Gene expression patterns and chromatin h3k4. Medical search. Frequent questions

A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. (ox.ac.uk)
Trimethylation of histone H3 lysine 4 (H3K4me3) marks transcription start sites of virtually all active genes. (ox.ac.uk)
These results strongly suggest that WDR5 and NURF function in a common biological pathway in vivo, and that NURF-mediated ATP-dependent chromatin remodelling is directly coupled to H3K4 trimethylation to maintain Hox gene expression patterns during development. (ox.ac.uk)
Most importantly it was found by inhibiting MLL1 it changes the global H3K4 methylation pattern increasing the monomethylation and decreasing trimethylation at H3K4 positions. (nitrkl.ac.in)
H3K4 trimethylation is an active gene mark present in various oncogenes during cancer progression. (nitrkl.ac.in)
A stable gene expression during plant and animal development is maintained by opposite functions of Polycomb group (PcG) chromatin remodeling factors that represses target gene expression through H3K27 trimethylation and trithorax group (trxG) chromatin remodeling factors that maintain transcription of target gene loci by H3K4-trimethylation (Schwartz and Pirrotta. (grassius.org)
Background: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. (researchgate.net)
Central to this is the transient increase in H3K4-trimethylation at developmental genes during G1, thereby creating a 'window of opportunity' for cell-fate specification. (researchgate.net)
We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
By establishing the trimethylation pattern of H3K4me3 residues of the nucleosomes, ATX1/SDG27 (Arabidopsis Homolog of Trithorax) regulates the SA/JA signaling pathway for plant defense against bacterial pathogens by activating the expression of the WRKY70, which was a critical transcription factor15. (achrinhibitor.com)
Increased trimethylation of H3 lysine 4 and acetylation of H3 lysine 9 and 18 both globally and in the promoter region of the securin gene were observed by increasing the levels of lysine-N-methyltransferase 2A, lysine-acetyltransferase, EP-300 and PCAF after RAN treatment. (biomedcentral.com)
Additional sex combs interacts with enhancer of zeste and trithorax and modulates levels of trimethylation on histone H3K4 and H3K27 during transcription of hsp70. (jefferson.edu)

The effects of DNA methylation and the histone code are due, at least in part, to modification-specific recruitment of factors, such as heterochromatin-associated proteins (HP1) and methyl-binding domain proteins, which establish and maintain higher order of chromatin structure. (aacrjournals.org)
Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. (cornell.edu)
DNA meth-ylation represses transcription by interfering with transcription factor binding and indirectly by recruiting methyl-CpG-binding proteins and reducing chromatin remodeling activities ( 12 ). (spandidos-publications.com)
Epigenetic regulation refers to the multiple chemical modifications of DNA or DNA-associated proteins that alter chromatin structure and DNA accessibility in a heritable manner, without changing DNA sequence. (frontiersin.org)
The protein encoded by this gene contains an ATPase/helicase domain, and thus it belongs to the SWI/SNF family of chromatin remodeling proteins. (arigobio.com)
The prions use themselves as a template and then edit the folding of normal proteins to match their own folding pattern. (cloudfront.net)
The inhibition of Torc1 by rapamycin mimics nutrient starvation and causes an array of physiological changes that include global changes in gene expression, phosphorylation/dephosphorylation of various factors, decreased cell growth, degradation of proteins, and ultimately cell cycle arrest in the G 1 phase [4, 9-11]. (researchsquare.com)
Yu, X., Martin, P. G. P. & Michaels, S. D. BORDER proteins protect expression of neighboring genes by promoting 3′ Pol II pausing in plants. (nature.com)
Our studies have demonstrated that several of the proteins encoded by cellular oncogenes function in fundamental aspects of gene regulation. (stanford.edu)
Histones are proteins that help package DNA in the nucleus of cells, and their modification plays a crucial role in regulating gene transcription. (agefluidman.com)
Histone modification refers to the addition or removal of chemical groups to histone proteins, which can alter the structure of chromatin and thereby influence gene expression. (agefluidman.com)
Phosphorylation of specific serine or threonine residues on histones can lead to changes in chromatin structure, allowing or preventing the binding of transcription factors and other regulatory proteins. (agefluidman.com)
By altering the structure of chromatin, histone modifications can either promote or hinder the binding of transcription factors and other regulatory proteins to specific gene loci. (agefluidman.com)
Methylation of specific lysine residues, such as H3K4, can also promote gene activation by recruiting proteins that facilitate transcription. (agefluidman.com)
Despite extensive studies on the effect of these genes on the development pathways, some MSY genes have remained as missing proteins with no experimental protein evidence due to highly transient and spatio-temporal restricted expression patterns. (biomedcentral.com)
While transcription factors bind and recruit chromatin-modifying and remodeling proteins, the relative contribution of individual cis elements residing within clusters of cis elements to the transcriptional control of endogenous loci is incompletely understood. (prolekarniky.cz)
Frequent translocation of the gene in acute leukemia results in the formation of chimeric proteins with aberrant transcriptional activity12. (biobender.com)

