Interactions histones. Medical search. Frequent questions

In fact, biological outcomes are often due to physical interactions between proteins that are so highly selective that seemingly minor chemical modifications (i.e. methylation, acetylation or phosphorylation) can completely abolish biomolecular recognition processes and redirect signaling pathways. (mtu.edu)
A thermodynamic model for acetylation-dependent polybromo-histone interactions. (mtu.edu)
Thermodynamic analysis of acetylation-dependent Pb1 bromodomain - histone H3 interactions. (mtu.edu)
Deciphering the histone acetylation code for human Polybromo-1. (mtu.edu)
Thomas had been studying the roles of histone acetylation in Huntington's disease and began to wonder whether similar mechanisms of gene regulation might also be important in schizophrenia. (neurosciencenews.com)
Compared to healthy brains, the brain samples from subjects with schizophrenia showed lower levels of acetylation in certain histone portions that would block gene expression. (neurosciencenews.com)
Histone acetylation is mediated by histone acetyltransferases (HATs) that leads to chromatin decondensation (accessible chromatin) and transcription activation. (wjgnet.com)
Unlike methylation, acetylation weakens histones' interaction with DNA and loosens the chromatin to make it accessible to transcription factors. (jove.com)
Histone acetyltransferases and deacetylases catalyze acetylation and deacetylation. (jove.com)
In htz1Delta cells, Sir2 and Sir3 spread into flanking euchromatic regions, producing changes in histone H4 acetylation and H3 4-methylation indicative of ectopic heterochromatin formation. (sdbonline.org)
Acetylation of all histone residues are activating, and H3K4 is no exception. (epigenie.com)
We performed chromatin immunoprecipitation sequencing (ChIP-seq) using a histone 3 lysine 9 acetylation (H3K9ac) mark in peripheral blood mononuclear cells from patients with atherosclerosis with T2D (n = 8) or without T2D (ND, n = 10). (lu.se)

Histone methyltransferases (HMT) are histone-modifying enzymes (e.g., histone-lysine N-methyltransferases and histone-arginine N-methyltransferases), that catalyze the transfer of one, two, or three methyl groups to lysine and arginine residues of histone proteins. (wikipedia.org)
The octamer is formed of two copies each of the histone proteins H2A, H2B, H3 and H4. (usherbrooke.ca)
Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. (nih.gov)
Multiple posttranslational modifications (PTMs) of histone proteins including site-specific phosphorylation of serine and threonine residues govern the accessibility of chromatin. (edu.sa)
According to the histone code theory, PTMs recruit regulatory proteins or block their access to chromatin. (edu.sa)
The formaldehyde-based in vivo mapping techniques described in this work are generally applicable, and can be used both to probe proteinDNA interactions within specific genes and to determine the genomic location of specific chromosomal proteins. (uthscsa.edu)
By using fluorescent fusion proteins, we show that TAF10 does not have an intrinsic nuclear localization signal (NLS) and needs one of its three interaction partners to be transported into the nucleus. (hal.science)
In addition to nucleosomes, chromatin contains non-histone chromatin-associated proteins, of which the high-mobility group proteins are the most abundant. (nature.com)
Chromatin is composed of nucleosomes-structures consisting of DNA wound around histone proteins. (jove.com)
Histone variants can replace the major histone proteins, leading to chromatin remodeling. (jove.com)
The histone H2A.F/Z (H2AZ) variant is a functionally distinct, highly conserved histone subgroup that likely represents a separate evolutionary lineage of histone H2A proteins. (sdbonline.org)
KRT23 has direct interactions with proteins and molecules. (creativebiomart.net)

Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. (nih.gov)
The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. (nih.gov)
Here we show that high-mobility group AT-hook 2 protein (HMGA2) induces DNA nicks at the transcription start site, which are required by the histone chaperone FACT complex to incorporate nucleosomes containing the histone variant H2A.X. Further, phosphorylation of H2A.X at S139 (γ-H2AX) is required for repair-mediated DNA demethylation and transcription activation. (nature.com)
Genome-wide studies in Saccharomyces cerevisiae , for example, have revealed that promoters of most actively transcribed genes are depleted of nucleosomes and that histone density is inversely proportional to the transcription rate within coding regions, suggesting that nucleosomes are dynamically disassembled and reassembled at each passage of the polymerase ( 16 ). (asm.org)
Chromatin-remodeling ATPases modulate histones-DNA interactions within nucleosomes and regulate transcription. (whiterose.ac.uk)
During remodeling, the histones are modified by specific enzymes, and entire nucleosomes relocate, altering gene expression. (jove.com)
Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. (sdbonline.org)
Histone variant H2A.Z (Htz1 in yeast) replaces conventional H2A in many nucleosomes. (sdbonline.org)
How histone variants such as H2AZ are incorporated into nucleosomes has been obscure. (sdbonline.org)
These advances establish a third mechanism of chromatin reconfiguration, raising fundamental questions about the stability of nucleosomes in nonreplicative phases of the cell cycle and the cellular machinery responsible for incorporating histone variants into nucleosomes (Mizuguchi, 2004). (sdbonline.org)

The level of chromatin compaction depends heavily on histone methylation and other post-translational modifications of histones. (wikipedia.org)
Histone modifications associated with somatic hypermutation. (nih.gov)
Chromatin-mediated regulation of transcription involves DNA methylation and histone modifications. (nature.com)
Histone "tails" regularly undergo chemical modifications to either relax the DNA or repack it. (neurosciencenews.com)
Although it is clear that switching among BESs does not involve DNA rearrangements and that regulation is probably epigenetic, it remains unknown why BESs are transcribed by Pol I and what roles are played by chromatin structure and histone modifications. (asm.org)
Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
In mammalian cells, active and silent rDNA promoters are characterized by specific histone modifications, DNA methylation, and positioning of the promoter-bound nucleosome (reviewed in reference 22 ). (asm.org)
A: Schematic of DNA methylation and histone modifications in neural stem cells (NSCs). (wjgnet.com)
Chromatin modifying enzymes deposit functionally important histone modifications in a spatiotemporal manner. (frontiersin.org)
Methylation of this fourth amino acid residue from the N-terminus of histone H3 is one of the most studied histone modifications, and with good reason: it's tightly associated with the promoters of active genes. (epigenie.com)
Set9, a novel histone H3 methyltransferase that facilitates transcription by precluding histone tail modifications required for heterochromatin formation. (epigenie.com)
have discovered that one difference between susceptible and resilient mice is activation of Sirt1, a histone deacetylase that produces epigenetic modifications. (jneurosci.org)

In addition to canonical histones (H1, H2A, H2B, H3 and H4), there are so called histone variants for all histones except for H4. (nature.com)

Although histone deacetylase (HDAC) inhibitors are known to suppress synovial sarcoma in vitro and in vivo , the exact mechanism is not clear. (nature.com)
2006). Anticancer activities of histone deacetylase inhibitors. (nature.com)
Inhibitors of histone deacetylase (HDAC) restore the p53 pathway in neuroblastoma cells. (nature.com)
In principle, development of small molecule inhibitors of interactions of specific transcriptional activators (or repressors) with DNA or with the basal transcription machinery could provide highly selective regulators of gene expression and thus highly selective therapeutic agents (e.g., antiviral agents based on disabling essential viral gene expression). (mtu.edu)
Synergistic antileukemic interactions between 2-medroxyestradiol (2-ME) and histone deacetylase inhibitors involve Akt down-regulation and oxidative stress. (cdc.gov)
We are studying how apoptotic cells are recognized by C1q and complement inhibitors and what are functional consequences of these interactions. (lu.se)

