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histone crotonylation

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https://www.readbyqxmd.com/read/29584949/a-chemical-probe-for-protein-crotonylation
#1
Jeffrey Bos, Tom W Muir
Protein lysine crotonylation has emerged as an important post-translational modification (PTM) in the regulation of gene transcription through epigenetic mechanisms. Here we introduce a chemical probe, based on a water-soluble phosphine warhead, which specifically reacts with the crotonyl modification. We show that this reagent is complementary to antibody-based tools allowing detection of endogenous cellular proteins such as histones carrying the crotonylation PTM. The tool is also used to show that the histone acylation activity of the transcriptional co-activator, p300, can be activated by pre-existing lysine crotonylation through a positive feedback mechanism...
March 27, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29548294/modulation-of-nucleosomal-dna-accessibility-via-charge-altering-post-translational-modifications-in-histone-core
#2
Andrew T Fenley, Ramu Anandakrishnan, Yared H Kidane, Alexey V Onufriev
BACKGROUND: Controlled modulation of nucleosomal DNA accessibility via post-translational modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs in the globular histone core-including acetylation, phosphorylation, crotonylation, propionylation, butyrylation, formylation, and citrullination-can alter the strong electrostatic interactions between the oppositely charged nucleosomal DNA and the histone proteins and thus modulate accessibility of the nucleosomal DNA, affecting processes that depend on access to the genetic information, such as transcription...
March 16, 2018: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/29534238/targeting-epigenetic-dna-and-histone-modifications-to-treat-kidney-disease
#3
Miguel Fontecha-Barriuso, Diego Martin-Sanchez, Olga Ruiz-Andres, Jonay Poveda, Maria Dolores Sanchez-Niño, Lara Valiño-Rivas, Marta Ruiz-Ortega, Alberto Ortiz, Ana Belén Sanz
Epigenetics refers to heritable changes in gene expression patterns not caused by an altered nucleotide sequence, and includes non-coding RNAs and covalent modifications of DNA and histones. This review focuses on functional evidence for the involvement of DNA and histone epigenetic modifications in the pathogenesis of kidney disease and the potential therapeutic implications. There is evidence of activation of epigenetic regulatory mechanisms in acute kidney injury (AKI), chronic kidney disease (CKD) and the AKI-to-CKD transition of diverse aetiologies, including ischaemia-reperfusion injury, nephrotoxicity, ureteral obstruction, diabetes, glomerulonephritis and polycystic kidney disease...
March 9, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29483630/first-profiling-of-lysine-crotonylation-of-myofilament-proteins-and-ribosomal-proteins-in-zebrafish-embryos
#4
Oh Kwang Kwon, Sun Joo Kim, Sangkyu Lee
Zebrafish embryos are translucent and develop rapidly in individual eggs ex utero; they are widely used as models for embryogenesis and organ development for human diseases and drug discovery. Lysine crotonylation (Kcr) is a type of histone post-translational modifications discovered in 2011. Kcr dynamics are involved in gene expression regulation and acute kidney injury; however, little is known about the effects of Kcr on non-histone proteins. In the present study, we conducted the first proteome-wide profiling of Kcr in zebrafish larvae and identified 557 Kcr sites on 218 proteins, representing the Kcr event in zebrafish...
February 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29457784/hiv-latency-is-reversed-by-acss2-driven-histone-crotonylation
#5
Guochun Jiang, Don Nguyen, Nancie M Archin, Steven A Yukl, Gema Méndez-Lagares, Yuyang Tang, Maher M Elsheikh, George R Thompson, Dennis J Hartigan-O'Connor, David M Margolis, Joseph K Wong, Satya Dandekar
Eradication of HIV-1 (HIV) is hindered by stable viral reservoirs. Viral latency is epigenetically regulated. While the effects of histone acetylation and methylation at the HIV long-terminal repeat (LTR) have been described, our knowledge of the proviral epigenetic landscape is incomplete. We report that a previously unrecognized epigenetic modification of the HIV LTR, histone crotonylation, is a regulator of HIV latency. Reactivation of latent HIV was achieved following the induction of histone crotonylation through increased expression of the crotonyl-CoA-producing enzyme acyl-CoA synthetase short-chain family member 2 (ACSS2)...
