scholarly journals Tidying-up the plant nuclear space: domains, functions, and dynamics

2020 ◽  
Vol 71 (17) ◽  
pp. 5160-5178
Author(s):  
Ana Paula Santos ◽  
Valérie Gaudin ◽  
Iva Mozgová ◽  
Frédéric Pontvianne ◽  
Daniel Schubert ◽  
...  
Keyword(s):  
Regulation Of Gene Expression ◽  
Nuclear Periphery ◽  
Plant Genome ◽  
Nuclear Space ◽  
Major Question ◽  
3D Genome ◽  
Technological Advances ◽  
Nuclear Domains ◽  
Remarkable Progress

Abstract Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.

scholarly journals Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

2020 ◽  
Author(s):  
Cristiana Bersaglieri ◽  
Jelena Kresoja-Rakic ◽  
Shivani Gupta ◽  
Dominik Bär ◽  
Rostyslav Kuzyakiv ◽  
...  
Keyword(s):  
Nuclear Periphery ◽  
Interaction Strength ◽  
Nuclear Lamina ◽  
Nuclear Space ◽  
Chromosome Architecture ◽  
Neural Genes ◽  
Repressive Chromatin ◽  
Genome Wide ◽  
Nuclear Environment

AbstractEukaryotic chromosomes are folded into hierarchical domains, enabling the organization of the genome into functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks thought to contribute to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for genome-wide maps of nucleolar associated domains (NADs). Here we established a method based on a Dam-fused engineered nucleolar histone H2B that marks DNA contacting the nucleolus. NAD-maps of ESCs and neural progenitors revealed layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs showed higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation, chromosomes around the nucleolus acquire a more compact, rigid architecture whereas NADs specific for ESCs decrease their interaction strength within the repressive B-compartment strength, unlocking neural genes from repressive nuclear environment. The methodologies here developed will make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function.

scholarly journals Chromatin Organization and Function in Drosophila

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2362
Author(s):  
Palmira Llorens-Giralt ◽  
Carlos Camilleri-Robles ◽  
Montserrat Corominas ◽  
Paula Climent-Cantó
Keyword(s):  
Cell Nucleus ◽  
Regulation Of Gene Expression ◽  
Temporal Distribution ◽  
Chromatin Organization ◽  
Small Scale ◽  
Nuclear Space ◽  
And Function ◽  
High Order Chromatin ◽  
Eukaryotic Genomes

Eukaryotic genomes are packaged into high-order chromatin structures organized in discrete territories inside the cell nucleus, which is surrounded by the nuclear envelope acting as a barrier. This chromatin organization is complex and dynamic and, thus, determining the spatial and temporal distribution and folding of chromosomes within the nucleus is critical for understanding the role of chromatin topology in genome function. Primarily focusing on the regulation of gene expression, we review here how the genome of Drosophila melanogaster is organized into the cell nucleus, from small scale histone–DNA interactions to chromosome and lamina interactions in the nuclear space.

scholarly journals Lamin C regulates genome organization after mitosis

2020 ◽  
Author(s):  
X Wong ◽  
VE Hoskins ◽  
JC Harr ◽  
M Gordon ◽  
KL Reddy
Keyword(s):  
Genome Organization ◽  
Mammalian Cells ◽  
Regulation Of Gene Expression ◽  
Nuclear Periphery ◽  
Nuclear Lamina ◽  
Lamin A ◽  
3D Genome ◽  
Cellular Processes ◽  
Genomic Regions ◽  
In Cells