We have previously demonstrated that crosstalk between lysine-specific demethylase 1 (LSD1) and histone deacetylases (HDACs) facilitates breast cancer proliferation. (johnshopkins.edu)

and 3) non-histone targets of histone-modifying enzymes. (childrensnational.org)
Chromatin endogenous cleavage (ChEC) and psoralen experiments indicated that active rDNA is devoid of histones ( 23 ), whereas chromatin immunoprecipitation (ChIP) and genetic studies led to the conclusion that active rDNA has at least a few histones and is associated with chromatin-remodeling enzymes ( 15 , 31 , 34 ). (asm.org)
therefore, scientists can add histone-modifying enzymes, histone variants, and chromatin remodeling complexes to somatic cells to aid reprogramming into pluripotent stem (iPS) cells. (jove.com)
Enzymes, such as histone demethylases and acetyltransferases, are often added during reprogramming to loosen the chromatin, making the DNA more accessible to transcription factors. (jove.com)
To counteract constraints imposed by nucleosome structure, cells deploy two major classes of multiprotein enzymes, which covalently modify the nucleosome core histones or catalyze nucleosome mobility in an adenosine triphosphate (ATP)-dependent fashion. (sdbonline.org)

Instead of SET, non-SET domain-containing histone methyltransferase utilizes the enzyme Dot1. (wikipedia.org)
Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate. (cornell.edu)

However, contrary to earlier in vitro evidence that histones may be absent from actively transcribed genes, we show directly, by immunoprecipitation of in vivocrosslinked chromatin fragments, that at least histone H4 remains bound to hsp70 DNA in vivo, irrespective of its rate of transcription. (uthscsa.edu)
When histones are acetylated, portions of DNA are exposed so that the genes can be used. (neurosciencenews.com)
The histone-DNA complexes, known as chromatin, are constantly relaxing and condensing to expose different genes, so there is no single right or wrong configuration. (neurosciencenews.com)
If portions of that guide remain closed when they shouldn't because histones are not acetylated properly, then genes can be effectively turned off when they shouldn't be with any number of detrimental effects. (neurosciencenews.com)
Methylation strengthens the interaction between histones and DNA, suppressing transcription of genes involved in differentiation. (jove.com)
In contrast, histone demethylases remove methyl groups to activate genes involved in pluripotency. (jove.com)
This synthetic genetic interaction is seen at the level of single genes and acts downstream of promoter nucleosome reorganization. (sdbonline.org)
Swr1 is required for the deposition of histone H2AZ at specific chromosome locations in vivo, and Swr1 and H2AZ commonly regulate a subset of yeast genes. (sdbonline.org)
Their published paper is titled "Driver mutations in histone H3.3 and chromatin remodeling genes in pediatric glioblastoma. (genengnews.com)
A model based which contains the Oct4/Sox2/Nanog core as well its interaction upon regulatory mechanisms inferred from ChIP-on-chip and with a few other key genes. (lu.se)

Histone variants differ from the canonical histones in their amino acid sequence and have specific and fundamental functions that cannot be performed by canonical histones. (nature.com)
Recent studies have revealed that variants of histone H2A and histone H3 play important roles not only in gene expression but also in the repair of DNA breaks and the assembly of chromosome centromeres. (sdbonline.org)
We describe genetic alterations in isocitrate dehydrogenase, ATRX, the telomerase promoter, and histone H3 variants that promote GBM tumorigenesis and have altered GBM categorization. (medscape.com)

Much of the current understanding of these processes is derived from analyses of nucleosomal histones that represent the major histone species within cells. (sdbonline.org)

The attachment of methyl groups occurs predominantly at specific lysine or arginine residues on histones H3 and H4. (wikipedia.org)
DNA is compressed through interactions with histones and methyl groups (M) are added to cytosine-guanine (CpGs) dinucleotides in regulatory regions. (wjgnet.com)

Histone methylation is a principal epigenetic modification of chromatin that determines gene expression, genomic stability, stem cell maturation, cell lineage development, genetic imprinting, DNA methylation, and cell mitosis. (wikipedia.org)
One critical area of epigenetic research is tied to histones. (neurosciencenews.com)
Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers. (mpg.de)
Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. (epigenie.com)
Our results present novel evidence on the interaction between genetics and epigenetics, as well as epigenetic changes related to immunity in patients with T2D and advanced atherosclerotic disease. (lu.se)

