Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Chromatin loop”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources
PubMed1995

Lineage-restricted regulation of the murine SCL/TAL-1 promoter.

The SCL/TAL-1 gene encodes a basic helix-loop-helix transcription factor that is expressed in multipotent hematopoietic progenitors before lineage commitment. Its expression is maintained during differentiation along erythroid, mast, and megakaryocytic lineages, but is repressed after commitment to nonexpressing lineages. To begin to address the molecular mechanisms underlying this complex pattern of expression, we have studied the regulation of the murine SCL promoter in erythroid and T-cell lines. Analysis of the methylation and chromatin structure of the SCL promoter region showed that SCL mRNA expression correlated with DNase hypersensitive sites and methylation status of the promoter. Transient reporter assays showed that promoter 1a was active in erythroid cells but not in T cells. Sequences between -187 and +26 were sufficient for lineage-restricted activity of promoter 1a. A joint promoter construct containing both promoter 1a and promoter 1b also exhibited lineage-restricted activity. Conserved GATA (-37), MAZ (+242), and ETS (+264) motifs were all shown to contribute to SCL promoter activity in erythroid cells, but several other motifs were not required for full promoter activity. The pattern of complexes binding to the +242 MAZ and +264 ETS sites were the same in erythroid and T cells. However, GATA-1 bound the -37 GATA site in erythroid cells, whereas in T cells GATA-3 was only able to bind weakly, if at all. Moreover, GATA-1 but not GATA-2 or GATA-3 was able to transactivate SCL promoter 1a in a T-cell environment. These results suggest that inactivity of SCL promoter 1a in T cells reflected the absence of GATA-1 rather than the presence of trans-dominant negative regulators.

Amino Acid Sequence↗
PubMed2003

Coordinated control of cholesterol catabolism to bile acids and of gluconeogenesis via a novel mechanism of transcription regulation linked to the fasted-to-fed cycle.

Bile acid metabolism plays an essential role in cholesterol homeostasis and is critical for the initiation of atherosclerotic disease. However, despite the recent advances, the molecular mechanisms whereby bile acids regulate gene transcription and cholesterol homeostasis in mammals still need further investigations. Here, we show that bile acids suppress transcription of the gene (CYP7A1) encoding cholesterol 7alpha-hydroxylase, the rate-limiting enzyme in bile acid biosynthesis, also through an unusual mechanism not involving the bile acid nuclear receptor, farnesoid X receptor. By performing cell-based reporter assays, protein/protein interaction, and chromatin immunoprecipitation assays, we demonstrate that bile acids impair the recruitment of peroxisome proliferator-activated receptor-gamma coactivator-1alpha and cAMP response element-binding protein-binding protein by hepatocyte nuclear factor-4alpha, a master regulator of CYP7A1. We also show for the first time that bile acids inhibit transcription of the gene (PEPCK) encoding phosphoenolpyruvate carboxykinase, the rate-limiting enzyme in gluconeogenesis, through the same farnesoid X receptor-independent mechanism. Chromatin immunoprecipitation assay revealed that bile acid-induced dissociation of coactivators from hepatocyte nuclear factor-4alpha decreased the recruitment of RNA polymerase II to the core promoter and downstream in the 3'-untranslated regions of these two genes, reflecting the reduction of gene transcription. Finally, we found that Cyp7a1 expression was stimulated in fasted mice in parallel to Pepck, whereas the same genes were repressed by bile acids. Collectively, these results reveal a novel regulatory mechanism that controls gene transcription in response to extracellular stimuli and argue that the transcription regulation by bile acids of genes central to cholesterol and glucose metabolism should be viewed dynamically in the context of the fasted-to-fed cycle.

3' Untranslated Regions↗
PubMed2001

High-affinity DNA binding of HU protein from the hyperthermophile Thermotoga maritima.