Lysine methylation of histones is recognized as an important component of an epigenetic indexing system demarcating transcriptionally active and inactive chromatin domains. (ox.ac.uk)
Acts as negative regulator of chromatin incorporation of transcriptionally repressive histone H2AFY, particularily at telomeres and the alpha-globin cluster in erythroleukemic cells. (arigobio.com)
Our study also identifies a pool of genes that may be transcriptionally regulated by AR only in the absence of p53, and that may contribute to the CRPC phenotype. (oncotarget.com)

Alternatively, the incorporation of histone variants into chromatin can provide another way to drastically alter the structure of chromatin. (biomedcentral.com)

For example, genes involved in blood pressure regulation and the development of the inner ear's semicircular canal are highly methylated in humans, but not in apes. (wikipedia.org)
Mechanism study reveals FQM killing bacteria by direct-contact ROS attack and gene regulation. (bvsalud.org)
The present study investigated the methylation of CpG sites in the cyclooxygenase (COX)‑2 promoter via nuclear factor (NF)‑κB transcriptional regulation and elucidated its effect on the COX‑2 transcriptional expression in a ketamine‑induced ulcerative cystitis (KIC) animal model. (spandidos-publications.com)
Moreover, DNA hypomethylation of the COX‑2 promoter region located from ‑1,522 to ‑829 bp might contribute to transcriptional regulation of COX‑2 expression and induce a pro‑inflammatory response in KIC. (spandidos-publications.com)
The mechanism of epigenetic regulation involves the CpG site methylation of promoter regions and the modification of DNA and histones by altering chromatin structure ( 9 - 11 ). (spandidos-publications.com)
Tracing the molecular marks on DNA and histone 3 for understanding the mechanism of gene regulation by ChIP analyses leads to a paradoxical result that shows DNA methylation adjacent to active histone marking (enrichment of H3K4me3) silence miR- 152 gene. (nitrkl.ac.in)
The epigenetic regulation of spatiotemporal gene expression is crucial for human development. (researchgate.net)
This protein is found to undergo cell cycle-dependent phosphorylation, which regulates its nuclear matrix and chromatin association, and suggests its involvement in the gene regulation at interphase and chromosomal segregation in mitosis. (arigobio.com)
Involved in transcriptional regulation and chromatin remodeling. (arigobio.com)
There are mechanisms by which environmental exposures induces epigenetic changes by affecting regulation and gene expression. (cloudfront.net)
Pelechano, V. & Steinmetz, L. M. Gene regulation by antisense transcription. (nature.com)
We are studying the role that normal chromatin structure plays in gene regulation in hematopoietic cells and how its disruption leads to altered development and cancer. (stanford.edu)
Ubiquitination is a less-studied histone modification but is gaining attention for its role in gene regulation. (agefluidman.com)
To better understand the interconnectedness of histone modifications and their impact on gene regulation, let's explore some examples of how different modifications can work together. (agefluidman.com)
This gene thus plays a role in both cell-cycle and epigenetic regulation. (cancerindex.org)
Epigenetic memory in gene regulation and immune response. (tskimlab.com)
The role of MSY genes in important cellular processes such as transcription regulation, translation, and protein stability in males is vital not only in sex determination but also in sex-dependent organ development [ 3 ]. (biomedcentral.com)
Various levels of regulation, including epigenetic modifications and transcription factors, play important roles in coordinating the expression of genes. (biorxiv.org)
Models of gene regulation have led to an attractive paradigm in which repression occurs in sequential stages of increasing stability [4] . (prolekarniky.cz)
Stem cell specificity is maintained by tight regulation of CD133 expression at both transcriptional and post-translational levels. (biomedcentral.com)
Significantly, in both benign and malignant prostate primary tissues, regulation of CD133 is independent of DNA methylation, but is under the dynamic control of chromatin condensation. (biomedcentral.com)
Epigenetic regulation of gene expression is a dynamic mechanism, which permits precise regulation throughout differentiation [ 1 ]. (biomedcentral.com)

For example, methylation of lysine 4 on histone H3 (H3K4) is associated with gene activation, while methylation of lysine 9 (H3K9) or lysine 27 (H3K27) is associated with gene repression. (agefluidman.com)
For instance, acetylation of H3K9 combined with methylation of H3K4 is associated with active gene transcription, while methylation of H3K9 combined with deacetylation of H3K27 is associated with gene repression. (agefluidman.com)
We observe preferential methylation of H3K9 in the Y chromosome chromatin whereas H3K27 methylation is more prominent in the X and autosomal chromatin. (biomedcentral.com)