AbstractThe dynamic 3D organization of the genome is central to the regulation of gene expression and developmental progression, with its disruption being implicated in various diseases. The nuclear lamina, a proteinaceous meshwork underlying the nuclear envelope (NE), provides both structural and regulatory influences on genome organization through the tethering of large inactive genomic regions, called Lamina Associated Domains (LADs), to the nuclear periphery. Evidence suggests that the A type lamins, lamins A and C, are the predominant lamins involved in the peripheral association of LADs, with these two isotypes forming distinct networks and potentially involved in different cellular processes. Here we tested whether lamins A and C have distinct roles in genome organization by examining chromosome architecture in cells in which lamin C or lamin A are specifically down-regulated. We find that lamin C (not lamin A) is required for the 3D organization of LADs and overall chromosome organization in the cell nucleus. Striking differences in the localization of lamin A and lamin C are present as cells exit mitosis that persist through early G1. Whereas lamin A associates with the nascent NE during telophase, lamin C remains in the interior surrounding nucleoplasmic LAD clusters. Lamin C association with the NE is delayed until several hours into G1 and correlates temporally and spatially with the post-mitotic NE association of LADs. Post-mitotic LAD association with the NE, and consequently global 3D genome organization, is perturbed only in cells depleted of lamin C, and not in cells depleted of lamin A. We conclude that lamin C regulates LAD dynamics after mitosis and is a key regulator of genome organization in mammalian cells. These findings reveal an unexpectedly central role for lamin C in genome organization, including both inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE.

Value-driven issues throughout the development of sociological theory

2020 ◽  
pp. 147-160
Author(s):  
Gulbarshyn Chepurko ◽  
Valerii Pylypenko
Keyword(s):  
Social Interactions ◽  
Social System ◽  
Sociological Theory ◽  
Social Scientists ◽  
Social Sphere ◽  
Technological Advances ◽  
The Social ◽  
The Individual ◽  
Different Levels

The paper examines and compares how the major sociological theories treat axiological issues. Value-driven topics are analysed in view of their relevance to society in times of crisis, when both societal life and the very structure of society undergo dramatic change. Nowadays, social scientists around the world are also witnessing such a change due to the emergence of alternative schools of sociological thought (non-classical, interpretive, postmodern, etc.) and, subsequently, the necessity to revise the paradigms that have been existed in sociology so far. Since the above-mentioned approaches are often used to address value-related issues, building a solid theoretical framework for these studies takes on considerable significance. Furthermore, the paradigm revision has been prompted by technological advances changing all areas of people’s lives, especially social interactions. The global human community, integral in nature, is being formed, and production of human values now matters more than production of things; hence the “expansion” of value-focused perspectives in contemporary sociology. The authors give special attention to collectivities which are higher-order units of the social system. These units are described as well-organised action systems where each individual performs his/her specific role. Just as the role of an individual is distinct from that of the collectivity (because the individual and the collectivity are different as units), so too a distinction is drawn between the value and the norm — because they represent different levels of social relationships. Values are the main connecting element between the society’s cultural system and the social sphere while norms, for the most part, belong to the social system. Values serve primarily to maintain the pattern according to which the society is functioning at a given time; norms are essential to social integration. Apart from being the means of regulating social processes and relationships, norms embody the “principles” that can be applied beyond a particular social system. The authors underline that it is important for Ukrainian sociology to keep abreast of the latest developments in the field of axiology and make good use of those ideas because this is a prerequisite for its successful integration into the global sociological community.

The Role of microRNAs in the Viral Infections

2019 ◽  
Vol 24 (39) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mona Fani ◽  
Milad Zandi ◽  
Majid Rezayi ◽  
Nastaran Khodadad ◽  
Hadis Langari ◽  
...  
Keyword(s):  
Viral Infections ◽  
Rna Viruses ◽  
Regulation Of Gene Expression ◽  
Molecular Structures ◽  
Main Function ◽  
Cellular Functions ◽  
Viral Genes ◽  
Non Coding Rnas ◽  
Post Transcriptional Regulation

MicroRNAs (miRNAs) are non-coding RNAs with 19 to 24 nucleotides which are evolutionally conserved. MicroRNAs play a regulatory role in many cellular functions such as immune mechanisms, apoptosis, and tumorigenesis. The main function of miRNAs is the post-transcriptional regulation of gene expression via mRNA degradation or inhibition of translation. In fact, many of them act as an oncogene or tumor suppressor. These molecular structures participate in many physiological and pathological processes of the cell. The virus can also produce them for developing its pathogenic processes. It was initially thought that viruses without nuclear replication cycle such as Poxviridae and RNA viruses can not code miRNA, but recently, it has been proven that RNA viruses can also produce miRNA. The aim of this articles is to describe viral miRNAs biogenesis and their effects on cellular and viral genes.

scholarly journals Education in developing countries and reducing maternal mortality: a forgotten piece of the puzzle?