Mutations in the major core histones relieve transcriptional repression and bypass the requirement for SNF/SWI and SAGA. (sdbonline.org)

The St. Jude-Washington University team reports its findings in Nature Genetics in a paper titled "Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and nonbrainstem glioblastomas. (genengnews.com)

The individual unit of chromatin is the nucleosome, which is composed of 146 bp of DNA wrapped 1,75 times around a protein complex called the core histone octamer. (usherbrooke.ca)

There are three different types of protein arginine methyltransferases (PRMTs) and three types of methylation that can occur at arginine residues on histone tails. (wikipedia.org)

Histone H2B as a functionally important plasminogen receptor on macrophages. (nih.gov)
Here we show that SETD2 accumulation results in a non-canonical deposition of the functionally important H3K36me3 histone mark, which includes its reduced enrichment over gene bodies and exons. (frontiersin.org)

Phosphorylation of histone H2B at DNA double-strand breaks. (nih.gov)
It also suggests that histones, signaling through toll-like receptor 2 (TLR2) on T cells, result in phosphorylation of signal transducer and activate transcription 3 (STAT3) and retinoic acid-related orphan receptor gamma t (RORγt). (scienceboard.net)
The data further highlight that histone, the key protein component of NETs, directly interact with TLR2 expressed on T cells, directly inducing phosphorylation of STAT3, which in the presence of Th17 cell-promoting cytokines, stimulates Th17 cell differentiation and activity. (scienceboard.net)

In the absence of CYLD, gene transcription of HGF in hepatic stellate cells was repressed through binding of histone deacetylase 7 (HDAC7) to the promoter of HGF. (uni-regensburg.de)
It was found that the variant histone H2A.Z regulates gene transcription. (usherbrooke.ca)
The histone chaperone FACT (facilitates chromatin transcription) is a heterodimeric complex, consisting of SUPT16 and SSRP1 (Spt16 and Pob3 in yeast) that is responsible for the deposition of H2A/H2B-dimers onto DNA 11 , 12 . (nature.com)
methylates H3, including histones in the HOX area for allowing chromatin to be open to transcription. (atlasgeneticsoncology.org)
The variant histone H2A.Z regulates gene transcription, and deletion of the gene encoding H2A.Z strongly increases the requirement for SNF/SWI and SAGA. (sdbonline.org)
These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure (Santisteban, 2000). (sdbonline.org)
While this is still an active area of research, it is clear that specific histone methylation states regulate transcription by promoting the binding of positive transcription factors and blocking negative ones. (epigenie.com)

Both teams suggest their respective works are the first to identify somatic mutations in histone H3. (genengnews.com)

Differential pull-down experiments with H3-tails synthesized from l- and d-amino acids uncovered that histone acetyltransferase 1 (HAT1) and retinoblastoma-binding protein 7 (RBBP7) are part of the protein network, which interacts with the unmodified H3-tail. (edu.sa)
In addition, the outlined methodology is generally applicable for studying specific binding partners of unmodified histone tails. (edu.sa)

CONCLUSIONS: We conclude that ASF1 is critically required to load H3.3-H4 dimers on the HIRA complex prior to histone deposition on paternal DNA. (ens-lyon.fr)

Two major types of histone methyltranferases exist, lysine-specific (which can be SET (Su(var)3-9, Enhancer of Zeste, Trithorax) domain containing or non-SET domain containing) and arginine-specific. (wikipedia.org)
The class of lysine-specific histone methyltransferases is subdivided into SET domain-containing and non-SET domain-containing. (wikipedia.org)

The conserved histone variant H2AZ has an important role in the regulation of gene expression and the establishment of a buffer to the spread of silent heterochromatin. (sdbonline.org)

This study has found that Swr1, a Swi2/Snf2-related adenosine triphosphatase, is the catalytic core of a multisubunit, histone-variant exchanger that efficiently replaces conventional histone H2A with histone H2AZ in nucleosome arrays. (sdbonline.org)