Prokaryotic genomes are compacted by association with small basic proteins, generating what has been termed bacterial chromatin. The ubiquitous DNA-binding protein HU serves this function. DNA-binding properties of HU from the hyperthermophilic eubacterium Thermotoga maritima are shown here to differ significantly from those characteristic of previously described HU homologs. Electrophoretic mobility shift analyses show that T. maritima HU (TmHU) binds double-stranded DNA with high affinity (K(d)=5.6(+/-0.7) nM for 37 bp DNA). Equivalent affinity is observed between 4 degrees C and 45 degrees C. TmHU has higher affinity for DNA containing a set of 4 nt loops separated by 9 bp (K(d)=1.4(+/-0.3) nM), consistent with its introduction of two DNA kinks. Using DNA probes of varying length, the optimal binding site for TmHU is estimated at 37 bp, in sharp contrast to the 9-10 bp binding site reported for other HU homologs. Alignment of >60 HU sequences demonstrates significant sequence conservation: A DNA-intercalating proline residue is almost universally conserved, and it is preceded by arginine and asparagine in most sequences, generating a highly conserved RNP motif; V substitutes for R only in HU from Thermotoga, Thermus and Deinococcus. A fivefold increase in DNA-binding affinity is observed for TmHU in which V is replaced with R (TmHU-V61R; K(d)=1.1(+/-0.2) nM), but a change in the trajectory of DNA flanking the sites of DNA intercalation is inferred from analysis of TmHU-V61R binding to DNA modified with 4 nt loops or with substitutions of 5-hydroxymethyluracil for thymine. Survival in extreme environments places unique demands on protection of genomic DNA from thermal destabilization and on access of DNA to the cellular machinery, demands that may be fulfilled by the specific DNA-binding properties of HU and by the fine structure of the bacterial chromatin.

Amino Acid Motifs↗
PubMed1997

Architectural accommodation in the complex of four p53 DNA binding domain peptides with the p21/waf1/cip1 DNA response element.

High resolution chemical footprinting and cross-linking experiments have provided a basis for elucidating the overall architecture of the complex between the core DNA binding domain of p53 (p53DBD, amino acids 98-309) and the p21/waf1/cip1 DNA response element implicated in the G1/S phase cell cycle checkpoint. These studies complement both a crystal structure and earlier biophysical studies and provide the first direct experimental evidence that four subunits of p53DBD bind to the response element in a regular staggered array having pseudodyad symmetry. The invariant guanosines in the highly conserved C(A/T)|(T/A)G parts of the consensus half-sites are critical to the p53DBD-DNA binding. Molecular modeling of the complex using the observed peptide-DNA contacts shows that when four subunits of p53DBD bind the response element, the DNA has to bend approximately 50 degrees to relieve steric clashes among different subunits, consistent with recent DNA cyclization studies. The overall lateral arrangement of the four p53 subunits with respect to the DNA loop comprises a novel nucleoprotein assembly that has not been reported previously in other complexes. We suggest that this kind of nucleoprotein superstructure may be important for p53 binding to response elements packed in chromatin and for subsequent transactivation of p53-mediated genes.

Base Sequence↗
PubMed2005

Mechanisms underlying the transcriptional regulation of skeletal myogenesis.

During skeletal myogenesis, chromatin-modifying enzymes are engaged at discrete genomic regions by transcription factors that recognize sequence-specific DNA motifs located at muscle gene regulatory regions. The composition of the chromatin-bound protein complexes and their temporally and spatially regulated recruitment influence gene expression. Recent findings are consistent with the concept that chromatin modifiers play an important role in regulating skeletal muscle gene expression and cellular differentiation.

Animals↗
PubMed2004

Basic helix-loop-helix transcription factor Tcfl5 interacts with the Calmegin gene promoter in mouse spermatogenesis.

In mouse spermatogenesis, differentiating germ line cells initiate expression of specific genes at subsequent developmental steps. The Calmegin (Clgn) gene is first expressed in meiotic prophase, in primary spermatocytes, and encodes a protein that acts as a chaperone. To identify testis-specific transcription factors that control expression of the Clgn gene in spermatogenesis, we performed a yeast one-hybrid screening with a Clgn promoter sequence as bait DNA. This screening resulted in the identification of mouse Tcfl5 as a candidate Clgn promoter-binding protein. Tcfl5 is a member of the basic helix-loop-helix (bHLH) family of transcription factors, and mouse Tcfl5 shows 83% amino acid sequence identity with human TCFL5. Gel-shift and yeast one-hybrid experiments showed that Tcfl5 interacts with a non-canonical CACGCG site that is present in the Clgn promoter. By using northern blot, RT-PCR and in situ hybridization, mouse Tcfl5 mRNA was detected only in testis, with the highest expression level in primary spermatocytes and round spermatids. The highest level of Tcfl5 protein was found in primary spermatocytes at the diplotene stage of meiotic prophase, where the protein colocalizes with transcriptionally active chromatin.