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Vedran Stefanovic
Keyword(s):  
Developing Countries ◽  
Maternal Mortality ◽  
Meta Analysis ◽  
Perinatal Care ◽  
Substantial Improvement ◽  
Global Strategy ◽  
Perinatal Medicine ◽  
Technological Advances ◽  
Women's Role

Abstract Despite substantial improvement in reducing maternal mortality during the recent decades, we constantly face tragic fact that maternal mortality (especially preventable deaths) is still unacceptably too high, particularly in the developing countries, where 99% of all maternal deaths worldwide occur. Poverty, lack of proper statistics, gender inequality, beliefs and corruption-associated poor governmental policies are just few of the reasons why decline in maternal mortality has not been as sharp as it was wished and expected. Education has not yet been fully recognized as the way out of poverty, improvement of women’s role in the society and consequent better perinatal care and consequent lower maternal mortality. Education should be improved on all levels including girls, women and their partners, medical providers, religious and governmental authorities. Teaching the teachers should be also an essential part of global strategy to lower maternal mortality. This paper is mostly a commentary, not a systematic review nor a meta-analysis with the aim to rise attention (again) to the role of different aspects of education in lowering maternal mortality. The International Academy of Perinatal Medicine should play a crucial role in pushing the efforts on this issue as the influential instance that promotes reflection and dialog in perinatal medicine, especially in aspects such as bioethics, the appropriate use of technological advances, and the sociological and humanistic dimensions of this specific problem of huge magnitude. The five concrete steps to achieve these goals are listed and discussed.

scholarly journals The Role of Capsid in HIV-1 Nuclear Entry

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1425
Author(s):  
Anabel Guedán ◽  
Eve R. Caroe ◽  
Genevieve C. R. Barr ◽  
Kate N. Bishop
Keyword(s):  
Nuclear Pore ◽  
Outer Face ◽  
Nuclear Entry ◽  
Nuclear Compartment ◽  
Critical Step ◽  
Technological Advances ◽  
Dividing Cells ◽  
Hiv 1 ◽  
Gain Access

HIV-1 can infect non-dividing cells. The nuclear envelope therefore represents a barrier that HIV-1 must traverse in order to gain access to the host cell chromatin for integration. Hence, nuclear entry is a critical step in the early stages of HIV-1 replication. Following membrane fusion, the viral capsid (CA) lattice, which forms the outer face of the retroviral core, makes numerous interactions with cellular proteins that orchestrate the progress of HIV-1 through the replication cycle. The ability of CA to interact with nuclear pore proteins and other host factors around the nuclear pore determines whether nuclear entry occurs. Uncoating, the process by which the CA lattice opens and/or disassembles, is another critical step that must occur prior to integration. Both early and delayed uncoating have detrimental effects on viral infectivity. How uncoating relates to nuclear entry is currently hotly debated. Recent technological advances have led to intense discussions about the timing, location, and requirements for uncoating and have prompted the field to consider alternative uncoating scenarios that presently focus on uncoating at the nuclear pore and within the nuclear compartment. This review describes recent advances in the study of HIV-1 nuclear entry, outlines the interactions of the retroviral CA protein, and discusses the challenges of investigating HIV-1 uncoating.

scholarly journals Histone lactylation drives oncogenesis by facilitating m6A reader protein YTHDF2 expression in ocular melanoma

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jie Yu ◽  
Peiwei Chai ◽  
Minyue Xie ◽  
Shengfang Ge ◽  
Jing Ruan ◽  
...  
Keyword(s):  
Macrophage Polarization ◽  
Regulation Of Gene Expression ◽  
Metabolic Stress ◽  
Ocular Melanoma ◽  
Rna Modifications ◽  
M1 Macrophage ◽  
Melanoma Therapy

