Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression

Kharerin, Hungyo; Bhat, Paike Jayadeva; Marko, John F.; Padinhateeri, Ranjith

doi:10.1038/srep20319

Cited by 8 publications

(11 citation statements)

References 62 publications

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“…In comparison, in the absence of pausing and sliding, the inheritance is poor—it leads to reduced coverage of TATA box (see Figure 3C ). In our simulations, we rarely got configurations that are devoid of nucleosomes implying that such nucleosome free states are only possible with active remodeling ( 7 , 41 ).…”

Section: Resultsmentioning

confidence: 91%

“…Further, we examined the promoter region of PHO5 gene which is known to show diverse behaviour ( 7 , 41 ). For example, if the TATA protein binding site is covered with a nucleosome, the promoter will mostly be in the ‘off’ (inactive) state; on the other hand if TATA site is exposed, then the promoter will mostly be in the ‘on’ (active) state.…”

Section: Resultsmentioning

confidence: 99%

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Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer

Bameta

Das

Padinhateeri

2018

Nucleic Acids Research

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Positioning of nucleosomes along the genomic DNA is crucial for many cellular processes that include gene regulation and higher order packaging of chromatin. The question of how nucleosome-positioning information from a parent chromatin gets transferred to the daughter chromatin is highly intriguing. Accounting for experimentally known coupling between replisome movement and nucleosome dynamics, we propose a model that can obtain de novo nucleosome assembly similar to what is observed in recent experiments. Simulating nucleosome dynamics during replication, we argue that short pausing of the replication fork, associated with nucleosome disassembly, can be a event crucial for communicating nucleosome positioning information from parent to daughter. We show that the interplay of timescales between nucleosome disassembly (τp) at the replication fork and nucleosome sliding behind the fork (τs) can give rise to a rich ‘phase diagram’ having different inherited patterns of nucleosome organization. Our model predicts that only when τp ≥ τs the daughter chromatin can inherit nucleosome positioning of the parent.

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Section: Resultsmentioning

confidence: 91%

Section: Resultsmentioning

confidence: 99%

Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer

Bameta

Das

Padinhateeri

2018

Nucleic Acids Research

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“…Further, we illustrate how binding and unbinding of nucleosomes from the DNA backbone, can speed up diffusion of cohesin by upto two orders of magnitude compared to the static case. There is widespread experimental evidence that cells can tune the binding-unbinding kinetics of nucleosomes in response to different signals, and in general, active genes are characterised by more dynamic nucleosomes [12, 30, 32, 49]. We show that this offers the cells a route to controlling the speed of loop formation by varying the nucleosome kinetics and hence linker length.…”

Section: Discussionmentioning

confidence: 90%

The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

Maji¹,

Padinhateeri²,

Mitra³

2019

Preprint

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An important question in the context of the 3D organization of chromosomes is the mechanism of formation of large loops between distant base pairs. Recent experiments suggest that the formation of loops might be mediated by Loop Extrusion Factor proteins like cohesin. Experiments on cohesin have shown that cohesins walk diffusively on the DNA, and that nucleosomes act as obstacles to the diffusion, lowering the permeability and hence reducing the effective diffusion constant. An estimation of the times required to form the loops of typical sizes seen in Hi-C experiments using these low effective diffusion constants leads to times that are unphysically large. The puzzle then is the following, how does a cohesin molecule diffusing on the DNA backbone achieve speeds necessary to form the large loops seen in experiments? We propose a simple answer to this puzzle, and show that while at low densities, nucleosomes act as barriers to cohesin diffusion, beyond a certain concentration, they can reduce loop formation times due to a subtle interplay between the nucleosome size and the mean linker length. This effect is further enhanced on considering stochastic binding kinetics of nucleosomes on the DNA backbone, and leads to predictions of lower loop formation times than might be expected from a naive obstacle picture of nucleosomes. 2 structure inside the nucleus remains an important open question [16, 40, 41, 62]. An 3 ubiquitous structural motif, as observed through 14, 25, 47] and other 4 experiments [34, 36, 50] are the formation of large loops, ranging from kilobases to 5 megabases. These loops play both a structural as well as functional roles, bringing 6 together regions of the DNA that are widely spaced along the backbone [1, 9, 35]. In 7 recent years, much work has been done in trying to understand the mechanism of 8 formation of these large loops. There is now a significant body of experimental 9 observations that implicate a class of proteins called the Structural maintenance of 10 chromosome (SMC) protein complexes -such as cohesin and condensin in the formation 11 and maintenance of these large chromosomal loops [19, 20, 28, 33, 54, 55, 58, 59, 64]. 12 Structural maintenance of chromosome (SMC) protein complexes are known to play 13 a major role in chromosome segregation in interphase and mitosis . Both cohesin and 14 condensin consists of SMC subunits and share structural similarities. SMC subunits 15 1/15 (SMC1, SMC3 in cohesin and SMC2, SMC4 in condensin) fold back on themselves to 16 form approximately a 50nm long arm. These two arms are then connected at one end 17 by a hinge domain and other two ends which have ATPase activity are connected by a 18 kleisin subunit (RAD21 in cohesin and condensin-associated protein H2 [CAPH2] in 19condensin)to form a ring like structure of the whole complex [5, 21, 26, 27, 42, 43, 48]. 20This ring like structure has been hypothesized to form a topological association with the 21 DNA backbone [38, 46]. In particular, experiments on cohesin have shown that such 22 topol...

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“…Moreover, they may coordinate with remodeling complexes to reposition the nearby nucleosomes and alter the NDR sizes. To take these effects into consideration, we modified the energy landscape by adding a Gaussian function with height h and width w in the vicinity of RSC or RSC + top 30 TFs ( Fig 4A ) [ 44 , 45 ]. The “ h ” is assumed to be proportional to the occupancy of the factor, and it can be either positive or negative, representing scenarios where the remodeler repels or attracts nucleosomes.…”

Section: Resultsmentioning

confidence: 99%

Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast

Kharerin

Bai

2021

PLoS Comput Biol

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Nucleosome positioning in the genome is essential for the regulation of many nuclear processes. We currently have limited capability to predict nucleosome positioning in vivo, especially the locations and sizes of nucleosome depleted regions (NDRs). Here, we present a thermodynamic model that incorporates the intrinsic affinity of histones, competitive binding of sequence-specific factors, and nucleosome remodeling to predict nucleosome positioning in budding yeast. The model shows that the intrinsic affinity of histones, at near-saturating histone concentration, is not sufficient in generating NDRs in the genome. However, the binding of a few factors, especially RSC towards GC-rich and poly(A/T) sequences, allows us to predict ~ 66% of genome-wide NDRs. The model also shows that nucleosome remodeling activity is required to predict the correct NDR sizes. The validity of the model was further supported by the agreement between the predicted and the measured nucleosome positioning upon factor deletion or on exogenous sequences introduced into yeast. Overall, our model quantitatively evaluated the impact of different genetic components on NDR formation and illustrated the vital roles of sequence-specific factors and nucleosome remodeling in this process.

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Role of transcription factor-mediated nucleosome disassembly in PHO5 gene expression

Cited by 8 publications

References 62 publications

Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer

Coupling of replisome movement with nucleosome dynamics can contribute to the parent–daughter information transfer

The accidental ally: Nucleosomal barriers can accelerate cohesin mediated loop formation in chromatin

Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast

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