scholarly journals DNA Binding Site Selection of Dimeric and Tetrameric Stat5 Proteins Reveals a Large Repertoire of Divergent Tetrameric Stat5a Binding Sites

2000 ◽  
Vol 20 (1) ◽  
pp. 389-401 ◽  
Author(s):  
Elisabetta Soldaini ◽  
Susan John ◽  
Stefano Moro ◽  
Julie Bollenbacher ◽  
Ulrike Schindler ◽  
...  

ABSTRACT We have defined the optimal binding sites for Stat5a and Stat5b homodimers and found that they share similar core TTC(T/C)N(G/A)GAA interferon gamma-activated sequence (GAS) motifs. Stat5a tetramers can bind to tandemly linked GAS motifs, but the binding site selection revealed that tetrameric binding also can be seen with a wide range of nonconsensus motifs, which in many cases did not allow Stat5a binding as a dimer. This indicates a greater degree of flexibility in the DNA sequences that allow binding of Stat5a tetramers than dimers. Indeed, in an oligonucleotide that could bind both dimers and tetramers, it was possible to design mutants that affected dimer binding without affecting tetramer binding. A spacing of 6 bp between the GAS sites was most frequently selected, demonstrating that this distance is favorable for Stat5a tetramer binding. These data provide insights into tetramer formation by Stat5a and indicate that the repertoire of potential binding sites for this transcription factor is broader than expected.

1994 ◽  
Vol 14 (9) ◽  
pp. 5986-5996
Author(s):  
S P Hunger ◽  
R Brown ◽  
M L Cleary

The t(17;19) translocation in acute lymphoblastic leukemias results in creation of E2A-hepatic leukemia factor (HLF) chimeric proteins that contain the DNA-binding and protein dimerization domains of the basic leucine zipper (bZIP) protein HLF fused to a portion of E2A proteins with transcriptional activation properties. An in vitro binding site selection procedure was used to determine DNA sequences preferentially bound by wild-type HLF and chimeric E2A-HLF proteins isolated from various t(17;19)-bearing leukemias. All were found to selectively bind the consensus sequence 5'-GTTACGTAAT-3' with high affinity. Wild-type and chimeric HLF proteins also bound closely related sites identified previously for bZIP proteins of both the proline- and acidic amino acid-rich (PAR) and C/EBP subfamilies; however, E2A-HLF proteins were significantly less tolerant of certain deviations from the HLF consensus binding site. These differences were directly attributable to loss of an HLF ancillary DNA-binding domain in all E2A-HLF chimeras and were further exacerbated by a zipper mutation in one isolate. Both wild-type and chimeric HLF proteins displayed transcriptional activator properties in lymphoid and nonlymphoid cells on reporter genes containing HLF or C/EBP consensus binding sites. But on reporter genes with nonoptimal binding sites, their transcriptional properties diverged and E2A-HLF competitively inhibited activation by wild-type PAR proteins. These findings establish a spectrum of binding site-specific transcriptional properties for E2A-HLF which may preferentially activate expression of select subordinate genes as a homodimer and potentially antagonize expression of others through heteromeric interactions.


2015 ◽  
Author(s):  
Javier Estrada ◽  
Teresa Ruiz-Herrero ◽  
Clarissa Scholes ◽  
Zeba Wunderlich ◽  
Angela DePace

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/


1994 ◽  
Vol 14 (9) ◽  
pp. 5986-5996 ◽  
Author(s):  
S P Hunger ◽  
R Brown ◽  
M L Cleary

The t(17;19) translocation in acute lymphoblastic leukemias results in creation of E2A-hepatic leukemia factor (HLF) chimeric proteins that contain the DNA-binding and protein dimerization domains of the basic leucine zipper (bZIP) protein HLF fused to a portion of E2A proteins with transcriptional activation properties. An in vitro binding site selection procedure was used to determine DNA sequences preferentially bound by wild-type HLF and chimeric E2A-HLF proteins isolated from various t(17;19)-bearing leukemias. All were found to selectively bind the consensus sequence 5'-GTTACGTAAT-3' with high affinity. Wild-type and chimeric HLF proteins also bound closely related sites identified previously for bZIP proteins of both the proline- and acidic amino acid-rich (PAR) and C/EBP subfamilies; however, E2A-HLF proteins were significantly less tolerant of certain deviations from the HLF consensus binding site. These differences were directly attributable to loss of an HLF ancillary DNA-binding domain in all E2A-HLF chimeras and were further exacerbated by a zipper mutation in one isolate. Both wild-type and chimeric HLF proteins displayed transcriptional activator properties in lymphoid and nonlymphoid cells on reporter genes containing HLF or C/EBP consensus binding sites. But on reporter genes with nonoptimal binding sites, their transcriptional properties diverged and E2A-HLF competitively inhibited activation by wild-type PAR proteins. These findings establish a spectrum of binding site-specific transcriptional properties for E2A-HLF which may preferentially activate expression of select subordinate genes as a homodimer and potentially antagonize expression of others through heteromeric interactions.


