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1.
Mol Cell ; 81(2): 239-254.e8, 2021 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-33301730

RESUMO

Metazoan transcription factors typically regulate large numbers of genes. Here we identify via a CRISPR-Cas9 genetic screen ZNF410, a pentadactyl DNA-binding protein that in human erythroid cells directly activates only a single gene, the NuRD component CHD4. Specificity is conveyed by two highly evolutionarily conserved clusters of ZNF410 binding sites near the CHD4 gene with no counterparts elsewhere in the genome. Loss of ZNF410 in adult-type human erythroid cell culture systems and xenotransplantation settings diminishes CHD4 levels and derepresses the fetal hemoglobin genes. While previously known to be silenced by CHD4, the fetal globin genes are exposed here as among the most sensitive to reduced CHD4 levels.. In vitro DNA binding assays and crystallographic studies reveal the ZNF410-DNA binding mode. ZNF410 is a remarkably selective transcriptional activator in erythroid cells, and its perturbation might offer new opportunities for treatment of hemoglobinopathies.


Assuntos
DNA/genética , Células Precursoras Eritroides/metabolismo , Hemoglobina Fetal/genética , Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/genética , Fatores de Transcrição/genética , Animais , Sítios de Ligação , Células COS , Sistemas CRISPR-Cas , Chlorocebus aethiops , DNA/metabolismo , Células Precursoras Eritroides/citologia , Células Precursoras Eritroides/transplante , Sangue Fetal/citologia , Sangue Fetal/metabolismo , Hemoglobina Fetal/metabolismo , Feto , Edição de Genes , Células HEK293 , Xenoenxertos , Humanos , Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/química , Complexo Mi-2 de Remodelação de Nucleossomo e Desacetilase/metabolismo , Camundongos , Modelos Moleculares , Células-Tronco Embrionárias Murinas/citologia , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo , Ativação Transcricional
2.
Genes Dev ; 34(21-22): 1546-1558, 2020 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-33004415

RESUMO

The de novo DNA methyltransferases Dnmt3a and Dnmt3b play crucial roles in developmental and cellular processes. Their enzymatic activities are stimulated by a regulatory protein Dnmt3L (Dnmt3-like) in vitro. However, genetic evidence indicates that Dnmt3L functions predominantly as a regulator of Dnmt3a in germ cells. How Dnmt3a and Dnmt3b activities are regulated during embryonic development and in somatic cells remains largely unknown. Here we show that Dnmt3b3, a catalytically inactive Dnmt3b isoform expressed in differentiated cells, positively regulates de novo methylation by Dnmt3a and Dnmt3b with a preference for Dnmt3b. Dnmt3b3 is equally potent as Dnmt3L in stimulating the activities of Dnmt3a2 and Dnmt3b2 in vitro. Like Dnmt3L, Dnmt3b3 forms a complex with Dnmt3a2 with a stoichiometry of 2:2. However, rescue experiments in Dnmt3a/3b/3l triple-knockout (TKO) mouse embryonic stem cells (mESCs) reveal that Dnmt3b3 prefers Dnmt3b2 over Dnmt3a2 in remethylating genomic sequences. Dnmt3a2, an active isoform that lacks the N-terminal uncharacterized region of Dnmt3a1 including a nuclear localization signal, has very low activity in TKO mESCs, indicating that an accessory protein is absolutely required for its function. Our results suggest that Dnmt3b3 and perhaps similar Dnmt3b isoforms facilitate de novo DNA methylation during embryonic development and in somatic cells.


Assuntos
DNA (Citosina-5-)-Metiltransferases/metabolismo , Metilação de DNA/genética , Isoenzimas/metabolismo , Animais , DNA (Citosina-5-)-Metiltransferases/genética , DNA Metiltransferase 3A , Embrião de Mamíferos , Desenvolvimento Embrionário/genética , Células-Tronco Embrionárias , Camundongos , Camundongos Knockout , DNA Metiltransferase 3B
3.
Mol Cell ; 65(3): 447-459.e6, 2017 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-28111016