Histone methylation reactions are catalyzed by histone methyltransferases (HMTs) and the reverse process is mediated by histone demethylases (HDMs). (wjgnet.com)

In both types of histone methyltransferases, S-Adenosyl methionine (SAM) serves as a cofactor and methyl donor group. (wikipedia.org)

The graph depicts the binding of the antibody to pre-coated crotonyl histone H3 (Lys9) peptide in the presence of increasing concentrations of various competitor peptides. (cellsignal.com)
As shown, the butyryl and crotonyl histone H3 (Lys9) peptides completely competed away the antibody and there was partial competition with the crotonyl histone H3 (Lys27) peptide. (cellsignal.com)

Unlike the SET domain, which targets the lysine tail region of the histone, Dot1 methylates a lysine residue in the globular core of the histone, and is the only enzyme known to do so. (wikipedia.org)

Histone alterations have been much more difficult to study because such research requires that the histones and DNA remain chemically intact. (neurosciencenews.com)

Collectively, these data highlight a biological role for SMRT in mediating DNA damage responses and suggest a model where p53 binding to the DAD limits HDAC3 interaction with this coregulator, thereby facilitating SMRT coactivation of p53-dependent gene expression. (nih.gov)

The in vitro experiment in the study showed that histones, a protein component in NETs, directly stimulate Th17 cells, which is shown by an effect ameliorated by β-methyl-cellobioside sulfate, a first-in-class histone inhibitor. (scienceboard.net)
The data will impact pathogenic aspects of this feed-forward loop in various conditions, suggesting that interrupting this loop using a direct histone inhibitor or through targeting of TLR2 provides an alternate therapeutic target for the treatment of autoimmune conditions. (scienceboard.net)

In order for the reaction to proceed, S-Adenosyl methionine (SAM) and the lysine residue of the substrate histone tail must first be bound and properly oriented in the catalytic pocket of the SET domain. (wikipedia.org)
The C-terminal is important for the substrate specificity and binding of Dot1 because the region carries a positive charge, allowing for a favorable interaction with the negatively charged backbone of DNA. (wikipedia.org)

The paper demonstrates how some specific protein interactions with H3K4me3 direct the formation of the preinitiation complex at p53 regulated promoters. (epigenie.com)

Human TAF10, a subunit of both TFIID and TFTC, has three histone fold-containing interaction partners: TAF3, TAF8, and SPT7Like (SPT7L). (hal.science)

The silencing mediator of retinoic acid and thyroid hormone receptors (SMRT) is an established histone deacetylase 3 (HDAC3)-dependent transcriptional corepressor. (nih.gov)
Depletion of GPS2 and TBL1, components of the SMRT corepressor complex, but not histone deacetylase 3 (HDAC3) decreased p21-luciferase activity. (nih.gov)
Here, we show that the histone deacetylase Hdac3 controls oligodendrocyte-specification gene Olig2 expression and functions as a molecular switch for oligodendrocyte and astrocyte lineage determination. (elsevierpure.com)

The genomic DNA of eukaryotes associates with histones to form chromatin. (wikipedia.org)

We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucleosome complex. (cornell.edu)
Surprisingly, we find that a basic N-terminal extension to the SET domain plays an even more prominent role in nucleosome binding, possibly by making an arginine anchor interaction with the nucleosome H2A/H2B acidic patch. (cornell.edu)

Solomon, MJ , Larsen, PL & Varshavsky, A 1988, ' Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene ', Cell , vol. 53, no. 6, pp. 937-947. (uthscsa.edu)
The in vivo experiment also showed the role of histones in promoting a rapid Th17 cell-specific response. (scienceboard.net)

H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. (epigenie.com)

The book also contains a new chapter on genome stability, highlighting current understanding of vitamin-genome interactions in the evolution of the human genome and the functional consequences of human genetic variation. (routledge.com)
High-resolution profiling of histone methylations in the human genome. (epigenie.com)
This is a key paper defining the localization of all common histone methylations in the human genome. (epigenie.com)

