An improved SELEX-Seq strategy for characterizing DNA-binding specificity of transcription factor: NF-κB as an example

Therapeutic Interventions into Innate Immune Diseases by Means of Aptamers

The immune system plays a crucial role in the body's defense system against various pathogens, such as bacteria, viruses, and parasites, as well as recognizes non-self- and self-molecules. The innate immune system is composed of special receptors known as pattern recognition receptors, which play a crucial role in the identification of pathogen-associated molecular patterns from diverse microorganisms. Any disequilibrium in the activation of a particular pattern recognition receptor leads to various inflammatory, autoimmune, or immunodeficiency diseases. Aptamers are short single-stranded deoxyribonucleic acid or ribonucleic acid molecules, also termed "chemical antibodies," which have tremendous specificity and affinity for their target molecules. Their features, such as stability, low immunogenicity, ease of manufacturing, and facile screening against a target, make them preferable as therapeutics. Immune-system-targeting aptamers have a great potential as a targeted therapeutic strategy against immune diseases. This review summarizes components of the innate immune system, aptamer production, pharmacokinetic characteristics of aptamers, and aptamers related to innate-immune-system diseases.

Increased vaccine tolerability and protection via NF-κB modulation

Improving adjuvant responses is a promising pathway to develop vaccines against some pathogens (e.g., HIV or dengue). One challenge in adjuvant development is modulating the inflammatory response, which can cause excess side effects, while maintaining immune activation and protection. No approved adjuvants yet have the capability to independently modulate inflammation and protection. Here, we demonstrate a method to limit inflammation while retaining and often increasing the protective responses. To accomplish this goal, we combined a partial selective nuclear factor kappa B (NF-kB) inhibitor with several current adjuvants. The resulting vaccines reduce systemic inflammation and boost protective responses. In an influenza challenge model, we demonstrate that this approach enhances protection. This method was tested across a broad range of adjuvants and antigens. We anticipate these studies will lead to an alternative approach to vaccine formulation design that may prove broadly applicable to a wide range of adjuvants and vaccines.

A Krüppel-like factor 1 (KLF1) Mutation Associated with Severe Congenital Dyserythropoietic Anemia Alters Its DNA-Binding Specificity

Krüppel-like factor 1 (KLF1/EKLF) is a transcription factor that globally activates genes involved in erythroid cell development. Various mutations are identified in the human KLF1 gene. The E325K mutation causes congenital dyserythropoietic anemia (CDA) type IV, characterized by severe anemia and non-erythroid-cell-related symptoms. The CDA mutation is in the second zinc finger of KLF1 at a position functionally involved in its interactions with DNA. The molecular parameters of how CDA-KLF1 exerts its biological effects have not been addressed. Here, using an in vitro selection strategy, we determined the preferred DNA-binding site for CDA-KLF1. Binding to the deduced consensus sequence is supported by in vitro gel shifts and by in vivo functional reporter gene studies. Two significant changes compared to wild-type (WT) binding are observed: G is selected as the middle nucleotide, and the 3' portion of the consensus sequence is more degenerate. As a consequence, CDA-KLF1 did not bind the WT consensus sequence. However, activation of ectopic sites is promoted. Continuous activation of WT target genes occurs if they fortuitously contain the novel CDA site nearby. Our findings provide a molecular understanding of how a single mutation in the KLF1 zinc finger exerts effects on erythroid physiology in CDA type IV.

SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding

BACKGROUND

Aptamers, single-stranded DNAs or RNAs, can be selected from a library containing random sequences using a method called Systematic Evolution of Ligands by EXponential Enrichment (SELEX). In SELEX, monitoring the enriching statuses of aptamer candidates during the process is a key step until today. Conformational change of an aptamer caused by target-binding in gel can be used to indicate its statuses of binding.