RESUMO

Chromatin remodelers use a helicase-like ATPase motor to reposition and reorganize nucleosomes along genomic DNA. Yet, how the ATPase motor communicates with other remodeler domains in the context of the nucleosome has so far been elusive. Here, we report for the Chd1 remodeler a unique organization of domains on the nucleosome that reveals direct domain-domain communication. Site-specific cross-linking shows that the chromodomains and ATPase motor bind to adjacent SHL1 and SHL2 sites, respectively, on nucleosomal DNA and pack against the DNA-binding domain on DNA exiting the nucleosome. This domain arrangement spans the two DNA gyres of the nucleosome and bridges both ends of a wrapped, ∼90-bp nucleosomal loop of DNA, suggesting a means for nucleosome assembly. This architecture illustrates how Chd1 senses DNA outside the nucleosome core and provides a basis for nucleosome spacing and directional sliding away from transcription factor barriers.


Assuntos
Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Animais , Montagem e Desmontagem da Cromatina , DNA/química , Nucleossomos/genética , Ligação Proteica , Domínios Proteicos , Xenopus laevis
4.
Nucleic Acids Res ; 51(4): 1674-1686, 2023 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-36660822

RESUMO

ZNF410 is a highly-conserved transcription factor, remarkable in that it recognizes a 15-base pair DNA element but has just a single responsive target gene in mammalian erythroid cells. ZNF410 includes a tandem array of five zinc-fingers (ZFs), surrounded by uncharacterized N- and C-terminal regions. Unexpectedly, full-length ZNF410 has reduced DNA binding affinity, compared to that of the isolated DNA binding ZF array, both in vitro and in cells. AlphaFold predicts a partially-folded N-terminal subdomain that includes a 30-residue long helix, preceded by a hairpin loop rich in acidic (aspartate/glutamate) and serine/threonine residues. This hairpin loop is predicted by AlphaFold to lie against the DNA binding interface of the ZF array. In solution, ZNF410 is a monomer and binds to DNA with 1:1 stoichiometry. Surprisingly, the single best-fit model for the experimental small angle X-ray scattering profile, in the absence of DNA, is the original AlphaFold model with the N-terminal long-helix and the hairpin loop occupying the ZF DNA binding surface. For DNA binding, the hairpin loop presumably must be displaced. After combining biophysical, biochemical, bioinformatic and artificial intelligence-based AlphaFold analyses, we suggest that the hairpin loop mimics the structure and electrostatics of DNA, and provides an additional mechanism, supplementary to sequence specificity, of regulating ZNF410 DNA binding.


Assuntos
Fatores de Transcrição , Animais , Sequência de Aminoácidos , Inteligência Artificial , Mamíferos/genética , Ligação Proteica , Domínios Proteicos , Dedos de Zinco/genética , Fatores de Transcrição/química , Fatores de Transcrição/metabolismo
5.
J Biol Chem ; 299(2): 102885, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36626981

RESUMO

ZBTB7A belongs to a small family of transcription factors having three members in humans (7A, 7B, and 7C). They share a BTB/POZ protein interaction domain at the amino end and a zinc-finger DNA-binding domain at the carboxyl end. They control the transcription of a wide range of genes, having varied functions in hematopoiesis, oncogenesis, and metabolism (in particular glycolysis). ZBTB7A-binding profiles at gene promoters contain a consensus G(a/c)CCC motif, followed by a CCCC sequence in some instances. Structural and mutational investigations suggest that DNA-specific contacts with the four-finger tandem array of ZBTB7A are formed sequentially, initiated from ZF1-ZF2 binding to G(a/c)CCC before spreading to ZF3-ZF4, which bind the DNA backbone and the 3' CCCC sequence, respectively. Here, we studied some mutations found in t(8;21)-positive acute myeloid leukemia patients that occur within the ZBTB7A DNA-binding domain. We determined that these mutations generally impair ZBTB7A DNA binding, with the most severe disruptions resulting from mutations in ZF1 and ZF2, and the least from a frameshift mutation in ZF3 that results in partial mislocalization. Information provided here on ZBTB7A-DNA interactions is likely applicable to ZBTB7B/C, which have overlapping functions with ZBTB7A in controlling primary metabolism.