In mammalian cells, histone H3 Lys 9 (H3K9) methylation and histone hypoacetylation are usually associated with methylated DNA, heterochromatin, and gene silencing. (aacrjournals.org)
Its heterochromatin targeting is proposed to involve a combinatorial readout of histone H3 modifications (specifically methylation states of H3K9 and H3K4) and association with CBX5. (arigobio.com)
First, the state of global histone methylation at selected methylation sites (histone 3 lysine 9 H3K9 and histone 3 lysine 4 H3K4) was examined post oxygen glucose deprivation. (fu-berlin.de)
Chromatin immunoprecipitation followed by sequencing revealed altered histone 3 (H3K9) modification states in promoter regions of certain genes upon SUV39H1 and G9a inhibition via Chaetocin. (fu-berlin.de)
This is the initial discovery of a histone demethylase responsible for eliminating mono- and dimethyl modifications from histones 3 lysine 4 (H3K4), histone 3 lysine 9 (H3K9), and histone 4 lysine 20 (H4K20). (biomedcentral.com)
Upon complexing with AR, LSD1 demethylates the repressive H3K9 and thereby promotes gene activation [ 11 ]. (biomedcentral.com)

Bivalent promoters are defined by the presence of both activating (H3K4me3) and repressive (H3K27me3) chromatin marks. (researchgate.net)
Some lncRNAs originate from intragenic enhancers which, when active, behave as alternative promoters producing transcripts that are processed using the canonical signals of their host gene. (biomedcentral.com)
ChIP analysis showed that NCL1 induced H3K9me2 accumulation at the promoters of androgen-responsive genes. (oncotarget.com)

Recently, we reported that the WD40-repeat protein WDR5 is important for global levels of H3K4me3 and control of HOX gene expression. (ox.ac.uk)
Here we show that a plant homeodomain (PHD) finger of nucleosome remodelling factor (NURF), an ISWI-containing ATP-dependent chromatin-remodelling complex, mediates a direct preferential association with H3K4me3 tails. (ox.ac.uk)
Depletion of H3K4me3 causes partial release of the NURF subunit, BPTF (bromodomain and PHD finger transcription factor), from chromatin and defective recruitment of the associated ATPase, SNF2L (also known as ISWI and SMARCA1), to the HOXC8 promoter. (ox.ac.uk)
Interestingly, within actively transcribed protein-coding genes, H3T3ph density was minimal in 5' genic regions, coincidental with a peak of H3K4me3 accumulation. (nih.gov)
Consistent with an increased fraction of heterochromatin observed in elderly individuals of different species [ 12 ], Wood and colleagues reported a reduction of histone marks associated with active chromatin, including tri-methylated lysine 4 of histone H3 (H3K4me3), and an increase of those histone marks linked to silencing of transcription, such as H3K27me3, in old D. melanogaster [ 13 ]. (aging-us.com)
Likewise, C. elegans with increased activity of the H3K4 methylase ASH-2/trithorax complex 9 and high levels of H3K4me3 showed accelerated aging [ 15 ]. (aging-us.com)

Epigenetics is the study of changes in gene expression that occur via mechanisms such as DNA methylation, histone acetylation, and microRNA modification. (wikipedia.org)
Recent advances in understanding the role that epigenetics plays in cancer pathogenesis and understanding the mechanisms through which these processes regulate gene expression have stimulated considerable interest in developing clinically viable antineoplastic agents that target enzymatic components of transcriptional regulatory complexes responsible for the establishment of pathologic epigenetic modifications that lead to deregulated gene expression in cancer. (aacrjournals.org)
Although genetics have played a dominant role in cancer research, epigenetics (heritable changes in gene function that do not involve alterations in DNA sequence) has become equally important in this field. (aacrjournals.org)
Cancer epigenetics is a general term for various abnormalities related to tumors that do not involve changes in nucleic acid sequences but can cause changes in heritable gene expression. (creativebiomart.net)
Epigenetics is a field of study that focuses on changes in gene expression that do not involve alterations to the DNA sequence itself. (agefluidman.com)

2014). AGAMOUS (AG) gene encodes MADS family of transcription factors which plays a role in specifying reproductive organ identity and acts in a negative feedback loop to limit floral stem cell proliferation. (grassius.org)
Both p53 and AR are transcription factors and can affect the expression of a broad array of genes. (oncotarget.com)
Histone modifications associated with gene activation, such as acetylation of histones, can create a more relaxed chromatin structure, allowing transcription factors and RNA polymerase to access the DNA and initiate gene transcription. (agefluidman.com)
On the other hand, histone modifications associated with gene repression, such as methylation of lysine 9 or 27, can lead to a more condensed chromatin structure, preventing the binding of transcription factors and RNA polymerase and effectively silencing gene expression. (agefluidman.com)
Transcription factors in these networks occupy specific cis elements at target gene loci where they modulate chromatin remodeling and modification, and thereby transcription. (prolekarniky.cz)