RESULTS

In this study, an easy-to-implement gel-based diffusion method (GBDM) was developed to monitor the interaction between enriched aptamer candidates and their targets. In order to prove the concept, characterization of aptamers targeting their targets including protein (thrombin) and non-protein molecules (acetamiprid, ATP, atrazine, profenofos and roxithromycin), respectively, were performed using mini gels. Our method has advantages over the common methods including easy performed with labor- and time- saving in experimental operation. The concept has been proven by monitoring enrichment of dynamic aptamer candidate libraries targeting a small molecule 2,2-bis(4-chlorophenyl) acetic acid (DDA) during SELEX process. A mini gel cassette was designed and fabricated by our laboratory to make mini agarose gels for diffusion with different directions.

CONCLUSIONS

These results indicate that GBDM, in particular, chasing diffusion is suitable for monitoring the interaction between enriched aptamer candidates and their targets. These pioneering efforts are helpful for novel aptamer selection by breaking through the technical bottleneck of aptamer development and helpful for development of novel aptasensors.

[Evaluation of the diversity of random DNA-libraries by the shape of amplification curves for estimation of the efficiency of aptamer selection]

Using random (combinatorial) DNA-libraries with various degrees of diversity, it was shown that their amplification by polymerase chain reaction in real time resulted in appearance of a maximum on amplification curves. The relative decrease of fluorescence after passing the maximum was directly proportional to the logarithm of the number of oligonucleotide sequence variants in the random DNA-library provided that this number was within in the interval from 1 to 104 and remained practically unaltered when the number of variants was in the interval from 105 to 108. The obtained dependence was used in the course of SELEX to evaluate changes in the diversity of random DNA-libraries from round to round in selection of DNA-aptamers to the recombinant SMAD4 protein. As a result, oligonucleotides containing sequences able to form a site of SMAD4-DNA interactions known as SBE (SMAD-binding element) have been selected thus indicating that the SMAD4-SBE interaction dominates the aptamer selection.

Inside the Black Box: What Makes SELEX Better?

Aptamers are small oligonucleotides that are capable of binding specifically to a target, with impressive potential for analysis, diagnostics, and therapeutics applications. Aptamers are isolated from large nucleic acid combinatorial libraries using an iterative selection process called SELEX (Systematic Evolution of Ligands by EXponential enrichment). Since being implemented 30 years ago, the SELEX protocol has undergone many modifications and improvements, but it remains a laborious, time-consuming, and costly method, and the results are not always successful. Each step in the aptamer selection protocol can influence its results. This review discusses key technical points of the SELEX procedure and their influence on the outcome of aptamer selection.

Rapid and easy method for in vitro determination of transcription factor binding core motifs

We introduce a rapid method for easily elucidating transcription factor (TF) cis-elements by adopting a highly efficient in vitro protein synthesis method and identifying protein-DNA interactions using PCR. We determined two cis-elements for plant TFs using this method, and the results confirmed our method as an easy and time-saving alternative for elucidating TF cis-elements using common laboratory procedures.

Cryptic glucocorticoid receptor-binding sites pervade genomic NF-κB response elements

Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself-tethering in a DNA binding-independent manner-represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.

Improving transcriptional activity of human cytomegalovirus major immediate-early promoter by mutating NF-κB binding sites

Many mammalian gene expression vectors express the transferred genes under the control of the cytomegalovirus (CMV) major immediate-early promoter (MIEP). The human MIEP has been known as the strongest promoter in mammalian cells and utilized widely in mammalian expression systems. There are four NF-κB binding sites (named as κBs) in the human MIEP. In this study, we have constructed multiple mutated MIEPs by changing the natural κBs in the human MIEP into the high-affinity artificial sequences that were in vitro selected by using systematic evolution of ligands by exponential enrichment (SELEX) and predicted by bioinformatics. With various transcriptional activity evaluations, we found three mutated MIEPs with the transcriptional activity higher than the wild-type MIEP, which should be useful and widely applicable in many mammalian transgene expression fields such as gene engineering, gene therapy and gene editing. This study provides a useful approach for promoter engineering in biotechnology. This study also produced a series of mutated MIEPs with various transcriptional activities, which may be used for the fine control of gene expression output in the future synthetic biology.

