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histone crotonylation

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https://www.readbyqxmd.com/read/28429772/global-profiling-of-crotonylation-on-non-histone-proteins
#1
Weizhi Xu, Junhu Wan, Jun Zhan, Xueying Li, Huiying He, Zhaomei Shi, Hongquan Zhang
No abstract text is available yet for this article.
April 21, 2017: Cell Research
https://www.readbyqxmd.com/read/28300602/yeats-domain-a-histone-acylation-reader-in-health-and-disease
#2
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 readout of PTMs on histones. The YEATS domain is an emerging reader module that selectively recognizes histone lysine acylation with a preference for crotonylation over acetylation...
March 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28283358/identify-and-analysis-crotonylation-sites-in-histone-by-using-support-vector-machines
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/27089029/the-taf14-yeats-domain-is-a-reader-of-histone-crotonylation
#15
Forest H Andrews, Stephen A Shinsky, Erin K Shanle, Joseph B Bridgers, Anneliese Gest, Ian K Tsun, Krzysztof Krajewski, Xiaobing Shi, Brian D Strahl, Tatiana G Kutateladze
The discovery of new histone modifications is unfolding at startling rates; however, the identification of effectors capable of interpreting these modifications has lagged behind. Here we report the YEATS domain as an effective reader of histone lysine crotonylation, an epigenetic signature associated with active transcription. We show that the Taf14 YEATS domain engages crotonyllysine via a unique π-π-π-stacking mechanism and that other YEATS domains have crotonyllysine-binding activity.
June 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/26820416/histone-h1-variants-in-arabidopsis-are-subject-to-numerous-post-translational-modifications-both-conserved-and-previously-unknown-in-histones-suggesting-complex-functions-of-h1-in-plants
#16
Maciej Kotliński, Kinga Rutowicz, Łukasz Kniżewski, Antoni Palusiński, Jacek Olędzki, Anna Fogtman, Tymon Rubel, Marta Koblowska, Michał Dadlez, Krzysztof Ginalski, Andrzej Jerzmanowski
Linker histones (H1s) are conserved and ubiquitous structural components of eukaryotic chromatin. Multiple non-allelic variants of H1, which differ in their DNA/nucleosome binding properties, co-exist in animal and plant cells and have been implicated in the control of genetic programs during development and differentiation. Studies in mammals and Drosophila have revealed diverse post-translational modifications of H1s, most of which are of unknown function. So far, it is not known how this pattern compares with that of H1s from other major lineages of multicellular Eukaryotes...
2016: PloS One
https://www.readbyqxmd.com/read/26694698/crystal-structure-of-the-nucleosome-containing-histone-h3-with-crotonylated-lysine-122
#17
Yuya Suzuki, Naoki Horikoshi, Daiki Kato, Hitoshi Kurumizaka
The crotonylation of histones is an important post-translational modification, and epigenetically functions in the regulation of genomic DNA activity. The histone modifications in the structured "histone-fold" domains are considered to have an especially important impact on the nucleosome structure and dynamics. In the present study, we reconstituted the human nucleosome containing histone H3.2 crotonylated at the Lys122 residue, and determined its crystal structure at 2.56 Å resolution. We found that the crotonylation of the H3 Lys122 residue does not affect the overall nucleosome structure, but locally impedes the formation of the water-mediated hydrogen bond with the DNA backbone...
January 15, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/26365797/a-subset-of-human-bromodomains-recognizes-butyryllysine-and-crotonyllysine-histone-peptide-modifications
#18
E Megan Flynn, Oscar W Huang, Florence Poy, Mariano Oppikofer, Steve F Bellon, Yong Tang, Andrea G Cochran
Bromodomains are epigenetic readers that are recruited to acetyllysine residues in histone tails. Recent studies have identified non-acetyl acyllysine modifications, raising the possibility that these might be read by bromodomains. Profiling the nearly complete human bromodomain family revealed that while most human bromodomains bind only the shorter acetyl and propionyl marks, the bromodomains of BRD9, CECR2, and the second bromodomain of TAF1 also recognize the longer butyryl mark. In addition, the TAF1 second bromodomain is capable of binding crotonyl marks...
October 6, 2015: Structure
https://www.readbyqxmd.com/read/25884364/greetings-from-the-planet-croton
#19
COMMENT
Allyson Evans
In this issue of Molecular Cell, Sabari et al. (2015) discover that levels of intracellular crotonyl-CoA impact the histone acylation landscape, providing deeper insight into the exotic histone modification, crotonylation, and exploring new avenues by which cellular metabolism can influence gene expression.
April 16, 2015: Molecular Cell
https://www.readbyqxmd.com/read/25870829/histone-acylation-beyond-acetylation-terra-incognita-in-chromatin-biology
#20
REVIEW
Sophie Rousseaux, Saadi Khochbin
Histone acetylation, one of the first and best studied histone post-translational modifications (PTMs), as well as the factors involved in its deposition (writers), binding (readers) and removal (erasers), have been shown to act at the heart of regulatory circuits controlling essential cellular functions. The identification of a variety of competing histone lysine-modifying acyl groups including propionyl, butyryl, 2-hydroxyisobutyryl, crotonyl, malonyl, succinyl and glutaryl, raises numerous questions on their functional significance, the molecular systems that manage their establishment, removal and interplay with the well-known acetylation-based mechanisms...
2015: Cell Journal
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