Eukaryotic chromosomes are made up of a large nucleoprotein complex called chromatin. Chromatin contains millions of repeating nucleosome subunits, each consisting of approximately 150 base pairs of double-stranded (ds) DNA wrapped around several highly conserved core structural proteins. These proteins, called core histones, form a flattened cylindrical coil that serves to compress dsDNA for storage in the microscopic cell nucleus. The core nucleosome contains two copies of each of the core histones H2A, H2B, H3 and H4, with histone H1 attached to the ends of the DNA entering and exiting the nucleosome , . While most of each histone strand is structured and involved in protein-protein or protein-DNA contacts, the first twenty N-terminal histone residues, called histones, arecruzThey are not structured. Reversible post-translational modifications (PTM) of histone tails, also called histonesto noticethey play a key role in the regulation of higher-order chromatin structure and gene expression . A large number of different histonesto noticeare presented as the basis of ahiston-codein eukaryotes, in which different sets of histone PTMs act as signals for specific DNA patterning processes. This histone code is implemented by a large familyauteurproteins that set up chemically distinct PTMs. family ofdocentproteins interpret different histone MTPs andgomproteins remove any PTM when the histone code needs to be erased and rewritten. Many, but not all, histone MTPs are located on lysine side-chain amines at the N- and C-termini of histones; including methylation , acetylation , ubiquitylation  and sumoylation . In fact, the small ubiquitin-like modifier (SUMO) is the largest histone PTM known to date. The consequences of some of themto noticeon chromatin structure and gene transcription were assessed with homogeneously modified semi-synthetic histones generated by different synthetic pathways , , . A common theme in these semi-synthetic approaches was the splitting of the target histone into two fragments. A smaller N- or C-terminal peptide fragment containing the PTM was prepared by solid phase peptide synthesis (SPPS), and a second larger histone fragment was heterologously expressed and purified from bacteria. The two fragments merged, orconnected, using the Native Chemical Ligation (NCL) technique . for largeto noticelike ubiquitin or SUMO, a recombinant protein modifier is installed on a specific lysine side chain with an additional ligation reaction .
We used semi-synthetic histones to determine the effectsto noticeabout chromatin structure, gene transcription and biochemical cross-talk with othersto notice(Figure 1) , , , , , , , , . Sedimentation rate analysis with reconstituted arrays of nucleosomes containing modified synthetic histones showed that SUMO conjugated to histone H4 on lysine 12, H4K12su  and ubiquitin bound to histone H2B on lysine 120 , H2BK120ub , inhibit chromatin compaction . Cell-free transcription assays with chromatinized plasmids containing semisynthetic histones also revealed that H4K12su directly suppresses gene transcription . In addition, demethylation assays with H4K12-containing mononucleosomes showed inhibition of H3K4 methylation and stimulation of lysine-specific demethylase 1 (LSD1) activity at H3 lysine 4, H3K4me2 . Many hypothesis-driven experiments, based on observations in different cell types and tissues, have used semi-synthetic histones to elucidate the biophysical and biochemical basis of the histone code. However, new approaches based on chemical biology are also needed to complement genetic experiments that can identify key enzymes that write and erase the dynamic histone code.
Although mutations in the active site of a known chromatin-modifying enzyme have been used to enhance binding to histones , it remains difficult to identify all, or even most, of the histone-writer/eraser interactions for specific modifications. To address this gap in our understanding of histone PTMs, particularly for histone ubiquitylation, we now report the synthesis of covalent histone-based probes that can be used to capture chromatin-binding enzymes. The covalent warheads we present have already been successful in investigating the biochemistry of ubiquitin  and in the characterization of binding-specific deubiquitylase enzymes , , , . Therefore, we present a general semi-synthetic method to obtain homogeneously ubiquitous histones with an oxidizable cysteine residue or an electrophilic dehydroalanine residue at the H2B-ubiquitin junction in H2BK120ub that can be used to generate active site thiols in chromatin-associated enzymes. to catch. which operate on H2BK120ub.
Demethylation of the H3K4me2 character
Lysine ε-amines on histones can be modified by mono-, di-, or trimethylation, and these modification states occur at different loci on chromatin . Each methylation state is interpreted by specific sets of reading enzymes , . Dimethylation at lysine 4 on histone H3 (H3K4me2) is enriched at the transcription start site (TSS) of many actively transcribed genes , , , . Set1-associated protein complex (COMPASS) is responsible for H3K4 methylation in yeast,
Half-synthesis of H2BK120ub(G76A), H2BK120ub(G76C) and H2BK120ub(G76Dha) can be achieved in three to four linear steps with two identical peptide and protein fragments. This provides rapid access to any desired protein form for biochemical and structural studies. For example, H2BK120ub(G76A) was first used in mechanistic studies of the biochemical cross-talk between H3K79 ubiquitylation and methylation by Dot1L and can be easily obtained in one step from H2BK120ub(G76C) as
Ophiston-codefor gene regulation was first proposed at the beginning of the 21st centuryto callcentury. Over the past two decades, we have collectively gained a strong understanding of the critical role that epigenetic marks, including approximately 30 chemically distinct histone PTMs and DNA methylation, play in orchestrating numerous DNA-directed processes in cells. eukaryotes. Although most of the histone marks discovered to date have been examined by site-directed mutagenesis, Western blots with site and
No external data were used for the research described in the article. All information mentioned in the manuscript is available for inspection upon reasoned request.
