Extended and dynamic linker histone-DNA Interactions control chromatosome compaction

Rudnizky, Sergei; Khamis, Hadeel; Ginosar, Yuval; Goren, Efrat; Melamed, Philippa; Kaplan, Ariel

doi:10.1016/j.molcel.2021.06.006

Cited by 15 publications

(18 citation statements)

References 76 publications

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“…The binding mode of H1 may switch and/or the CTD may either remain unbound from nucleosomal DNA, or given the unstructured and flexible nature of the CTD, it may bind to the other DNA linker. One study using an optical trap to measure DNA unzipping found that mouse H1.0 binds on dyad, but when one side of the nucleosome is repeatedly unzipped without causing nucleosome dissociation, H1 may switch to an off dyad binding mode . Unfortunately, the design of our FRET experiments and the nature of FRET make quantitative determination of the population of H1 in each binding mode difficult due to multiple affects.…”

Section: Discussionmentioning

confidence: 99%

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

et al. 2022

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The linker histone H1 is a highly prevalent protein that compacts chromatin and regulates DNA accessibility and transcription. However, the mechanisms behind H1 regulation of transcription factor (TF) binding within nucleosomes are not well understood. Using in vitro fluorescence assays, we positioned fluorophores throughout human H1 and the nucleosome, then monitored the distance changes between H1 and the histone octamer, H1 and nucleosomal DNA, or nucleosomal DNA and the histone octamer to monitor the H1 movement during TF binding. We found that H1 remains bound to the nucleosome dyad, while the C terminal domain (CTD) releases the linker DNA during nucleosome partial unwrapping and TF binding. In addition, mutational studies revealed that a small 16 amino acid region at the beginning of the H1 CTD is largely responsible for altering nucleosome wrapping and regulating TF binding within nucleosomes. We then investigated physiologically relevant post-translational modifications (PTMs) in human H1 by preparing fully synthetic H1 using convergent hybrid phase native chemical ligation. Both individual PTMs and combinations of phosphorylation and citrullination of H1 had no detectable influence on nucleosome binding and nucleosome wrapping, and had only a minor impact on H1 regulation of TF occupancy within nucleosomes. This suggests that these H1 PTMs function by other mechanisms. Our results highlight the importance of the H1 CTD, in particular, the first 16 amino acids, in regulating nucleosome linker DNA dynamics and TF binding within the nucleosome.

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Section: Discussionmentioning

confidence: 99%

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

et al. 2022

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“…According to the DNA footprinting data ( Figure 4 A, region +(35–60)), the strong contacts affecting RNAP’s progression through the +24 position can be found near +(60–70) region (SHL-1). The region of strong DNA-histone contacts is present at the SHL-1 region [ 70 , 71 ]. Therefore, RNAP pauses near position +24 and backtracking might occur.…”

Section: Discussionmentioning

confidence: 99%

Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription

Герасимова

Volokh

Pestov

et al. 2022

Cells

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Transcription through chromatin by RNA polymerase II (Pol II) is accompanied by the formation of small intranucleosomal DNA loops containing the enzyme (i-loops) that are involved in survival of core histones on the DNA and arrest of Pol II during the transcription of damaged DNA. However, the structures of i-loops have not been determined. Here, the structures of the intermediates formed during transcription through a nucleosome containing intact or damaged DNA were studied using biochemical approaches and electron microscopy. After RNA polymerase reaches position +24 from the nucleosomal boundary, the enzyme can backtrack to position +20, where DNA behind the enzyme recoils on the surface of the histone octamer, forming an i-loop that locks Pol II in the arrested state. Since the i-loop is formed more efficiently in the presence of SSBs positioned behind the transcribing enzyme, the loop could play a role in the transcription-coupled repair of DNA damage hidden in the chromatin structure.

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“…Our method is based on monitoring the thermal fluctuations of DNA, which are suppressed upon protein binding. With the ability to obtain the full probability distribution for the binding and residence times of a TF to a known site, while at the same time offering the possibility to gradually increase the complexity of the system and follow binding in the vicinity of nucleosomes ( 65 ) and chromatosomes ( 66 ), we expect this method to offer important mechanistic insights to complement the information obtained from live cell measurements.…”

Section: Discussionmentioning

confidence: 99%

Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation

Khamis

Rudnizky

Melamed

et al. 2021

Nucleic Acids Research

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The interaction of transcription factors with their response elements in DNA is emerging as a highly complex process, whose characterization requires measuring the full distribution of binding and dissociation times in a well-controlled assay. Here, we present a single-molecule assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. We demonstrate this new approach by following the binding of Egr1 to its consensus motif and the three binding sites found in the promoter of the Lhb gene, and find that both association and dissociation are modulated by the 9 bp core motif and the sequences around it. In addition, CpG methylation modulates the dissociation kinetics in a sequence and position-dependent manner, which can both stabilize or destabilize the complex. Together, our findings show how variations in sequence and methylation patterns synergistically extend the spectrum of a protein's binding properties, and demonstrate how the proposed approach can provide new insights on the function of transcription factors.

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Extended and dynamic linker histone-DNA Interactions control chromatosome compaction

Cited by 15 publications

References 76 publications

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

H1.0 C Terminal Domain Is Integral for Altering Transcription Factor Binding within Nucleosomes

Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription

Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation

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