NMR monitoring of the SELEX process to confirm enrichment of structured RNA

RNA aptamers are RNA molecules that bind to a target molecule with high affinity and specificity using uniquely-folded tertiary structures. RNA aptamers are selected from an RNA pool typically comprising up to 1015 different sequences generated by iterative steps of selection and amplification known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Over several rounds of SELEX, the diversity of the RNA pool decreases and the aptamers are enriched. Hence, monitoring of the enrichment of these RNA pools is critical for the successful selection of aptamers, and several methods for monitoring them have been developed. In this study, we measured one-dimensional imino proton NMR spectra of RNA pools during SELEX. The spectrum of the initial RNA pool indicates that the RNAs adopt tertiary structures. The structural diversity of the RNA pools was shown to depend highly on the design of the primer-binding sequence. Furthermore, we demonstrate that enrichment of RNA aptamers can be monitored using NMR. The RNA pools can be recovered from the NMR tube after measurement of NMR spectra. We also can monitor target binding in the NMR tubes. Thus, we propose using NMR to monitor the enrichment of structured aptamers during the SELEX process.

SELMAP - SELEX affinity landscape MAPping of transcription factor binding sites using integrated microfluidics

Transcription factors (TFs) alter gene expression in response to changes in the environment through sequence-specific interactions with the DNA. These interactions are best portrayed as a landscape of TF binding affinities. Current methods to study sequence-specific binding preferences suffer from limited dynamic range, sequence bias, lack of specificity and limited throughput. We have developed a microfluidic-based device for SELEX Affinity Landscape MAPping (SELMAP) of TF binding, which allows high-throughput measurement of 16 proteins in parallel. We used it to measure the relative affinities of Pho4, AtERF2 and Btd full-length proteins to millions of different DNA binding sites, and detected both high and low-affinity interactions in equilibrium conditions, generating a comprehensive landscape of the relative TF affinities to all possible DNA 6-mers, and even DNA10-mers with increased sequencing depth. Low quantities of both the TFs and DNA oligomers were sufficient for obtaining high-quality results, significantly reducing experimental costs. SELMAP allows in-depth screening of hundreds of TFs, and provides a means for better understanding of the regulatory processes that govern gene expression.

SELEX of Cell-Specific RNA Aptamers

This chapter focuses on the selection of RNA aptamers, which bind to specific cell surface components and thus can be internalized receptor mediated. Such aptamers discriminate between different tissues, e.g., detect malignant cells, and target them or induce apoptosis through drug internalization. However, before starting the selection process the choice of an ideal target can be challenging. To give an example for the selection of cell specific aptamers, we here used the interleukin-6 receptor (IL-6R) as a target, which is presented on hepatocytes, neutrophils, monocytes, and macrophages.

A Robust Analytical Pipeline for Genome-Wide Identification of the Genes Regulated by a Transcription Factor: Combinatorial Analysis Performed Using gSELEX-Seq and RNA-Seq

For identifying the genes that are regulated by a transcription factor (TF), we have established an analytical pipeline that combines genomic systematic evolution of ligands by exponential enrichment (gSELEX)-Seq and RNA-Seq. Here, SELEX was used to select DNA fragments from an Aspergillus nidulans genomic library that bound specifically to AmyR, a TF from A. nidulans. High-throughput sequencing data were obtained for the DNAs enriched through the selection, following which various in silico analyses were performed. Mapping reads to the genome revealed the binding motifs including the canonical AmyR-binding motif, CGGN8CGG, as well as the candidate promoters controlled by AmyR. In parallel, differentially expressed genes related to AmyR were identified by using RNA-Seq analysis with samples from A. nidulans WT and amyR deletant. By obtaining the intersecting set of genes detected using both gSELEX-Seq and RNA-Seq, the genes directly regulated by AmyR in A. nidulans can be identified with high reliability. This analytical pipeline is a robust platform for comprehensive genome-wide identification of the genes that are regulated by a target TF.