February 19, 2018: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/29395068/intracellular-crotonyl-coa-stimulates-transcription-through-p300-catalyzed-histone-crotonylation
#6
Benjamin R Sabari, Zhanyun Tang, He Huang, Vladimir Yong-Gonzalez, Henrik Molina, Ha Eun Kong, Lunzhi Dai, Miho Shimada, Justin R Cross, Yingming Zhao, Robert G Roeder, C David Allis
No abstract text is available yet for this article.
February 1, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29317660/microbiota-derived-short-chain-fatty-acids-promote-histone-crotonylation-in-the-colon-through-histone-deacetylases
#7
Rachel Fellows, Jérémy Denizot, Claudia Stellato, Alessandro Cuomo, Payal Jain, Elena Stoyanova, Szabina Balázsi, Zoltán Hajnády, Anke Liebert, Juri Kazakevych, Hector Blackburn, Renan Oliveira Corrêa, José Luís Fachi, Fabio Takeo Sato, Willian R Ribeiro, Caroline Marcantonio Ferreira, Hélène Perée, Mariangela Spagnuolo, Raphaël Mattiuz, Csaba Matolcsi, Joana Guedes, Jonathan Clark, Marc Veldhoen, Tiziana Bonaldi, Marco Aurélio Ramirez Vinolo, Patrick Varga-Weisz
The recently discovered histone post-translational modification crotonylation connects cellular metabolism to gene regulation. Its regulation and tissue-specific functions are poorly understood. We characterize histone crotonylation in intestinal epithelia and find that histone H3 crotonylation at lysine 18 is a surprisingly abundant modification in the small intestine crypt and colon, and is linked to gene regulation. We show that this modification is highly dynamic and regulated during the cell cycle. We identify class I histone deacetylases, HDAC1, HDAC2, and HDAC3, as major executors of histone decrotonylation...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29107015/ikcr-pseens-identify-lysine-crotonylation-sites-in-histone-proteins-with-pseudo-components-and-ensemble-classifier
#8
Wang-Ren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Jian-Hua Jia, Kuo-Chen Chou
Lysine crotonylation (Kcr) is an evolution-conserved histone posttranslational modification (PTM), occurring in both human somatic and mouse male germ cell genomes. It is important for male germ cell differentiation. Information of Kcr sites in proteins is very useful for both basic research and drug development. But it is time-consuming and expensive to determine them by experiments alone. Here, we report a novel predictor called iKcr-PseEns that is established by incorporating five tiers of amino acid pairwise couplings into the general pseudo amino acid composition...
October 26, 2017: Genomics
https://www.readbyqxmd.com/read/28971554/p-b-desulfurization-an-enabling-method-for-protein-chemical-synthesis-and-site-specific-deuteration
#9
Kang Jin, Tianlu Li, Hoi Yee Chow, Han Liu, Xuechen Li
Cysteine-mediated native chemical ligation is a powerful method for protein chemical synthesis. Herein, we report an unprecedentedly mild system (TCEP/NaBH4 or TCEP/LiBEt3 H; TCEP=tris(2-carboxyethyl)phosphine) for chemoselective peptide desulfurization to achieve effective protein synthesis via the native chemical ligation-desulfurization approach. This method, termed P-B desulfurization, features usage of common reagents, simplicity of operation, robustness, high yields, clean conversion, and versatile functionality compatibility with complex peptides/proteins...
October 2, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28886434/prediction-of-lysine-crotonylation-sites-by-incorporating-the-composition-of-k-spaced-amino-acid-pairs-into-chou-s-general-pseaac
#10
Zhe Ju, Jian-Jun He
As one of the most important and common histones post-translational modifications, crotonylation plays a key role in regulating various biological processes. The accurate identification of crotonylation sites is crucial to elucidate the underlying molecular mechanisms of crotonylation. In this study, a novel bioinformatics tool named CKSAAP_CrotSite is developed to predict crotonylation sites. The highlight of CKSAAP_CrotSite is to adopt the composition of k-spaced amino acid pairs as input encoding, and the support vector machine is employed as the classifier...
