, we harnessed single-molecule footprinting to quantify distinct steps of initiation in vivo throughout the Drosophila genome. This identifies the impact of promoter structure on initiation dynamics in relation to nucleosomal occupancy. Additionally, perturbation of transcriptional initiation reveals an unexpectedly high turnover of polymerases at paused promoters-an observation confirmed at the level of nascent RNAs. These observations argue that absence of elongation is largely caused by premature termination rather than by stable polymerase stalling. In support of this non-processive model, we observe that induction of the paused heat shock promoter depends on continuous initiation. Our study provides a framework to quantify protein binding at single-molecule resolution and refines concepts of transcriptional pausing.
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Affiliation(s)
- Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
| | - Dilek Imanci
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Faculty of Sciences, Petersplatz 1, 4001 Basel, Switzerland.
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Wang L, Lu H, Wang Y, Yang S, Xu H, Cheng K, Zhao Y, Tian B, Hua Y. An Improved Method for Identifying Specific DNA-Protein-Binding Sites In Vitro. Mol Biotechnol 2017; 59:59-65. [PMID: 28132389 DOI: 10.1007/s12033-017-9993-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Binding of proteins to specific DNA sequences is essential for a variety of cellular processes such as DNA replication, transcription and responses to external stimuli. Chromatin immunoprecipitation is widely used for determining intracellular DNA fragments bound by a specific protein. However, the subsequent specific or accurate DNA-protein-binding sequence is usually determined by DNA footprinting. Here, we report an alternative method for identifying specific sites of DNA-protein-binding (designated SSDP) in vitro. This technique is mainly dependent on antibody-antigen immunity, simple and convenient, while radioactive isotope labeling and optimization of partial degradation by deoxyribonuclease (DNase) are avoided. As an example, the specific binding sequence of a target promoter by DdrO (a DNA damage response protein from Deinococcus radiodurans) in vitro was determined by the developed method. The central sequence of the binding site could be easily located using this technique.
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Bordiya Y, Kang HG. Genome-Wide Analysis of Chromatin Accessibility in Arabidopsis Infected with Pseudomonas syringae. Methods Mol Biol 2017; 1578:263-272. [PMID: 28220432 DOI: 10.1007/978-1-4939-6859-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Changes in chromatin accessibility are an important aspect of the molecular changes that occur in eukaryotic cells responding to stress, and they appear to play a critical role in stress-induced transcriptional activation/reprogramming and epigenetic changes. In plants, pathogen infection has been shown to induce rapid and drastic transcriptional reprogramming; growing evidence suggests that chromatin remodeling plays an essential role in this phenomenon. The recent development of genomic tools to assess chromatin accessibility presents a significant opportunity to investigate the relationship between chromatin dynamicity and gene expression. In this protocol, we have adopted a popular chromatin accessibility assay, DNase-seq, to measure chromatin accessibility in Arabidopsis infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). DNase-seq provides information on chromatin accessibility through the sequencing of DNA fragments generated by DNase I digestion of open chromatin, followed by mapping these sequences on a reference genome. Of the two popular DNase-seq approaches, we based our method on the Stamatoyannopoulos protocol, which involves two DNase cleavages rather than a single cleavage, followed by size fractionation. Please note that this two-cleavage approach is widely accepted and has been used extensively by ENCODE (Encyclopedia of DNA Elements) project, a public research consortium investigating cis- and trans-elements in the transcriptional regulation in animal cells. To enhance the quality of the chromatin accessibility assay, we modified this protocol by including two centrifugation steps for nuclear enrichment and size fractionation and an extra washing step for removal of chloroplasts and Pst. The outcomes obtained by this approach are also discussed.
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Affiliation(s)
- Yogendra Bordiya
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX, 78748, USA
| | - Hong-Gu Kang
- Department of Biology, Texas State University, 601 University Dr., San Marcos, TX, 78748, USA.
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Matteau D, Rodrigue S. Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo). Methods Mol Biol 2015; 1334:173-193. [PMID: 26404150 DOI: 10.1007/978-1-4939-2877-4_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA-binding proteins play a crucial role in all living organisms by interacting with various DNA sequences across the genome. While several methods have been used to study the interaction between DNA and proteins in vitro, chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard technique for identifying the genome-wide location of DNA-binding proteins in vivo. However, the resolution of standard ChIP-seq methodology is limited by the DNA fragmentation process and presence of contaminating DNA. A significant improvement of the ChIP-seq technique results from the addition of an exonuclease treatment during the immunoprecipitation step (ChIP-exo) that lowers background noise and more importantly increases the identification of binding sites to a level near to single-base resolution by effectively footprinting DNA-bound proteins. By doing so, ChIP-exo offers new opportunities for a better characterization of the complex and fascinating architecture that resides in DNA-proteins interactions and provides new insights for the comprehension of important molecular mechanisms.
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Affiliation(s)
- Dominick Matteau
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1
| | - Sébastien Rodrigue
- Département de biologie, Faculté des sciences, Université de Sherbrooke, 2500 boulevard de l'Université, Sherbrooke, QC, Canada, J1K 2R1.
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Wittayanarakul K, Anthony NG, Treesuwan W, Hannongbua S, Alniss H, Khalaf AI, Suckling CJ, Parkinson JA, Mackay SP. Ranking ligand affinity for the DNA minor groove by experiment and simulation. ACS Med Chem Lett 2010; 1:376-80. [PMID: 24900221 DOI: 10.1021/ml100047n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2010] [Accepted: 07/12/2010] [Indexed: 11/30/2022] Open
Abstract
The structural and thermodynamic basis for the strength and selectivity of the interactions of minor groove binders (MGBs) with DNA is not fully understood. In 2003, we reported the first example of a thiazole-containing MGB that bound in a phase-shifted pattern that spanned six base pairs rather than the usual four (for tricyclic distamycin-like compounds). Since then, using DNA footprinting, NMR spectroscopy, isothermal titration calorimetry, and molecular dynamics, we have established that the flanking bases around the central four being read by the ligand have subtle effects on recognition. We have investigated the effect of these flanking sequences on binding and the reasons for the differences and established a computational method to rank ligand affinity against varying DNA sequences.
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Affiliation(s)
- Kitiyaporn Wittayanarakul
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Nahoum G. Anthony
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Witcha Treesuwan
- Chemistry Department and Center of Nanotechnology, Kasetsart University, Bangkok 10900, Thailand
| | - Supa Hannongbua
- Chemistry Department and Center of Nanotechnology, Kasetsart University, Bangkok 10900, Thailand
| | - Hasan Alniss
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
| | - Abedawn I. Khalaf
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Colin J. Suckling
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John A Parkinson
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Simon P. Mackay
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 27 Taylor Street, Glasgow G4 0NR, United Kingdom
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