CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Clarkson, Christopher T.; Deeks, Emma A.; Samarista, Ralph; Mamayusupova, Hulkar; Zhurkin, Victor B.; Teif, Vladimir B.

doi:10.1093/nar/gkz908

Cited by 55 publications

(60 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…4b), and this is not an artifact of any averaging process (supplementary note 16). The fact that the length of a structured DNA region exceeds the CTCF consensus motif has been recently reported 64 . As nucleosome formation requires extensive DNA bending, our finding suggests that the sequence-encoded property of CTCF binding sites as being highly cyclizable may favor the formation of nucleosomes.…”

Section: Applications Of the Predictive Model For The Sequence-dependmentioning

confidence: 95%

Deciphering the mechanical code of genome and epigenome

Basu

Cieza

et al. 2020

Preprint

View full text Add to dashboard Cite

Sequence features have long been known to influence the local mechanical properties and shapes of DNA. However, a mechanical code (i.e. a comprehensive mapping between DNA sequence and mechanical properties), if it exists, has been difficult to experimentally determine because direct means of measuring the mechanical properties of DNA are typically limited in throughput. Here we use Loop-seq – a recently developed technique to measure the intrinsic cyclizabilities (a proxy for bendability) of DNA fragments in genomic-scale throughput – to characterize the mechanical code. We tabulate how DNA sequence features (distribution patterns of all possible dinucleotides and dinucleotide pairs) influence intrinsic cyclizability, and build a linear model to predict intrinsic cyclizability from sequence. Using our model, we predict that DNA mechanical landscape shapes nucleosome organization around the promoters of various organisms and at the binding site of the transcription factor CTCF, and that hyperperiodic DNA in C. elegans leads to globally curved DNA segments. By performing loop-seq on random libraries in the presence or absence of CpG methylation, we show that CpG methylation leads to global stiffening of DNA in a wide sequence context, and predict based on our model that CpG methylation widely changes the mechanical landscape around mouse promoters. It suggests how epigenetic modifications of DNA might alter gene expression and mediate cellular adaptation by affecting critical processes around promoters that require mechanical deformations of DNA, such as nucleosome organization and transcription initiation. Finally, we show that the genetic code and the mechanical code are linked: sequence-dependent mechanical properties of coding DNA constrains the amino acid sequence despite the degeneracy in the genetic code. Our measurements explain why the pattern of nucleosome organization along genes influences the distribution of amino acids in the translated polypeptide.

show abstract

Section: Applications Of the Predictive Model For The Sequence-dependmentioning

confidence: 95%

Deciphering the mechanical code of genome and epigenome

Basu

Cieza

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…First, CTCF is uniquely able to position ~20 nucleosomes around its DNA-binding sites [ 91 – 95 ], suggesting a mechanism whereby CTCF binding generates a unique chromatin microenvironment that could potentially serve as a steric hindrance pause signal. Consistently, CTCF has been reported to form a highly unusual DNA structure where it binds [ 96 ].…”

Section: One-step Vs Multi-step Ctcf-cohesin Interactions To Explainmentioning

confidence: 99%

“…Third, CTCF is subject to a number of post-translational modifications [ 66 ], some of which are quite large such as SUMOylation [ 98 ] and poly-ADP-ribosylation [ 99 – 101 ]. Early reports suggested that poly-ADP-ribosylation contributes to the insulation function of CTCF [ 99 , 100 ], and mutation of the 11 amino acids in the N-terminus reported to be poly-ADP-ribosylated as well as treatment with a PARP inhibitor, moderately decreased CTCF’s ability to stabilize cohesin at its binding sites as measured by ChIP-Seq [ 39 ].…”

Section: One-step Vs Multi-step Ctcf-cohesin Interactions To Explainmentioning

confidence: 99%

CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism

Hansen

2020

Nucleus

View full text Add to dashboard Cite

Mammalian genome structure is closely linked to function. At the scale of kilobases to megabases, CTCF and cohesin organize the genome into chromatin loops. Mechanistically, cohesin is proposed to extrude chromatin loops bidirectionally until it encounters occupied CTCF DNA-binding sites. Curiously, loops form predominantly between CTCF binding sites in a convergent orientation. How CTCF interacts with and blocks cohesin extrusion in an orientation-specific manner has remained a mechanistic mystery. Here, we review recent papers that have shed light on these processes and suggest a multi-step interaction between CTCF and cohesin. This interaction may first involve a pausing step, where CTCF halts cohesin extrusion, followed by a stabilization step of the CTCF-cohesin complex, resulting in a chromatin loop. Finally, we discuss our own recent studies on an internal RNA-Binding Region (RBRi) in CTCF to elucidate its role in regulating CTCF clustering, target search mechanisms and chromatin loop formation and future challenges.

show abstract

“…NRL is defined as the average distance (bp) between the dyad axes of adjacent nucleosomes and is traditionally used as an integrative parameter characterizing local nucleosome packing. Previous publications suggest that NRL is different near binding sites of transcription factors [42] and affected by the presence of linker histones, although the role of different H1 variants is not clear [43]. Figure 8 presents normalized calculations of the NRL in regions enriched for the H1 variants, using the NucTools algorithm [27].…”

Section: Influence Of H12/h15 Enrichment On the Nucleosome Repeat Lmentioning

confidence: 99%

Linker histone epitopes are hidden by in situ higher-order chromatin structure

Teif

Gould

Clarkson

et al. 2020

Epigenetics & Chromatin

Self Cite

View full text Add to dashboard Cite

Background: Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higherorder structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements. Results: We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde. Conclusion: Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized

show abstract

CTCF-dependent chromatin boundaries formed by asymmetric nucleosome arrays with decreased linker length

Cited by 55 publications

References 83 publications

Deciphering the mechanical code of genome and epigenome

Deciphering the mechanical code of genome and epigenome

CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism

Linker histone epitopes are hidden by in situ higher-order chromatin structure

Contact Info

Product

Resources

About