• Thus CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes. (wikipedia.org)
  • In further study, we find that even though transcription factors and histone modifications offer similar effects on expression levels of genome-wide genes, the effects of transcription factors and histone modifications on predictive abilities are different for genes in independent biological processes. (oncotarget.com)
  • Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the candidate reference genes were significantly enriched in cellular metabolic process, protein metabolic process and ribosome in early development and normal adult tissues as well as in cellular localization and endocytosis in the hindgut under sulfide stress. (biomedcentral.com)
  • Subunit of the Set3 complex, which is a meiotic-specific repressor of sporulation specific genes tha. (yeastrc.org)
  • Forkhead box protein M1 (FOXM1) is a key transcription factor (TF) that regulates a common set of genes related to the cell cycle in various cell types. (mdpi.com)
  • However, Yaf2 knockout promotes neural differentiation and leads to redistribution of RYBP binding, increases enrichment of RYBP and H2AK119ub on the RYBP-YAF2 cotargeted genes, and prevents ectopic derepression of nonneuroectoderm-associated genes in neural-differentiated cells. (bvsalud.org)
  • This loss is accompanied with an increased expression of the histone demethylase Jmjd3 and with the recruitment of the MLL1 protein, and correlates with the expression of the Ink4a/Arf genes. (plos.org)
  • Promoters of housekeeping genes contain built-in activating motifs for factors such as GABPA and YY1, which decrease the responsiveness of promoters to distal enhancers. (nature.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)
  • Furthermore, gene-gene and gene-metabolite network analyses discovered that the light-responsive expression of genes encoding bHLH, MYB, WRKY, NAC, and MADS-box transcription factors, and proteins involved in genetic information processing and epigenetic regulation such as nucleosome assembly and histone acetylation, showed a high positive correlation with grape berry phenolic accumulation in response to different light regimes. (biomedcentral.com)
  • LncRNAs are a class of ncRNAs that are more than 200 nucleotides in length, and although lncRNAs do not possess protein-coding capability, they play vital roles in modulating protein-coding genes at the transcriptional or posttranscriptional level [ 10 , 11 ]. (biomedcentral.com)
  • Cis-acting DNA sequences which can increase transcription of genes. (lookformedical.com)
  • ncRNAs with more than 200 nucleotides are considered as lncRNAs, which originate from intronic and exonic regions of protein-coding genes in both sense and antisense strands, as well as from the intergenic regions [ 21 ]. (biomedcentral.com)
  • A-kinase anchoring protein 5 [Source:HG. (gsea-msigdb.org)
  • Active mTORC1 phosphorylates the eukaryotic initiation factor 4E-binding protein-1 (4E-BP1) and 40S ribosomal protein S6 kinase 1 (S6K1) to promote protein synthesis [ 3 , 4 ]. (springer.com)
  • Conversely, during starvation mTORC1 is inhibited and autophagy is induced by AMP-activated protein kinase (AMPK), leading to generation of intracellular nutrients and energy during degradation of non-functional or non-essential organelles or protein aggregates [ 4 , 6 ], in turn contributing to cell survival. (springer.com)
  • CDK4 is a member of the Ser/Thr protein kinase family. (thermofisher.com)
  • It is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression. (thermofisher.com)
  • The activity of this kinase is restricted to the G1-S phase, which is controlled by the regulatory subunits D-type cyclins and CDK inhibitor p16(INK4a). (thermofisher.com)
  • The adaptor protein Grb2 is able to enhance the activity of the cytoplasmic tyrosine kinase Btk through a novel mechanism, revealing a new role for Grb2 in B-cell signaling. (elifesciences.org)
  • In most organisms, the opened euchromatin is enriched in tri-methylation of lysine 4 and lysine 36 (H3K4me3 and H3K36me3), two concomitant modifications associated with active transcription [ 2 ]. (biomedcentral.com)
  • We generated the corresponding histone methyltransferase null mutants and showed an interdependence of H3K9me3 and H3K27me3 marks. (biomedcentral.com)
  • Structural insights into histone binding and nucleosome assembly by chromatin assembly factor-1. (ucsf.edu)