Amino Acid Sequence↗
PubMed1996

The leucine zipper may induce electrophoretic mobility anomalies without DNA bending.

Numerous proteins bend DNA upon binding, a phenomenon of potential significance for regulation of gene expression and chromatin. DNA bending is commonly predicted from the presence of electrophoretic mobility anomalies in protein-DNA complexes. However, as compared with electrophoretic methods, several DNA binding oncoprotein families do not display comparable evidence of DNA bends in x-ray structural studies. Herein, circularization kinetics and affinity measurements with prebent DNA templates were employed to assess bending and DNA structural preferences for Max and other basic helix-loop-helix/leucine zipper proteins. In this way, proteins in the Myc/Max basic helix-loop-helix/ leucine zipper family were found not to bend DNA in solution but to actually stabilize DNA in an unbent configuration that resists circularization. The mobility anomaly was found to be induced by the leucine zipper protein motif, rather than structural distortions of DNA. Thus rigid protein domain structures may induce anomalous electrophoretic mobility. Moreover, the energetic preference of non-DNA bending proteins for unbent templates suggests mechanisms whereby chromatin structure may regulate transcription.

Binding Sites↗
PubMed2003

Functional inactivation of a transcriptional corepressor by a signaling kinase.

The C-terminal binding protein 1 (CtBP) is a ubiquitous corepressor linking the recruitment of DNA- and histone-modifying proteins to sequence-specific DNA-binding proteins and facilitating gene regulation during development and oncogenesis. We describe here the binding, phosphorylation and functional regulation of CtBP by the p21-activated kinase 1 (Pak1). Pak1 phosphorylates CtBP selectively on Ser158 within a putative regulatory loop, triggering CtBP cellular redistribution and blocking CtBP corepressor functions. A S158A substitution in CtBP or Pak1 knockdown by short interference RNA blocked CtBP phosphorylation, redistribution and attenuation of CtBP corepressor functions in reporter and chromatin assays. In the presence of NADH, Pak1 superphosphorylates CtBP and inhibits CtBP dehydrogenase activity, suggesting that preferential phosphorylation of active CtBP may alter secondary structures and influence both enzymatic and corepressor functions. Pak1 regulation of CtBP represents a new model of corepressor regulation whereby cellular signaling cascades may influence gene expression in mammalian cells.

Alcohol Oxidoreductases↗
PubMed1998

A preferred target DNA structure for retroviral integrase in vitro.

The retroviral integrase protein catalyzes the insertion of linear viral DNA ends into the host cell DNA. Although integration in vivo is not site-specific, the detection of local and regional preferences within cellular DNA suggests that the integration reaction can be influenced by specific features of host DNA or chromatin. Here we describe highly preferred in vitro integration sites for avian sarcoma virus and human immunodeficiency virus-1 integrases within the stems of plasmid DNA cruciform structures. The preferred sites are adjacent to the loops in the cruciform and are strand-specific. We suggest that the observed preference is due to the end-like character of the stem loop structure that allows DNA unpairing. From these results we propose that such unpairing may enhance both the processing and the joining steps in the integration reaction, and perhaps other cellular recombination reactions as well.

Avian Sarcoma Viruses↗
PubMed1998

Assembly of lampbrush chromosomes from sperm chromatin.