2020 ◽  
Vol 8 ◽  
Author(s):  
Chinmayee Choudhury ◽  
Anshu Bhardwaj

Antimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200 ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 1,563,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.


2020 ◽  
Vol 95 (1) ◽  
Author(s):  
Tetyana Lukash ◽  
Tatiana Agback ◽  
Francisco Dominguez ◽  
Nikita Shiliaev ◽  
Chetan Meshram ◽  
...  

ABSTRACT Decades of insufficient control have resulted in unprecedented spread of chikungunya virus (CHIKV) around the globe, and millions have suffered from the highly debilitating disease. Nevertheless, the current understanding of CHIKV-host interactions and adaptability of the virus to replication in mosquitoes and mammalian hosts is still elusive. Our new study shows that four-and-a-half LIM domain protein (FHL1) is one of the host factors that interact with the hypervariable domain (HVD) of CHIKV nsP3. Unlike G3BPs, FHL1 is not a prerequisite of CHIKV replication, and many commonly used cell lines do not express FHL1. However, its expression has a detectable stimulatory effect(s) on CHIKV replication, and Fhl1 knockout (KO) cell lines demonstrate slower infection spread. Nuclear magnetic resonance (NMR)-based studies revealed that the binding site of FHL1 in CHIKV nsP3 HVD overlaps that of another proviral host factor, CD2AP. The structural data also demonstrated that FHL1-HVD interaction is mostly determined by the LIM1 domain of FHL1. However, it does not mirror binding of the entire protein, suggesting that other LIM domains are involved. In agreement with previously published data, our biological experiments showed that interactions of CHIKV HVD with CD2AP and FHL1 have additive effects on the efficiency of CHIKV replication. This study shows that CHIKV mutants with extensive modifications of FHL1- or both FHL1- and CD2AP-binding sites remain viable and develop spreading infection in multiple cell types. Our study also demonstrated that other members of the FHL family can bind to CHIKV HVD and thus may be involved in viral replication. IMPORTANCE Replication of chikungunya virus (CHIKV) is determined by a wide range of host factors. Previously, we have demonstrated that the hypervariable domain (HVD) of CHIKV nsP3 contains linear motifs that recruit defined families of host proteins into formation of functional viral replication complexes. Now, using NMR-based structural and biological approaches, we have characterized the binding site of the cellular FHL1 protein in CHIKV HVD and defined the biological significance of this interaction. In contrast to previously described binding of G3BP to CHIKV HVD, the FHL1-HVD interaction was found to not be a prerequisite of viral replication. However, the presence of FHL1 has a stimulatory effect on CHIKV infectivity and, subsequently, the infection spread. FHL1 and CD2AP proteins were found to have overlapping binding sites in CHIKV HVD and additive proviral functions. Elimination of the FHL1-binding site in the nsP3 HVD can be used for the development of stable, attenuated vaccine candidates.


2021 ◽  
Author(s):  
Chen Chen ◽  
Jie Hou ◽  
Xiaowen Shi ◽  
Hua Yang ◽  
James A. Birchler ◽  
...  

Abstract BackgroundDue to the complexity of the biological systems, the prediction of the potential DNA binding sites for transcription factors remains a difficult problem in computational biology. Genomic DNA sequences and experimental results from parallel sequencing provide available information about the affinity and accessibility of genome and are commonly used features in binding sites prediction. The attention mechanism in deep learning has shown its capability to learn long-range dependencies from sequential data, such as sentences and voices. Until now, no study has applied this approach in binding site inference from massively parallel sequencing data. The successful applications of attention mechanism in similar input contexts motivate us to build and test new methods that can accurately determine the binding sites of transcription factors.ResultsIn this study, we propose a novel tool (named DeepGRN) for transcription factors binding site prediction based on the combination of two components: single attention module and pairwise attention module. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets. The results show that DeepGRN achieves higher unified scores in 6 of 13 targets than any of the top four methods in the DREAM challenge. We also demonstrate that the attention weights learned by the model are correlated with potential informative inputs, such as DNase-Seq coverage and motifs, which provide possible explanations for the predictive improvements in DeepGRN.ConclusionsDeepGRN can automatically and effectively predict transcription factor binding sites from DNA sequences and DNase-Seq coverage. Furthermore, the visualization techniques we developed for the attention modules help to interpret how critical patterns from different types of input features are recognized by our model.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3811-3811 ◽  
Author(s):  
Amanda J Favreau ◽  
Fariba Shaffiey ◽  
Erin Cross ◽  
Pradeep Sathyanarayana

