RUNX1 regulates site specificity of DNA demethylation by recruitment of DNA demethylation machineries in hematopoietic cells

Key PointsEctopic expression of RUNX1 induces binding site–directed DNA demethylation, in which hematopoietic gene promoters are included. RUNX1 binding sites are enriched in demethylated regions during hematopoietic development.

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An Empirical Prior Improves Accuracy for Bayesian Estimation of Transcription Factor Binding Site Frequencies within Gene Promoters

Bioinformatics and Biology Insights ◽

10.4137/bbi.s29330 ◽

2015 ◽

Vol 9S4 ◽

pp. BBI.S29330

Author(s):

Stephen A. Ramsey

Keyword(s):

Transcription Factor ◽

Binding Site ◽

Transcription Factor Binding Site ◽

Binding Sites ◽

Transcription Factor Binding ◽

Regulatory Sequences ◽

Gene Promoters ◽

Sequence Pattern ◽

Factor Binding Site ◽

Factor Binding

A Bayesian method for sampling from the distribution of matches to a precompiled transcription factor binding site (TFBS) sequence pattern (conditioned on an observed nucleotide sequence and the sequence pattern) is described. The method takes a position frequency matrix as input for a set of representative binding sites for a transcription factor and two sets of noncoding, 5’ regulatory sequences for gene sets that are to be compared. An empirical prior on the frequency A (per base pair of gene-vicinal, noncoding DNA) of TFBSs is developed using data from the ENCODE project and incorporated into the method. In addition, a probabilistic model for binding site occurrences conditioned on λ is developed analytically, taking into account the finite-width effects of binding sites. The count of TFBS β (conditioned on the observed sequence) is sampled using Metropolis-Hastings with an information entropybased move generator. The derivation of the method is presented in a step-by-step fashion, starting from specific conditional independence assumptions. Empirical results show that the newly proposed prior on β improves accuracy for estimating the number of TFBS within a set of promoter sequences.

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Ectopic expression of Delta4 impairs hematopoietic development and leads to lymphoproliferative disease

Blood ◽

10.1182/blood.v100.6.2046 ◽

2002 ◽

Vol 100 (6) ◽

pp. 2046-2055 ◽

Cited By ~ 46

Author(s):

Marion Dorsch ◽

Gang Zheng ◽

David Yowe ◽

Prakash Rao ◽

Yanjun Wang ◽

...

Keyword(s):

B Cells ◽

Critical Role ◽

Ectopic Expression ◽

Hematopoietic Cells ◽

Lymphoproliferative Disease ◽

Rapid Expansion ◽

Soluble Form ◽

Hematopoietic Stem ◽

Hematopoietic Development ◽

Cd8 Cells

Abstract Notch signaling plays a critical role in cell fate determination in many developmental systems, including the hematopoietic system. We and others have recently cloned a novel Notch ligand called Delta4. In this study, we show the effect of retrovirus-mediated ectopic expression of Delta4 in hematopoietic cells. Lethally irradiated mice transplanted with bone marrow cells expressing Delta4 initially suffered from leukopenia and thrombocytopenia. Although all lineages were affected, the deficit in B cells and platelets was the most durable and profound. A rapid expansion of CD4+CD8+ cells occurred shortly after transplantation. CD4+CD8+ cells progressively invaded all tissues analyzed except the thymus, which surprisingly was atrophic. CD4+CD8+cells were mainly non–Delta4-transduced cells, strongly suggesting that the disease was not cell autonomous. Around 15 weeks after transplantation, mice died from this severe lymphoproliferative disorder, which was not transplantable in late-stage disease into secondary recipients. Mice transduced with a soluble form of Delta4 behaved like control mice. Characterization of early hematopoietic development revealed that Delta4 expression impaired formation of day-12 spleen colony-forming units (CFU-Ss) and, to a greater extent, pre–CFU-Ss. No effect was observed on myeloid colony-forming cells (CFU-Cs), indicating that Delta4 specifically acted on the earliest hematopoietic stem cell compartment. These results show that constitutive expression of Delta4 in hematopoietic cells impairs the development of B cells, platelets, and early stem cells and induces a lethal lymphoproliferative disease.