Ketamine treatment increased the binding of NF‑κB and permissive histone H3 lysine‑4 (H3K4)m3, but caused a decrease in the repressive histone H3K27m3 and H3K36m3 on the COX‑2 promoter ranging from ‑1,522 to ‑1,331 bp as determined by a chromatin immunoprecipitation assay. (spandidos-publications.com)
The present findings revealed that there was a hypomethylation pattern of the COX‑2 promoter in association with the level of COX‑2 transcription in KIC. (spandidos-publications.com)
Silencing of the miR-152 gene due to promoter DNA methylation alter the expression pattern of several other genes. (nitrkl.ac.in)
CDH1 gene is downregulated by promoter DNA methylation during cancer progression. (nitrkl.ac.in)
Thus in response to cold treatment, enrichment of OsULT1 occupancy and decrease in H3K27me3 at promoter region of OsDREB1b gene (Dehydration Response Element Binding 1b) was observed resulting in antagonizing the repressive effect of PcG complex on OsDREB1b for its transcription activation. (grassius.org)
In contrast, in the case of ''true'' bivalency, virtually all cells in the population carry both marks simultaneously at the promoter in question, leading to low, if any, expression for that gene in all cells. (researchgate.net)
It is mainly manifested in the reduction of whole-genome DNA methylation level, hypermethylation of the promoter region, changes in specific histone modification, abnormal chromatin conformation, changes in non-coding RNA (ncRNA) molecules, etc . (creativebiomart.net)
CpG-rich regions are unevenly distributed in the genome, and they often appear in gene promoter regions. (creativebiomart.net)
CpG sites located in the promoter region are usually not methylated, while CpG outside the regulatory region of genes is methylated. (creativebiomart.net)
Moreover, DNA hypermethylation can also occur during the development of cancer, especially in CpG islands of the promoter region, resulting in transcriptional silencing of affected genes, such as tumor suppressor genes. (creativebiomart.net)
Activating promoter marks occurred together with elevated mRNA levels of the genes vascular endothelial growth factor (VEGF) and brain derived neurotrophic factor (BDNF). (fu-berlin.de)
Since the molecular mechanism underlying securin upregulation remains unclear, this study intended to investigate the association of securin upregulation with the Rb-E2F1 circuit and epigenetic histone (H3) modification patterns both globally and in the promoter region of the securin gene. (biomedcentral.com)
ChIP-qPCR assays were performed to evaluate the recruitment of different histone modifications in the core promoter region of securin gene as well as its upstream and downstream regions. (biomedcentral.com)
RAN-mediated pRb-inactivation induced securin upregulation, a putative E2F1 target, by inducing misregulation in chromatin remodeling in its promoter region, which led to transcriptional activation and subsequent development of chromosomal instability. (biomedcentral.com)
We found that CD133 expression is repressed by DNA methylation in the majority of prostate epithelial cell lines examined, where the promoter is heavily CpG hypermethylated, whereas in primary prostate cancer and benign prostatic hyperplasia, low levels of DNA methylation, accompanied by low levels of mRNA, were found. (biomedcentral.com)
CD133 is tightly regulated by DNA methylation only in cell lines, where promoter methylation and gene expression inversely correlate. (biomedcentral.com)