Abstract The recent discovery of new molecular lesions with prognostic significance in acute myeloid leukemia (AML) is enhancing our understanding of leukemia biology and our ability to identify new therapeutic targets. Previously, using the unique leukemic myeloid progenitor line AML-193, we profiled IL-3-, GM-CSF-, and G-CSF-regulated miRNA signatures. 301 miRNAs were commonly regulated by these three cytokines, and the most highly induced miRNA was miR-590-5p. Herein, we have attempted to define the functional role and clinical relevance of miR-590 in AML. We first examined the relative miR-590 expression in steady state hematopoiesis and showed it was highest at CD34+ and declined its expression through myeloid lineage differentiation (ANOVA, p<0.0001). To functionally determine the role of increased miR-590 expression, we generated a gain-of-function model in human CD34+ hematopoietic stem cells (HSC) via lentivirus transduction. Increased expression of miR-590 in CD34+ cells resulted in significant increases in CFU-GM colonies, strongly suggesting that dysregulation of miR-590 expression may be myeloproliferative. In AML (n=33) and control (n=9) bone marrow samples, miR-590 expression was determined via RT-qPCR. miR-590-5p expression was highly upregulated in 22 of the samples (67%) compared to control subjects. In silico analysis of the miR-590-5p promoter revealed three potential binding sites for STAT5 (-249, -749, -1499). To functionally determine whether STAT5 directly regulates miR-590-5p expression, we performed a ChIP assay, which showed that STAT5 binds to the -749 region of miR-590-5p promoter. To conclusively determine the STAT5 binding sites, we cloned the miR-590 promoter in a luciferase vector and performed site directed mutagenesis for each potential binding site. This assay confirmed that the -749 binding site was the major STAT5 regulatory site for miR-590 (p<0.002). Importantly, constitutive activation of STAT5 is a hallmark of AML associated with FLT3 mutations, therefore, we set out to determine if specific STAT5 and FLT3 inhibitors could decrease miR-590 expression. We pretreated MV4-11 cells, which harbors the FLT-ITD mutation and has increased STAT5 activation, with 100uM STAT5 inhibitor (N′-((4-Oxo-4H-chromen-3-yl)methylene)nicotinohydrazide) for 90 minutes or 100nM FLT3 inhibitor (EMD Millipore, 343020) for 12 hours, both of which resulted in significant inhibition of miR-590-5p expression (p<0.05). To evaluate whether the AML samples with high miR-590 expression also possess elevated phospho-STAT5 or phospho-FLT3 levels, we performed immunohistochemistry analysis on a custom-made tissue microarray. In AML samples with high miR-590 levels, increased activation of FLT3 and STAT5 was observed compared to controls. Since FLT3 mutations result in decreased survival and poorer prognosis in AML, it may be that miR-590-5p plays an important role in the pathology of AML associated with dysregulated FLT3 and STAT5. To understand the complete functional role of miR-590 in AML, the predicted targets need to be identified and validated for their roles in leukemogenesis. Upon molecular screening of several predicted targets, FasL was experimentally found to be a conserved target of miR-590. More specifically, 3’UTR analysis of FasL revealed three potential seed sequences for miR-590 which have been verified experimentally via luciferase assay. Furthermore, significantly increased levels of FasL protein and transcript expression was detected in the MV4-11 cells stably expressing anti-miR-590 compared to control cells. Additionally, we identified the levels of Fas/CD95 (FasL receptor) on AML-193 and MV4-11 cell lines and found these cells had high Fas/CD95 expression on the cell surface as analyzed via flow cytometry. In order to determine the physiological significance of Fas/FasL, these cells were treated with soluble FasL (100ng) for 24 hours and apoptosis was analyzed via Annexin V staining. FasL treatment induced increased apoptosis compared to the untreated cells. Taken together, we have identified miR-590 as a candidate oncomiR that is regulated via the STAT5 pathway and targets FasL to promote cell survival. Thus, our data suggests that further understanding of miR-590’s role in AML may lead to development of novel anti-miR-590 therapeutic strategies in AML associated with dysregulated STAT5. Disclosures: No relevant conflicts of interest to declare.


Sign in / Sign up

Export Citation Format

Share Document