  • Here, using a CRISPRi screen targeting chromatin factors, we identified the nucleosome-remodeling factor (NURF) subunit BPTF as an essential regulator of AML cell survival. (x-mol.com)
  • From Protein Complexes to Subunit Backbone Fragments: a Novel Approach to Native Mass Spectrometry. (chicagobiomedicalconsortium.org)
  • Genomic sites of DNA methylation can be bound by methyl-CpG-binding domain proteins (MBDs) and specific zinc finger proteins, which can recruit co-repressor complexes to silence transcription on targeted loci. (biomedcentral.com)
  • When cells enter senescence the binding to RD of both PRC1 and PRC2 complexes is lost leading to a decreased level of histone H3K27 trimethylation (H3K27me3). (plos.org)
  • First identified in Drosophila, the conserved Polycomb group (Pc-G) protein complexes were shown to be both writers (Polycomb Repressive Complex 2, PRC2) and readers (Polycomb Repressive Complex 1, PRC1) of H3K27me3 [ 19 , 20 , 21 ]. (biomedcentral.com)
  • The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)
  • p16 Ink4a downregulation leads to an activation of PKA-CREB-PGC1α signaling through increased phosphorylation of PKA regulatory subunits. (diabetesjournals.org)
  • Relatively little is known about regulatory mechanisms in HIF signalling, especially with regards to HIF-2 but other putative mechanisms for the maintenance of HIF expression include stabilisation through binding of the molecular chaperone heat shock protein, HSP90 [ 28 ]. (biomedcentral.com)
  • protein phosphatase 1 regulatory subuni. (gsea-msigdb.org)
  • 7 VSIG4 can suppress T cell proliferation and promote Foxp3 + regulatory T cell (Tregs) differentiation by binding an unidentified receptor on T cells [ 9 ]. (thno.org)
  • E7 from human papil omavirus type 16 cooperate to cancer: the European prospective investigation into doi:10.1093/carcin/bgp321 PMID:20047954 target the PDZ protein Na/H exchange regulatory cancer and nutrition study. (who.int)
  • Signaling is initiated when the Wnt ligand binds to the Frizzled receptor on the cell membrane and the LDL receptor-associated protein 5/6 (LRP5/6) co-receptor. (frontiersin.org)
  • Ligand and G-protein selectivity in the κ-opioid receptor. (ucsf.edu)
  • DNA cleavage is inhibited where the ligand binds to DNA. (lookformedical.com)
  • Transcriptional activation of the orphan nuclear receptor Nurr1 by ligands targeting its heterodimer partner retinoid X receptor alpha (RXRα) occurs through a nonclassical pharmacological mechanism involving ligand-binding domain protein-protein interaction inhibition. (elifesciences.org)
  • Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism. (bvsalud.org)
  • Upon senescence, Jmjd3 is overexpressed and the MLL1 protein is recruited to the locus provoking the dissociation of Polycomb from the INK4/ARF locus, its transcriptional activation and its replication during early S-phase. (plos.org)
  • We integrated high-resolution maps of transcriptional initiation and transcription to annotate a conservative set of intergenic lncRNAs expressed in mouse erythroblasts. (biomedcentral.com)
  • We subclassified intergenic lncRNAs according to chromatin status at transcriptional initiation regions, defined by relative levels of histone H3K4 mono- and trimethylation. (biomedcentral.com)
  • Coordinated transcriptional changes in the light signaling components CRY2 and HY5/HYHs, transcription regulator MYBA1, and enzymes LAR, ANR, UFGT and FLS4, coincided well with light-responsive biosynthesis of the corresponding flavonoids. (biomedcentral.com)
  • Previous studies have demonstrated that lncRNAs act as one of the molecular mechanisms for the post-transcriptional regulation and modulation of protein function. (biomedcentral.com)
  • Finally, we demonstrate that Polycomb proteins and associated epigenetic marks are crucial for the control of the replication timing of the INK4a/ARF locus during senescence. (plos.org)
  • Post-translational modifications (PTMs) of proteins, including phosphorylation, acetylation, ubiquitination, and SUMOylation, can regulate the function of proteins, determine the active state and subcellular location of proteins, and dynamically interact with other proteins related to carcinogenesis and progression ( 17 - 20 ). (frontiersin.org)
  • Histone modifications regulate pioneer transcription factor cooperativity. (ucsf.edu)