August 24, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28882038/ultradeep-lysine-crotonylome-reveals-the-crotonylation-enhancement-on-both-histones-and-nonhistone-proteins-by-saha-treatment
#11
Quan Wu, Wenting Li, Chi Wang, Pingsheng Fan, Lejie Cao, Zhiwei Wu, Fengsong Wang
Lysine crotonylation is a newly discovered protein post-translational modification and was reported to share transferases and deacylases with lysine acetylation. The acetyltransferase p300 was reported to also contain crotonyltransferase activity, and class I histone deacetylases were demonstrated to be the major histone decrotonylases. However, the decrotonylases for nonhistone proteins are unclear. Moreover, because of the lack of high-quality pan-antibodies, large-scale analysis of crotonylome still remains a challenge...
September 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28803779/chromodomain-protein-cdyl-acts-as-a-crotonyl-coa-hydratase-to-regulate-histone-crotonylation-and-spermatogenesis
#12
Shumeng Liu, Huajing Yu, Yongqing Liu, Xinhua Liu, Yu Zhang, Chen Bu, Shuai Yuan, Zhe Chen, Guojia Xie, Wanjin Li, Bosen Xu, Jianguo Yang, Lin He, Tong Jin, Yundong Xiong, Luyang Sun, Xiaohui Liu, Chunsheng Han, Zhongyi Cheng, Jing Liang, Yongfeng Shang
Lysine crotonylation (Kcr) is a newly identified histone modification that is associated with active transcription in mammalian cells. Here we report that the chromodomain Y-like transcription corepressor CDYL negatively regulates histone Kcr by acting as a crotonyl-CoA hydratase to convert crotonyl-CoA to β-hydroxybutyryl-CoA. We showed that the negative regulation of histone Kcr by CDYL is intrinsically linked to its transcription repression activity and functionally implemented in the reactivation of sex chromosome-linked genes in round spermatids and genome-wide histone replacement in elongating spermatids...
September 7, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28644004/intricate-effects-of-%C3%AE-amino-and-lysine-modifications-on-arginine-methylation-of-the-n-terminal-tail-of-histone-h4
#13
Melody D Fulton, Jing Zhang, Maomao He, Meng-Chiao Ho, Y George Zheng
Chemical modifications of the DNA and nucleosomal histones tightly control the gene transcription program in eukaryotic cells. The "histone code" hypothesis proposes that the frequency, combination, and location of post-translational modifications (PTMs) of the core histones compose a complex network of epigenetic regulation. Currently, there are at least 23 different types and >450 histone PTMs that have been discovered, and the PTMs of lysine and arginine residues account for a crucial part of the histone code...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28592803/first-comprehensive-proteome-analysis-of-lysine-crotonylation-in-seedling-leaves-of-nicotiana-tabacum
#14
Hangjun Sun, Xiaowei Liu, Fangfang Li, Wei Li, Jing Zhang, Zhixin Xiao, Lili Shen, Ying Li, Fenglong Wang, Jinguang Yang
Histone crotonylation is a new lysine acylation type of post-translational modification (PTM) enriched at active gene promoters and potential enhancers in yeast and mammalian cells. However, lysine crotonylation in nonhistone proteins and plant cells has not yet been studied. In the present study, we performed a global crotonylation proteome analysis of Nicotiana tabacum (tobacco) using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity purification. A total of 2044 lysine modification sites distributed on 637 proteins were identified, representing the most abundant lysine acylation proteome reported in the plant kingdom...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28580166/mof-as-an-evolutionarily-conserved-histone-crotonyltransferase-and-transcriptional-activation-by-histone-acetyltransferase-deficient-and-crotonyltransferase-competent-cbp-p300
#15
Xiaoguang Liu, Wei Wei, Yuting Liu, Xueli Yang, Jian Wu, Yang Zhang, Qiao Zhang, Tieliu Shi, James X Du, Yingming Zhao, Ming Lei, Jin-Qiu Zhou, Jiwen Li, Jiemin Wong
Recent studies indicate that histones are subjected to various types of acylation including acetylation, propionylation and crotonylation. CBP and p300 have been shown to catalyze multiple types of acylation but are not conserved in evolution, raising the question as to the existence of other enzymes for histone acylation and the functional relationship between well-characterized acetylation and other types of acylation. In this study, we focus on enzymes catalyzing histone crotonylation and demonstrate that among the known histone acetyltransferases, MOF, in addition to CBP and p300, also possesses histone crotonyltransferase (HCT) activity and this activity is conserved in evolution...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28562590/genetic-wiring-maps-of-single-cell-protein-states-reveal-an-off-switch-for-gpcr-signalling
#16
Markus Brockmann, Vincent A Blomen, Joppe Nieuwenhuis, Elmer Stickel, Matthijs Raaben, Onno B Bleijerveld, A F Maarten Altelaar, Lucas T Jae, Thijn R Brummelkamp
As key executers of biological functions, the activity and abundance of proteins are subjected to extensive regulation. Deciphering the genetic architecture underlying this regulation is critical for understanding cellular signalling events and responses to environmental cues. Using random mutagenesis in haploid human cells, we apply a sensitive approach to directly couple genomic mutations to protein measurements in individual cells. Here we use this to examine a suite of cellular processes, such as transcriptional induction, regulation of protein abundance and splicing, signalling cascades (mitogen-activated protein kinase (MAPK), G-protein-coupled receptor (GPCR), protein kinase B (AKT), interferon, and Wingless and Int-related protein (WNT) pathways) and epigenetic modifications (histone crotonylation and methylation)...