Assuntos
Leucemia Mieloide Aguda , Fatores de Transcrição , Humanos , Linhagem Celular Tumoral , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Leucemia Mieloide Aguda/genética , Mutação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Dedos de Zinco/genética , Domínios Proteicos/genética , Ligação Proteica/genética
6.
Nano Lett ; 23(24): 11438-11446, 2023 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-38051760

RESUMO

Single-molecule antigen detection using nanopores offers a promising alternative for accurate virus testing to contain their transmission. However, the selective and efficient identification of small viral proteins directly in human biofluids remains a challenge. Here, we report a nanopore sensing strategy based on a customized DNA molecular probe that combines an aptamer and an antibody to enhance the single-molecule detection of mpox virus (MPXV) A29 protein, a small protein with an M.W. of ca. 14 kDa. The formation of the aptamer-target-antibody sandwich structures enables efficient identification of targets when translocating through the nanopore. This technique can accurately detect A29 protein with a limit of detection of ∼11 fM and can distinguish the MPXV A29 from vaccinia virus A27 protein (a difference of only four amino acids) and Varicella Zoster Virus (VZV) protein directly in biofluids. The simplicity, high selectivity, and sensitivity of this approach have the potential to contribute to the diagnosis of viruses in point-of-care settings.


Assuntos
Mpox , Nanoporos , Humanos , Proteínas/química , Nanotecnologia/métodos , DNA/química , Anticorpos , Oligonucleotídeos
7.
Wei Sheng Yan Jiu ; 53(3): 455-464, 2024 May.
Artigo em Zh | MEDLINE | ID: mdl-38839588

RESUMO

OBJECTIVE: To establish an ultra-performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS) method for simultaneous determination of 11 nutritional components(thiamine, riboflavin, nicotinamide, nicotinic acid, pantothenic acid, pyridoxine, pyridoxal, pyridoxamine, biotin, choline, L-carnitine) in liquid milk. METHODS: Milk samples were shaken with 20 mmol/L ammonium formate solution and heated in a water bath at 100 ℃ for 30 min, then incubated with papain and acid phosphatase at 45 ℃ for 16 h, the lower liquid was collected after centrifugation for analysis. UPLC separation was performed on an ACQUITY~(TM) HSS T3(3.0 mm×150 mm, 1.8 µm) column, 2 mmol/L ammonium formate(containing 0.1% formic acid) solution and acetonitrile(containing 0.1% formic acid) were used as mobile phase. Quantitative detection was performed by internal standard method. RESULTS: 11 nutritional components can be effectively separated and detected in 12 min, and the linear correlation coefficients(R~2) were all above 0.995. The limits of detection(LODs) were between 0.05 and 0.50 µg/L, and the limits of quantification(LOQs) were between 0.20 and 1.25 µg/L. The recovery rates of three-level addition were 85.6%-119.3%, and the precision RSDs were between 3.68% and 7.82%(n=6). Based on the detection of 60 liquid milk samples from 5 different animals, it was found that the contents of 11 nutrients in liquid milk from different milk sources were significantly different, but pyridoxine could not be detected. CONCLUSION: The method can quantitatively detect 11 water-soluble nutrients, including free and bound forms, by effective enzymolysis. It is sensitive, reproducible and can meet the needs of quantitative detection.


Assuntos
Leite , Espectrometria de Massas em Tandem , Leite/química , Espectrometria de Massas em Tandem/métodos , Animais , Cromatografia Líquida de Alta Pressão/métodos , Niacinamida/análise , Riboflavina/análise , Nutrientes/análise , Ácido Pantotênico/análise , Bovinos , Piridoxina/análise , Niacina/análise , Carnitina/análise
8.
J Am Chem Soc ; 145(11): 6371-6382, 2023 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-36897933

RESUMO

The analysis at the single-molecule level of proteins and their interactions can provide critical information for understanding biological processes and diseases, particularly for proteins present in biological samples with low copy numbers. Nanopore sensing is an analytical technique that allows label-free detection of single proteins in solution and is ideally suited to applications, such as studying protein-protein interactions, biomarker screening, drug discovery, and even protein sequencing. However, given the current spatiotemporal limitations in protein nanopore sensing, challenges remain in controlling protein translocation through a nanopore and relating protein structures and functions with nanopore readouts. Here, we demonstrate that supercharged unstructured polypeptides (SUPs) can be genetically fused with proteins of interest and used as molecular carriers to facilitate nanopore detection of proteins. We show that cationic SUPs can substantially slow down the translocation of target proteins due to their electrostatic interactions with the nanopore surface. This approach enables the differentiation of individual proteins with different sizes and shapes via characteristic subpeaks in the nanopore current, thus facilitating a viable route to use polypeptide molecular carriers to control molecular transport and as a potential system to study protein-protein interactions at the single-molecule level.


