In situ chromatin interactomics using a chemical bait and trap approach

Burton, Antony J.; Haugbro, Michael; Gates, Leah; Bagert, John D.; Allis, C. David; Muir, Tom W.

doi:10.1038/s41557-020-0474-8

Cited by 64 publications

(51 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our biochemical and structural studies established that PHF14 is an unmodified histone H3 reader that is sensitive to active histone marks such as H3K4me3, H3R8me2a, and H3K23ac, but tolerates repressive marks such as H3K9me3 and H3K27me3. Other groups also found that PHF14 is repelled by H3K4me3 ( 34–36 ). These results together support a primary function of PHF14 as an epigenetic repressor.…”

Section: Discussionmentioning

confidence: 93%

Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14

Zheng

Chen

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

Histone recognition constitutes a key epigenetic mechanism in gene regulation and cell fate decision. PHF14 is a conserved multi-PHD finger protein that has been implicated in organ development, tissue homeostasis, and tumorigenesis. Here we show that PHF14 reads unmodified histone H3(1–34) through an integrated PHD1-ZnK-PHD2 cassette (PHF14PZP). Our binding, structural and HDX-MS analyses revealed a feature of bipartite recognition, in which PHF14PZP utilizes two distinct surfaces for concurrent yet separable engagement of segments H3-Nter (e.g. 1–15) and H3-middle (e.g. 14–34) of H3(1–34). Structural studies revealed a novel histone H3 binding mode by PHD1 of PHF14PZP, in which a PHF14-unique insertion loop but not the core β-strands of a PHD finger dominates H3K4 readout. Binding studies showed that H3-PHF14PZP engagement is sensitive to modifications occurring to H3 R2, T3, K4, R8 and K23 but not K9 and K27, suggesting multiple layers of modification switch. Collectively, our work calls attention to PHF14 as a ‘ground’ state (unmodified) H3(1–34) reader that can be negatively regulated by active marks, thus providing molecular insights into a repressive function of PHF14 and its derepression.

show abstract

Section: Discussionmentioning

confidence: 93%

Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14

Zheng

Chen

et al. 2021

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…The combination of chemical methods to modify histones together with mass spectrometry (MS) has been proven powerful in identifying the relevant writers, readers, and erasers for specific (core) histone-PTMs 15,[26][27][28] , as chemical protein synthesis allows for the generation of histones of defined, homogeneous modification states 15,29,30 . Methods include cysteine bioconjugation 31,32 , protein semisynthesis, such as native chemical ligation 33,34 , expressed protein ligation 35 or sortase-mediated ligation 36 , as well as genetic code expansion 37,38 .…”

mentioning

confidence: 99%

Site-specific ubiquitylation acts as a regulator of linker histone H1

et al. 2021

View full text Add to dashboard Cite

Decoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.

show abstract

“…This group further presented a synthetic approach termed “chemical bait and trap” to assemble engineered histone proteins, using ultrafast Cfa split-intein that assists in the incorporation of desired histone post-translational modifications (hPTMs) and cross-linkers. The split inteins present in the truncated histone and the delivery cargo assemble upon PTS, precisely joining the modified histone on the native chromatin [ 147 ]. The engineering of reporter proteins was done by Kawase et al by constructing engineered Npu DnaE split intein variants, where the N-intein sequence was modified by inducing Gly4Tyr and Asp5Glu mutations and the C-inteins variants were selected from libraries created by error-prone PCR.…”

Section: Intein Applicationsmentioning

confidence: 99%

Inteins in Science: Evolution to Application

et al. 2020

View full text Add to dashboard Cite

Inteins are mobile genetic elements that apply standard enzymatic strategies to excise themselves post-translationally from the precursor protein via protein splicing. Since their discovery in the 1990s, recent advances in intein technology allow for them to be implemented as a modern biotechnological contrivance. Radical improvement in the structure and catalytic framework of cis- and trans-splicing inteins devised the development of engineered inteins that contribute to various efficient downstream techniques. Previous literature indicates that implementation of intein-mediated splicing has been extended to in vivo systems. Besides, the homing endonuclease domain also acts as a versatile biotechnological tool involving genetic manipulation and control of monogenic diseases. This review orients the understanding of inteins by sequentially studying the distribution and evolution pattern of intein, thereby highlighting a role in genetic mobility. Further, we include an in-depth summary of specific applications branching from protein purification using self-cleaving tags to protein modification, post-translational processing and labelling, followed by the development of intein-based biosensors. These engineered inteins offer a disruptive approach towards research avenues like biomaterial construction, metabolic engineering and synthetic biology. Therefore, this linear perspective allows for a more comprehensive understanding of intein function and its diverse applications.

show abstract

In situ chromatin interactomics using a chemical bait and trap approach

Cited by 64 publications

References 53 publications

Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14

Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14

Site-specific ubiquitylation acts as a regulator of linker histone H1

Inteins in Science: Evolution to Application

Contact Info

Product

Resources

About