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DNA binding site specificity of the Neurospora global nitrogen regulatory protein NIT2: Analysis with mutated binding sites

MGG Molecular & General Genetics ◽

10.1007/bf00302264 ◽

1994 ◽

Vol 245 (4) ◽

pp. 512-516 ◽

Cited By ~ 13

Author(s):

Tso-Yu Chiang ◽

Rajendra Rai ◽

Terrance G. Cooper ◽

George A. Marzluf

Keyword(s):

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Regulatory Protein ◽

Site Specificity ◽

Dna Binding Site

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Uterine binding sites for LH/hCG can be modulated by hormonal status in rabbits and rats

Acta Endocrinologica ◽

10.1530/acta.0.1240322 ◽

1991 ◽

Vol 124 (3) ◽

pp. 322-330 ◽

Cited By ~ 11

Author(s):

Arleen L. Sawitzke ◽

William D. Odell

Keyword(s):

Binding Site ◽

Binding Sites ◽

Hormonal Status ◽

Site Specificity ◽

Estrus Cycle ◽

Uterine Tissue ◽

High Affinity ◽

Site Number ◽

Serum Lh ◽

Specific Manner

Abstract. High-affinity LH/hCG binding sites have been identified in both porcine and rabbit uteri. We have now identified these binding sites in rat uteri. We have assessed the binding site specificity and modulation and have searched for binding sites for a related glycoprotein. Radioreceptor assays were performed with membrane homogenates of uterine tissue, and were analysed for binding site specificity, affinity, and capacity. The rabbit and rat LH/hCG binding sites did not bind human TSH or human FSH. Rabbit uterine tissue contained no binding sites for FSH, as determined with 125I-labelled FSH and unlabelled FSH. Pretreatment of rabbits with hCG decreased their uterine binding site capacity from 1.30±0.29 to 0.46±0.01 fmol/mg protein. Pretreatment of castrated rabbits with estrogen or estrogen combined with progesterone did not alter the binding site affinity or capacity. In rats, the uterine binding site number was shown to vary inversely with the serum LH concentration and directly with the ovarian LH/hCG bindig site number during the estrus cycle. Hypophysectomy resulted in a significant increase in uterine binding site capacity in rats. Estrogen treatment prevented this hypophysectomy-induced increase. The function of these LH/hCG binding sites remains uncertain; however, the lack of binding sites for a related glycoprotein and the modulation of these binding sites by hormonal factors strengthen the concept that uterine tissue might respond in a specific manner to direct LH/hCG stimulation.

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Ectopic expression of Delta4 impairs hematopoietic development and leads to lymphoproliferative disease

Blood ◽

10.1182/blood.v100.6.2046.h81802002046_2046_2055 ◽

2002 ◽

Vol 100 (6) ◽

pp. 2046-2055 ◽

Cited By ~ 3

Author(s):

Marion Dorsch ◽

Gang Zheng ◽

David Yowe ◽

Prakash Rao ◽

Yanjun Wang ◽

...

Keyword(s):

B Cells ◽

Critical Role ◽

Ectopic Expression ◽

Hematopoietic Cells ◽

Lymphoproliferative Disease ◽

Rapid Expansion ◽

Soluble Form ◽

Hematopoietic Stem ◽

Hematopoietic Development ◽

Cd8 Cells

Notch signaling plays a critical role in cell fate determination in many developmental systems, including the hematopoietic system. We and others have recently cloned a novel Notch ligand called Delta4. In this study, we show the effect of retrovirus-mediated ectopic expression of Delta4 in hematopoietic cells. Lethally irradiated mice transplanted with bone marrow cells expressing Delta4 initially suffered from leukopenia and thrombocytopenia. Although all lineages were affected, the deficit in B cells and platelets was the most durable and profound. A rapid expansion of CD4+CD8+ cells occurred shortly after transplantation. CD4+CD8+ cells progressively invaded all tissues analyzed except the thymus, which surprisingly was atrophic. CD4+CD8+cells were mainly non–Delta4-transduced cells, strongly suggesting that the disease was not cell autonomous. Around 15 weeks after transplantation, mice died from this severe lymphoproliferative disorder, which was not transplantable in late-stage disease into secondary recipients. Mice transduced with a soluble form of Delta4 behaved like control mice. Characterization of early hematopoietic development revealed that Delta4 expression impaired formation of day-12 spleen colony-forming units (CFU-Ss) and, to a greater extent, pre–CFU-Ss. No effect was observed on myeloid colony-forming cells (CFU-Cs), indicating that Delta4 specifically acted on the earliest hematopoietic stem cell compartment. These results show that constitutive expression of Delta4 in hematopoietic cells impairs the development of B cells, platelets, and early stem cells and induces a lethal lymphoproliferative disease.

