scholarly journals Now open: Evolving insights to the roles of lysine acetylation in chromatin organization and function

2022 ◽  
Author(s):  
Ying-Jiun C. Chen ◽  
Evangelia Koutelou ◽  
Sharon Y.R. Dent
Keyword(s):  
Chromatin Organization ◽  
Lysine Acetylation ◽  
And Function

Functions of the nuclear envelope and lamina in development and disease

2008 ◽  
Vol 36 (6) ◽  
pp. 1329-1334 ◽  
Author(s):  
Tatiana V. Cohen ◽  
Lidia Hernandez ◽  
Colin L. Stewart
Keyword(s):  
Transcriptional Regulation ◽  
Nuclear Envelope ◽  
Chromatin Organization ◽  
Signalling Pathways ◽  
Mechanical Integrity ◽  
Inherited Diseases ◽  
And Function

Recent findings that some 24 inherited diseases and anomalies are caused by defects in proteins of the NE (nuclear envelope) and lamina have resulted in a fundamental reassessment of the functions of the NE and underlying lamina. Instead of just regarding the NE and lamina as a molecular filtering device, regulating the transfer of macromolecules between the cytoplasm and nucleus, we now envisage the NE/lamina functioning as a key cellular ‘hub’ in integrating critical functions that include chromatin organization, transcriptional regulation, mechanical integrity of the cell and signalling pathways, as well as acting as a key component in the organization and function of the cytoskeleton.

The winged-helix transcription factor JUMU regulates development, nucleolus morphology and function, and chromatin organization of Drosophila melanogaster

2010 ◽  
Vol 18 (3) ◽  
pp. 307-324 ◽  
Author(s):  
Annemarie Hofmann ◽  
Madeleine Brünner ◽  
Alexander Schwendemann ◽  
Martin Strödicke ◽  
Sascha Karberg ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Drosophila Melanogaster ◽  
Chromatin Organization ◽  
Winged Helix ◽  
And Function ◽  
Winged Helix Transcription Factor

scholarly journals Ion counting demonstrates a high electrostatic field generated by the nucleosome

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Magdalena Gebala ◽  
Stephanie L Johnson ◽  
Geeta J Narlikar ◽  
Dan Herschlag
Keyword(s):  
Electrostatic Field ◽  
Nuclear Dna ◽  
Chromatin Organization ◽  
Computational Studies ◽  
Compaction Process ◽  
Histone Protein ◽  
Dna Compaction ◽  
Nucleosome Formation ◽  
And Function ◽  
Positively Charged

In eukaryotes, a first step towards the nuclear DNA compaction process is the formation of a nucleosome, which is comprised of negatively charged DNA wrapped around a positively charged histone protein octamer. Often, it is assumed that the complexation of the DNA into the nucleosome completely attenuates the DNA charge and hence the electrostatic field generated by the molecule. In contrast, theoretical and computational studies suggest that the nucleosome retains a strong, negative electrostatic field. Despite their fundamental implications for chromatin organization and function, these opposing views of nucleosome electrostatics have not been experimentally tested. Herein, we directly measure nucleosome electrostatics and find that while nucleosome formation reduces the complex charge by half, the nucleosome nevertheless maintains a strong negative electrostatic field. Our studies highlight the importance of considering the polyelectrolyte nature of the nucleosome and its impact on processes ranging from factor binding to DNA compaction.

Quantitative Analysis of Lysine Acetylation in Vero Cells Infected With Peste Des Petits Ruminants Virus

2021 ◽  
Author(s):  
Xuelian Meng ◽  
Xueliang Zhu ◽  
Rui Zhang ◽  
Zhidong Zhang
Keyword(s):  
Rna Virus ◽  
Small Ruminants ◽  
Vero Cells ◽  
Host Cells ◽  
Lysine Acetylation ◽  
Peste Des Petits Ruminants ◽  
Bioinformatics Analyses ◽  
Protein Protein Interaction ◽  
Quantification Analysis ◽  
And Function

Abstract Background: Peste des petits ruminants virus (PPRV) is a negative-stranded RNA virus belonging to the Paramyxoviridae family and causes acute, highly contagious disease in small ruminants. Lysine acetylation plays central role in regulating gene expression. However, the extent and function of lysine acetylation in host cells during PPRV infection remains unknown. Methods: Lysine acetylation of PPRV-infected Vero cells was tested and differentially expressed lysine acetylation was found. The acetylated peptides were enriched using specific antibody and labeled with demethylation. Proteins with acetylation sites were identified. Subsequently, intensive bioinformatics analysis of succinylome of PPRV-infected Vero cells was were performed. In this study, intensive proteomic quantification analysis of the proteome and acetylome of PPRV-infected Vero cells was performed using dimethylation labeling-based quantitative proteomics. Results: We identified 4729 cellular proteins and 1068 proteins with 2641 modification sites quantifiable detected by mass spectrometry, of which 304 proteins with 410 acetylation sites were significantly acetylated in response to PPRV infection. Bioinformatics analyses revealed that the differentially acetylated proteins mainly participated in carbohydrate catabolic and DNA metabolic process, and were associated with multifarious functions, suggesting that intracellular activities were extensively changed after PPRV infection. Protein-protein interaction (PPI) network of the identified proteins further indicated that a variety of chaperone and ribosome processes were modulated by acetylation. Conclusions: To our knowledge, this is the first study on acetylome in host cell infected with PPRV. It provides an important baseline to future study the roles of acetylation in the host response to PPRV replication.

