scholarly journals The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes

Acta Naturae ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 15-33
Author(s):  
L. S. Melnikova ◽  
P. G. Georgiev ◽  
A. K. Golovnin
Keyword(s):  
Experimental Data ◽  
Long Range ◽  
Regulatory Elements ◽  
Mechanisms Of Action ◽  
Topologically Associating Domains ◽  
Long Range Interactions ◽  
Chromosomal Architecture ◽  
Enhancer Blocking ◽  
Higher Eukaryotes ◽  
Auxiliary Role

The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of Drosophila and mammals, and it also briefly characterizes the proteins responsible for their functional activity. It was initially believed that the main properties of insulators are blocking of enhancers and the formation of independent transcription domains. We present experimental data proving that the chromatin loops formed by insulators play only an auxiliary role in enhancer blocking. The review also discusses the mechanisms involved in the formation of topologically associating domains and their role in the formation of the chromosomal architecture and regulation of gene transcription.

scholarly journals A Description of Transverse Momentum Distributions in p+p Collisions at RHIC and LHC Energies

2019 ◽  
Vol 2019 ◽  
pp. 1-9
Author(s):  
Jia-Qi Hui ◽  
Zhi-Jin Jiang
Keyword(s):  
Experimental Data ◽  
Transverse Momentum ◽  
Long Range ◽  
Collective Motion ◽  
Good Description ◽  
Dense Matter ◽  
Relativistic Hydrodynamics ◽  
Nonextensive Statistics ◽  
Long Range Interactions ◽  
Momentum Distributions

It has long been debated whether the hydrodynamics is suitable for the smaller colliding systems such as p+p collisions. In this paper, by assuming the existence of longitudinal collective motion and long-range interactions in the hot and dense matter created in p+p collisions, the relativistic hydrodynamics incorporating with the nonextensive statistics is used to analyze the transverse momentum distributions of the particles. The investigations of the present paper show that the hybrid model can give a good description of the currently available experimental data obtained in p+p collisions at RHIC and LHC energies, except for p and p¯ produced in the range of pT>3.0 GeV/c at s=200 GeV.

scholarly journals Chromosome looping at the human α-globin locus is mediated via the major upstream regulatory element (HS −40)

Blood ◽  
2009 ◽  
Vol 114 (19) ◽  
pp. 4253-4260 ◽  
Author(s):  
Douglas Vernimmen ◽  
Fatima Marques-Kranc ◽  
Jacqueline A. Sharpe ◽  
Jacqueline A. Sloane-Stanley ◽  
William G. Wood ◽  
...  
Keyword(s):  
Long Range ◽  
Regulatory Element ◽  
Globin Gene ◽  
Regulatory Elements ◽  
Chromosome Conformation ◽  
Long Range Interactions ◽  
Upstream Regulatory Element ◽  
Physical Interactions ◽  
Globin Promoter

Abstract Previous studies in the mouse have shown that high levels of α-globin gene expression in late erythropoiesis depend on long-range, physical interactions between remote upstream regulatory elements and the globin promoters. Using quantitative chromosome conformation capture (q3C), we have now analyzed all interactions between 4 such elements lying 10 to 50 kb upstream of the human α cluster and their interactions with the α-globin promoter. All of these elements interact with the α-globin gene in an erythroid-specific manner. These results were confirmed in a mouse model of human α globin expression in which the human cluster replaces the mouse cluster in situ (humanized mouse). We have also shown that expression and all of the long-range interactions depend largely on just one of these elements; removal of the previously characterized major regulatory element (called HS −40) results in loss of all the interactions and α-globin expression. Reinsertion of this element at an ectopic location restores both expression and the intralocus interactions. In contrast to other more complex systems involving multiple upstream elements and promoters, analysis of the human α-globin cluster during erythropoiesis provides a simple and tractable model to understand the mechanisms underlying long-range gene regulation.

scholarly journals Community effects in regulation of translation

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Paul M Macdonald ◽  
Matt Kanke ◽  
Andrew Kenny
Keyword(s):  
Long Range ◽  
Translational Regulation ◽  
Regulatory Elements ◽  
Community Effects ◽  
Particle Assembly ◽  
Cis Acting ◽  
Long Range Interactions ◽  
In Trans ◽  
Single Transcript ◽  
In Cis

Certain forms of translational regulation, and translation itself, rely on long-range interactions between proteins bound to the different ends of mRNAs. A widespread assumption is that such interactions occur only in cis, between the two ends of a single transcript. However, certain translational regulatory defects of the Drosophila oskar (osk) mRNA can be rescued in trans. We proposed that inter-transcript interactions, promoted by assembly of the mRNAs in particles, allow regulatory elements to act in trans. Here we confirm predictions of that model and show that disruption of PTB-dependent particle assembly inhibits rescue in trans. Communication between transcripts is not limited to different osk mRNAs, as regulation imposed by cis-acting elements embedded in the osk mRNA spreads to gurken mRNA. We conclude that community effects exist in translational regulation.

Long-range interactions between topologically associating domains shape the four-dimensional genome during differentiation

2019 ◽  
Vol 51 (5) ◽  
pp. 835-843 ◽  
Author(s):  
Jonas Paulsen ◽  
Tharvesh M. Liyakat Ali ◽  
Maxim Nekrasov ◽  
Erwan Delbarre ◽  
Marie-Odile Baudement ◽  
...  
Keyword(s):  
Long Range ◽  
Topologically Associating Domains ◽  
Long Range Interactions

scholarly journals Structural Changes in the Acceptor Site of Photosystem II upon Ca2+/Sr2+ Exchange in the Mn4CaO5 Cluster Site and the Possible Long-Range Interactions

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 371
Author(s):  
Koua
Keyword(s):  
Crystal Structure ◽  
Photosystem Ii ◽  
Long Range ◽  
Electron Acceptor ◽  
Structural Changes ◽  
Acceptor Site ◽  
Oxygen Evolving Complex ◽  
Long Range Interactions ◽  
Structural Perturbations ◽  
Oxygen Evolving

The Mn4CaO5 cluster site in the oxygen-evolving complex (OEC) of photosystem II (PSII) undergoes structural perturbations, such as those induced by Ca2+/Sr2+ exchanges or Ca/Mn removal. These changes have been known to induce long-range positive shifts (between +30 and +150 mV) in the redox potential of the primary quinone electron acceptor plastoquinone A (QA), which is located 40 Å from the OEC. To further investigate these effects, we reanalyzed the crystal structure of Sr-PSII resolved at 2.1 Å and compared it with the native Ca-PSII resolved at 1.9 Å. Here, we focus on the acceptor site and report the possible long-range interactions between the donor, Mn4Ca(Sr)O5 cluster, and acceptor sites.

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