Epigenetic histone modifications control a key adaptive trait in Arabidopsis thaliana, and their pattern changes rapidly during evolution associated with reproductive strategy. (wikipedia.org)
Histone modifications and chromatin-associated protein complexes are crucially involved in the control of gene expression, supervising cell fate decisions and differentiation. (researchgate.net)
Histone modifications related to both active and inhibitory chromatin can be observed during cancer progression, and these modifications can occur simultaneously. (creativebiomart.net)
On the maternal allele, required for the chromatin occupancy of SMC1 and CTCTF within the H19 imprinting control region (ICR) and involved in esatblishment of histone tails modifications in the ICR. (arigobio.com)
More than a thousand post-translational histone modifications, also known as histone marks, have been identified, many of which are associated with different chromatin states [ 1 ]. (aging-us.com)
Histone modifications in which the structure of chromatin and its transcriptional state is regulated. (cloudfront.net)
It encompasses a wide range of modifications that can influence gene activity, including histone modifications. (agefluidman.com)
Each of these modifications can have different effects on gene activity. (agefluidman.com)
The histone code hypothesis proposes that specific combinations of histone modifications can act as a "code" that determines the functional state of a gene. (agefluidman.com)
Here, we identified regulatory patterns of 16 epigenetic modifications across metabolism in Arabidopsis thaliana . (biorxiv.org)
Surprisingly, specialized metabolic genes, often involved in defense, were predominantly regulated by two modifications that have opposite effects on gene expression, H3K27me3 (repression) and H3K18ac (activation). (biorxiv.org)
Using camalexin biosynthesis genes as an example, we confirmed that these two modifications were co-localized to form bivalent chromatin. (biorxiv.org)
Mutants defective in H3K27m3 and H3K18ac modifications showed that both modifications are required to determine the normal transcriptional kinetics of these genes upon stress stimuli. (biorxiv.org)
To see if there are any interactions between epigenetic modifications across metabolic genes, we computed pairwise Pearson's correlation coefficients between the 16 epigenetic modifications based on their relative abundance at each metabolic gene region. (biorxiv.org)
Groups I and II included mainly the epigenetic modifications that activate gene expression. (biorxiv.org)
Group III included only the modifications that repress expression, such as H3K9me2 and H3K27me1. (biorxiv.org)
Interestingly, group IV included two modifications that have opposite effects on expression: H3K18ac, an activation mark, and H3K27me3, a repression mark. (biorxiv.org)
Enrichment of modifications in each metabolic domain, relative to all the genes in the genome, revealed both shared and diverse patterns. (biorxiv.org)
The enrichment patterns of epigenetic modifications were consistent with expression levels of genes involved in each domain under healthy conditions (Fig. S1A). (biorxiv.org)
As the field continues to learn more about the dynamic interplay between histone tails and DNA, and the impact of various chromatin modifications 13-15 , it has become clear that a linear peptide may not provide the ideal substrate for testing histone PTM antibody binding. (chromatinantibodies.com)
During the meiotic prophase some modifications expected in active chromatin are not found or are found at low level. (biomedcentral.com)
The majority of modifications persist until the early spermatid nuclei, and only a minority further persist until the final chromatin compaction stages before individualization of the spermatozoa. (biomedcentral.com)
Postmeiotically, we observed a highly complex pattern of the histone modifications until late spermatid nuclear elongation stages. (biomedcentral.com)
Condensation and decondensation of chromatin is to a large extent controlled or accompanied by both postranslational modifications of nucleosomal histones and sometimes by DNA methylation. (biomedcentral.com)
This observation, the special characteristics of the first meiotic prophase in Drosophila and the availability of antibodies specific for particular histone modifications [ 15 ] led us to study the patterns of histone modifications in the male germ line. (biomedcentral.com)
Our observations reveal that the male germ line of Drosophila shows a characteristic pattern of histone modifications. (biomedcentral.com)

2) We have discovered a group of oncoproteins that are implicated in long-term maintenance of gene expression through their effects on the state of chromatin. (stanford.edu)

A comparative analysis of CpG methylation patterns between humans and primates found that there were more than 800 genes that varied in their methylation patterns among orangutans, gorillas, chimpanzees, and bonobos. (wikipedia.org)
Since humans and the great apes share 99% of their DNA, it is thought that the differences in methylation patterns account for their distinction. (wikipedia.org)
Changes in DNA methylation patterns are the first epigenetic event to be described in human cancer and have been observed in both early and late-stage tumors. (creativebiomart.net)
Interestingly, different types of cancer exhibit different methylation patterns, so further studies are needed to clarify the differential methylation patterns of specific cancer types and the correlation of epigenomic mapping with underlying pathology. (creativebiomart.net)
Hyeonju Woo, Junsoo Oh, Jung-Shin Lee, TaeSoo Kim* , N-terminal actylation of Set1-COMPASS by NatA fine-tunes H3K4 methylation patterns. (tskimlab.com)
Determinants of Histone H3K4 Methylation Patterns. (tskimlab.com)

Different correlations between the levels of elncRNAs, plncRNAs and expression of neighboring genes suggest that functional lncRNAs from the two classes may play contrasting roles in regulating the transcript abundance of local or distal loci. (biomedcentral.com)

Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. (cornell.edu)
This modification is generally associated with gene activation, as it loosens the interaction between histones and DNA, allowing access to the transcriptional machinery. (agefluidman.com)
Methylation of lysine residues on histones can lead to gene activation or repression, depending on which lysine residue is modified. (agefluidman.com)

