Synthesis of ADP-Ribosylated Histones Reveals Site-Specific Impacts on Chromatin Structure and Function

2021 ◽  
Author(s):  
Nir Hananya ◽  
Sara K. Daley ◽  
John D. Bagert ◽  
Tom W. Muir
Keyword(s):  
Chromatin Structure ◽  
Structure And Function ◽  
Site Specific ◽  
And Function

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.

Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length

2006 ◽  
Vol 14 (1) ◽  
pp. 17-25 ◽  
Author(s):  
Christopher L. Woodcock ◽  
Arthur I. Skoultchi ◽  
Yuhong Fan
Keyword(s):  
Chromatin Structure ◽  
Structure And Function ◽  
Linker Histone ◽  
Repeat Length ◽  
And Function

scholarly journals Synaptic transmission induces site-specific changes in sialylation on N-linked glycoproteins in rat nerve terminals

2020 ◽  
Author(s):  
Inga Boll ◽  
Pia Jensen ◽  
Veit Schwämmle ◽  
Martin R. Larsen
Keyword(s):  
Synaptic Transmission ◽  
Structure And Function ◽  
Synaptic Proteins ◽  
Nerve Terminals ◽  
Membrane Glycoproteins ◽  
Site Specific ◽  
Specific Alteration ◽  
And Function ◽  
Rat Nerve ◽  
Stimulation Of

AbstractSynaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show a novel potential modulator of synaptic transmission, sialylation of N-linked glycosylation. The negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after five seconds depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.

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 Regional, watershed, and site-specific environmental influences on fish assemblage structure and function in western Lake Superior tributaries

2005 ◽  
Vol 62 (6) ◽  
pp. 1254-1270 ◽  
Author(s):  
John C Brazner ◽  
Danny K Tanner ◽  
Naomi E Detenbeck ◽  
Sharon L Batterman ◽  
Stacey L Stark ◽  
...  
Keyword(s):  
Fish Assemblage ◽  
Brook Trout ◽  
Fish Assemblages ◽  
Lake Superior ◽  
Structure And Function ◽  
Assemblage Structure ◽  
Fish Assemblage Structure ◽  
Site Specific ◽  
Western Lake ◽  
And Function

The relative importance of regional, watershed, and in-stream environmental factors on fish assemblage structure and function was investigated in western Lake Superior tributaries. We selected 48 second- and third-order watersheds from two hydrogeomorphic regions to examine fish assemblage response to differences in forest fragmentation, watershed storage, and a number of other watershed, riparian, and in-stream habitat conditions. Although a variety of regional, fragmentation, and storage-related factors had significant influences on the fish assemblages, water temperature appeared to be the single most important environmental factor. We found lower water temperatures and trout–sculpin assemblages at lower fragmentation sites and higher temperatures and minnow–sucker–darter assemblages as storage increased. Factors related to riparian shading and flow separated brook trout streams from brown trout (Salmo trutta) – rainbow trout (Oncorhynchus mykiss) streams. Functionally, fish assemblages at lower fragmentation sites were dominated by cold-water fishes that had low silt tolerance and preferred moderate current speeds, while fishes with higher silt tolerances, warmer temperature preferences, and weaker sustained swimming capabilities were most common at higher storage sites. Our results suggest that site-specific environmental conditions are highly dependent on regional- and watershed-scale characters and that a combination of these factors operates in concert to influence the structure and function of stream fish assemblages.

scholarly journals Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function

2018 ◽  
Vol 46 (17) ◽  
pp. 8665-8678 ◽  
Author(s):  
Rajbir Singh ◽  
Emily Bassett ◽  
Arnab Chakravarti ◽  
Mark R Parthun
Keyword(s):  
Chromatin Structure ◽  
Structure And Function ◽  
And Function
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