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Covalent-Fragment Screening of Brd4 Identifies a Ligandable Site Orthogonal to the Acetyl-Lysine Binding Sites

10.26434/chemrxiv.8859098 ◽

2019 ◽

Author(s):

Michael Olp ◽

Daniel Sprague ◽

Stefan Kathman ◽

Ziyang Xu ◽

Alexandar Statsyuk ◽

...

Keyword(s):

Mass Spectrometry ◽

Binding Site ◽

Binding Sites ◽

Computational Prediction ◽

Chemical Probes ◽

Computational Docking ◽

Fragment Screening ◽

Covalent Inhibitors ◽

Bet Protein ◽

Proof Of Principle

<p>Brd4, a member of the bromodomain and extraterminal domain (BET) family, has emerged as a promising epigenetic target in cancer and inflammatory disorders. All reported BET family ligands bind within the bromodomain acetyl-lysine binding sites and competitively inhibit BET protein interaction with acetylated chromatin. Alternative chemical probes that act orthogonally to the highly-conserved acetyl-lysine binding sites may exhibit selectivity within the BET family and avoid recently reported toxicity in clinical trials of BET bromodomain inhibitors. Here, we report the first identification of a ligandable site on a bromodomain outside the acetyl-lysine binding site. Inspired by our computational prediction of hotspots adjacent to non-homologous cysteine residues within the <i>C</i>-terminal Brd4 bromodomain (Brd4-BD2), we performed a mid-throughput mass spectrometry screen to identify cysteine-reactive fragments that covalently and selectively modify Brd4. Subsequent mass spectrometry, NMR and computational docking analyses of electrophilic fragment hits revealed a novel ligandable site near Cys356 that is unique to Brd4 among all human bromodomains. This site is orthogonal to the Brd4-BD2 acetyl-lysine binding site as Cys356 modification did not impact binding of the pan-BET bromodomain inhibitor JQ1 in fluorescence polarization assays. Finally, we tethered covalent fragments to JQ1 and performed NanoBRET assays to provide proof of principle that this orthogonal site can be covalently targeted in intact human cells. Overall, we demonstrate the potential of targeting sites orthogonal to bromodomain acetyl-lysine binding sites to develop bivalent and covalent inhibitors that displace Brd4 from chromatin.</p>

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Effects of Multiple Binding Sites on Studies of Hydrogen Bonding between Nitroxide Radicals and Solvent Molecules

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19930047 ◽

1993 ◽

Vol 58 (1) ◽

pp. 47-52 ◽

Cited By ~ 2

Author(s):

Imad Al-Bala'a ◽

Richard D. Bates

Keyword(s):

Hydrogen Bonding ◽

Magnetic Resonance ◽

Binding Site ◽

Binding Sites ◽

Hyperfine Coupling Constant ◽

Hydrogen Donor ◽

Complex Formation Constants ◽

Multiple Binding Sites ◽

Multiple Binding ◽

Solvent Molecules

The role of more than one binding site on a nitroxide free radical in magnetic resonance determinations of the properties of the complex formed with a hydrogen donor is examined. The expression that relates observed hyperfine couplings in EPR spectra to complex formation constants and concentrations of each species in solution becomes much more complex when multiple binding sites are present, but reduces to a simpler form when binding at the two sites occurs independently and the binding at the non-nitroxide site does not produce significant differences in the hyperfine coupling constant in the complexed radical. Effects on studies of hydrogen bonding between multiple binding site nitroxides and hydrogen donor solvent molecules by other magnetic resonance methods are potentially more extreme.

