scholarly journals Plant Histone HTB (H2B) Variants in Regulating Chromatin Structure and Function

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1435
Author(s):  
Janardan Khadka ◽  
Anat Pesok ◽  
Gideon Grafi
Keyword(s):  
Arabidopsis Thaliana ◽  
Chromatin Structure ◽  
Developmental Stages ◽  
Histone Variants ◽  
Structure And Function ◽  
Core Histone ◽  
Histone H2b ◽  
Histone Proteins ◽  
Genes Encoding ◽  
And Function

Besides chemical modification of histone proteins, chromatin dynamics can be modulated by histone variants. Most organisms possess multiple genes encoding for core histone proteins, which are highly similar in amino acid sequence. The Arabidopsis thaliana genome contains 11 genes encoding for histone H2B (HTBs), 13 for H2A (HTAs), 15 for H3 (HTRs), and 8 genes encoding for histone H4 (HFOs). The finding that histone variants may be expressed in specific tissues and/or during specific developmental stages, often displaying specific nuclear localization and involvement in specific nuclear processes suggests that histone variants have evolved to carry out specific functions in regulating chromatin structure and function and might be important for better understanding of growth and development and particularly the response to stress. In this review, we will elaborate on a group of core histone proteins in Arabidopsis, namely histone H2B, summarize existing data, and illuminate the potential function of H2B variants in regulating chromatin structure and function in Arabidopsis thaliana.

scholarly journals Methylation of H3 K4 and K79 is not strictly dependent on H2B K123 ubiquitylation

2009 ◽  
Vol 184 (5) ◽  
pp. 631-638 ◽  
Author(s):  
Elinor R. Foster ◽  
Jessica A. Downs
Keyword(s):  
Ubiquitin Ligase ◽  
Chromatin Structure ◽  
Methylation Status ◽  
Structure And Function ◽  
Effector Proteins ◽  
Original Strain ◽  
Histone Proteins ◽  
Specific Modification ◽  
Covalent Modifications ◽  
And Function

Covalent modifications of histone proteins have profound consequences on chromatin structure and function. Specific modification patterns constitute a code read by effector proteins. Studies from yeast found that H3 trimethylation at K4 and K79 is dependent on ubiquitylation of H2B K123, which is termed a “trans-tail pathway.” In this study, we show that a strain unable to be ubiquitylated on H2B (K123R) is still proficient for H3 trimethylation at both K4 and K79, indicating that H3 methylation status is not solely dependent on H2B ubiquitylation. However, additional mutations in H2B result in loss of H3 methylation when combined with htb1-K123R. Consistent with this, we find that the original strain used to identify the trans-tail pathway has a genomic mutation that, when combined with H2B K123R, results in defective H3 methylation. Finally, we show that strains lacking the ubiquitin ligase Bre1 are defective for H3 methylation, suggesting that there is an additional Bre1 substrate that in combination with H2B K123 facilitates H3 methylation.

scholarly journals The Art of War: harnessing the epigenome against cancer

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 141 ◽  
Author(s):  
Jonathan Nye ◽  
Daniël P. Melters ◽  
Yamini Dalal
Keyword(s):  
Cancer Cells ◽  
Chromatin Structure ◽  
Histone Variants ◽  
Structure And Function ◽  
Histone Chaperones ◽  
Growth And Survival ◽  
Art Of War ◽  
Chromatin Interactions ◽  
And Function ◽  
Target Cancer

Histone chaperones are indispensable regulators of chromatin structure and function. Recent work has shown that they are frequently mis-regulated in cancer, which can have profound consequences on tumor growth and survival. Here, we focus on chaperones for the essential H3 histone variants H3.3 and CENP-A, specifically HIRA, DAXX/ATRX, DEK, and HJURP. This review summarizes recent studies elucidating their roles in regulating chromatin and discusses how cancer-specific chromatin interactions can be exploited to target cancer cells.

Role of histone modifications in defining chromatin structure and function

2008 ◽  
Vol 389 (4) ◽  
pp. 353-363 ◽  
Author(s):  
Kathy A. Gelato ◽  
Wolfgang Fischle
Keyword(s):  
Histone Modifications ◽  
Chromatin Structure ◽  
Eukaryotic Cell ◽  
Structure And Function ◽  
Cell Nuclei ◽  
Histone Proteins ◽  
Post Translational Modifications ◽  
And Function ◽  
Molecular Components

AbstractChromosomes in eukaryotic cell nuclei are not uniformly organized, but rather contain distinct chromatin elements, with each state having a defined biochemical structure and biological function. These are recognizable by their distinct architectures and molecular components, which can change in response to cellular stimuli or metabolic requirements. Chromatin elements are characterized by the fundamental histone and DNA components, as well as other associated non-histone proteins and factors. Post-translational modifications of histone proteins in particular often correlate with a specific chromatin structure and function. Patterns of histone modifications are implicated as having a role in directing the level of chromatin compaction, as well as playing roles in multiple functional pathways directing the readout of distinct regions of the genome. We review the properties of various chromatin elements and the apparent links of histone modifications with chromatin organization and functional output.

scholarly journals Impact of DNA methylation on 3D genome structure

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana Buitrago ◽  
Mireia Labrador ◽  
Juan Pablo Arcon ◽  
Rafael Lema ◽  
Oscar Flores ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromatin Structure ◽  
Chromatin Condensation ◽  
Genome Structure ◽  
Dna Methyltransferases ◽  
Model System ◽  
Structure And Function ◽  
3D Genome ◽  
Cellular Machinery ◽  
And Function

AbstractDetermining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, that lacks DNA methylation machinery making it a perfect model system to study the intrinsic role of DNA methylation in chromatin structure and function. We expressed the murine DNA methyltransferases in Saccharomyces cerevisiae and analyzed the correlation between DNA methylation, nucleosome positioning, gene expression and 3D genome organization. Despite lacking the machinery for positioning and reading methylation marks, induced DNA methylation follows a conserved pattern with low methylation levels at the 5’ end of the gene increasing gradually toward the 3’ end, with concentration of methylated DNA in linkers and nucleosome free regions, and with actively expressed genes showing low and high levels of methylation at transcription start and terminating sites respectively, mimicking the patterns seen in mammals. We also see that DNA methylation increases chromatin condensation in peri-centromeric regions, decreases overall DNA flexibility, and favors the heterochromatin state. Taken together, these results demonstrate that methylation intrinsically modulates chromatin structure and function even in the absence of cellular machinery evolved to recognize and process the methylation signal.

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