We have examined the behavior of demembranated sperm heads when injected into the germinal vesicle (GV) of amphibian oocytes. Xenopus sperm heads injected into Xenopus GVs swelled immediately and within hours began to stain with an antibody against RNA polymerase II (Pol II). Over time each sperm head became a loose mass of chromosome-like threads, which by 24-48 h resolved into individually recognizable lampbrush chromosomes (LBCs). Although LBCs derived from sperm are unreplicated single chromatids, their morphology and immunofluorescent staining properties were strikingly similar to those of the endogenous lampbrush bivalents. They displayed typical transcriptionally active loops extending from an axis of condensed chromomeres, as well as locus-specific "landmarks. " Experiments with [3H]GTP and actinomycin D demonstrated that transcription was not necessary for the initial swelling of the sperm heads and acquisition of Pol II but was required for maintenance of the lampbrush loops. Splicing was not required at any stage during formation of sperm LBCs. When Xenopus sperm heads were injected into GVs of the newt Notophthalmus, the resulting sperm LBCs displayed very long loops with pronounced Pol II axes, like those of the endogenous newt LBCs; as expected, they stained with antibodies against newt-specific proteins. Other heterologous injections, including sperm heads of the frog Rana pipiens and the zebrafish Danio rerio in Xenopus GVs, confirm that LBCs can be derived from taxonomically distant organisms. The GV system should help identify both cis- and trans-acting factors needed to convert condensed chromatin into transcriptionally active LBCs. It may also be useful in producing cytologically analyzable chromosomes from organisms whose oocytes do not go through a typical lampbrush phase or cannot be manipulated by current techniques.

Animals↗
PubMed2004

Gelsolin gene silencing involving unusual hypersensitivities to dimethylsulfate and KMnO4 in vivo footprinting on its promoter region.

We previously reported that gelsolin gene expression is reduced in various tumors. In an effort to gain further insights into the mechanism of gelsolin downregulation in tumors, we examined the in vivo properties of the gelsolin promoter in urinary bladder cancer cell lines. Neither mutation nor hypermethylation was responsible for gene silencing at the promoter. After exposure to trichostatin A (TSA), a histone deacetylase inhibitor, gelsolin promoter activity was markedly enhanced in the cancer cells, not in cells derived from normal tissue. Chromatin immunoprecipitation assays revealed that both histones H3 and H4 were hypoacetylated in the promoter region of the cancer cells, and the accumulation of acetylated histones was detected by TSA treatment. In vivo footprinting analysis revealed the presence of dimethylsulfate (DMS) hypersensitive site in the untranslated region around nucleotide--35 only in the cancer cells but not in cells derived from normal tissue, and analysis of KMnO4 reactive nucleotides showed that the stem loop structure could be formed in vivo of the cancer cells. This novel stem loop structure may play a part in regulating the transcription of the gelsolin gene in the cancer cells. These results suggest that nucleosome accessibility through histone deacetylation and structural changes (DMS hypersensitivity and stem loop structure) in the promoter region form the basis of the mechanism leading to the silencing of gelsolin gene in human bladder cancer.

Base Sequence↗
PubMed2006

Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation.

Both prokaryotic and eukaryotic organisms contain DNA bridging proteins, which can have regulatory or architectural functions. The molecular and mechanical details of such proteins are hard to obtain, in particular if they involve non-specific interactions. The bacterial nucleoid consists of hundreds of DNA loops, shaped in part by non-specific DNA bridging proteins such as histone-like nucleoid structuring protein (H-NS), leucine-responsive regulatory protein (Lrp) and SMC (structural maintenance of chromosomes) proteins. We have developed an optical tweezers instrument that can independently handle two DNA molecules, which allows the systematic investigation of protein-mediated DNA-DNA interactions. Here we use this technique to investigate the abundant non-specific nucleoid-associated protein H-NS, and show that H-NS is dynamically organized between two DNA molecules in register with their helical pitch. Our optical tweezers also allow us to carry out dynamic force spectroscopy on non-specific DNA binding proteins and thereby to determine an energy landscape for the H-NS-DNA interaction. Our results explain how the bacterial nucleoid can be effectively compacted and organized, but be dynamic in nature and accessible to DNA-tracking motor enzymes. Finally, our experimental approach is widely applicable to other DNA bridging proteins, as well as to complex DNA interactions involving multiple DNA molecules.

Bacterial Proteins↗
PubMed1989

Competence growth factors can cause modification in higher-order chromatin structure in mouse embryo 3T3 fibroblasts.

