Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes
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Capturing Binding Location and Speed: Transcription factor–binding sites in chromatin can be mapped by the chromatin immunoprecipitation (ChIP) assay, which analyzes formaldehyde-fixed chromatin fragments obtained from cells. However, the standard ChIP assay does not provide information about how stable the inter-actions are. Other approaches, including live-cell imaging, can reveal aspects of the dynamic behavior of transcription factors but are limited either in location precision or time resolution. Poorey et al. (p. 369 , published online 3 October) developed a model to explain how the ChIP signal relates to formaldehyde cross-linking time, and they developed a method to measure chromatin site–specific binding dynamics with high temporal resolution.
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ChIP signals vary relative to formaldehyde crosslinking time.
“and ChIP signals vary in general relative to formaldehyde crosslinking time.140, 141”
From Census and evaluation of p53 target genes (2017) · cites this paper as [140]
The ChIP technique in general can produce false findings.
“Notably, the ChIP technique in general can produce false findings.”
From Census and evaluation of p53 target genes (2017) · cites this paper as [140]
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“Formaldehyde is very water soluble, is rapidly taken up into cells, and its reaction kinetics are fast 23,24 .”
The N-Terminal Tail of Histone H3 Regulates Copper Homeostasis in Saccharomyces cerevisiae
Singh, S., Sahu, R. K., & Tomar, R. S. (2020) · Molecular and Cellular Biology · doi:10.1128/mcb.00210-20 · Cited by 18 · see citing works
“Although Ace1 binds very transiently, its fast cycling at the promoter leads to transcription bursts of CUP1 (16, 17, 57).”
BackgroundGenome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function
de Jonge, W. J., Brok, M. O., Lijnzaad, P., Kemmeren, P., & Holstege, F. C. P. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209885 · Cited by 17 · see citing works
“DIVORSEQ directly measures off-rates and has been designed for application alongside on-rate measurement by cross-linking kinetic analyses (Poorey et al, 2013), that has yet to be applied at the genomic scale (Zaidi et al, 2017).”
Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions
Molitor, J., Mallm, J., Rippe, K., & Erdel, F. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2017.01.001 · Cited by 17 · see citing works
Second-generation method for analysis of chromatin binding with formaldehyde–cross-linking kinetics
Zaidi, H., Hoffman, E. A., Shetty, S. J., Bekiranov, S., & Auble, D. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.m117.796441 · Cited by 17 · see citing works
“This long lifetime is consistent with both prior CLK and live-imaging data (15).”
BackgroundMethodInfluentialSelf-citationXL-DNase-seq: improved footprinting of dynamic transcription factors
Oh, K.-S., Ha, J., Baek, S., & Sung, M.-H. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0277-6 · Cited by 11 · see citing works
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Dynamic Chromatin Regulation from a Single Molecule Perspective
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Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP–DNA dissociation
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“These results are consistent with recent studies on Mot1 function implicating that it mainly removes weakly bound TBP (44,45).”
BackgroundResultInfluentialSelf-citationRNA synthesis is associated with multiple TBP-chromatin binding events
Zaidi, H., Auble, D., & Bekiranov, S. (2017) · Scientific Reports · doi:10.1038/srep39631 · Cited by 10 · see citing works
Self-citationMolecular Mechanism of Mot1, a TATA-binding Protein (TBP)-DNA Dissociating Enzyme
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“erentially increases the dynamics of less stably bound TBP molecules at diverse sites (36).”
BackgroundSelf-citationRecruitment of RAG1 and RAG2 to Chromatinized DNA during V(D)J Recombination
Shetty, K. S., & Schatz, D. G. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00219-15 · Cited by 9 · see citing works
“A technique that provides high temporal resolution, such as a modified ChIP assay that relies on short formaldehyde cross-linking incubation times (48) or single-molecule imaging (49), would be necessary to dissect such features of RAG binding.”
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“However, some concerns have been raised recently [76,77].”
BackgroundAnalysis of chromatin binding dynamics using the crosslinking kinetics (CLK) method
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“Previously, we used a formaldehyde crosslinking kinetic approach, called CLK, to measure chromatin binding dynamics (Poorey et al, 2013).”
