Epigenetic Preparation of Future Gene Induction Kinetics.

Decoding the Epigenetic Language of Neuronal Plasticity

Chromatin Remodeling Is a Key Mechanism Underlying Cocaine-Induced Plasticity in Striatum

Histone Modifications and Chromatin Remodeling during Bacterial Infections

Epigenetics in Male Germ Cells

Epigenomics in COVID-19; the link between DNAmethylation, histone modifications and SARS-CoV-2 infection.

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells

Gene expression is regulated by the dynamic nature of DNA modification, histone modification, and recruitment of activating and repressing protein complexes at specific loci. Chromatin itself is further organized structurally into regions of varying accessibility, an aspect of which includes transient or sustained redistribution of portions of the genome from the nucleoplasm to the nuclear periphery. Targeting of genes to the nuclear membrane, frequently via association with components of the nuclear pore complex (NPC), has both positive and negative effects on the timing and magnitude of gene expression [1]. Moreover, chromatin localization to the nuclear membrane endows certain genes with a form of multigenerational transcriptional memory after inactivation, allowing faster reactivation in the progeny upon return to inducing conditions [2]. The mechanisms underlying these various phenomena are beginning to be understood at the molecular level, perhaps best exemplified by studies in the baker’s yeast Saccharomyces cerevisiae, where precise manipulation of environmental conditions can be coupled with state of the art single-cell imaging and genetics. For example, genes have been found to localize to the nuclear periphery in response to nutrient shift (GAL1-10, INO1, SUC2, HXK1) and heat shock (HSP104, TSA2) (summarized in ref [3]). This dynamic association requires NPC proteins and, in the case of INO1, two sequence elements (gene recruitment sequence I and II; GRS) in the promoter [4]. While the role of GRSII remains unclear, GRSI recruits the Put3 transcription factor as an intermediary for NPC targeting [5]. After shift to repressing conditions, the INO1 locus remains associated with the nuclear periphery for multiple generations, conferring transcriptional memory via stabilization of a poised RNA polymerase II complex [6, 7]. This phenomenon requires a different promoter element termed the memory recruitment sequence (MRS) and a different nuclear pore protein (Nup100) than those involved in GRS recruitment [6]. Therefore, unique “DNA zip codes” dictate targeting of a gene to the nuclear periphery via distinct protein interactions. Importantly, these targeting events are independent of each other – GRSI, II and Put3 are not required during memory and the MRS is apparently dispensable for localization during gene activation [6]. The Brickner laboratory has paved the way in our understanding of these events, and elucidated much of the molecular detail. Central to their discoveries has been the development of methods to quantitatively assess subnuclear chromatin positioning. These approaches utilize DNA arrays consisting of Lac (LacO) and Tet (TetO) Operator elements integrated at loci of interest paired with fluorescent protein-DNA binding protein fusions. Cells bearing these endogenous and/or ectopic constructs can then be visualized with confocal microscopy and intra-nuclear distances measured (i.e., gene-gene or gene-nuclear periphery) for individual cells within a population. A key observation derived from these analyses was that two copies of the same locus, for example INO1/INO1 in a diploid cell, identified with different color fluorophores, were found to cluster together in three-dimensional space [8]. Moreover, two independent loci, each bearing a GRSI element, likewise cluster during activation [8]. In the article published in this issue of Microbial Cell, Brickner and co-workers reveal that clustering also occurs during transcriptional memory [9]. Multiple aspects of INO1 memory clustering differentiate this phenomenon from that observed upon gene activation. Transcriptional memory at the GAL1-10 locus requires the nuclear basket protein Mlp1, in contrast to INO1 which targets to the NPC through Nup100 [6, 10]. Consistently, GAL1 and INO1, when differentially labeled, were found not to cluster after shift to repressing conditions, indicating specificity [9]. The MRS zip code was also shown to be required for clustering, functionally linking this feature with targeting to the nuclear periphery during memory. Fascinatingly, the MRS was seen in this study to be insufficient for memory-based clustering – both GRSI and GRSII elements are also required. The same held true for the role of the GRSI binding protein Put3 and the gene activation nuclear periphery recruitment protein Nup100 [9]. Therefore, clustering during transcriptional memory requires previous clustering during gene activation, and each process relies on its own previ-