Assuntos
Nanoporos , Peptídeos/química , Proteínas , Sequência de Aminoácidos , Nanotecnologia
9.
Opt Express ; 31(5): 7900-7906, 2023 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-36859911

RESUMO

InGaAs/AlGaAs multiple quantum well lasers grown on silicon (001) by molecular beam epitaxy have been demonstrated. By inserting InAlAs trapping layers into AlGaAs cladding layers, misfit dislocations easily located in the active region can be effectively transferred out of the active region. For comparison, the same laser structure without the InAlAs trapping layers was also grown. All these as-grown materials were fabricated into Fabry-Perot lasers with the same cavity size of 20 × 1000 µm2. The laser with trapping layers achieved a 2.7-fold reduction in threshold current density under pulsed operation (5 µs-pulsed width, 1%-duty cycle) compared to the counterpart, and further realized a room-temperature continuous-wave lasing with a threshold current of 537 mA which corresponds to a threshold current density of 2.7 kA/cm2. When the injection current reached 1000 mA, the single-facet maximum output power and slope efficiency were 45.3 mW and 0.143 W/A, respectively. This work demonstrates significantly improved performances of InGaAs/AlGaAs quantum well lasers monolithically grown on silicon, providing a feasible solution to optimize the InGaAs quantum well structure.

10.
Appl Opt ; 62(4): 1057-1065, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36821163

RESUMO

A modified uni-traveling carrier photodiode with an electric field control layer is proposed to achieve high-speed and high-power performance at a lower bias voltage. By inserting the 10 nm p-type InGaAs electric field control layer between the intrinsic absorption layer and space layer, the electric field distribution in the depleted absorption layer and depleted non-absorption layer can be changed. It is beneficial for reducing power consumption and heat generation, meanwhile suppressing the space-charge effect. Compared with the original structure without the electric field control layer, the 3 dB bandwidth of the 20 µm diameter novel structure, to the best of our knowledge, is improved by 27.1% to 37.5 GHz with a reverse bias of 2 V, and the RF output power reaches 23.9 dBm at 30 GHz. In addition, under 8 V bias voltage, the bandwidth reaches 47.3 GHz.

11.
Zygote ; 31(4): 393-401, 2023 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-37212062

RESUMO

Although ethanol treatment is widely used to activate oocytes, the underlying mechanisms are largely unclear. Roles of intracellular calcium stores and extracellular calcium in ethanol-induced activation (EIA) of oocytes remain to be verified, and whether calcium-sensing receptor (CaSR) is involved in EIA is unknown. This study showed that calcium-free ageing (CFA) in vitro significantly decreased intracellular stored calcium (sCa) and CaSR expression, and impaired EIA, spindle/chromosome morphology and developmental potential of mouse oocytes. Although EIA in oocytes with full sCa after ageing with calcium does not require calcium influx, calcium influx is essential for EIA of oocytes with reduced sCa after CFA. Furthermore, the extremely low EIA rate in oocytes with CFA-downregulated CaSR expression and the fact that inhibiting CaSR significantly decreased the EIA of oocytes with a full complement of CaSR suggest that CaSR played a significant role in the EIA of ageing oocytes. In conclusion, CFA impaired EIA and the developmental potential of mouse oocytes by decreasing sCa and downregulating CaSR expression. Because mouse oocytes routinely treated for activation (18 h post hCG) are equipped with a full sCa complement and CaSR, the present results suggest that, while calcium influx is not essential, CaSR is required for the EIA of oocytes.