The authors compared sedimentation rates of nucleoids from mouse embryo 3T3 fibroblasts cultured in the presence or absence of different cell growth factors. The results clearly showed that rapidly sedimenting nucleoids are obtained only when cells are supplied with any of the following competence growth factors: platelet-derived growth factor (PDGF), fibroblast growth factor (FGF), or the product of the oncogene v-sis (a peptide homologous to PDGF). The tumor promoter phorbol 12-myristate 13-acetate, an activator of protein kinase C and a partial mitogen, shares this property with the competence growth factors. Removal of these factors from the medium causes cells to enter Go and nucleoids to sediment at a slower rate. Protein synthesis is required for growth factor induction of change in nucleoid sedimentation, but inhibition of either DNA synthesis or DNA repair does not antagonize the effect of growth factors. Titration of nucleoids with ethidium bromide indicates that one possible mechanism for the nucleoid change is the unwinding of DNA in supercoiled loops. The results indicated that the nucleoid change constitutes a cell response to competence factors that might have an important role in cell proliferation.

Animals↗
PubMed2026

JNK acts as a molecular brake of the CDC73 positive feedback loop to modulate osteosarcoma malignant progression via UBR5.

CDC73 is a well-characterized tumor suppressor regulated by stress stimuli, governing progression of diverse human malignancies. Although previous studies have shown that E3 ubiquitin ligase UBR5 drives CDC73 ubiquitination and degradation to modulate tumorigenesis, the mechanisms by which stress-responsive pathways regulate UBR5-mediated CDC73 inactivation and transcriptional reprogramming remain elusive. Here, via integrated analyses of public datasets, multi-omics profiling (assay for transposase-accessible chromatin with sequencing [ATAC-seq], cleavage under targets and tagmentation [CUT&Tag], mRNA sequencing [mRNA-seq]), in vitro/in vivo assays, and molecular approaches including co-immunoprecipitation (Co-IP) and molecular docking, we demonstrate that UBR5 depletion profoundly alters chromatin accessibility and genome-wide transcriptional profiles in a CDC73-dependent manner. UBR5 ablation markedly suppresses osteosarcoma malignant phenotypes in cultured cells and xenograft models, with these effects fully rescued by concurrent CDC73 silencing. Mechanistically, we identify the JNK cascade as the critical upstream regulator: JNK activation sustains CDC73 stability by antagonizing UBR5-mediated CDC73 polyubiquitination, and map Lys257 as the key residue for UBR5-dependent CDC73 ubiquitination and degradation. Collectively, our findings define a novel JNK-dependent UBR5-CDC73 axis that acts as a molecular brake of the CDC73 positive feedback loop to orchestrate transcriptional programs, providing new mechanistic insights into CDC73 post-translational regulation in tumorigenesis and promising therapeutic targets for CDC73-dysregulated diseases.

Journal Article↗
PubMed1999

cDNA of the yeast retrotransposon Ty5 preferentially recombines with substrates in silent chromatin.

The yeast retrotransposon Ty5 preferentially integrates into regions of silent chromatin. Ty5 cDNA also recombines with homologous sequences, generating tandem elements or elements that have exchanged markers between cDNA and substrate. In this study, we demonstrate that Ty5 integration depends upon the conserved DD(35)E domain of integrase and cis-acting sequences at the end of the long terminal repeat (LTR) implicated in integrase binding. cDNA recombination requires Rad52p, which is responsible for homologous recombination. Interestingly, Ty5 cDNA recombines at least three times more frequently with substrates in silent chromatin than with a control substrate at an internal chromosomal locus. This preference depends upon the Ty5 targeting domain that is responsible for integration specificity, suggesting that localization of cDNA to silent chromatin results in the enhanced recombination. Recombination with a telomeric substrate occasionally generates highly reiterated Ty5 arrays, and mechanisms for tandem element formation were explored by using a plasmid-based recombination assay. Point mutations were introduced into plasmid targets, and recombination products were characterized to determine recombination initiation sites. Despite our previous observation of the importance of the LTR in forming tandem elements, recombination cannot simply be explained by crossover events between the LTRs of substrate and cDNA. We propose an alternative model based on single-strand annealing, where single-stranded cDNA initiates tandem element formation and the LTR is required for strand displacement to form a looped intermediate. Retrotransposons are increasingly found associated with chromosome ends, and amplification of Ty5 by both integration and recombination exemplifies how retroelements can contribute to telomere dynamics.

