Variations in Nucleosome Structure and Organization among Eukaryotes

2021 ◽  
Vol 16 (10) ◽  
pp. 171-178
Author(s):  
Shruti Sinha ◽  
K.V. Chaitanya
Keyword(s):  
Posttranslational Modifications ◽  
Crucial Role ◽  
Chromatin Assembly ◽  
Proper Function ◽  
Histone Binding ◽  
Histone Fold ◽  
Nucleosome Structure ◽  
Nucleosome Organization ◽  
Eukaryotic Dna ◽  
Structure And Functions

Folding eukaryotic DNA by chromatin is a vital process necessary for the proper function of DNA. This is achieved by the fundamental unit of chromatin, known as a nucleosome. The position of a nucleosome and its interaction with DNA plays a crucial role in regulating the vital processes involved in DNA function. Factors such as variations in nucleosome and its core structure and histone fold variations will help to understand nucleosome functions and their role in DNA replication, transcription, translation, posttranslational modifications, re-combinations and repair. The present review focuses on recent findings in understanding the variations in the structure and functions of nucleosomes across eukaryotes. Variations in the nucleosome organization and its assembly have also been discussed by stating the contribution of histone binding factors and chromatin assembly factors.

scholarly journals The role of micro-RNAs in the female reproductive tract

Reproduction ◽  
2012 ◽  
Vol 143 (5) ◽  
pp. 559-576 ◽  
Author(s):  
Warren B Nothnick
Keyword(s):  
Posttranslational Modifications ◽  
Reproductive Tract ◽  
Current Knowledge ◽  
Female Reproductive Tract ◽  
Micro Rna ◽  
Proper Function ◽  
Posttranscriptional Gene Regulation ◽  
Micro Rnas ◽  
And Function

Proper development and function of the female reproductive tract are essential for successful reproduction. Regulation of the differentiated functions of the organs that make up the female reproductive tract is well established to occur at multiple levels including transcription, translation, and posttranslational modifications. Micro-RNA (miRNA)-mediated posttranscriptional gene regulation has emerged as a fundamental mechanism controlling normal tissue development and function. Emerging evidence indicates that miRNAs are expressed within the organs of the female reproductive tract where they function to regulate cellular pathways necessary for proper function of these organs. In this review, the functional significance of miRNAs in the development and function of the organs of the female reproductive tract is discussed. Initial discussion focuses on the role of miRNAs in the development of the organs of the female reproductive tract highlighting recent studies that clearly demonstrate that mice with disrupted Dicer1 expression are sterile, fail to develop uterine glands, and have muted estrogen responsiveness. Next, emphasis moves to discussion on our current knowledge on the characterization of miRNA expression in each of the organs of the female reproductive tract. When possible, information is presented and discussed with respect to regulation, function, and/or functional targets of these miRNA within each specific organ of the female reproductive tract.

scholarly journals BM28, a human member of the MCM2-3-5 family, is displaced from chromatin during DNA replication.

1995 ◽  
Vol 129 (6) ◽  
pp. 1433-1445 ◽  
Author(s):  
I T Todorov ◽  
A Attaran ◽  
S E Kearsey
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Posttranslational Modifications ◽  
S Phase ◽  
Present Evidence ◽  
Nuclear Binding ◽  
Eukaryotic Dna ◽  
Triton X ◽  
Related Proteins ◽  
Phase Proceeds

We have recently cloned and characterized a human member (BM28) of the MCM2-3-5 family of putative relication factors (Todorov, I.T., R. Pepperkok, R.N. Philipova, S. Kearsey, W. Ansorge, and D. Werner. 1994. J. Cell Sci. 107:253-265). While this protein is located in the nucleus throughout interphase, we report here a dramatic alteration in its nuclear binding during the cell cycle. BM28 is retained in the nucleus after Triton X-100 extraction in G1 and early S phase cells, but is progressively lost as S phase proceeds, and little BM28 is retained in detergent-extracted G2 nuclei. BM28 that is resistant to extraction in G1 nuclei is removed by DNase I digestion, suggesting that the protein is chromatin associated. In addition, we present evidence for variations in the electrophoretic mobility of BM28 that may reflect posttranslational modifications of BM28 during the cell cycle. During mitosis, BM28 is present as a fast-migrating form, but on entry into G1, the protein is converted into a slow-migrating form. With the onset of S phase, the slow-migrating form is progressively converted into the fast form. BM28 is phosphorylated at all stages of the cell cycle, but during interphase the fast form is hyperphosphorylated compared with the slow form. These apparent changes in modification may reflect or effect changes in the nuclear binding of BM28. The behavior of BM28 is not dissimilar to related proteins in Saccharomyces cerevisiae, such as Mcm2p, which are excluded from the nucleus after DNA replication. We speculate that BM28 may be involved in the control that limits eukaryotic DNA replication to one round per cell cycle.

