scholarly journals Guided nuclear exploration increases CTCF target search efficiency

2018 ◽  
Author(s):  
Anders S. Hansen ◽  
Assaf Amitai ◽  
Claudia Cattoglio ◽  
Robert Tjian ◽  
Xavier Darzacq
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Target Search ◽  
Single Molecule Tracking ◽  
Search Mechanism ◽  
Binding Factor ◽  
Target Sites ◽  
Mammalian Genomes

Mammalian genomes are enormous. For a DNA-binding protein, this means that the number of non-specific, off-target sites vastly exceeds the number of specific, cognate sites. How mammalian DNA-binding proteins overcome this challenge to efficiently locate their target sites is not known. Here through live-cell single-molecule tracking, we show that CCCTC-binding factor, CTCF, is repeatedly trapped in small zones in the nucleus in a manner that is largely dependent on its RNA-binding region (RBR). Integrating theory, we devise a new model, Anisotropic Diffusion through transient Trapping in Zones (ADTZ), to explain this. Functionally, transient RBR-mediated trapping increases the efficiency of CTCF target search by ∼2.5 fold. Since the RBR-domain also mediates CTCF clustering, our results suggest a “guided” mechanism where CTCF clusters concentrate diffusing CTCF proteins near cognate binding sites, thus increasing the local ON-rate. We suggest that local “guiding” may represent a general target search mechanism in mammalian cells.

scholarly journals A nonequilibrium strategy for fast target search on the genome

2020 ◽  
Author(s):  
F. Cagnetta ◽  
D. Michieletto ◽  
D. Marenduzzo
Keyword(s):  
Dna Repair ◽  
Dna Binding ◽  
Kinetic Parameter ◽  
Thermodynamic Equilibrium ◽  
Dna Binding Proteins ◽  
Biological Processes ◽  
Target Search ◽  
Search Mechanism ◽  
Target Sites ◽  
Parameter Values

Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on “chromophoresis”, the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colours (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled - a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform undirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and “dive” deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for DNA repair.

scholarly journals How p53 Molecules Solve the Target DNA Search Problem: A Review

2020 ◽  
Vol 21 (3) ◽  
pp. 1031 ◽  
Author(s):  
Kiyoto Kamagata ◽  
Yuji Itoh ◽  
Dwiky Rendra Graha Subekti
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Search Problem ◽  
Target Search ◽  
Cellular Processes ◽  
Target Dna ◽  
Target Sites ◽  
Dna Strands ◽  
Single Molecule Studies

Interactions between DNA and DNA-binding proteins play an important role in many essential cellular processes. A key function of the DNA-binding protein p53 is to search for and bind to target sites incorporated in genomic DNA, which triggers transcriptional regulation. How do p53 molecules achieve “rapid” and “accurate” target search in living cells? The search dynamics of p53 were expected to include 3D diffusion in solution, 1D diffusion along DNA, and intersegmental transfer between two different DNA strands. Single-molecule fluorescence microscopy enabled the tracking of p53 molecules on DNA and the characterization of these dynamics quantitatively. Recent intensive single-molecule studies of p53 succeeded in revealing each of these search dynamics. Here, we review these studies and discuss the target search mechanisms of p53.

scholarly journals Roles of Emerging RNA-Binding Activity of cGAS in Innate Antiviral Response

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuying Ma ◽  
Xiaohui Wang ◽  
Weisheng Luo ◽  
Ji Xiao ◽  
Xiaowei Song ◽  
...  
Keyword(s):  
Dna Binding ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Binding Protein ◽  
Structural Similarity ◽  
Antiviral Response ◽  
Binding Activity ◽  
Type I Interferons ◽  
Type I ◽  
Innate Antiviral Response

cGAS, a DNA sensor in mammalian cells, catalyzes the generation of 2’-3’-cyclic AMP-GMP (cGAMP) once activated by the binding of free DNA. cGAMP can bind to STING, activating downstream TBK1-IRF-3 signaling to initiate the expression of type I interferons. Although cGAS has been considered a traditional DNA-binding protein, several lines of evidence suggest that cGAS is a potential RNA-binding protein (RBP), which is mainly supported by its interactions with RNAs, RBP partners, RNA/cGAS-phase-separations as well as its structural similarity with the dsRNA recognition receptor 2’-5’ oligoadenylate synthase. Moreover, two influential studies reported that the cGAS-like receptors (cGLRs) of fly Drosophila melanogaster sense RNA and control 3′-2′-cGAMP signaling. In this review, we summarize and discuss in depth recent studies that identified or implied cGAS as an RBP. We also comprehensively summarized current experimental methods and computational tools that can identify or predict RNAs that bind to cGAS. Based on these discussions, we appeal that the RNA-binding activity of cGAS cannot be ignored in the cGAS-mediated innate antiviral response. It will be important to identify RNAs that can bind and regulate the activity of cGAS in cells with or without virus infection. Our review provides novel insight into the regulation of cGAS by its RNA-binding activity and extends beyond its DNA-binding activity. Our review would be significant for understanding the precise modulation of cGAS activity, providing the foundation for the future development of drugs against cGAS-triggering autoimmune diseases such as Aicardi-Gourtières syndrome.