Amino Acid Sequence↗
PubMed2005

The basic domain of ATH5 mediates neuron-specific promoter activity during retina development.

In the developing retina, the gene encoding the beta3 subunit of the neuronal nicotinic receptor, a specific marker of retinal ganglion cells, is under the direct control of the atonal homolog 5 (ATH5) basic helix-loop-helix (bHLH) transcription factor. Although quite short (143 bp in length), the beta3 promoter has the remarkable capacity to discriminate between ATH5 and the other neuronal bHLH proteins expressed in the developing nervous system. We have identified three amino acids within the basic domain that confer specificity to the ATH5 protein. These residues do not mediate direct DNA binding but are required for interaction between ATH5 and chromatin-associated proteins during retina development. When misexpressed in neurons, the myogenic bHLH factor MyoD is also able to activate the beta3 gene. This, however, is achieved not by binding of the protein to the promoter but by dimerization of MyoD with a partner, a process that depends not on the basic domain but on the HLH domain. By sequestering an E-box-binding protein, MyoD relieves the active repression that blocks the beta3 promoter in most neurons. The mechanisms used by bHLH proteins to activate beta3 thus highlight how ATH5 is selected by the beta3 promoter and coordinates the derepression and transcriptional activation of the beta3 gene during the specification of retinal ganglion cells.

Amino Acid Motifs↗
PubMed2003

Distinct strategies to make nucleosomal DNA accessible.

One hallmark of ATP-dependent remodeling complexes is the ability to make nucleosomal DNA accessible to regulatory factors. We have compared two prominent human ATP-dependent remodelers, BRG1 from the SWI/SNF family and SNF2h from the ISWI family, for their abilities to make a spectrum of nucleosomal sites accessible. By measuring rates of remodeling at seven different sites on a mononucleosome and at six different sites on the central nucleosome of a trinucleosome, we have found that BRG1 opens centrally located sites more than an order of magnitude better than SNF2h. We provide evidence that this capability of BRG1 is caused by its ability to create DNA loops on the surface of a nucleosome, even when that nucleosome is constrained by adjacent nucleosomes. This specialized ability to make central sites accessible should allow SWI/SNF family complexes to facilitate binding of nuclear factors in chromatin environments where adjacent nucleosomes might otherwise constrain mobility.

Adenosine Triphosphate↗
PubMed1997

Stable co-occupancy of transcription factors and histones at the HIV-1 enhancer.

To investigate mechanisms yielding DNase I-hypersensitive sites (DHSs) at gene regulatory regions, we have initiated a biochemical analysis of transcription factor binding and nucleosome remodeling with a region of the human immunodeficiency virus 1 (HIV-1) 5' long terminal repeat (LTR) that harbors constitutive DHSs in vivo. In vitro reconstitution of an HIV-1 5' LTR fragment into nucleosome core particles demonstrates that Sp1, NF-kappaB1, LEF-1, ETS-1 and USF can gain access to their binding sites in HIV-1 nucleosomal DNA. The factor-bound mononucleosomes resist histone displacement from the DNA by the chromatin remodeling activity, SW1-SNF, or the histone chaperone, nucleoplasmin, suggesting that the binding of these factors to nucleosomal HIV-1 sequences forms a stable complex that includes the underlying histones. However, when the HIV-1 5' LTR fragment is incorporated into a nucleosomal array, Sp1 and NF-kappaB1 binding produce regions of enhanced DNase I sensitivity specifically at the HIV-1 nucleosome. These regions resemble the observed in vivo DHSs, yet the HIV-1 nucleosome remains intact even in the presence of nucleoplasmin. Thus, the constitutive DHSs identified at the HIV-1 enhancer in native chromatin may reflect the presence of a ternary complex composed of transcriptional activators, histones and DNA.

Binding Sites↗