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

Evolve and resequence (E&R) experiments use experimental evolution to adapt populations to a novel environment, then next-generation sequencing to analyse genetic changes. They enable molecular evolution to be monitored in real time on a genome-wide scale. Here, we review the field of E&R experiments across diverse systems, ranging from simple non-living RNA to bacteria, yeast and the complex multicellular organism Drosophila melanogaster. We explore how different evolutionary outcomes in these systems are largely consistent with common population genetics principles. Differences in outcomes across systems are largely explained by different starting population sizes, levels of pre-existing genetic variation, recombination rates and adaptive landscapes. We highlight emerging themes and inconsistencies that future experiments must address.

Emulsion PCR significantly improves nonequilibrium capillary electrophoresis of equilibrium mixtures-based aptamer selection: allowing for efficient and rapid selection of aptamer to unmodified ABH2 protein

Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM), a homogeneous approach to select DNA aptamers, is among the most efficient partitioning techniques. In contrast with surface-based systematic evolution of ligands by exponential enrichment (SELEX) approaches, the ability of NECEEM to select aptamers to unmodified proteins in solution is preferable for identifying aptamers for eventual in vivo use. The high stringency and low sample volumes of NECEEM, although generally beneficial, can result in binding of very few aptamers, requiring highly efficient amplification to propagate them. When amplified with standard PCR, detectable library enrichment can fail due to the fast conversion of the aptamers into byproducts and preferential amplification of nonbinders. As an alternative, we proposed the use of emulsion PCR (ePCR), which is known to reduce byproduct formation, as a PCR mode for coupling with NECEEM partitioning. For the first time, we tested the advantages of ePCR in NECEEM-based aptamer selection to a medically relevant DNA repair enzyme, ABH2. We report that the combination of ePCR with NECEEM allowed for the selection of aptamers in the first three rounds of SELEX, while SELEX with conventional PCR failed in a number of attempts. Selected aptamers to an unmodified ABH2 protein have potential use in diagnostics and as leads for anticancer cotherapies, used as enhancements of alkylating agents in chemotherapy.

Single-nucleotide mutation matrix: a new model for predicting the NF-κB DNA binding sites

In this study, we established a single nucleotide mutation matrix (SNMM) model based on the relative binding affinities of NF-κB p50 homodimer to a wild-type binding site (GGGACTTTCC) and its all single-nucleotide mutants detected with the double-stranded DNA microarray. We evaluated this model by scoring different groups of 10-bp DNA sequences with this model and analyzing the correlations between the scores and the relative binding affinities detected with three wet experiments, including the electrophoresis mobility shift assay (EMSA), the protein-binding microarray (PBM) and the systematic evolution of ligands by exponential enrichment-sequencing (SELEX-Seq). The results revealed that the SNMM scores were strongly correlated with the detected binding affinities. We also scored the DNA sequences with other three models, including the principal coordinate (PC) model, the position weight matrix scoring algorithm (PWMSA) model and the Match model, and analyzed the correlations between the scores and the detected binding affinities. In comparison with these models, the SNMM model achieved reliable results. We finally determined 0.747 as the optimal threshold for predicting the NF-κB DNA-binding sites with the SNMM model. The SNMM model thus provides a new alternative model for scoring the relative binding affinities of NF-κB to the 10-bp DNA sequences and predicting the NF-κB DNA-binding sites.