scholarly journals A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9

2017 ◽  
Author(s):  
Yavuz S. Dagdas ◽  
Janice S. Chen ◽  
Samuel H. Sternberg ◽  
Jennifer A. Doudna ◽  
Ahmet Yildiz
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Dna Cleavage ◽  
Genome Engineering ◽  
Divalent Cations ◽  
Guide Rna ◽  
Single Molecule Fret ◽  
Target Sites ◽  
Multiple Conformations ◽  
Dna Binding And Cleavage

AbstractThe Cas9 endonuclease is widely utilized for genome engineering applications by programming its single-guide RNA and ongoing work is aimed at improving the accuracy and efficiency of DNA targeting. DNA cleavage of Cas9 is controlled by the conformational state of the HNH nuclease domain, but the mechanism that governs HNH activation at on-target DNA while reducing cleavage activity at off-target sites remains poorly understood. Using single-molecule FRET, we identified an intermediate state of S. pyogenes Cas9, representing a conformational checkpoint between DNA binding and cleavage. Upon DNA binding, the HNH domain transitions between multiple conformations before docking into its active state. HNH docking requires divalent cations, but not strand scission, and this docked conformation persists following DNA cleavage. Sequence mismatches between the DNA target and guide RNA prevent transitions from the checkpoint intermediate to the active conformation, providing selective avoidance of DNA cleavage at stably bound off-target sites.

scholarly journals Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins

2020 ◽  
Author(s):  
Mathew Stracy ◽  
Jakob Schweizer ◽  
David J Sherratt ◽  
Achillefs N Kapanidis ◽  
Stephan Uphoff ◽  
...  
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Binding Proteins ◽  
Search Time ◽  
Dna Binding Proteins ◽  
Protein Diffusion ◽  
Chromosomal Dna ◽  
Dna Interactions ◽  
Target Search ◽  
Molecular Weights

ABSTRACTDespite their diverse biochemical characteristics and functions, all DNA-binding proteins share the ability to accurately locate their target sites among the vast excess of non-target DNA. Towards identifying universal mechanisms of the target search, we used single-molecule tracking of 11 diverse DNA-binding proteins in living Escherichia coli. The mobility of these proteins during the target search was dictated by DNA interactions, rather than by their molecular weights. By generating cells devoid of all chromosomal DNA, we discovered that the nucleoid does not pose a physical barrier for protein diffusion, but significantly slows the motion of DNA-binding proteins through frequent short-lived DNA interactions. The representative DNA-binding proteins (irrespective of their size, concentration, or function) spend the majority (58-99%) of their search time bound to DNA and occupy as much as ∼30% of the chromosomal DNA at any time. Chromosome-crowding likely has important implications for the function of all DNA-binding proteins.

scholarly journals Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Davide Normanno ◽  
Lydia Boudarène ◽  
Claire Dugast-Darzacq ◽  
Jiji Chen ◽  
Christian Richter ◽  
...  
Keyword(s):  
Dna Binding ◽  
Mammalian Cells ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Target Search

scholarly journals A Study of p53 Action on DNA at the Single Molecule Level

2021 ◽  
Author(s):  
Kiyoto Kamagata
Keyword(s):  
Dna Binding ◽  
Single Molecule ◽  
Dynamic Properties ◽  
Diffusion Mechanism ◽  
Target Search ◽  
Single Molecule Level ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Biophysical Study ◽  
Model Protein

The transcription factor p53 searches for and binds to target sequences within long genomic DNA, to regulate downstream gene expression. p53 possesses multiple disordered and DNA-binding domains, which are frequently observed in DNA-binding proteins. Owing to these properties, p53 is used as a model protein for target search studies. It counters cell stress by utilizing a facilitated diffusion mechanism that combines 3D diffusion in solution, 1D sliding along DNA, hopping/jumping along DNA, and intersegmental transfer between two DNAs. Single-molecule fluorescence microscopy has been used to characterize individual motions of p53 in detail. In addition, a biophysical study has revealed that p53 forms liquid-like droplets involving the functional switch. In this chapter, the target search and regulation of p53 are discussed in terms of dynamic properties.

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