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Biochemistry. Biokhimii︠a︡

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https://www.readbyqxmd.com/read/29626931/who-needs-this-junk-or-genomic-dark-matter
#1
REVIEW
O I Podgornaya, D I Ostromyshenskii, N I Enukashvily
Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species - chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC)...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626930/link-between-double-strand-dna-break-hotspots-and-transcription-regulation-forum-domains-50-250-kb-chromosome-regions-containing-coordinately-expressed-genes
#2
REVIEW
N A Tchurikov, Y V Kravatsky, O V Kretova
The data on forum domains formed by DNA double-strand break (DSB) hotspots are reviewed including forum domain identification by pulsed-field gel electrophoresis, whole genome mapping of these domains using deep sequencing strategies, analysis of gene expression in forum domains, and binding of nuclear proteins to their boundaries. Earlier unpublished data by the authors are presented. The "piano playing" hypothesis is suggested based on coordinated active transcription in some of the forum domains and coordinated silencing in the majority of them...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626929/structure-and-functions-of-the-mediator-complex
#3
REVIEW
E V Putlyaev, A N Ibragimov, L A Lebedeva, P G Georgiev, Y V Shidlovskii
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626928/protein-protein-interactions-in-dna-base-excision-repair
#4
REVIEW
N A Moor, O I Lavrik
The system of base excision repair (BER) ensures correction of the most abundant DNA damages in mammalian cells and plays an important role in maintaining genome stability. Enzymes and protein factors participate in the multistage BER in a coordinated fashion, which ensures repair efficiency. The suggested coordination mechanisms are based on formation of protein complexes stabilized via either direct or indirect DNA-mediated interactions. The results of investigation of direct interactions of the proteins participating in BER with each other and with other proteins are outlined in this review...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626927/effect-of-environmental-factors-on-nuclear-organization-and-transformation-of-human-b-lymphocytes
#5
REVIEW
F B Sall, D Germini, A P Kovina, V Ribrag, J Wiels, A O Toure, O V Iarovaia, M Lipinski, Y Vassetzky
Chromosomal translocations have long been known for their association with malignant transformation, particularly in hematopoietic disorders such as B-cell lymphomas. In addition to the physiological process of maturation, which creates double strand breaks in immunoglobulin gene loci, environmental factors including the Epstein-Barr and human immunodeficiency viruses, malaria-causing parasites (Plasmodium falciparum), and plant components (Euphorbia tirucalli latex) can trigger a reorganization of the nuclear architecture and DNA damage that together will facilitate the occurrence of deleterious chromosomal rearrangements...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626926/interpreting-chromosomal-rearrangements-in-the-context-of-3-dimentional-genome-organization-a-practical-guide-for-medical-genetics
#6
REVIEW
V S Fishman, P A Salnikov, N R Battulin
In this exciting era of "next-gen cytogenetics", the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626925/genetic-and-epigenetic-mechanisms-of-%C3%AE-globin-gene-switching
#7
REVIEW
O V Iarovaia, A P Kovina, N V Petrova, S V Razin, E S Ioudinkova, Y S Vassetzky, S V Ulianov
Vertebrates have multiple forms of hemoglobin that differ in the composition of their polypeptide chains. During ontogenesis, the composition of these subunits changes. Genes encoding different α- and β-polypeptide chains are located in two multigene clusters on different chromosomes. Each cluster contains several genes that are expressed at different stages of ontogenesis. The phenomenon of stage-specific transcription of globin genes is referred to as globin gene switching. Mechanisms of expression switching, stage-specific activation, and repression of transcription of α- and β-globin genes are of interest from both theoretical and practical points of view...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626924/unsolvable-problems-of-biology-it-is-impossible-to-create-two-identical-organisms-to-defeat-cancer-or-to-map-organisms-onto-their-genomes
#8
REVIEW
E D Sverdlov
The review is devoted to unsolvable problems of biology. 1) Problems unsolvable due to stochastic mutations occurring during DNA replication that make it impossible to create two identical organisms or even two identical complex cells (Sverdlov, E. D. (2009) Biochemistry (Moscow), 74, 939-944) and to "defeat" cancer. 2) Problems unsolvable due to multiple interactions in complex systems leading to the appearance of unpredictable emergent properties that prevent establishment of unambiguous relationships between the genetic architecture and phenotypic manifestation of the genome and make impossible to predict with certainty responses of the organism, its parts, or pathological processes to external factors...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626923/role-of-nuclear-lamina-in-gene-repression-and-maintenance-of-chromosome-architecture-in-the-nucleus
#9
REVIEW
Y Y Shevelyov, S V Ulianov
Nuclear lamina is a protein meshwork composed of lamins and lamin-associated proteins that lines the nuclear envelope from the inside and forms repressive transcription compartment. The review presents current data on the contribution of nuclear lamina to the repression of genes located in this compartment and on the mechanisms of chromatin attachment to the nuclear envelope.