Assuntos
Cálcio , Etanol , Camundongos , Animais , Cálcio/metabolismo , Etanol/farmacologia , Oócitos/fisiologia , Receptores de Detecção de Cálcio/genética , Receptores de Detecção de Cálcio/metabolismo , Envelhecimento
12.
Adv Exp Med Biol ; 1389: 295-315, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36350515

RESUMO

The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine-5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine-have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine-N4-methylcytosine and N6-methyladenine-are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, several crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA.


Assuntos
5-Metilcitosina , Metilação de DNA , DNA , 5-Metilcitosina/química , Citosina/química , DNA/metabolismo , Epigênese Genética , Eucariotos/genética , Eucariotos/metabolismo
13.
Bioorg Chem ; 109: 104710, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33611137

RESUMO

A series of 8-substituted sampangine derivatives have been designed, synthesized and tested for their ability to inhibit cholinesterase and penetrate the blood-brain barrier. Their chelating ability toward Zn2+ and other biologically relevant metal ions was also demonstrated by isothermal titration calorimetry. The new derivatives exhibited high acetylcholinesterase inhibitory activity, high blood-brain barrier penetration ability and high chelating selectivity for Zn2+. Moreover, compound 10 with the strongest binding affinity to Zn2+ was selected for further research. Western blotting analysis, transmission electron microscopy, DCFH-DA assay and paralysis experiment indicated that compound 10 suppressed the formation of Zn2+-Aß complexes, alleviated the Zn2+ induced neurotoxicity and inhibited the production of ROS catalyzed by Zn2+ in Aß42 transgenic C. elegans. Furthermore, compound 10 also inhibited the expressions of pro-inflammatory cytokines, such as NO, TNF-α, IL-6 and IL-1ß, induced by Zn2+ + Aß1-42 in BV2 microglial cells. In general, this work provided new insights into the design and development of potent metal-chelating agents for Alzheimer's disease treatment.


Assuntos
Alcaloides/química , Peptídeos beta-Amiloides/antagonistas & inibidores , Peptídeos beta-Amiloides/química , Caenorhabditis elegans/efeitos dos fármacos , Compostos Heterocíclicos de 4 ou mais Anéis/química , Naftiridinas/química , Zinco/química , Animais , Animais Geneticamente Modificados , Citocinas/genética , Citocinas/metabolismo , Regulação da Expressão Gênica/efeitos dos fármacos , Ibuprofeno , Microglia , Oxirredução , Ratos , Espécies Reativas de Oxigênio
14.
J Reprod Dev ; 67(1): 43-51, 2021 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-33310974

RESUMO

It has been reported in recent studies that restraint stress on pregnant mice during the preimplantation stage elevated corticotrophin-releasing hormone (CRH) and glucocorticoid levels in the serum and oviducts; furthermore, CRH and corticosterone (CORT) impacted preimplantation embryos indirectly by triggering the apoptosis of oviductal epithelial cells (OECs) through activation of the Fas system. However, it remains unclear whether TNF-α signaling is involved in CRH- and/or glucocorticoid-induced apoptosis of OECs. In the present study, it was shown that culture with either CRH or CORT induced significant apoptosis of OECs. The culture of OECs with CRH augmented both FasL expression and TNF-α expression. However, culture with CORT increased FasL, but decreased TNF-α, expression significantly. Although knocking down/knocking out FasL expression in OECs significantly ameliorated the proapoptotic effects of both CRH and CORT, knocking down/knocking out TNF-α expression relieved only the proapoptotic effect of CRH but not that of CORT. Taken together, our results demonstrated that CRH-induced OEC apoptosis involved both Fas signaling and TNF-α signaling. Conversely, CORT-induced OEC apoptosis involved only the Fas, but not the TNF-α, signaling pathway. The data obtained are crucial for our understanding of the mechanisms by which various categories of stress imposed on pregnant females impair embryo development, as well as for the development of measures to protect the embryo from the adverse effects of stress.


