Defining TP53 pioneering capabilities with competitive nucleosome binding assays

Yu, Xinyang; Buck, Michael

doi:10.1101/gr.234104.117

Cited by 47 publications

(73 citation statements)

References 73 publications

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“…As to the rotational setting of the Sox2 binding motif, a more accessible minor groove (facing away from the histone octamer) generally corresponds to a higher affinity. A preference for specific motif positioning in the nucleosome context has also been suggested for other TFs, such as p53, which favors exposed sites (Cui and Zhurkin, 2014) and nucleosome edges (Yu and Buck, 2019).…”

Section: Discussionmentioning

confidence: 83%

“…Despite extensive research, the capacity of and mutual relationship between Sox2 and Oct4, and PFs in general, in targeting nucleosomal DNA remains a matter of debate (Biddle et al, 2019; Chronis et al, 2017; Franco et al, 2015; Iwafuchi-Doi et al, 2016; Soufi et al, 2015; Swinstead et al, 2016). Recent data suggested that the pioneer activity of a given TF may be conditional and dependent on the local chromatin environment (King and Klose, 2017; Liu and Kraus, 2017; Soufi et al, 2015; Swinstead et al, 2016; Yu and Buck, 2019). Popular methods of choice for studying TF-chromatin interaction, such as genome-wide binding and bulk biochemical assays, lack sufficient temporal resolution to inform the time order of binding events (usually occurring on the order of seconds) by multiple TFs.…”

Section: Introductionmentioning

confidence: 99%

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Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

Zheng

Zhao

2019

Cell Reports

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SUMMARYCooperative binding of transcription factors (TFs) to chromatin orchestrates gene expression programming and cell fate specification. However, the biophysical principles of TF cooperativity remain incompletely understood. Here we use single-molecule fluorescence microscopy to study the partnership between Sox2 and Oct4, two core members of the pluripotency gene regulatory network. We find that the ability of Sox2 to target DNA inside nucleosomes is strongly affected by the translational and rotational positioning of its binding motif. In contrast, Oct4 can access nucleosomal sites with equal capacities. Furthermore, the Sox2-Oct4 pair displays nonreciprocal cooperativity, with Oct4 modulating interaction of Sox2 with the nucleosome but not vice versa. Such cooperativity is conditional upon the composite motif’s residing at specific nucleosomal locations. These results reveal that pioneer factors possess distinct chromatin-binding properties and suggest that the same set of TFs can differentially regulate gene activities on the basis of their motif positions in the nucleosomal context.

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Section: Discussionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

Zheng

Zhao

2019

Cell Reports

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“…S4F). It has been shown that P53 has pioneering activity [ 64 , 65 ] and is capable of binding nucleosomal DNA [ 66 – 68 ]. Hence, we performed nucleosome occupancy and phasing analysis using ATAC- [ 69 ] and MNAse-seq [ 70 , 71 ] and observed strong nucleosome phasing at P53 peaks compared to OSN-bound or randomly selected loci (Fig.…”

Section: Resultsmentioning

confidence: 99%

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells

et al. 2020

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Background Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for identifying putative enhancers and for describing their activity levels and dynamics. Results Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in “ground-state” (2i+LIF; 2iL) and “metastable” (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq libraries for common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and increases their propensity to differentiate towards the endodermal fate. STARR-seq also reveals enhancers that are not accessible, masked by a repressive chromatin signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac under specific conditions, such as after treatment with Nocodazol, or transiently during reprogramming from fibroblasts to pluripotency. Conclusions In conclusion, loci identified as active by STARR-seq often overlap with those identified by chromatin accessibility and active epigenetic marking, yet a significant fraction is epigenetically repressed or display condition-specific enhancer activity.

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“…The LFY target site is near the nucleosome dyad, where it resides in vivo (Fig. 1a) and where histone-DNA interactions are strongest 58, 59 . LFY did not bind the nucleosomal substrate when its consensus motif was mutated, indicating that LFY binds the nucleosome in a sequence specific manner (Fig.…”

Section: Resultsmentioning

confidence: 99%

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

Jin

Klasfeld

García

et al. 2020

Preprint

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Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet no bonafide pioneer transcription factor has -been identified in this kingdom. Here we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds in a sequence-specific manner and with high affinity to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1, where it co-occupies DNA with histones. Moreover, the LFY DNA contact helix shares defining properties with those of strong nucleosome binding pioneer factors. At the AP1 locus, LFY unlocks chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later and require activity of additional, non-pioneer transcription, factors. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between plant and animal pioneer transcription factors. Further analyses aimed at elucidating the defining characteristics of pioneer transcription factors will allow harnessing these for enhanced cell fate reprogramming.Chromatin prevents expression of inappropriate or detrimental gene expression programs, allowing formation of distinct cell types from the same genome 1. The basic unit of chromatin is the nucleosome comprised of 150 base-pairs of DNA wrapped nearly two turns around the histone octamer 2. Chromatin is further compacted by nucleosome/nucleosome interactions and by the linker histone H1, which associates with the dyad (midpoint) of the nucleosome 3. During cell fate reprogramming in eukaryotes, master transcription factors silence and activate new gene expression programs in the context of chromatin 4-6. While it is easy to imagine how master transcription factors bind to active genes in open chromatin to trigger silencing, it is difficult to envision how these sequence-specific binding proteins can access their cognate motifs in silent chromatin to activate gene expression. This is because nucleosomes are refractory for most transcription factor binding 7-10 11. However, a special class of transcription factors, termed pioneer transcription factors, can access their cognate binding motifs in the nucleosome 1,4,12-17. These pioneer transcription factors play important roles in cell fate reprogramming. For example, the mammalian pioneer transcription factor FoxA reprograms fibroblast to hepatocytes 16,18-20, while the Oct4, Klf4 and Sox2 pioneer transcription factors reprogram fibroblasts to induced pluripotent stem ...

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Defining TP53 pioneering capabilities with competitive nucleosome binding assays

Cited by 47 publications

References 73 publications

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells

LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

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