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626922/the-role-of-chromosome-nuclear-envelope-attachments-in-3d-genome-organization
#10
REVIEW
I V Sharakhov, S M Bondarenko, G N Artemov, A V Onufriev
Chromosomes are intricately folded and packaged in the cell nucleus and interact with the nuclear envelope. This complex nuclear architecture has a profound effect on how the genome works and how the cells function. The main goal of review is to highlight recent studies on the effect of chromosome-nuclear envelope interactions on chromatin folding and function in the nucleus. The data obtained suggest that chromosome-nuclear envelope attachments are important for the organization of nuclear architecture in various organisms...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626921/banding-pattern-of-polytene-chromosomes-as-a-representation-of-universal-principles-of-chromatin-organization-into-topological-domains
#11
REVIEW
T D Kolesnikova
Drosophila polytene chromosomes are widely used as a model of eukaryotic interphase chromosomes. The most noticeable feature of polytene chromosome is transverse banding associated with alternation of dense stripes (dark or black bands) and light diffuse areas that encompass alternating less compact gray bands and interbands visible with an electron microscope. In recent years, several approaches have been developed to predict location of morphological structures of polytene chromosomes based on the distribution of proteins on the molecular map of Drosophila genome...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626920/crowding-entropic-forces-and-confinement-crucial-factors-for-structures-and-functions-in-the-cell-nucleus
#12
REVIEW
R Hancock
The view of the cell nucleus as a crowded system of colloid particles and that chromosomes are giant self-avoiding polymers is stimulating rapid advances in our understanding of its structure and activities, thanks to concepts and experimental methods from colloid, polymer, soft matter, and nano sciences and to increased computational power for simulating macromolecules and polymers. This review summarizes current understanding of some characteristics of the molecular environment in the nucleus, of how intranuclear compartments are formed, and of how the genome is highly but precisely compacted, and underlines the crucial, subtle, and sometimes unintuitive effects on structures and reactions of entropic forces caused by the high concentration of macromolecules in the nucleus...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626919/the-4d-nucleome-genome-compartmentalization-in-an-evolutionary-context
#13
REVIEW
T Cremer, M Cremer, C Cremer
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626918/structural-functional-domains-of-the-eukaryotic-genome
#14
REVIEW
S V Razin, A A Gavrilov
It is well known that DNA folding in the eukaryotic cell nucleus is tightly coupled with the operation of epigenetic mechanisms defining the repertoires of the genes expressed in different types of cells. To understand these mechanisms, it is important to know how DNA is packaged in chromatin. About 30 years ago a hypothesis was formulated, according to which epigenetic mechanisms operate not at the level of individual genes, but rather groups of genes localized in structurally and functionally isolated genomic segments that were called structural and functional domains...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626917/structural-functional-organization-of-the-eukaryotic-cell-nucleus-and-transcription-regulation-introduction-to-this-special-issue-of-biochemistry-moscow
#15
S V Razin
This issue of Biochemistry (Moscow) is devoted to the cell nucleus and mechanisms of transcription regulation. Over the years, biochemical processes in the cell nucleus have been studied in isolation, outside the context of their spatial organization. Now it is clear that segregation of functional processes within a compartmentalized cell nucleus is very important for the implementation of basic genetic processes. The functional compartmentalization of the cell nucleus is closely related to the spatial organization of the genome, which in turn plays a key role in the operation of epigenetic mechanisms...