  • Similarly, primary cilia have been implicated in regulation of mTOR signaling, in which Tuberous Sclerosis Complex proteins 1 and 2 (TSC1/2) negatively regulate protein synthesis by inactivating the mTOR complex 1 (mTORC1) at energy limiting states. (springer.com)
  • Together, this systematic assessment of enhancer-promoter compatibility suggests a multiplicative model tuned by enhancer and promoter class to control gene transcription in the human genome. (nature.com)
  • Transcription factors and histone modifications are vital for the regulation of gene expression. (oncotarget.com)
  • Hence, to estimate the effects of transcription factors binding and histone modifications on gene expression, we construct a statistical model for the genome-wide 15 transcription factors binding data, 10 histone modifications profiles and DNase-I hypersensitivity data in three mammalian. (oncotarget.com)
  • And H3K4me3, H3K27me3 and H3K9ac are more reliable predictors than other histone modifications in human embryonic stem cells. (oncotarget.com)
  • Moreover, genome-wide statistical redundancies exist within and between transcription factors and histone modifications, and these phenomena may be caused by the regulation mechanism. (oncotarget.com)
  • Earlier studies [ 1 - 4 ] showed transcription factors (TFs) binding and histone modifications (HMs) were critical for gene expression, and the abnormities of TFs binding and HMs may affect the cell fate such as differentiation and apoptosis [ 5 ]. (oncotarget.com)
  • The binding to methylated DNA may be regulated by post-translational MBD modifications. (biomedcentral.com)
  • Histones are subjected to a variety of post-translational covalent modifications [ 1 ] that may impact the overall degree of packing of the genome. (biomedcentral.com)
  • In contrast, histones present in the compacted heterochromatin are enriched in either tri-methylated H3K27 (H3K27me3) or tri-methylated H3K9 (H3K9me3) [ 3 ]. (biomedcentral.com)
  • However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells. (bvsalud.org)
  • Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for HOS4 . (yeastrc.org)
  • Towards in silico CLIP-seq : predicting protein-RNA interaction via sequence-to-signal learning. (ki.si)
  • The miniF plasmid C protein: sequence, purification and DNA binding. (shengsci.com)
  • A method for determining the sequence specificity of DNA-binding proteins. (lookformedical.com)
  • TFs can activate or block the initiation of gene transcription by binding to specific DNA sequences in enhancers or promoters [ 14 , 15 ] or recruiting some chromatin-modifying enzymes to induce the changes of chromatin structure [ 16 ]. (oncotarget.com)
  • HMs are recognized to activate or inhibit transcription by either modulating the local chromatin structure to control TFs accessibility [ 17 ] or directly recruiting related enzymes [ 18 ]. (oncotarget.com)
  • Canonical regulation of HIF abundance is governed after transcription and translation in part due to the action of oxygen sensitive enzymes, the hif-α prolyl hydroxylases. (biomedcentral.com)
  • These enzymes tag HIFs prior to Von Hippel Lindau protein (vHL) ubiquitination and destruction in the proteosome. (biomedcentral.com)
  • BACKGROUND: Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. (bvsalud.org)
  • The mitochondria have their own chaperones and proteolytic enzymes that remove damaged or unfolded proteins [ 18 - 20 ]. (hindawi.com)
  • Reduced SMO-dependent expression of Gli1 was demonstrated in both Tsc1 −/− and Tsc2 −/− cells, and we found that Tsc1 is required for TGF-β induced phosphorylation of SMAD2/3 and subsequent expression of the HH signaling effector and transcription factor GLI2. (springer.com)
  • Structural basis of mitochondrial protein import by the TIM23 complex. (ucsf.edu)
  • A fish oil diet induces mitochondrial uncoupling and mitochondrial unfolded protein response in epididymal white adipose tissue of mice. (omrf.org)
  • In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
  • Moreover, we show that the Polycomb protein BMI1 interacts with CDC6, an essential regulator of DNA replication in eukaryotic cells. (plos.org)
  • Eukaryotic High-Mobility Group B (HMGB) proteins alter DNA elasticity while facilitating transcription, replication and DNA repair. (shengsci.com)