scholarly journals SIRT2 deacetylase regulates the activity of GSK3 isoforms independent of inhibitory phosphorylation

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Mohsen Sarikhani ◽  
Sneha Mishra ◽  
Sangeeta Maity ◽  
Chaithanya Kotyada ◽  
Donald Wolfgeher ◽  
...  
Keyword(s):  
Glycogen Synthase ◽  
Serine Phosphorylation ◽  
Glycogen Synthase Kinase 3 ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Dynamics Simulations ◽  
And Function ◽  
Reduced Activity ◽  
Deficient Mice

Glycogen synthase kinase 3 (GSK3) is a critical regulator of diverse cellular functions involved in the maintenance of structure and function. Enzymatic activity of GSK3 is inhibited by N-terminal serine phosphorylation. However, alternate post-translational mechanism(s) responsible for GSK3 inactivation are not characterized. Here, we report that GSK3α and GSK3β are acetylated at Lys246 and Lys183, respectively. Molecular modeling and/or molecular dynamics simulations indicate that acetylation of GSK3 isoforms would hinder both the adenosine binding and prevent stable interactions of the negatively charged phosphates. We found that SIRT2 deacetylates GSK3β, and thus enhances its binding to ATP. Interestingly, the reduced activity of GSK3β is associated with lysine acetylation, but not with phosphorylation at Ser9 in hearts of SIRT2-deficient mice. Moreover, GSK3 is required for the anti-hypertrophic function of SIRT2 in cardiomyocytes. Overall, our study identified lysine acetylation as a novel post-translational modification regulating GSK3 activity.

scholarly journals Linker histones regulate fine-scale chromatin organization and modulate developmental decisions in Arabidopsis

2018 ◽  
Author(s):  
Kinga Rutowicz ◽  
Maciej Lirski ◽  
Benoît Mermaz ◽  
Jasmin Schubert ◽  
Gianluca Teano ◽  
...  
Keyword(s):  
Chromatin Organization ◽  
Fine Scale ◽  
Developmental Transitions ◽  
Linker Histones ◽  
Lateral Root Initiation ◽  
Control Gene Expression ◽  
Nucleosome Density ◽  
And Function ◽  
Epigenetic Patterns ◽  
The Impact

AbstractChromatin in eukaryotes provides a tunable platform to control gene expression and convey an epigenetic memory throughout cell divisions. H1 linker histones are abundant components with an intrinsic potential in influencing chromatin structure and function. We detail the impact of H1 depletion in Arabidopsis on fine-scale chromatin organization, transcription and development. While required for chromocenter assembly, H1s are dispensable for transposable element (TE) silencing and peripheral positioning of heterochromatin. In euchromatin, H1 regulates nucleosome density, mobility, and regular distribution of nanoscale chromatin domains. While necessary to maintain epigenetic patterns, H1 only moderately affects transcription. Its depletion is associated with failures in transitional fate changes such as lateral root initiation, root hair production, stomata patterning but also flowering and dormancy regulation. Therefore, Arabidopsis H1 variants are chromatin architects mediating nano‐ and microscale levels-of-organization operating downstream of epigenetic and transcriptional establishment processes and contribute to epigenetic reorientations in developmental transitions.

Nonhistone targets of KAT2A and KAT2B implicated in cancer biology

2019 ◽  
Vol 97 (1) ◽  
pp. 30-45 ◽  
Author(s):  
Emma Bondy-Chorney ◽  
Alix Denoncourt ◽  
Yuka Sai ◽  
Michael Downey
Keyword(s):  
Protein Function ◽  
Cancer Biology ◽  
Protein Complexes ◽  
Lysine Acetylation ◽  
Large Protein ◽  
Nonhistone Proteins ◽  
Nonhistone Protein ◽  
Cancer Systems Biology ◽  
Cancer Phenotype ◽  
And Function

Lysine acetylation is a critical post-translation modification that can impact a protein’s localization, stability, and function. Originally thought to only occur on histones, we now know thousands of nonhistone proteins are also acetylated. In conjunction with many other proteins, lysine acetyltransferases (KATs) are incorporated into large protein complexes that carry out these modifications. In this review we focus on the contribution of two KATs, KAT2A and KAT2B, and their potential roles in the development and progression of cancer. Systems biology demands that we take a broad look at protein function rather than focusing on individual pathways or targets. As such, in this review we examine KAT2A/2B-directed nonhistone protein acetylations in cancer in the context of the 10 “Hallmarks of Cancer”, as defined by Hanahan and Weinberg. By focusing on specific examples of KAT2A/2B-directed acetylations with well-defined mechanisms or strong links to a cancer phenotype, we aim to reinforce the complex role that these enzymes play in cancer biology.

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