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histone crotonylation

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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
#1
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 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28592803/first-comprehensive-proteome-analysis-of-lysine-crotonylation-in-seedling-leaves-of-nicotiana-tabacum
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28283358/identify-and-analysis-crotonylation-sites-in-histone-by-using-support-vector-machines
#9
Wang-Ren Qiu, Bi-Qian Sun, Hua Tang, Jian Huang, Hao Lin
OBJECTIVE: Lysine crotonylation (Kcr) is a newly discovered histone posttranslational modification, which is specifically enriched at active gene promoters and potential enhancers in mammalian cell genomes. Although lysine crotonylation sites can be correctly identified with high-resolution mass spectrometry, the experimental methods are time-consuming and expensive. Therefore, it is necessary to develop computational methods to deal with this problem. METHODS: We proposed a new encoding scheme named position weight amino acid composition to extract sequence information of histone around crotonylation sites...
March 7, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28150880/assays-for-acetylation-and-other-acylations-of-lysine-residues
#10
Nadine Pelletier, Serge Grégoire, Xiang-Jiao Yang
Lysine acetylation refers to addition of an acetyl moiety to the epsilon-amino group of a lysine residue and is important for regulating protein functions in various organisms from bacteria to humans. This is a reversible and precisely controlled covalent modification that either serves as an on/off switch or participates in a codified manner with other post-translational modifications to regulate different cellular and developmental processes in normal and pathological states. This unit describes methods for in vitro and in vivo determination of lysine acetylation...
February 2, 2017: Current Protocols in Protein Science
https://www.readbyqxmd.com/read/28108585/histone-h3k4-and-h3k36-methylation-independently-recruit-the-nua3-histone-acetyltransferase-in-saccharomyces-cerevisiae
#11
Benjamin J E Martin, Kristina L McBurney, Vicki E Maltby, Kristoffer N Jensen, Julie Brind'Amour, LeAnn J Howe
Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In Saccharomyces cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14; which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9, respectively...
March 2017: Genetics
https://www.readbyqxmd.com/read/27924077/metabolic-regulation-of-gene-expression-through-histone-acylations
#12
REVIEW
Benjamin R Sabari, Di Zhang, C David Allis, Yingming Zhao
Eight types of short-chain Lys acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggests that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this Review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, the acylation 'reader' proteins that mediate the effects of different acylations and their physiological functions, which include signal-dependent gene activation, spermatogenesis, tissue injury and metabolic stress...
February 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/27820805/structure-of-p300-in-complex-with-acyl-coa-variants
#13
Zuzanna Kaczmarska, Esther Ortega, Afsaneh Goudarzi, He Huang, Sunjoo Kim, José A Márquez, Yingming Zhao, Saadi Khochbin, Daniel Panne
Histone acetylation plays an important role in transcriptional activation. Histones are also modified by chemically diverse acylations that are frequently deposited by p300, a transcriptional coactivator that uses a number of different acyl-CoA cofactors. Here we report that while p300 is a robust acetylase, its activity gets weaker with increasing acyl-CoA chain length. Crystal structures of p300 in complex with propionyl-, crotonyl-, or butyryl-CoA show that the aliphatic portions of these cofactors are bound in the lysine substrate-binding tunnel in a conformation that is incompatible with substrate transfer...
January 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/27775714/selective-recognition-of-histone-crotonylation-by-double-phd-fingers-of-moz-and-dpf2
#14
Xiaozhe Xiong, Tatyana Panchenko, Shuang Yang, Shuai Zhao, Peiqiang Yan, Wenhao Zhang, Wei Xie, Yuanyuan Li, Yingming Zhao, C David Allis, Haitao Li
Recognition of histone covalent modifications by 'reader' modules constitutes a major mechanism for epigenetic regulation. A recent upsurge of newly discovered histone lysine acylations, such as crotonylation (Kcr), butyrylation (Kbu), and propionylation (Kpr), greatly expands the coding potential of histone lysine modifications. Here we demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylations with the strongest preference for Kcr...