  • A methylated DNA affinity precipitation method was implemented to assay binding of proteins to methylated DNA. (biomedcentral.com)
  • Description: This is Double-antibody Sandwich Enzyme-linked immunosorbent assay for detection of Human GA Binding Protein Transcription Factor Alpha (GABPa) in serum, plasma, tissue homogenates, cell lysates and other biological fluids. (therabio.org)
  • Description: Enzyme-linked immunosorbent assay based on the Double-antibody Sandwich method for detection of Human GA Binding Protein Transcription Factor Alpha (GABPa) in samples from serum, plasma, tissue homogenates, cell lysates and other biological fluids with no significant corss-reactivity with analogues from other species. (therabio.org)
  • Chromatin immunoprecipitation assay was performed to assess the bindings between protein and genomic DNA. (biomedcentral.com)
  • However, we uncovered an intriguing evolutionary fluidity in the repressive histone deposition machinery, which challenges canonical definitions of constitutive and facultative heterochromatin. (biomedcentral.com)
  • Hypoxia maintains HIFα protein expression through inhibition of prolyl hydroxylases and IL-1 is suggested to effect subunit expression at the level of transcription and in a similarly post-translational fashion [ 26 ]. (biomedcentral.com)
  • SUMOylation is a post-translational modification of proteins that has been found to play a major role in the Wnt/β-catenin signaling pathway. (frontiersin.org)
  • Arguably the two most prominent factors are genetic variability and immunologic status of the exposed individual. (hindawi.com)
  • Furthermore, accumulating data indicate that alterations of immune responsiveness are partly dependent on genetic factors [ 4 ]. (hindawi.com)
  • Some studies have suggested a role for this protein in maintaining centriole-nucleated sensory organelles termed primary cilia, and AS is now considered to belong to the growing class of human genetic disorders linked to ciliary dysfunction (ciliopathies). (springer.com)
  • Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process. (lookformedical.com)
  • Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. (biomedcentral.com)
  • The two enrichment strategies allow probing of methyl-CpG protein interactions in early vertebrate oocytes and embryos. (biomedcentral.com)
  • A number of methods to study DNA-protein interactions have been developed over the years. (biomedcentral.com)
  • Disruption of plant plasma membrane by Nep1-like proteins in pathogen/plant interactions. (ki.si)
  • We identified the replication licencing factor CDC6 as a new partner of the Polycomb group member BMI1. (plos.org)
  • Our results suggest that in young cells Polycomb proteins are recruited to the INK4/ARF locus through CDC6 and the resulting silent locus is replicated during late S-phase. (plos.org)
  • Endogenous MeCP2 and MBD3 were precipitated from Xenopus oocyte extracts and conditions for methylation-specific binding were optimized. (biomedcentral.com)
  • In the presence of nutrients, mTORC1 is activated and promotes cell growth, including protein synthesis and energy storage. (springer.com)
  • The proteostasis network (PN) is an assembly of distinct dynamic molecular pathways that control the functionality of the proteome (proteome homeodynamics) during protein synthesis, folding, trafficking, and degradation. (hindawi.com)
  • Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. (shengsci.com)
  • Their binding to DNA inhibits synthesis of nucleic acids. (lookformedical.com)
  • A cytotoxic polypeptide quinoxaline antibiotic isolated from Streptomyces echinatus that binds to DNA and inhibits RNA synthesis. (lookformedical.com)
  • Single-molecule kinetics reveal microscopic mechanism by which High-Mobility Group B proteins alter DNA flexibility. (shengsci.com)
  • GL7 encodes a protein homologous to LONGIFOLIA in Arabidopsis thaliana and increase grain length and improvement of grain appearance quality [12]. (researchsquare.com)
  • Proteins associated with the Wnt/β-catenin pathway have been identified as SUMOylated substrates, and evidences suggested that the initiation and progression of cancers depended on the function of the SUMOylation ( 23 ). (frontiersin.org)
  • DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. (lookformedical.com)
  • Evidence supporting the direct control of the cell cycle by Pc-G proteins in vertebrates came from studies on mouse Bmi1 mutants. (plos.org)