CFP10 and ESAT6 aptamers as effective Mycobacterial antigen diagnostic reagents

The development of effective Mycobacterial antigen diagnostic reagents remains a high priority. The 6-kDa early secreted antigenic target (ESAT6) and 10-kDa culture filtrate protein (CFP10) are secreted early by virulent Mycobacterium tuberculosis (M. tb) and are not present in the non-virulent Bacillus Calmette-Guerin (BCG). In this study, we used a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technique to screen for a functional ssDNA aptamer "antibody" that specifically bound to ESAT6-CFP10 (CE) protein. The selected single ssDNA aptamers (CE24 and CE15) demonstrated the highest specificity and binding affinity to CFP10 (CE24: Kd = 3.75 × 10(-7) M) and ESAT6 (CE15: Kd = 1.6 × 10(-7) M). We further detected CFP10 and ESAT6 proteins in serum samples from active pulmonary tuberculosis (TB) patients, extrapulmonary TB patients and healthy donors by using an enzyme-linked oligonucleotide assay (ELONA). The results showed that the sensitivity and specificity were 100% and 94.1% (using CE24 aptamer-based ELONA) and 89.6% and 94.1% (using CE15 aptamer-based ELONA), respectively. A good correlation was observed between aptamer-based ELONA and T-SPOT TB assay. Thus, our study suggests that CE24 and CE15 have potentially broad applications as early antigen diagnostic agents not only for active pulmonary TB, extrapulmonary TB, but also possibly for latent TB infection and TB with immune-deficiency.

Sensitive detection of transcription factors using near-infrared fluorescent solid-phase rolling circle amplification

This study describes a method for analyzing transcription factor (TF) activity, near-infrared fluorescent solid-phase rolling circle amplification (NIRF-sRCA). This method analyzes TF activity in four steps: (i) incubate DNA with protein sample and isolate TF-bound DNA, (ii) hybridize the TF-bound DNA and rolling circle to DNA microarray, (iii) amplify the TF-bound DNA with sRCA that contains biotin-labeled dUTP, and (iv) detect sRCA products by binding of NIRF-labeled streptavidin and NIRF imaging. This method was validated by proof-of-concept detection of purified TF protein and cell nuclear extract. Detection of purified TF protein demonstrated that NIRF-sRCA could quantitatively detect NF-κB p50 protein, and as little as 6.94 ng (∼140 fmol) of this protein was detected. Detection of nuclear extract revealed that NIRF-sRCA could specifically and quantitatively detect NF-κB p50 activity in HeLa cell nuclear extracts, and the activity of this TF in as little as 0.625 μg of nuclear extracts could be detected. Detection of nuclear extract also revealed that NIRF-sRCA could detect the relative activities of multiple TFs in HeLa cell nuclear extracts and the fold induction of multiple TFs in the TNFα-induced HeLa cell nuclear extracts. Therefore, this study provides a new tool for studying TFs.

Analyzing transcription factor activity using near infrared fluorescent bridge polymerase chain reaction

This study has developed a new method, near infrared fluorescent bridge polymerase chain reaction (NIRF-bPCR), for analyzing transcription factor (TF) activity. This method was first used to detect the activity of purified nuclear factor kappa B (NF-κB) p50. The results demonstrated that this method could quantitatively detect the activity of p50 protein at less than 115ng (∼ 2320fmol), and the detection limit reached as little as 6.94ng (∼ 140fmol) of p50 protein. This method was then used to detect TF activity in cell extracts. The results revealed that this method could specifically detect NF-κB activity in HeLa cell nuclear extracts. Finally, this method was used to detect the activities of multiple TFs in a protein sample. The results showed that this method could detect the activities of six TFs-NF-κB, AP-1, TFIID, CREB, NF-E2, and p53-in the TNFα-induced and -uninduced HeLa cell nuclear extracts. Calculation of the fold induction of six TFs revealed that NF-κB, CREB, and AP1 were activated by TNFα induction in HeLa cells, in agreement with the detection results of other methods. Therefore, this study provides a new tool for analyzing TF activity. This study also revealed that NIRF-bPCR may be used as a new method for detecting DNA molecules.