December 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27760772/downregulation-of-kidney-protective-factors-by-inflammation-role-of-transcription-factors-and-epigenetic-mechanisms
#15
REVIEW
Olga Ruiz-Andres, Maria Dolores Sanchez-Niño, Juan Antonio Moreno, Marta Ruiz-Ortega, Adrian Mario Ramos, Ana Belen Sanz, Alberto Ortiz
Chronic kidney disease (CKD) is associated to an increased risk of death, CKD progression, and acute kidney injury (AKI) even from early stages, when glomerular filtration rate (GFR) is preserved. The link between early CKD and these risks is unclear, since there is no accumulation of uremic toxins. However, pathological albuminuria and kidney inflammation are frequent features of early CKD, and the production of kidney protective factors may be decreased. Indeed, Klotho expression is already decreased in CKD category G1 (normal GFR)...
December 1, 2016: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/27661789/yeats-domain-linking-histone-crotonylation-to-gene-regulation
#16
Yuanyuan Li, Dan Zhao, Zhonglei Chen, Haitao Li
Recent research reveals that the YEATS domains preferentially recognize crotonylated lysines on histones. Here, we discuss the molecular mechanisms that enable this recognition and the biological significances of this interaction. The dynamics of histone crotonylation and its potential roles in the regulation of gene expression will also be discussed.
January 2017: Transcription
https://www.readbyqxmd.com/read/27545619/structural-insights-into-histone-crotonyl-lysine-recognition-by-the-af9-yeats-domain
#17
Qiang Zhang, Lei Zeng, Chengcheng Zhao, Ying Ju, Tsuyoshi Konuma, Ming-Ming Zhou
Histone lysine acylations play an important role in the regulation of gene transcription in chromatin. Unlike histone acetyl-lysine, molecular recognition of a recently identified crotonyl-lysine mark is much less understood. Here, we report that the YEATS domain of AF9 preferentially binds crotonyl-lysine over acetyl-lysine in histone H3. Nuclear magnetic resonance structural analysis reveals that crotonyl-lysine of histone H3 lysine 18 is engulfed deep in an aromatic cage of the YEATS domain where the carbonyl oxygen of crotonyl-lysine forms a hydrogen bond with the backbone amide of protein residue Tyr78...
September 6, 2016: Structure
https://www.readbyqxmd.com/read/27125278/histone-lysine-crotonylation-during-acute-kidney-injury-in-mice
#18
Olga Ruiz-Andres, Maria Dolores Sanchez-Niño, Pablo Cannata-Ortiz, Marta Ruiz-Ortega, Jesus Egido, Alberto Ortiz, Ana Belen Sanz
Acute kidney injury (AKI) is a potentially lethal condition for which no therapy is available beyond replacement of renal function. Post-translational histone modifications modulate gene expression and kidney injury. Histone crotonylation is a recently described post-translational modification. We hypothesized that histone crotonylation might modulate kidney injury. Histone crotonylation was studied in cultured murine proximal tubular cells and in kidneys from mice with AKI induced by folic acid or cisplatin...
June 1, 2016: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/27105114/molecular-coupling-of-histone-crotonylation-and-active-transcription-by-af9-yeats-domain
#19
Yuanyuan Li, Benjamin R Sabari, Tatyana Panchenko, Hong Wen, Dan Zhao, Haipeng Guan, Liling Wan, He Huang, Zhanyun Tang, Yingming Zhao, Robert G Roeder, Xiaobing Shi, C David Allis, Haitao Li
Recognition of histone covalent modifications by chromatin-binding protein modules ("readers") constitutes a major mechanism for epigenetic regulation, typified by bromodomains that bind acetyllysine. Non-acetyl histone lysine acylations (e.g., crotonylation, butyrylation, propionylation) have been recently identified, but readers that prefer these acylations have not been characterized. Here we report that the AF9 YEATS domain displays selectively higher binding affinity for crotonyllysine over acetyllysine...
April 21, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27103431/yeats2-is-a-selective-histone-crotonylation-reader
#20
Dan Zhao, Haipeng Guan, Shuai Zhao, Wenyi Mi, Hong Wen, Yuanyuan Li, Yingming Zhao, C David Allis, Xiaobing Shi, Haitao Li
No abstract text is available yet for this article.
May 2016: Cell Research
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