  • C protein binds strongly to pifO, and weakly to sequences in the ori-1 region. (shengsci.com)
  • Samples are mixed with a cocktail of biotinylated detection antibodies (Step 1) and then incubated with the array membrane which is spotted in duplicate with capture antibodies to specific target proteins (Step 2) . (rndsystems.com)
  • Structural model for factor X inhibition of IgM and complement-mediated neutralization of adenovirus. (ucsf.edu)
  • This recruitment and the associated cilia elongation is not inhibited by blockade of HIFα transcription activity or rescue of basal HIF-2α expression. (biomedcentral.com)
  • cilia and flagella associated protein 6. (gsea-msigdb.org)
  • Primary cilia are sensory organelles that coordinate multiple cellular signaling pathways, including Hedgehog (HH), Wingless/Int (WNT) and Transforming Growth Factor-β (TGF-β) signaling. (springer.com)
  • The nuclear transport receptor Importin-11 is a tumor suppressor that maintains PTEN protein. (omrf.org)
  • Such assays can be used to study binding affinity and recruitment specificity of either recombinant or cellular proteins [ 27 , 28 ]. (biomedcentral.com)
  • SUMOylation of proteins is an important mechanism in cellular responses to environmental stress ( 21 , 22 ). (frontiersin.org)
  • Cells express a pool of thousands of different proteins that need to be tightly controlled for proper cellular structure, organization, and function. (hindawi.com)
  • In addition, the subcellular distribution of mitochondria can affect the cellular transcriptome and transcription rates. (hindawi.com)
  • Mutations in this gene as well as in its related proteins including D-type cyclins, p16(INK4a) and Rb were all found to be associated with tumorigenesis of a variety of cancers. (thermofisher.com)
  • The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION. (lookformedical.com)
  • There was also an upregulation in expression of positive regulators and key components of the AMPK pathway, autophagy, proteasome function, and the unfolded protein response. (nature.com)
  • Muscleblind-like proteins (MBNLs) are regulators of RNA metabolism. (shengsci.com)
  • The LINE-1 retrotransposon protein, ORF1p, forms a condensate on RNA that is essential for retrotransposition, and may explain cis -preference through a co-translational assembly mechanism. (elifesciences.org)
  • The RNA-binding protein Musashi-1 (MSI1) regulates the proliferation and differentiation of adult stem cells. (bvsalud.org)
  • We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. (bvsalud.org)
  • Accordingly, H3K9me3-dependent heterochromatin is considered as a barrier to cell fate changes, by preventing some transcription factors to bind DNA [ 18 ]. (biomedcentral.com)
  • Hypomorphic mutation to intraflagellar transport protein IFT88 results in limited ciliogenesis. (biomedcentral.com)
  • Alvares K, Stern PH, Veis A. Dentin Phosphoprotein Binds Annexin 2 and is Involved in Calcium Transport in Rat kidney Ureteric Bud Cells. (chicagobiomedicalconsortium.org)
  • In addition, its ability to function as a pioneer factor enables the reprogramming of somatic cells back into a pluripotent state. (bvsalud.org)
  • Furthermore, TSC1 was demonstrated to be required for the proper activation of the transforming growth factor-β (TGF-β)-SMAD2/3 pathway in HeLa cells [ 11 ]. (springer.com)
  • The C protein has been purified from cells carrying the Ptrp-C plasmid, and a preliminary study of C protein-DNA binding properties has been carried out. (shengsci.com)
  • Here, we report the presence of short C-terminal MSI1 (MSI1-C) proteins in early mouse embryos and mouse ESCs, but not in human ESCs, under conventional culture conditions. (bvsalud.org)
  • The phosphorylated form of 40S ribosome protein S6 is thus a marker for mTORC1 activity. (springer.com)
  • abraxas 1, BRCA1 A complex subunit [Sou. (gsea-msigdb.org)
  • The heterodimeric TSC complex negatively regulates mTORC1 activity via the GTPase activity of TSC2, towards the small G-protein RHEB (Ras homologue enriched in brain) [ 5 ]. (springer.com)
  • In line with a more complex picture, multiple isoforms of the protein likely exist and non-centrosomal sites of localisation have been reported. (springer.com)
  • Together, these results provide a unified model that integrates replication, transcription and epigenetics at the INK4/ARF locus. (plos.org)