scholarly journals Structural analysis of the chicken FANCM–MHF complex and its stability

2021 ◽  
Vol 77 (1) ◽  
Author(s):  
Sho Ito ◽  
Tatsuya Nishino
Keyword(s):  
Chromosomal Instability ◽  
Structural Basis ◽  
Hydrophilic Interactions ◽  
Histone Fold ◽  
Damage Recognition ◽  
Domain Loss ◽  
Eukaryotic Dna ◽  
Crystallization Conditions ◽  
The Stability ◽  
Dna Damage Recognition

FANCM is involved in eukaryotic DNA-damage recognition and activates the Fanconi anemia (FA) pathway through complex formation. MHF is one of the FANCM-associating components and contains a histone-fold DNA-binding domain. Loss of the FANCM–MHF interaction compromises the activation of the FA pathway, resulting in chromosomal instability. Thus, formation of the FANCM–MHF complex is important for function, but its nature largely remains elusive. Here, the aim was to reveal the molecular and structural basis for the stability of the FANCM–MHF complex. A recombinant tripartite complex containing chicken FANCM (MHF interaction region), MHF1 and MHF2 was expressed and purified. The purified tripartite complex was crystallized under various conditions and three different crystals were obtained from similar crystallization conditions. Unexpectedly, structure determination revealed that one of the crystals contained the FANCM–MHF complex but that the other two contained the MHF complex without FANCM. How FANCM dissociates from MHF was further investigated and it was found that the presence of 2-methyl-2,4-pentanediol (MPD) and an oxidative environment may have promoted its release. However, under these conditions MHF retained its complexed form. FANCM–MHF interaction involves a mixture of hydrophobic/hydrophilic interactions, and chicken FANCM contains several nonconserved cysteines within this region which may lead to aggregation with other FANCM–MHF molecules. These results indicate an unexpected nature of the FANCM–MHF complex and the data can be used to improve the stability of the complex for biochemical and structural analyses.

scholarly journals SUMO protease SENP1 deSUMOylates and stabilizes c-Myc

2018 ◽  
Vol 115 (43) ◽  
pp. 10983-10988 ◽  
Author(s):  
Xiao-Xin Sun ◽  
Yingxiao Chen ◽  
Yulong Su ◽  
Xiaoyan Wang ◽  
Krishna Mohan Chauhan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Cell Cycle ◽  
Cell Proliferation ◽  
Posttranslational Modifications ◽  
Crucial Role ◽  
Wild Type ◽  
Sumo Protease ◽  
Cycle Arrest ◽  
Cancer Tissues

Posttranslational modifications play a crucial role in the proper control of c-Myc protein stability and activity. c-Myc can be modified by small ubiquitin-like modifier (SUMO). However, how SUMOylation regulates c-Myc stability and activity remains to be elucidated. The deSUMOylation enzyme, SENP1, has recently been shown to have a prooncogenic role in cancer; however, mechanistic understanding of this is limited. Here we show that SENP1 is a c-Myc deSUMOylating enzyme. SENP1 interacts with and deSUMOylates c-Myc in cells and in vitro. Overexpression of wild-type SENP1, but not its catalytically inactive C603S mutant, markedly stabilizes c-Myc and increases its levels and activity. Knockdown of SENP1 reduces c-Myc levels, induces cell cycle arrest, and drastically suppresses cell proliferation. We further show that c-Myc can be comodified by both ubiquitination and SUMOylation. SENP1-mediated deSUMOylation reduces c-Myc polyubiquitination, suggesting that SUMOylation promotes c-Myc degradation through the proteasome system. Interestingly, SENP1-mediated deSUMOylation promotes the accumulation of monoubiquitinated c-Myc and its phosphorylation at serine 62 and threonine 58. SENP1 is frequently overexpressed, correlating with the high expression of c-Myc, in breast cancer tissues. Together, these results reveal that SENP1 is a crucial c-Myc deSUMOylating enzyme that positively regulates c-Myc’s stability and activity.

scholarly journals Genome-Wide Identification, Evolutionary, and Expression Analyses of Histone H3 Variants in Plants