Assuntos
Apoptose/efeitos dos fármacos , Corticosterona/farmacologia , Células Epiteliais/efeitos dos fármacos , Oviductos/efeitos dos fármacos , Animais , Células Cultivadas , Células Epiteliais/fisiologia , Feminino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Endogâmicos ICR , Camundongos Knockout , Oviductos/citologia , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/genética , Fator de Necrose Tumoral alfa/genética
15.
Nucleic Acids Res ; 47(4): 1774-1785, 2019 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-30566668

RESUMO

CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides. Methylation of the CpG and CpA sites generates a DNA element with every pyrimidine having a methyl group in the 5-carbon position (thymine or 5-methylcytosine (5mC)). To understand the effects of both CpG and CpA modification on a centrally-important transcription factor, we show that C/EBPß binds the methylated 8-bp element with modestly-increased (2.4-fold) binding affinity relative to the unmodified cognate sequence, while cytosine hydroxymethylation (particularly at the CpA sites) substantially decreased binding affinity (36-fold). The structure of C/EBPß DNA binding domain in complex with methylated DNA revealed that the methyl groups of the 5mCpA/TpG make van der Waals contacts with Val285 in C/EBPß. Arg289 recognizes the central 5mCpG by forming a methyl-Arg-G triad, and its conformation is constrained by Val285 and the 5mCpG methyl group. We substituted Val285 with Ala (V285A) in an Ala-Val dipeptide, to mimic the conserved Ala-Ala in many members of the basic leucine-zipper family of transcription factors, important in gene regulation, cell proliferation and oncogenesis. The V285A variant demonstrated a 90-fold binding preference for methylated DNA (particularly 5mCpA methylation) over the unmodified sequence. The smaller side chain of Ala285 permits Arg289 to adopt two alternative conformations, to interact in a similar fashion with either the central 5mCpG or the TpG of the opposite strand. Significantly, the best-studied cis-regulatory elements in RNA polymerase II promoters and enhancers have variable sequences corresponding to the central CpG or reduced to a single G:C base pair, but retain a conserved outer CpA sequence. Our analyses suggest an important modification-dependent CpA recognition by basic leucine-zipper transcription factors.


Assuntos
Proteína beta Intensificadora de Ligação a CCAAT/química , Metilação de DNA/genética , Proteínas de Ligação a DNA/química , DNA/genética , 5-Metilcitosina/metabolismo , Proteína beta Intensificadora de Ligação a CCAAT/genética , Sequência Conservada/genética , Ilhas de CpG/genética , Cristalografia por Raios X , Citosina/metabolismo , Proteínas de Ligação a DNA/genética , Elementos E-Box/genética , Regulação da Expressão Gênica , Regiões Promotoras Genéticas , Conformação Proteica , Timina/metabolismo , Fator de Transcrição AP-1/química , Fator de Transcrição AP-1/genética
16.
Nucleic Acids Res ; 47(16): 8388-8398, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31226215

RESUMO

ZBTB24, encoding a protein of the ZBTB family of transcriptional regulators, is one of four known genes-the other three being DNMT3B, CDCA7 and HELLS-that are mutated in immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome, a genetic disorder characterized by DNA hypomethylation and antibody deficiency. The molecular mechanisms by which ZBTB24 regulates gene expression and the biological functions of ZBTB24 are poorly understood. Here, we identified a 12-bp consensus sequence [CT(G/T)CCAGGACCT] occupied by ZBTB24 in the mouse genome. The sequence is present at multiple loci, including the Cdca7 promoter region, and ZBTB24 binding is mostly associated with gene activation. Crystallography and DNA-binding data revealed that the last four of the eight zinc fingers (ZFs) (i.e. ZF5-8) in ZBTB24 confer specificity of DNA binding. Two ICF missense mutations have been identified in the ZBTB24 ZF domain, which alter zinc-binding cysteine residues. We demonstrated that the corresponding C382Y and C407G mutations in mouse ZBTB24 abolish specific DNA binding and fail to induce Cdca7 expression. Our analyses indicate and suggest a structural basis for the sequence specific recognition by a transcription factor centrally important for the pathogenesis of ICF syndrome.


