Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries

Nguyen, Uyen; Bittova, Lenka; Müller, Matthias A.; Fierz, Beat; David, Yael; Houck-Loomis, Brian; Feng, Vanessa; Dann, Geoffrey P.; Muir, Tom W.

doi:10.1038/nmeth.3022

Cited by 139 publications

(168 citation statements)

References 56 publications

(83 reference statements)

Supporting

Mentioning

156

Contrasting

Unclassified

Order By: Relevance

“…Besides the 3D-carbene SPRi platform, other fluorescencebased peptide or reader microarray technologies have also been successfully applied for profiling epigenetic targets (29,30). Recently, DNA-barcoded designer nucleosome libraries (DNLs) have emerged as a unique technology that analyzes histone recognition and signaling, especially combinatorial histone modification readout at the nucleosome level (31). The kinetic and direct detection feature of the 3D-carbene SPRi platform complements well with other library-based methods for epigenetic discovery.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao

Yang

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chipbased surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant. The mechanisms leading to differential transcriptional and developmental outcomes under the same genetic background are known as epigenetics. Posttranslational modification (PTM) on histones is a major epigenetic regulatory mechanism such that more than 30 types of PTMs occur on histones, with new ones still being discovered (1). The well-studied histone PTMs include methylation, acetylation, phosphorylation, and most recently discovered nonacetyl acylations (2). Histone PTMs regulate transcription either by directly affecting the structure/stability of single nucleosome and the high-order folding of chromatin, or by recruiting specific effector proteins (also called histone readers) recognizing them (3, 4).The ever-expanding repertoire of histone readers are diverse in sequence and structure, and how they engage diversely modified chromatin is complicated, hard to predict, yet important for their functions. Often one type of reader domains can recognize different types of PTMs. For example, PHD finger proteins can recognize unmodified, methylated, or acylated lysine residue on histones (5, 6). Several YEATS domain proteins, originally identified as readers of lysine acetylation (Kac), in fact accommodate a wide range of lysine acylations with lysine crotonylation (Kcr) most preferred (7). These "mark-reader" interactions vary greatly in binding affinity, ranging from submicromolar to millimolar levels. To complicate the matter further, the recognition of marks by reader proteins is often either synergized or antagonized by other marks in close proximity (8). For instance, Spindlin1 recognizes histone H3 trimethylation of Lys-4 (H3K4me3) and asymmetrically dimethylation of Arg-8 (H3R8me2a) in concert, while phosphorylation of Ser-10 on H3 (H3S10ph) completely abrogates the binding of H3 Lys-9 trimethylation (H3K9me3) by HP1 protein (9, 10). BRDT protein binds neither histone H4 Lys-5 acetylation (H4K5ac) nor Lys-8 acetylation (H4K8ac) but engages H4 peptide bearing both marks with decent affinity (K...

show abstract

Section: Discussionmentioning

confidence: 99%

“…S1B). The ITC curve of histone H3 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) un, H3K4 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15) me3, H3.1 (28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41) K36me3, and H3.3 (28)(29)(30)(31)(32)(33)(34)(35)(36)…”

Section: Methodsunclassified

Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology

Zhao

Yang

Zhou

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…By incorporating more than one label into the same octamer, different histones within the same nucleosome could be monitored independently. Our assay using fluorescent histone labeling, along with other recently developed techniques such as fluorescent labeling of nucleosomal DNA (55) and DNA-barcoded nucleosome libraries (56), are particularly suited to addressing the mechanistic basis of histone crosstalk.…”

Section: Discussionmentioning

confidence: 99%

Nucleosome competition reveals processive acetylation by the SAGA HAT module

Ringel

Cieniewicz

Taverna

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex hyperacetylates histone tails in vivo in a manner that depends upon histone 3 lysine 4 trimethylation (H3K4me3), a histone mark enriched at promoters of actively transcribed genes. SAGA contains a separable subcomplex known as the histone acetyltransferase (HAT) module that contains the HAT, Gcn5, bound to Sgf29, Ada2, and Ada3. Sgf29 contains a tandem Tudor domain that recognizes H3K4me3-containing peptides and is required for histone hyperacetylation in vivo. However, the mechanism by which H3K4me3 recognition leads to lysine hyperacetylation is unknown, as in vitro studies show no effect of the H3K4me3 modification on histone peptide acetylation by Gcn5. To determine how H3K4me3 binding by Sgf29 leads to histone hyperacetylation by Gcn5, we used differential fluorescent labeling of histones to monitor acetylation of individual subpopulations of methylated and unmodified nucleosomes in a mixture. We find that the SAGA HAT module preferentially acetylates H3K4me3 nucleosomes in a mixture containing excess unmodified nucleosomes and that this effect requires the Tudor domain of Sgf29. The H3K4me3 mark promotes processive, multisite acetylation of histone H3 by Gcn5 that can account for the different acetylation patterns established by SAGA at promoters versus coding regions. Our results establish a model for Sgf29 function at gene promoters and define a mechanism governing crosstalk between histone modifications.T he different patterns of histone posttranslational modifications distributed across the genome are proposed to constitute a "histone code" that orchestrates distinct transcriptional programs by recruiting specific effector proteins (1-4). The phenomenon of histone code "crosstalk," whereby one type of histone modification directs the establishment of another, or through which several histone modifications are recognized in tandem, has emerged as an important and widespread mechanism regulating chromatin-templated processes (5, 6). The multifunctional complexes that activate transcription are thought to mediate crosstalk through "reader" domains that recognize particular chromatin marks as well as through catalytic subunits that deposit or remove histone modifications (5,7,8). As a result, distinct combinations of histone posttranslational modifications that correlate with transcriptional output cluster across the genome (9-11). High levels of histone 3 lysine 4 trimethylation (H3K4me3) and histone H3 hyperacetylation are present at the promoters of actively transcribed genes (9,11,12), and multiple lines of evidence support the existence of regulatory mechanisms coupling the two modifications. Studies using tandem mass spectrometry to sequence whole histone tails have shown that H3K4me3 is highly correlated with hyperacetylation of the same H3 tail (13,14). Deleting the yeast Set1 methyltransferase, which trimethylates H3K4, leads to dramatically lower levels of histone H3 tail acetylation overall (13, 15). These results are consistent with ...

show abstract

“…Zuschriften metrisch modifizierte Nukleosomen haben ein breites Anwendungsspektrum in der epigenetischen Forschung,z .B.i n mechanistischen oder Hochdurchsatz-In-vitro-Studien zur Wechselwirkung von Histon-PTMs [16] oder in der quantitativen Chromatin-Immunopräzipitation. [17] In dieser Studie haben wir eine Reihe von asymmetrischen Nukleosomen hergestellt und dazu verwendet, den Regulationsmechanismus von PRC2 durch die Kombination von H3K4me3 und H3K27me3 zu untersuchen.…”

Section: Angewandte Chemieunclassified