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Tuning of Electronic Properties in Conducting Polymers

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc20011208 ◽

2001 ◽

Vol 66 (8) ◽

pp. 1208-1218 ◽

Cited By ~ 3

Author(s):

Guofeng Li ◽

Mira Josowicz ◽

Jiří Janata

Keyword(s):

Hydrogen Bonding ◽

Binding Site ◽

Binding Sites ◽

Polymer Chains ◽

Electronic Transitions ◽

Weakly Bound ◽

Ordered Structures ◽

Doped Polymer ◽

Positively Charged ◽

Repeated Cycling

Structural and electronic transitions in poly(thiophenyleneiminophenylene), usually referred to as poly(phenylenesulfidephenyleneamine) (PPSA) upon electrochemical doping with LiClO4 have been investigated. The unusual electrochemical behavior of PPSA indicates that the dopant anions are bound in two energetically different sites. In the so-called "binding site", the ClO4- anion is Coulombically attracted to the positively charged S or N sites on one chain and simultaneously hydrogen-bonded with the N-H group on a neighboring polymer chain. This strong interaction causes a re-organization of the polymer chains, resulting in the formation of a networked structure linked together by these ClO4- Coulombic/hydrogen bonding "bridges". However, in the "non-binding site", the ClO4- anion is very weakly bound, involves only the electrostatic interaction and can be reversibly exchanged when the doped polymer is reduced. In the repeated cycling, the continuous and alternating influx and expulsion of ClO4- ions serves as a self-organizing process for such networked structures, giving rise to a diminishing number of available "non-binding" sites. The occurrence of these ordered structures has a major impact on the electrochemical activity and the morphology of the doped polymer. Also due to stabilization of the dopant ions, the doped polymer can be kept in a stable and desirable oxidation state, thus both work function and conductivity of the polymer can be electrochemically controlled.

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Genes encoding components of the olfactory signal transduction cascade contain a DNA binding site that may direct neuronal expression.

Molecular and Cellular Biology ◽

10.1128/mcb.13.9.5805 ◽

1993 ◽

Vol 13 (9) ◽

pp. 5805-5813 ◽

Cited By ~ 52

Author(s):

M M Wang ◽

R Y Tsai ◽

K A Schrader ◽

R R Reed

Keyword(s):

Signal Transduction ◽

Dna Binding ◽

Binding Site ◽

Binding Sites ◽

Consensus Sequence ◽

Initiation Site ◽

Olfactory Neuron ◽

Promoter Regions ◽

Transcriptional Initiation ◽

Genes Encoding

Genes which mediate odorant signal transduction are expressed at high levels in neurons of the olfactory epithelium. The molecular mechanism governing the restricted expression of these genes likely involves tissue-specific DNA binding proteins which coordinately activate transcription through sequence-specific interactions with olfactory promoter regions. We have identified binding sites for the olfactory neuron-specific transcription factor, Olf-1, in the sequences surrounding the transcriptional initiation site of five olfactory neuron-specific genes. The Olf-1 binding sites described define the consensus sequence YTCCCYRGGGAR. In addition, we have identified a second binding site, the U site, in the olfactory cyclic nucleotide gated channel and type III cyclase promoters, which binds factors present in all tissue examined. These experiments support a model in which expression of Olf-1 in the sensory neurons coordinately activates a set of olfactory neuron-specific genes. Furthermore, expression of a subset of these genes may be modulated by additional binding factors.

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Study of Endogen Substrates, Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Molecules ◽

10.3390/molecules26041051 ◽

2021 ◽

Vol 26 (4) ◽

pp. 1051

Author(s):

Edgardo Becerra ◽

Giovanny Aguilera-Durán ◽

Laura Berumen ◽

Antonio Romo-Mancillas ◽

Guadalupe García-Alcocer

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Binding Energy ◽

Binding Site ◽

Binding Sites ◽

Adenosine Monophosphate ◽

Competitive Inhibitor ◽

Umbrella Sampling ◽

Coarse Grained ◽

Nucleotide Polymorphisms

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.

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