Abstract Background Histone lactylation, a metabolic stress-related histone modification, plays an important role in the regulation of gene expression during M1 macrophage polarization. However, the role of histone lactylation in tumorigenesis remains unclear. Results Here, we show histone lactylation is elevated in tumors and is associated with poor prognosis of ocular melanoma. Target correction of aberrant histone lactylation triggers therapeutic efficacy both in vitro and in vivo. Mechanistically, histone lactylation contributes to tumorigenesis by facilitating YTHDF2 expression. Moreover, YTHDF2 recognizes the m6A modified PER1 and TP53 mRNAs and promotes their degradation, which accelerates tumorigenesis of ocular melanoma. Conclusion We reveal the oncogenic role of histone lactylation, thereby providing novel therapeutic targets for ocular melanoma therapy. We also bridge histone modifications with RNA modifications, which provides novel understanding of epigenetic regulation in tumorigenesis.

scholarly journals Role of microRNAs in Lung Carcinogenesis Induced by Asbestos

2021 ◽  
Vol 11 (2) ◽  
pp. 97
Author(s):  
Rakhmetkazhy Bersimbaev ◽  
Olga Bulgakova ◽  
Akmaral Aripova ◽  
Assiya Kussainova ◽  
Oralbek Ilderbayev
Keyword(s):  
Lung Cancer ◽  
Expression Profile ◽  
Regulation Of Gene Expression ◽  
International Agency ◽  
Oxygen Species ◽  
Lung Carcinogenesis ◽  
Mrna Targets ◽  
The World ◽  
Post Transcriptional Regulation

MicroRNAs are a class of small noncoding endogenous RNAs 19–25 nucleotides long, which play an important role in the post-transcriptional regulation of gene expression by targeting mRNA targets with subsequent repression of translation. MicroRNAs are involved in the pathogenesis of numerous diseases, including cancer. Lung cancer is the leading cause of cancer death in the world. Lung cancer is usually associated with tobacco smoking. However, about 25% of lung cancer cases occur in people who have never smoked. According to the International Agency for Research on Cancer, asbestos has been classified as one of the cancerogenic factors for lung cancer. The mechanism of malignant transformation under the influence of asbestos is associated with the genotoxic effect of reactive oxygen species, which initiate the processes of DNA damage in the cell. However, epigenetic mechanisms such as changes in the microRNA expression profile may also be implicated in the pathogenesis of asbestos-induced lung cancer. Numerous studies have shown that microRNAs can serve as a biomarker of the effects of various adverse environmental factors on the human body. This review examines the role of microRNAs, the expression profile of which changes upon exposure to asbestos, in key processes of carcinogenesis, such as proliferation, cell survival, metastasis, neo-angiogenesis, and immune response avoidance.

Speciation and changes in male gene expression in Drosophila

Genome ◽  
2020 ◽  
pp. 1-11
Author(s):  
Bahar Patlar ◽  
Alberto Civetta
Keyword(s):  
Gene Expression ◽  
Reproductive Isolation ◽  
Potential Role ◽  
Regulation Of Gene Expression ◽  
Drosophila Model ◽  
Depth Analysis ◽  
The Impact ◽  
Plastic Responses ◽  
Male Gene

It has long been acknowledged that changes in the regulation of gene expression may account for major organismal differences. However, we still do not fully understand how changes in gene expression evolve and how do such changes influence organisms’ differences. We are even less aware of the impact such changes might have in restricting gene flow between species. Here, we focus on studies of gene expression and speciation in the Drosophila model. We review studies that have identified gene interactions in post-mating reproductive isolation and speciation, particularly those that modulate male gene expression. We also address studies that have experimentally manipulated changes in gene expression to test their effect in post-mating reproductive isolation. We highlight the need for a more in-depth analysis of the role of selection causing disrupted gene expression of such candidate genes in sterile/inviable hybrids. Moreover, we discuss the relevance to incorporate more routinely assays that simultaneously evaluate the potential effects of environmental factors and genetic background in modulating plastic responses in male genes and their potential role in speciation.

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