Assuntos
Proteínas de Ciclo Celular/genética , Face/anormalidades , Genoma , Mutação de Sentido Incorreto , Proteínas Nucleares/genética , Doenças da Imunodeficiência Primária/genética , Proteínas Repressoras/química , Fatores de Transcrição/química , Dedos de Zinco/genética , Animais , Sítios de Ligação , Proteínas de Ciclo Celular/metabolismo , Clonagem Molecular , Escherichia coli/genética , Escherichia coli/metabolismo , Face/patologia , Expressão Gênica , Loci Gênicos , Vetores Genéticos , Humanos , Camundongos , Modelos Moleculares , Proteínas Nucleares/metabolismo , Motivos de Nucleotídeos , Doenças da Imunodeficiência Primária/metabolismo , Doenças da Imunodeficiência Primária/patologia , Regiões Promotoras Genéticas , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
17.
J Biol Chem ; 294(48): 18181-18191, 2019 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-31636125

RESUMO

Chromatin remodelers use helicase-like ATPase domains to reorganize histone-DNA contacts within the nucleosome. Like other remodelers, the chromodomain helicase DNA-binding protein 1 (Chd1) remodeler repositions nucleosomes by altering DNA topology at its internal binding site on the nucleosome, coupling different degrees of DNA twist and DNA movement to distinct nucleotide-bound states of the ATPase motor. In this work, we used a competition assay to study how variations in the bound nucleotide, Chd1, and the nucleosome substrate affect stability of Chd1-nucleosome complexes. We found that Chd1-nucleosome complexes formed in nucleotide-free or ADP conditions were relatively unstable and dissociated within 30 s, whereas those with the nonhydrolyzable ATP analog AMP-PNP had a mean lifetime of 4.8 ± 0.7 min. Chd1-nucleosome complexes were remarkably stable with ADP·BeF3- and the transition state analogs ADP·AlFX and ADP·MgFX, being resistant to competitor nucleosome over a 24-h period. For the tight ADP·BeF3--stabilized complex, Mg2+ was a critical component that did not freely exchange, and formation of these long-lived complexes had a slow, concentration-dependent step. The ADP·BeF3--stabilized complex did not require the Chd1 DNA-binding domain nor the histone H4 tail and appeared relatively insensitive to sequence differences on either side of the Widom 601 sequence. Interestingly, the complex remained stable in ADP·BeF3- even when nucleosomes contained single-stranded gaps that disrupted most DNA contacts with the guide strand. This finding suggests that binding via the tracking strand alone is sufficient for stabilizing the complex in a hydrolysis-competent state.


Assuntos
Difosfato de Adenosina/química , DNA Fúngico/química , Proteínas de Ligação a DNA/química , Fluoretos/química , Nucleossomos/química , Proteínas de Saccharomyces cerevisiae/química , Saccharomyces cerevisiae/química , Difosfato de Adenosina/genética , Difosfato de Adenosina/metabolismo , DNA Fúngico/genética , DNA Fúngico/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Magnésio/química , Nucleossomos/genética , Nucleossomos/metabolismo , Domínios Proteicos , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
18.
Anal Bioanal Chem ; 412(1): 203-222, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31802178

RESUMO

This study examines an improved and simplified method for solid-phase extraction (SPE), which offers rapid and accurate determination and identification of 44 pharmaceutically active compounds using ultra-performance liquid chromatography (UPLC) and tandem mass spectrometry (MS/MS). The common active compounds include four macrolides, seventeen sulfonamides, four quinolones, chloramphenicol, eight ß-lactams, four tetracyclines, lincomycin, amantadine, 4-acetamidophenol, phenylbutazone, trimethoprim, clenbuterol, and hydrocortisone in water samples. We optimized crucial parameters of MS/MS, UPLC, and SPE and studied the matrix effect related to the modified analytical process from water samples. The matrix-matched calibration curves were accomplished at seven concentration levels and a satisfactory linear relationship (r2 > 0.994) was observed within the range of 0.1-500 ng/mL. Results show varying limits of detection (0.0111-0.966 ng/L for different analytes based on signal-to-noise (S/N) = 3) and limits of quantitation (0.0382-3.26 ng/L). Recoveries of the spiked samples ranged from 75.7 to 108% with relative standard deviation lower than 9.6%. The proposed method was successfully applied to the analysis of real samples.