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625548/glutamic-acid-signal-synchronizes-protein-synthesis-kinetics-in-hepatocytes-from-old-rats-for-the-following-several-days-cell-metabolism-memory
#16
V Y Brodsky, L A Malchenko, D S Lazarev, N N Butorina, T K Dubovaya, N D Zvezdina
The kinetics of protein synthesis was investigated in primary cultures of hepatocytes from old rats in serum-free medium. The rats were fed mixed fodder supplemented with glutamic acid and then transferred to a regular mixed fodder. The amplitude of protein synthesis rhythm in hepatocytes isolated from these rats increased on average 2-fold in comparison with the rats not receiving glutamic acid supplement. Based on this indicator reflecting the degree of cell-cell interactions, the cells from old rats were not different from those of young rats...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625547/endonuclease-activity-of-mutl-protein-of-the-rhodobacter-sphaeroides-mismatch-repair-system
#17
M V Monakhova, A I Penkina, A V Pavlova, A M Lyaschuk, V V Kucherenko, A V Alexeevski, V G Lunin, P Friedhoff, G Klug, T S Oretskaya, E A Kubareva
We have purified the MutL protein from Rhodobacter sphaeroides mismatch repair system (rsMutL) for the first time. rsMutL demonstrated endonuclease activity in vitro, as predicted by bioinformatics analysis. Based on the alignment of 1483 sequences of bacterial MutL homologs with presumed endonuclease activity, conserved functional motifs and amino acid residues in the rsMutL sequence were identified: five motifs comprising the catalytic site responsible for DNA cleavage were found in the C-terminal domain; seven conserved motifs involved in ATP binding and hydrolysis and specific to the GHKL family of ATPases were found in the N-terminal domain...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625546/possible-role-of-escherichia-coli-protein-ybgi
#18
O V Sergeeva, D O Bredikhin, M V Nesterchuk, M V Serebryakova, P V Sergiev, O A Dontsova
Proteins containing the NIF3 domain are highly conserved and are found in bacteria, eukaryotes, and archaea. YbgI is an Escherichia coli protein whose gene is conserved among bacteria. The structure of YbgI is known; however, the function of this protein in cells remains obscure. Our studies of E. coli cells with deleted ybgI gene suggest that YbgI is involved in formation of the bacterial cell wall.
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625545/expression-of-soluble-active-interferon-%C3%AE-a-in-escherichia-coli-periplasm-by-fusion-with-thermostable-lichenase-using-the-domain-insertion-approach
#19
A A Tyurin, K V Kabardaeva, O N Mustafaev, O S Pavlenko, N S Sadovskaya, V S Fadeev, E A Zvonova, I V Goldenkova-Pavlova
A recombinant DNA in which the interferon αA (IFN-αA) gene sequence is integrated into a loop region of the gene coding thermostable lichenase was constructed. This approach of insertion fusion with thermostable lichenase is advantageous in terms of increasing the solubility, stability, and production of the fusion partner in soluble form in general and in the periplasm of bacterial cells in particular. Thus, the insertion of IFN-αA into the loop (53 a.a.) of thermostable lichenase from Clostridium thermocellum resulted in effective expression of the soluble form of the recombinant protein in the periplasm of Escherichia coli without any compromise in biological activity of IFN-αA, while the thermostable lichenase retained its ability for functional folding without dramatic loss of its basic activity and thermostability...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625544/identification-of-single-amino-acid-substitutions-in-proteogenomics
#20
REVIEW
S A Moshkovskii, M V Ivanov, K G Kuznetsova, M V Gorshkov
An important aim of proteogenomics, which combines data of high throughput nucleic acid and protein analysis, is to reliably identify single amino acid substitutions representing a main type of coding genome variants. Exact knowledge of deviations from the consensus genome can be utilized in several biomedical fields, such as studies of expression of mutated proteins in cancer, deciphering heterozygosity mechanisms, identification of neoantigens in anticancer vaccine production, search for RNA editing sites at the level of the proteome, etc...
March 2018: Biochemistry. Biokhimii︠a︡
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