June 8, 2017: Nature
https://www.readbyqxmd.com/read/28497810/class-i-histone-deacetylases-are-major-histone-decrotonylases-evidence-for-critical-and-broad-function-of-histone-crotonylation-in-transcription
#17
Wei Wei, Xiaoguang Liu, Jiwei Chen, Shennan Gao, Lu Lu, Huifang Zhang, Guangjin Ding, Zhiqiang Wang, Zhongzhou Chen, Tieliu Shi, Jiwen Li, Jianjun Yu, Jiemin Wong
Recent studies on enzymes and reader proteins for histone crotonylation support a function of histone crotonylation in transcription. However, the enzyme(s) responsible for histone decrotonylation (HDCR) remains poorly defined. Moreover, it remains to be determined if histone crotonylation is physiologically significant and functionally distinct from or redundant to histone acetylation. Here we present evidence that class I histone deacetylases (HDACs) rather than sirtuin family deacetylases (SIRTs) are the major histone decrotonylases, and that histone crotonylation is as dynamic as histone acetylation in mammalian cells...
July 2017: Cell Research
https://www.readbyqxmd.com/read/28459554/genetically-encoded-photoaffinity-histone-marks
#18
Xiao Xie, Xiao-Meng Li, Fangfei Qin, Jianwei Lin, Gong Zhang, Jingyi Zhao, Xiucong Bao, Rongfeng Zhu, Haiping Song, Xiang David Li, Peng R Chen
Posttranslational modifications (PTMs) of lysine are crucial histone marks that regulate diverse biological processes. The functional roles and regulation mechanism of many newly identified lysine PTMs, however, remain yet to be understood. Here we report a photoaffinity crotonyl lysine (Kcr) analogue that can be genetically and site-specifically incorporated into histone proteins. This, in conjunction with the genetically encoded photo-lysine as a "control probe", enables the capture and identification of enzymatic machinery and/or effector proteins for histone lysine crotonylation...
May 8, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28429772/global-profiling-of-crotonylation-on-non-histone-proteins
#19
Weizhi Xu, Junhu Wan, Jun Zhan, Xueying Li, Huiying He, Zhaomei Shi, Hongquan Zhang
No abstract text is available yet for this article.
July 2017: Cell Research
https://www.readbyqxmd.com/read/28300602/yeats-domain-a-histone-acylation-reader-in-health-and-disease
#20
REVIEW
Dan Zhao, Yuanyuan Li, Xiaozhe Xiong, Zhonglei Chen, Haitao Li
Histone post-translational modifications (PTMs) carry an epigenetic layer of message to regulate diverse cellular processes at the chromatin level. Many of these PTMs are selectively recognized by dedicated effector proteins for normal cell growth and development, while dysregulation of these recognition events is often implicated in human diseases, notably cancer. Thus, it is fundamentally important to elucidate the regulatory mechanism(s) underlying the readout of PTMs on histones. The Yaf9, ENL, AF9, Taf14, Sas5 (YEATS) domain is an emerging reader module that selectively recognizes histone lysine acylation with a preference for crotonylation over acetylation...
June 30, 2017: Journal of Molecular Biology
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