MethodSelf-citationChIP-seq Analysis of Condensin Complex in Cultured Mammalian Cells
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“Therefore, a single formaldehyde crosslinking step can substantially fi x and accumulate short-lived TF occupancy events, and compromise the measured spectrum of residence time across different TFs, and across different genomic sites for the same TF (Poorey et al, 2013).”
The changing chromatome as a driver of disease: A panoramic view from different methodologies
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“[6] Furthermore, the temporal residency of chromatin proteins can vary remarkably, ranging from a few milliseconds for transcription factors (TF) to several hours for stable histone proteins.[7,8] Perturbations in chromatome composition, protein distribution across the genome, and chromatin interaction dynamics aredir…”
BackgroundGenome-wide promoter assembly in E. coli measured at single-base resolutionPreprint
John, J. D., Jabbar, J., Badjatia, N., Rossi, M. J., Lai, W., & Pugh, B. F. (2022) · Genome Research · doi:10.1101/gr.276544.121 · Cited by 5 · see citing works
On the Ability of Formaldehyde to Act as a Tethering Catalyst in Water
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Fixated on fixation - using ChIP to interrogate the dynamics of chromatin interactions
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“[2] applied chemical reaction rate theory to model what happens during a ChIP experiment and have consequently adjusted the standard ChIP assay described above to allow the extraction of kinetic information.”
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“Yeast strains, wild type (WT) and overexpression (OE) for each TF of interest (see Poorey et al., 2013 and Zaidi et al., 2017 for strain lists) 21.”
InfluentialSelf-citationHeterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module
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Chromatin Immunoprecipitation Assays on Medulloblastoma Cell Line DAOY
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High-resolution mapping of transcription factor binding sites on native chromatin
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“To improve the temporal resolution of PdF, the cross-linking kinetic (CLK) technology (Poorey et al., 2013 ) might be used, by which the protein–DNA binding detection can be accomplished in a time scale of seconds.”
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Retrieving chromatin patterns from deep sequencing data using correlation functionsPreprint
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The smc5/6 complex : linking DNA replication with chromosome segregation
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Transcriptional Regulation by Mot1 and Spt16
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XL-DNase-Seq: Footprinting Analysis of Dynamic Transcription Factors
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“In contrast, TFs bind to DNA in a sequence dependent manner with highly variable affinities and dissociation rates to form TF-DNA complexes with residence times varying from seconds, for dynamic TFs, to hours for stable TFs [22, 27, 53].”
Discovery and analysis of silencers in Drosophila acting as enhancers in other cellular contexts
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- Authors
- Poorey, K., Viswanathan, R., Carver, M. N., Karpova, T. S., Cirimotich, S. M., McNally, J. G., Bekiranov, S., & Auble, D. T.
- Affiliations
- University of Virginia Health System (US)
- National Institutes of Health (US)
- Corresponding author
- Poorey, Kunal
- Viswanathan, Ramya
- Bekiranov, Stefan
- Auble, David T.
- ORCID
- Venue
- Science
- Published
- 2013-10-18
- Volume
- 342
- Issue
- 6156
- Pages
- 369-372
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3997053
- OpenAlex
- W2033265108
- Cited by
- 88
- References
- 37
- Citations by year
- 2026: 2 · 2024: 4 · 2022: 4 · 2021: 2 · 2020: 5 · 2019: 5 · 2018: 4 · 2017: 19 · 2016: 11 · 2015: 14 · 2014: 14 · 2013: 4
- FWCI
- 6.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM 55763, R01GM055763)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
- Keywords
- single-copy gene, chromatin immunoprecipitation, formaldehyde crosslinking, TATA-binding protein, promoter interactions, live-cell imaging
- MeSH terms
- Adenosine Triphosphatases, Chromatin, Cross-Linking Reagents, DNA-Binding Proteins, Formaldehyde, Gene Expression Regulation, Kinetics, Promoter Regions, Genetic, Transcription Factors, Gene Dosage, Saccharomyces cerevisiae Proteins, TATA-Box Binding Protein, TATA-Binding Protein Associated Factors, Chromatin Immunoprecipitation
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