Assuntos
Cromatografia Líquida/métodos , Preparações Farmacêuticas/análise , Extração em Fase Sólida/métodos , Espectrometria de Massas em Tandem/métodos , Poluentes Químicos da Água/análise , Limite de Detecção , Preparações Farmacêuticas/normas , Padrões de Referência , Reprodutibilidade dos Testes
19.
Nucleic Acids Res ; 46(10): 4978-4990, 2018 06 01.
Artigo em Inglês | MEDLINE | ID: mdl-29850894

RESUMO

Chromatin remodelers are ATP-dependent motors that reorganize DNA packaging by disrupting canonical histone-DNA contacts within the nucleosome. Here, we show that the Chd1 chromatin remodeler stimulates DNA unwrapping from the edge of the nucleosome in a nucleotide-dependent and DNA sequence-sensitive fashion. Nucleosome binding, monitored by stopped flow, was complex and sensitive to nucleotide, with AMP-PNP promoting faster binding than ADP·BeF3-. Nucleosome unwrapping by Chd1, examined by bulk FRET, occurred in the presence and absence of nucleotide and did not require the Chd1 DNA-binding domain. In AMP-PNP conditions, Chd1 unwrapped one side of the Widom 601 DNA more easily than the other, consistent with previous observations of 601 asymmetry and indicating that Chd1 amplifies intrinsic sequence properties of nucleosomal DNA. Using small angle X-ray scattering (SAXS) with contrast variation, we found distinct DNA conformations depending on the nucleotide analog bound to Chd1: with AMP-PNP, DNA primarily unwrapped in-plane with the nucleosomal disk, whereas with ADP·BeF3-, a significant fraction showed distinctive out-of-plane unwrapping as well. Taken together, our findings show tight coupling between entry/exit DNA of the nucleosome and the Chd1 ATPase motor, suggesting that dynamic nucleosome unwrapping is coupled to nucleosome binding and remodeling by Chd1.


Assuntos
Montagem e Desmontagem da Cromatina/fisiologia , DNA Fúngico/metabolismo , Proteínas de Ligação a DNA/metabolismo , Nucleossomos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Ligação a DNA/genética , Transferência Ressonante de Energia de Fluorescência , Nucleossomos/química , Nucleossomos/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Espalhamento a Baixo Ângulo , Difração de Raios X
20.
Plant Cell ; 27(12): 3367-82, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26672070

RESUMO

Cell division requires proper spindle assembly; a surveillance pathway, the spindle assembly checkpoint (SAC), monitors whether the spindle is normal and correctly attached to kinetochores. The SAC proteins regulate mitotic chromosome segregation by affecting CDC20 (Cell Division Cycle 20) function. However, it is unclear whether CDC20 regulates meiotic spindle assembly and proper homolog segregation. Here, we show that the Arabidopsis thaliana CDC20.1 gene is indispensable for meiosis and male fertility. We demonstrate that cdc20.1 meiotic chromosomes align asynchronously and segregate unequally and the metaphase I spindle has aberrant morphology. Comparison of the distribution of meiotic stages at different time points between the wild type and cdc20.1 reveals a delay of meiotic progression from diakinesis to anaphase I. Furthermore, cdc20.1 meiocytes exhibit an abnormal distribution of a histone H3 phosphorylation mark mediated by the Aurora kinase, providing evidence that CDC20.1 regulates Aurora localization for meiotic chromosome segregation. Further evidence that CDC20.1 and Aurora are functionally related was provided by meiosis-specific knockdown of At-Aurora1 expression, resulting in meiotic chromosome segregation defects similar to those of cdc20.1. Taken together, these results suggest a critical role for CDC20.1 in SAC-dependent meiotic chromosome segregation.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Proteínas Cdc20/genética , Pontos de Checagem do Ciclo Celular , Segregação de Cromossomos , Meiose , Anáfase , Ciclossomo-Complexo Promotor de Anáfase/genética , Ciclossomo-Complexo Promotor de Anáfase/metabolismo , Arabidopsis/citologia , Arabidopsis/fisiologia , Proteínas de Arabidopsis/metabolismo , Proteínas Cdc20/metabolismo , Técnicas de Silenciamento de Genes , Cinetocoros/metabolismo , Metáfase , Infertilidade das Plantas , Fuso Acromático/metabolismo
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