The book is intended for students studying medical and biological specialties. CHAPTER I. EPIGENETICS INTRODUCTION The science of epigenetics looks at the mechanisms of molecular modifications of histones and DNA that can regulate gene activity without affecting the nucleotide sequences in the DNA molecule. Recognized epigenetic regulators are DNA methylation, post-translational modifications of histones, and non-coding RNAs (nkRNAs). One of the most important differences between eukaryotic cells and prokaryotes is the presence of a complex nucleo-protein chromatin complex in eukaryotes. It is in this form that the DNA molecule is stored in our cells. On the one hand, the complex structural organization of chromatin provides a compact arrangement of DNA in the cell nucleus. On the other hand, chromatin is directly involved in the process of regulating gene expression. At the same time, the nucleosome depicted in Fig. 1 (a structural and functional unit of chromatin) is considered as a key component in the processes of regulating gene expression. The nucleus of the nucleosome is 8 histone proteins (octamers). The nucleus of the nucleosome consists of two copies of each of the histone proteins H2A, H2B, H3 and H4. The DNA chain, which includes 147 nucleotides, folds 1.65 times around the octamer of histones. The nucleosomes are arranged as a linear array along the DNA molecule in the form of "beads on a string". The linker section of DNA connecting adjacent nucleosomes (transcriptionally inactive) is sealed with H1-histone protein. The length of the linker section is 30 nm. Moreover, the site of the beginning of transcription is usually located inside the nucleosome. Consequently, the nucleosome serves as a gene repressor, preventing the initiation of transcription. That is, chromatin provides a total repression of genes. In contrast, transcription becomes possible as a result of chromatin remodeling factors that enable the "dismantling" of nucleosomes or otherwise alter their structure and organization. Thus, the repression (inactivation) of genes begins with wrapping the DNA molecule around the histones in the nucleosome, and the liberation of genes from repression (activation) involves freeing DNA from binding to histone proteins and unfolding DNA by chromatin remodeling factors (Lorch Y., Kornberg R. D., 2017). Thanks to this mechanism, selective expression of only those genes that are needed at a given time by the cell or tissue is possible. It should be emphasized that nucleosome repression extends not only to transcription, but also to most other biological processes associated with the DNA molecule, such as replication, mitotic division, repair of double-strand breaks, and maintenance of telomeres. Thus, epigenetic mechanisms control various physiological and pathological processes by regulating the expression of the corresponding genes by changing the availability of epigenetic control systems to chromatin. The scope of application of epigenetic research methods is rapidly expanding. Currently, we are witnessing the active introduction of epigenetic approaches in the field of practical medicine aimed at diagnosing and treating dangerous human diseases. CHAPTER II. TRANSCRIPTION FACTORS INTRODUCTION For the first time, the existence of transcription factors was revealed on the basis of a discovery that made it possible to establish in vitro purified RNA polymerase-II can initiate transcription on the DNA template in the presence of a cell extract (Weil P. A. et al., 1979). Further research aimed at the fractionation and identification of the general transcription factors (GTF) required to initiate transcription in vitro has identified similar factors in rats, Drosophila, and yeast and substantiated the assumption that GTFs are indeed "common" factors necessary for the expression of genes transcribed by RNA polymerase II. is highly conserved in a number of eukaryotic organisms (Matsui T. et al., 1980). We only mention RNA polymerase II because only this type of enzyme has the ability to synthesize mRNA. Whereas RNA polymerase I is responsible for the synthesis of pro-rRNA, and RNA polymerase III is responsible for the synthesis of tRNA and other non-coding cell RNAs. Meanwhile, the regulation of transcription in eukaryotes is quite complex, since it depends on chromatin remodeling complexes (Burns L. G., Peterson C. L., 1997) and covalent modification of histone proteins (Natsume-Kitatani Y., Mamitsuka H., 2016). In transcription initiation, the immediate target of GTF is a well-defined promo zone of a structural gene. In the structure of the promotra of eukaryotes, the main elements and regulatory elements can be distinguished. The main elements of the promotra (bark promoter, see Fig. 2.1) can be attributed to the site for assembling the transcription initiation complex (PIC), including the TATA sequence located above from the transcription start site (TSS ), and an initiating sequence (Inr) covering the start site. Promoters may include a TATA unit, an initiator sequence (Inr), or both (Hampsey M., 1998). A third major element, the downstream promoter element (DPE), was originally described in Drosophila and is located about 30 p.p. below TSS. The DPE promoter element appears to function in conjunction with the Inr element as a binding site for the transcription factor TFIID on non-TATA promoters. According to current research, the cellular (main) promoters of multicellular organisms that control the initiation of transcription by RNA polymerase II may contain short sequences of nucleotides called cow promoter elements (motifs) (e.g., the TATA block, the initiator (Inr), and the lower element of the cow promoter (DPE)) that recruit RNA polymerase II through a common transcription initiation mechanism (Dreos R. et al., 2021). The authors report that the classes of Promoters of Inr+DPE are not only present in the genome of Drosophila and humans and are structurally similar to each other, but may also be common to different species of multicellular organisms. The most studied element of the cow promoter is the TATA box, but the TATA box is found only in about 10-20% of multicellular cortical promoters. Therefore, along with the TATA sequence, it is necessary to name other possible key DNA sequences known as cortical promoter elements, which include: BRE, MTE, TST and DPE sequences. The two BRE (TFIIB recognition element) motifs are located either above (BREu) or below (BREd) elements of the TATA box. It should be emphasized that TBP, TATA box, and BRE demonstrate high levels of conservatism in the range from archaebacteria to humans (Kadonaga J. T., 2012). In doing so, BREu as well as BREd have both positive and negative effects on transcription activity. The downstream core promoter element (DPE) was detected in the analysis of non-TATA gene promoters in Drosophila. The MTE element (motif ten element), which is located directly in front of the DPE, was identified as an overrepresented sequence of a cow promoter called "motif 10" and then discovered, that it is a functional element of a cow promoter. The MTE and DPE motifs exhibit high conservatism in the range from Drosophila to humans, and both motifs appear to be directly recognized by the subunits of the main transcription factor TFIID, TAF proteins that resemble histone proteins in structure. In turn, the TCT sequence regulates the transcription of ribosomal protein genes in Drosophila and humans. Although there are no universal cortical promoter elements that are present in all promoters, the concept of a cow promoter of nuclear RNA polymerase II can be defined as a minimum stretch of DNA that is sufficient to accurately initiate transcription by RNA polymerase II (Kadonaga J. T., 2012; Haberle V., Stark A., 2018). It should be noted that the results of modern research will constantly supplement the list of all new components of the cow promoter, for example, DNA-replicatedrelated element (DRE), Ohler 1,6 and 7 motifs (Danino Y. M. et al., 2015; Haberle V., Stark A., 2018). According to the authors, the bark promoter may be transformed in the course of evolution. Due to this, gene expression levels can be modulated by the composition of cow promoter elements. Such modulation is directly achieved through the emergence of combinations of new elements of the cow promoter, as a result of which an additional level of transcription regulation is realized. To summarize the above facts, transcription is usually initiated at a specific position, the Transcription Initiation Site (TSS), at the 5' end of the gene. The TSS site is embedded in a bark promoter, which is a short sequence spanning 50 base pairs above and 50 below TSS. The cortical promoter serves as a binding platform for the components required to initiate transcription, including RNA polymerase II and related common transcription factors (GTFs). Regulatory elements. The cortical promoter is sufficient to initiate transcription, but such transcription has low basal activity, which can be further activated, generally by more distally arranged regulatory elements called enhancers (discussed below). Enhancers bind regulatory proteins known as transcription factors, recruit transcription cofactors, and can further enhance transcription. CHAPTER III. CELL SIGNALING PATHWAYS INTRODUCTION In a multicellular organism, the work of each cell is regulated by a large number of signals. These signals can be formed both in the organism itself, reflecting the specific needs of a living organism (metabolic state, stages of development, differentiation, reproduction), and in the form of a reaction to the effects of the external environment. The implementation of each of these signals encompasses all the biological and biochemical processes that lead from the cell's perception of the signal to the cell's response. A signal to a cell is something that is recogni