In eukaryotic cells, chromatin remodeling factors regulate chromatin structure by altering the assembly, disassembly, and relocalization of nucleosomes, thereby improving the local accessibility of transcription-related factors in their chromatin DNA, which further initiates or suppresses transcription of related genes. (creativebiomart.net)
May help stabilizing G-rich regions into regular chromatin structures by remodeling G4 DNA and incorporating H3.3-containing nucleosomes. (arigobio.com)
Catalytic component of the chromatin remodeling complex ATRX:DAXX which has ATP-dependent DNA translocase activity and catalyzes the replication-independent deposition of histone H3.3 in pericentric DNA repeats outside S-phase and telomeres, and the in vitro remodeling of H3.3-containing nucleosomes. (arigobio.com)
Nucleosomes containing core histone variants H3.3 or macroH2A have been associated with the active and inactive states of a gene, respectively. (biomedcentral.com)
[10] Chromatin consists of DNA and nucleosomes that comes together to form a histone octamer. (cloudfront.net)

Here, we present whole-genome chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. (researchgate.net)

Central to the epigenetic control of gene expression is the histone code through which input signals can be translated into a heritable pattern of gene expression defining cellular output states ( Fig. 1 ). (aacrjournals.org)
TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. (cornell.edu)
Ectopic expression of miR- 193a results in cell death, inhibition of cellular migration, and anchorage-independent growth of cancer cells. (nitrkl.ac.in)
The findings of this thesis demonstrate that manipulating aberrant histone methylation upon experimental ischemia can alter cellular gene expression patterns and improve neuronal viability. (fu-berlin.de)
We have previously shown that the peptidyl-prolyl isomerase Rrd1 is required to mediate cellular response to rapamycin by altering gene expression [6, 7, 19, 20]. (researchsquare.com)
This, in turn, affects gene expression and ultimately determines cellular identity and function. (agefluidman.com)
This information is crucial to understanding the role of chromatin structure in various cellular processes, as well as disease development. (chromatinantibodies.com)

2014). Arabidopsis gynoecium organ patterning along several axes is regulated by ULT1 and KAN1 (KANADI1) transcription factor. (grassius.org)
This pattern was not affected in the double mutant, implying the existence of additional H3T3 protein kinases in Arabidopsis. (nih.gov)
When Arabidopsis plants were exposed to cold temperature, H3K27me3 was significantly reduced in the area of chromatin containing COR15A (Cold-regulated15A) and ATGOLS3 (Galactinol Synthase 3) 17, which are cold stress response genes. (achrinhibitor.com)

FLD localizes to actively transcribed genes, where it colocalizes with elongating RNA polymerase II phosphorylated at the Ser2 or Ser5 sites. (nature.com)
Fig. 2: FLD localizes to the TTSs of actively transcribed genes. (nature.com)

2001) and B-box like motif near C-terminus that might play role in protein-protein or protein-DNA interaction and share similar expression pattern in embryonic shoot apical meristem, inflorescence and floral meristem and in developing stamens, carpels and ovules except in vegetative meristem and leaf primordia where only ULT1 mRNA accumulates (Carles et al. (grassius.org)
In nuclear transfer to Xenopus eggs, histone H3.3 participates in the transmission of an active state of a gene, even in embryonic lineages where genes should be silenced [ 4 ]. (biomedcentral.com)

according (PubMed:24500201) is not sufficient to decrease chromatin condensation at telomers nor to increase expression of telomeric RNA in fibroblasts. (arigobio.com)
This may be in part due to postmeiotic transcription and in part to differential histone replacement during chromatin condensation. (biomedcentral.com)

Further analysis revealed that a lower AR occupancy was accompanied by a reduction in FoxA1 binding at regulatory regions of AR-dependent genes. (oncotarget.com)
To determine how metabolism is regulated epigenetically, we first identified regulatory patterns of epigenetic modification across all metabolic domains. (biorxiv.org)
Metazoan development is characterized by complex transcriptional programs specified by gene regulatory networks [1] , [2] . (prolekarniky.cz)

Our findings demonstrate that the −1.8 kb site selectively maintains repression, confers a specific histone modification pattern and expels RNA Polymerase II from the locus. (prolekarniky.cz)

Our genome-wide chromatin profiling revealed that FLD, as well as its associating factor LUMINIDEPENDENS 9 , downregulates histone H3K4me1 in regions with convergent overlapping transcription. (nature.com)
Genome-wide transcription analyses suggest that FLD-mediated H3K4me1 removal negatively regulates the transcription of genes with high levels of antisense transcription. (nature.com)
Moreover, it modified the genome-wide binding pattern of AR. (oncotarget.com)
Bordet G, Lodhi N, Guo D, Kossenkov A, Tulin AV. Poly(ADP-ribose) polymerase 1 in genome-wide expression control in Drosophila. (jefferson.edu)