Work in our laboratory is supported by National Institutes of Health R01GM110430, R01HD097408, and National Science Foundation CHE-2107525.
no reference provided
Statement on CRediT's contribution
Madeline F. Currie:Writing: original draft, Writing: revision and editing.Sumeet K. Singh:Conceptualization, research, writing - review and publication.Meihuan-ji:Research, writing - reviewing and editing.Champak Chatterjee:Conceptualization, financing, mentoring, writing: revision and publication.
Declaration of Interest in the Contest
The authors declare that they have no conflicting financial interests or known personal relationships that could affect the work reported in this document.
Catching DUBs in action: new ubiquitin-based probes for targeting active sites
Current Opinion in Chemical Biology, Volume 23, 2014., p. 63-70 (weergave, rust).
Protein ubiquitylation is an important regulator of protein function, localization and half-life. It plays a key role in most cellular processes, including immune signaling. Dysregulation of this process is an important causative factor in many diseases. A breakthrough in the identification and characterization of ubiquitin-removing enzymes, deubiquitylases (DUBs), was achieved through the development of activity-based probes (ABPs). Recent advances in chemical protein synthesis and binding methodology have led to new reagents for use in ubiquitous research. We describe recent advances and discuss future directions in the development of reagents for the study of DUBs.(Video) Unit6B Epigenetics
A structural variant of human glycophorin DUP4 that protects against malaria shows somatic mosaicism and association with hemoglobin levels
The American Journal of Human Genetics, nummer 103, broj 5, 2018., str. 769-7
Glycophorin A and glycophorin B are proteins on the surface of red blood cells and both are receptors for the parasite.Plasmodium falciparum, the leading cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that contains extra copies of the glycophorin A and glycophorin B fusion gene and has a dramatic effect on the risk of malaria by reducing the risk of severe malaria by up to 40%. Using Fiber-FISH and Illumina sequencing, we confirmed the structural arrangement of the glycophorin locus in the DUP4 variant and detected the somatic copy number variation of the glycophorin B-glycophorin A fusion gene. By a simple, specific and PCR-based test for DUP4, we show that the DUP4 variant reaches a frequency of 13% in the population of a malaria-endemic village in southeastern Tanzania. We genotyped a significant portion of that village and demonstrated an association between DUP4 genotype and hemoglobin levels, a phenotype associated with malaria, using a family-based linkage test. Taken together, we show that DUP4 is a complex structural variant that may be subject to somatic variation and show that DUP4 is associated with a malaria-related phenotype in a longitudinally followed population.
Research article(Video) The Importance of Histone Tail Conformation and Dynamics in Chromatin Signaling and Disease
Non-histone-binding functions of PHD fingers
Trends in Biochemical Sciences, 2023
Plant homeodomain fingers (PHD) are a large and well-established family of epigenetic readers that recognize histone H3. A typical PHD finger binds to the unaltered or methylated amino terminal tail of H3. This interaction is highly specific and can be regulated by post-translational modifications (PTMs) in H3 and other domains present in the protein. Recently, however, a set of PHD fingers has been shown to bind to non-histone proteins, H3 mimetics and DNA. In this review, we highlight the molecular mechanisms by which PHD fingers interact with ligands other than the amino terminus of H3 and discuss similarities and differences in the interaction with histone and non-histone binding partners.
Unraveling germline POLN mutations in familial nasopharyngeal carcinoma: additional evidence from gene association and molecular studies
eBioMedicine, Volume 86, 2022, Article 104326
Research article(Video) Transcription Factors Histone Modification EDITED VERSION AT https://youtu.be/MdzUB0WWons
chemical ubiquity of chromatin
Current Opinion in Chemical Biology, Volume 45, 2018., p. 18-26 (weergave, rust).
Histone modifications dynamically regulate chromatin structure and function and mediate many processes that require access to DNA. Chemical protein synthesis has emerged as a powerful approach to generate homogeneously modified histone analogs in viable quantities for subsequent incorporation into nucleosome arrays for biochemical, functional and structural studies. This brief review focuses on the power of total protein chemical synthesis and semisynthetic approaches to generate ubiquitous histones in their natural or non-native forms and the utility of these analogs in deciphering the role of ubiquity in epigenetics.
Design of a neuroclinical assessment of empathy deficits in psychopathy based on the zipper model of empathy
Neuroscience and Biobehavior Reviews, Volume 151, 2023, Artikel 105244
The heterogeneity of the literature on empathy highlights its multidimensional and dynamic nature and contributes to vague descriptions of empathy in the context of psychopathology. The zipper model of empathy integrates current theories of empathy and proposes that the maturity of empathy depends on whether contextual and personal factors bring together or separate affective and cognitive processes. Therefore, this conceptual paper proposes a comprehensive set of physiological and behavioral measures to empirically assess empathy processing according to this model with application to psychopathic personality. We recommend using the following measures to assess each component of this model: (1) facial electromyography; (2) emotion recognition task; (3) empathy accuracy task and physiological measures (e.g., heart rate); (4) selection of theory of mind tasks and modified point perspective task, and; (5) a custom charity assignment. Ultimately, we hope that this article will serve as a starting point for discussion and debate on the definition and assessment of empathy processing, to encourage research to falsify and update this model to improve our understanding of empathy.(Video) (2022) MCB 182 Lecture 5 - Epigenomes
© 2023 Elsevier B.V. We are the real prisoners.