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Jinteng Cui ◽  
Zhanlu Zhang ◽  
Yang Shao ◽  
Kezhong Zhang ◽  
Pingsheng Leng ◽  
...  
Keyword(s):  
Chromosome Segregation ◽  
Posttranslational Modifications ◽  
Evolutionary History ◽  
Histone H3 ◽  
Purifying Selection ◽  
Histone Variants ◽  
Nucleosome Structure ◽  
Genome Wide ◽  
Eukaryotic Species ◽  
History Of

Histone variants alter the nucleosome structure and play important roles in chromosome segregation, transcription, DNA repair, and sperm compaction. Histone H3 is encoded by many genes in most eukaryotic species and is the histone that contains the largest variety of posttranslational modifications. Compared with the metazoan H3 variants, little is known about the complex evolutionary history of H3 variants proteins in plants. Here, we study the identification, evolutionary, and expression analyses of histone H3 variants from genomes in major branches in the plant tree of life. Firstly we identified all the histone three related (HTR) genes from the examined genomes, then we classified the four groups variants: centromeric H3, H3.1, H3.3 and H3-like, by phylogenetic analysis, intron information, and alignment. We further demonstrated that the H3 variants have evolved under strong purifying selection, indicating the conservation of HTR proteins. Expression analysis revealed that the HTR has a wide expression profile in maize and rice development and plays important roles in development.

Nietzsche’s Epiphenomenalism about RConsciousness

2021 ◽  
pp. 126-164
Author(s):  
Mattia Riccardi
Keyword(s):  
Social Norms ◽  
Crucial Role ◽  
Conscious State ◽  
Proper Function ◽  
Textual Evidence ◽  
Reflective Consciousness ◽  
Social Coordination

This chapter argues for an epiphenomenal reading of Nietzsche’s view of reflective consciousness. The position ascribed to Nietzsche is that no reflectively conscious state is among the causally efficacious antecedents of token actions. This reading is defended by showing it is compellingly supported by textual evidence. The chapter also argues that reflective consciousness’s proper function is in the realm of social coordination. More precisely, Rconscious states play a crucial role in the acquisition of social norms. That role, however, is not sufficient for the relevant norm to become behaviourally efficacious and, thus, cause our actions. For only internalized norms are behaviourally efficacious in that sense. In turn, though Rconscious states are often the channel through which we are presented with social norms, it depends on the arrangement of our drives and affects whether we internalize them or not. The chapter ends by surveying and rebutting a range of objections to epiphenomenal readings of Nietzsche.

scholarly journals The N-terminal Tail of C. elegans CENP-A Interacts with KNL-2 and is Essential for Centromeric Chromatin Assembly

2020 ◽  
Author(s):  
Christian de Groot ◽  
Jack Houston ◽  
Bethany Davis ◽  
Adina Gerson-Gurwitz ◽  
Joost Monen ◽  
...  
Keyword(s):  
Histone H3 ◽  
Direct Interaction ◽  
Chromatin Assembly ◽  
Nucleosome Assembly ◽  
Centromeric Chromatin ◽  
C Elegans ◽  
Histone Fold ◽  
Kinetochore Assembly ◽  
Histone H3 Variant ◽  
Evolutionary Variation

ABSTRACTCentromeres are epigenetically defined by the presence of the centromere-specific histone H3 variant CENP-A. A specialized loading machinery, including the histone chaperone HJURP/Scm3, participates in CENP-A nucleosome assembly. However, Scm3/HJURP is missing from multiple lineages, including nematodes, which rely on a CENP-A-dependent centromere. Here, we show that the extended N-terminal tail of C. elegans CENP-A contains a predicted structured region that is essential for centromeric chromatin assembly. Removal of this region of the CENP-A N-Tail prevents loading, resulting in failure of kinetochore assembly and defective chromosome condensation. By contrast, the N-Tail mutant CENP-A localizes normally in the presence of endogenous CENP-A. The portion of the N-Tail containing the predicted structured region binds to KNL-2, a conserved SANTA and Myb domain-containing protein (referred to as M18BP1 in vertebrates), that is specifically involved in CENP-A chromatin assembly. This direct interaction is conserved in the related nematode C. briggsae, despite divergence of the N-Tail and KNL-2 primary sequences. Thus, the extended N-Tail of CENP-A is essential for CENP-A chromatin assembly in C. elegans and partially substitutes for the function of Scm3/HJURP, in that it mediates an interaction of the specialized histone fold of CENP-A with KNL-2. These results highlight an evolutionary variation on centromeric chromatin assembly in the absence of a dedicated CENP-A-specific chaperone/targeting factor of the Scm3/HJURP family.

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