Chandrasekaran, R., and Thompson, M. (2007) Polybromo-1-bromodomains bind histone H3 at specific acetyl-lysine positions. (mtu.edu)
Polybromo-1 bromodomains bind histone H3 at specific acetyl-lysine positions. (mtu.edu)

Chromatin immunoprecipitations were performed with cross-linked chromatin from HeLa cells and either Butyryl/Crotonyl-Histone H3 (Lys9) (E9N8C) Rabbit mAb or Normal Rabbit IgG #2729, using SimpleChIP ® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) #9005. (cellsignal.com)
One such important histone mark is H3K36me3 which is deposited by the enzyme SETD2 in mammalian cells. (frontiersin.org)
February 4, 2022 -- Histones, a protein component of neutrophil extracellular traps (NETs), can directly stimulate T cells, specifically T helper 17 (Th17) cell differentiation, according to a recent Nature Communications research article. (scienceboard.net)
The interaction between Th17 cells and neutrophils is often considered bidirectional. (scienceboard.net)

Research in Drosophila and in yeast shows that the unique feature of H2A.Z does not reside in its histone fold but in its carboxy-terminal domain, termed M6, which is essential for the survival of that organism. (usherbrooke.ca)
Methyl-histone binding analysis of the yeast double chromodomain protein Chd1. (mtu.edu)
Those interactions were detected by several methods such as yeast two hybrid, co-IP, pull-down and so on. (creativebiomart.net)

The nuclear import of TAF10 is regulated by one of its three histone fold domain-containing interaction partners. (hal.science)

We describe a multifaceted approach to link the domain structure with function, using quantitative assays for DNA and histone binding, ATPase activity, shape reconstruction from solution scattering data, and single molecule translocation assays. (whiterose.ac.uk)

Ly6C high MC exhibited activated neutrophil degranulation, lysosome, cytokine production/receptor interaction and myeloid cell activation pathways, and Ly6C low MC presented features of lymphocyte immunity pathways in both mice. (frontiersin.org)

Independent researchers have identified mutations in the histone H3.3-coding gene H3F3A in a large proportion of pediatric cases of gliobastoma multiforme (GBM) and diffuse intrinsic pontine glioma (DIPG), an aggressive brainstem astrocytic tumor that occurs almost exclusively in children. (genengnews.com)

BACKGROUND: Anti-Silencing Factor 1 (ASF1) is a conserved H3-H4 histone chaperone involved in both Replication-Coupled and Replication-Independent (RI) nucleosomeassembly pathways. (ens-lyon.fr)

Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. (epigenie.com)

Additionally, the experiment showed the increase in Th17 cell differentiation by histones was obliterated in the absence of MyD88, which suggests a toll-like receptor, myeloid differentiation, primary response 88 (MyD88)-dependent mechanism. (scienceboard.net)

Anatomy25

Organisms15

Diseases2

Chemicals and Drugs115

Analytical, Diagnostic and Therapeutic Techniques and Equipment20

Phenomena and Processes86

Disciplines and Occupations1

Information Science3

Acetylation12

Proteins12

Nucleosomes10

Modifications12

Called histone variants1

Inhibitors6

Deacetylases1

Enzymes5

Methyltransferase2

Genes10

Variants3

Major histone1

Methyl groups2

Epigenetic5

Core histones1

Genetics1

Octamer1

Residues1

Functionally2

Phosphorylation3

Transcription7

Somatic1

Tails2

Deposition1

Lysine-specific2

Heterochromatin1

Variant1

Demethylases1

Methyltransferases1

Peptides2

Methylates1

Alterations1

Gene expression1

Inhibitor2

Substrate2

Promoters1

Subunit1

HDAC33

Eukaryotes1

Nucleosome2

Vivo2

TAF31

Human genome3

Bind2

Cells4

Yeast3

Fold1

Assays1

Neutrophil1

Pediatric1

Chaperone1

Specific1

Receptor1