DNA methylation and histone modification are two mechanisms used to regulate gene expression in plants. (wikipedia.org)
Mechanisms regulating INK4/ARF expression are not fully characterized. (plos.org)
The mechanisms underlying this phenomenon are not well understood but are likely to involve changes to chromatin. (biomedcentral.com)
In yeast, rapamycin inhibits the TORC1 kinase signaling pathway causing rapid alteration in gene expression and ultimately cell cycle arrest in G 1 through mechanisms that are not fully understood. (researchsquare.com)
Furthermore, the effect of FLD on transcription dynamics is antagonized by DNA topoisomerase I. Our study reveals chromatin-based mechanisms to cope with overlapping transcription, which may occur by modulating DNA topology. (nature.com)
In plants RNA interference or post transcriptional gene silencing (PTGS) acts as a natural anti-viral defense system for neutralizing pathogenic nucleic acids either through a change in RNA stability in the cytoplasm or through mechanisms that use the RNA itself to induce methylation and silencing of homologous nuclear genes [ 1 ]. (biomedcentral.com)
Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. (biomedcentral.com)
Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. (biomedcentral.com)
The Telomere and Chromatin lab aims at dissecting the telomere maintenance mechanisms linked to cancer, aging and telomere biology disorders. (crcm-marseille.fr)

Due to the questions surrounding the accuracy of histone peptide arrays, we decided to create a platform that directly examines the specificity of antibodies on a physiological chromatin substrate. (chromatinantibodies.com)

DNA is wrapped into a DNA-protein complex called chromatin in the nucleus of eukaryotic cells. (cloudfront.net)

The INK4/ARF locus encodes three tumor suppressor genes (p15 Ink4b , Arf and p16 Ink4a ) and is frequently inactivated in a large number of human cancers. (plos.org)
Mutations in histone-modifying enzymes in tumors, such as mutations of histone methylase, histone demethylase, and histone acetylase, can also cause abnormal gene expression and determine tumor cell phenotypes. (creativebiomart.net)
In the study of Ras-induced tumor development, the importance of chromatin remodeling changes in cancer is also evident, with the observation that chromatin conformation is more open in early-developing tumors and more accessible in late-stage tumor development. (creativebiomart.net)
Recently, it has become apparent that not only genetic mutations but also epigenetic alterations lead to the activation of oncogenes and the loss of function of tumor suppressor genes. (oncotarget.com)
Raw areca nut (RAN) consumption induces oral, esophageal and gastric cancers, which are significantly associated with the overexpression of pituitary tumor transforming gene 1/securin and chromosomal instability (CIN). (biomedcentral.com)

Forms of histone methylation cause repression of certain genes that are stably inherited through mitosis but that can also be erased during meiosis or with the progression of time. (wikipedia.org)
In mitosis prophase chromatin typically condenses progressively into the microscopically visible individual chromosomes, which can be seen in their fully condensed state at metaphase. (biomedcentral.com)

Here we show that bivalent domains and chromosome architecture for bivalent genes are dynamically regulated during the cell cycle in human pluripotent cells. (researchgate.net)
In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. (biomedcentral.com)
Their X homologs excessively escape X chromosome inactivation, thus researchers classified them as dose-sensitive and haplolethal genes. (biomedcentral.com)

Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. (cornell.edu)
It also divulges the reason for aberrant expression of miRNAs (miR-152, miR-148a, and miR-193a) in breast and prostate cancer. (nitrkl.ac.in)
Although Gata2 is normally repressed in late-stage erythroblasts, the −1.8 kb mutation unexpectedly resulted in reactivated Gata2 transcription, blocked differentiation, and an aberrant lineage-specific gene expression pattern. (prolekarniky.cz)

mRNA and protein expression profile of DNMT1 implicate that miR-152 targets DNMT1 mRNA and inhibits its protein expression. (nitrkl.ac.in)
Gera R, Mokbel L, Jiang WG, Mokbel K mRNA Expression of Cancer Genomics Proteomics. (cancerindex.org)
Our objective was to determine if CDK2AP1 mRNA expression levels were consistent with tumour-suppressive functions in breast cancer. (cancerindex.org)
To our knowledge, this is the first study in the literature to examine the mRNA expression of CDK2AP1 in human breast cancer over a long-term follow-up period. (cancerindex.org)
Thus, we investigated male mouse (m) PRL protein and mRNA expression in spermatozoa at various differentiation stages in the testes. (go.jp)

In January 2003, a workshop was held in Baltimore to discuss the therapeutic potential of several agents that can modify chromatin structure. (aacrjournals.org)
The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. (cornell.edu)
While each DNA blueprint, or gene, encodes for a different machine or structure, the genome, the collection of DNA wrapped up inside the nucleus, is much more active than a quiet library of neatly stacked blue-prints. (birmingham.ac.uk)
From these combined studies, it seems logical that the global gene expression pattern that ensues upon exposure to rapamycin must be governed by changes at the level of the chromatin structure. (researchsquare.com)
qRT-PCR was used to measure CD133 expression and chromatin structure was determined by ChIP. (biomedcentral.com)
They are made of repetitive DNA sequences that are folded into a particular chromatin structure organized by specific DNA-protein interactions. (crcm-marseille.fr)

Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. (biomedcentral.com)
In the male germ line of Drosophila chromatin remains decondensed and highly transcribed during meiotic prophase until it is rapidly compacted. (biomedcentral.com)

Nuclear reprogramming is characterized by a global shift in gene expression. (biomedcentral.com)

Of considerable interest, we found that expression of elncRNAs, but not plncRNAs, is associated with enhanced expression of neighboring protein-coding genes during erythropoiesis. (biomedcentral.com)
At least 50,000 lncRNAs are expressed from intergenic regions of the human genome, more than twice the number of protein-coding genes [ 5 ]. (biomedcentral.com)

Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. (arigobio.com)
For example, GATA-1 directly represses Gata2 transcription via displacing GATA-2 from chromatin sites at its own locus, a process termed a "GATA Switch" [6] , [7] . (prolekarniky.cz)

2004). Polycomb response elements (PRE) are not only recognized by the PcG complex to mediate gene silencing but also targeted by trxG complex to initiate transcription activation. (grassius.org)

By inhibiting H3K4, tri-methylation cancer progression can be repressed. (nitrkl.ac.in)

Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. (biomedcentral.com)
In contrast, metabolic genes involved in specialized and hormone metabolic domains, which are generally involved in interactions with biotic and abiotic environmental stimuli, showed distinct patterns with the enrichment of a repression mark H3K27me3 and an activation mark H3K18ac ( Fig. 1B ). (biorxiv.org)

We, therefore, searched a collection of 442 histone mutants [24] for ones that failed to respond to rapamycin in an attempt to identify molecular pathways critical for rapamycin response at the level of chromatin. (researchsquare.com)
Metabolism underpins development and physiology, but little is known about how metabolic genes and pathways are regulated, especially in multicellular organisms. (biorxiv.org)

Our study suggests that this type of bivalent chromatin, which we name a kairostat, controls the precise timing of gene expression upon stimuli. (biorxiv.org)

However, the overall amount of H3K27me3 in C. elegans was reported to decrease with age, and RNA interference of the H3K27me3 demethylase UTX-1 prolonged lifespan by suppressing the expression of genes of the insulin pathway [ 16 ]. (aging-us.com)
In euchromatin, methylation of histone H3K4, H3K36 and H3K27me3 were shown to be associated with gene regulations including transcriptional activation and gene silencing13. (achrinhibitor.com)

We investigated histone modification patterns in testes of D. melanogaster and D. hydei . (biomedcentral.com)
In somatic cells of the testis envelope and in germ cells these modification patterns differ from those typically seen in eu- and heterochromatin of other somatic cells. (biomedcentral.com)
Histone modification patterns in the male germ line differ from expected patterns. (biomedcentral.com)
The cell cycle-regulated histone variant H3.1 and H3.3, expressed throughout the cell cycle, also vary in their modification patterns. (biomedcentral.com)

We are seeking to understand how these genes are involved in telomere maintenance. (crcm-marseille.fr)

The 67 kDa Menin protein which binds to the N-terminus of MLL is essential for MLL target genes manifestation14 16 17 18 Small molecule inhibitors of menin-MLL connection can block MLL fusion protein-mediated leukemic transformation19. (biobender.com)

Anatomy34

Organisms20

Diseases3

Chemicals and Drugs67

Analytical, Diagnostic and Therapeutic Techniques and Equipment32

Phenomena and Processes100

Disciplines and Occupations4

Technology, Industry, Agriculture3

Information Science9

Health Care3

Trimethylation12

Proteins17

Transcriptionally3

Alter the structure of chromatin1

Regulation22

H3K273

H3K96

Promoters3

H3K4me36

Epigenetics5

Transcription Factors5

Promoter16

Modifications26

State of chromatin1

Methylation patterns6

Loci1

Histones3

Nucleosomes5

Immunoprecipitation followed1

Cellular7

Arabidopsis3

Actively transcribed genes2

Embryonic2

Condensation2

Regulatory3

Specific histone modification1

Genome-wide4

Mechanisms9

Specificity1

Eukaryotic1

Tumor5

Mitosis2

Chromosome3

Aberrant3

MRNA5

Structure6

Highly transcribed2

Nuclear1

Protein-codin2

Locus2

Polycomb1

Cancer progression1

Enrichment2

Pathways2

Bivalent1

H3K27me32

Modification patterns4

Involved in telomere maintenance1

Target genes1