Chromatin modifications, epigenetics, and how protozoan parasites regulate their lives

Characterization of Mammalian Cellular Memory.

Epigenetic regulation of oligodendrocyte identity

During ontogeny, cells progress through multiple alternate differentiation states by activating distinct gene regulatory networks. In this review, we highlight the important role of chromatin priming in facilitating gene activation during lineage specification and in maintaining an epigenetic memory of previous gene activation. We show that chromatin priming is part of a hugely diverse repertoire of regulatory mechanisms that genes use to ensure that they are expressed at the correct time, in the correct cell type, and at the correct level, but also that they react to signals. We also emphasize how increasing our knowledge of these principles could inform our understanding of developmental failure and disease.

Higher-order orchestration of hematopoiesis: Is cohesin a new player?

Epigenetics has evolved rapidly over the last two decades as a contemporary field of biology. In present day, it represents the heritable mitotic or even meiotic genetic change which does not alter the DNA sequence. Plants are considered as the masters of epigenetic regulation since they have the capability of rapid and reversible alteration of their epigenetic state and also maintaining a stable “memory” of it. Plants being sessile in nature are exposed to adverse environmental conditions which hampers their growth, development, productivity, and survival. They have developed intricate mechanisms at molecular level to withstand such stressful situations. Recent studies have documented the epigenetic control on stress-responsive mechanisms in response to various abiotic stresses. Several epigenetic mechanisms identified so far involve DNA methylation, histone modifications (acetylation, methylation, phosphorylation, ubiquitination, biotinylation, and sumoylation), chromatin remodeling, and small RNA (miRNA and siRNA) directed DNA methylation. Plants make wide use of DNA methylation as an epigenetic mark and undergo histone modifications to carry out transcriptional as well as posttranscriptional gene silencing programs. In this chapter, we have recapitulated the historical overview of the field of epigenetics followed by the various epigenetic mechanisms and lastly reviewed the studies related to various abiotic stress responses to understand the role of different epigenetic mechanisms in different plant species.

Methylation of Lysine 4 on Histone H3: Intricacy of Writing and Reading a Single Epigenetic Mark