Eukaryotic Transcription Factors Research Articles

MTF1 genetic variants are associated with lung cancer risk in the Chinese Han population

BackgroundMetal-regulatory transcription factor 1 (MTF1), a conserved metal-binding transcription factor in eukaryotes, regulates the proliferation of cancer cells by activating downstream target genes and then participates in the formation and progression of tumors, including lung cancer (LC). The expression level of MTF1 is down-regulated in LC, and high expression of MTF1 is associated with a good prognosis of LC. However, the association between MTF1 polymorphism and LC risk has not been explored.MethodsThe genotyping of MTF1 Single nucleotide polymorphisms (SNPs) including rs473279, rs28411034, rs28411352, and rs3748682 was identified by the Agena MassARRAY system among 670 healthy controls and 670 patients with LC. The odds ratio (OR) and 95% confidence intervals (CI) were calculated by logistics regression to assess the association of these SNPs with LC risk.ResultsMTF1 rs28411034 (OR 1.22, 95% CI 1.03–1.45, p = 0.024) and rs3748682 (OR 1.24, 95% CI 1.04–1.47, p = 0.014) were associated with higher LC susceptibility overall. Moreover, the effect of rs28411034 and rs3748682 on LC susceptibility was observed in males, subjects with body mass index (BMI) ≥ 24 kg/m2, smokers, drinkers, and patients with lung squamous carcinoma (OR and 95% CI > 1, p < 0.05). Besides, rs28411352 (OR 0.73, 95% CI 0.55–0.97, p = 0.028,) showed protective effect for reduced LC risk in drinkers.ConclusionsWe were first who reported that rs28411034 and rs3748682 tended to be relevant to increased LC susceptibility among the Chinese Han population. These results of this study could help to recognize the pathogenic mechanisms of the MTF1 gene in LC progress.

GAGA zinc finger transcription factor searches chromatin by 1D-3D facilitated diffusion.

To elucidate how eukaryotic sequence-specific transcription factors (TFs) search for gene targets on chromatin, we used multi-color smFRET and single-particle imaging to track the diffusion of purified GAGA-Associated Factor (GAF) on DNA and nucleosomes. Monomeric GAF DNA-binding domain (DBD) bearing one zinc finger finds its cognate site by 1D or 3D diffusion on bare DNA and rapidly slides back-and-forth between naturally clustered motifs for seconds before escape. Multimeric, full-length GAF also finds clustered motifs on DNA by 1D-3D diffusion, but remains locked on target for longer periods. Nucleosome architecture effectively blocks GAF-DBD 1D-sliding into the histone core but favors retention of GAF-DBD when targeting solvent-exposed sites by 3D-diffusion. Despite the occlusive power of nucleosomes, 1D-3D facilitated diffusion enables GAF to effectively search for clustered cognate motifs in chromatin, providing a mechanism for navigation to nucleosome and nucleosome-free sites by a member of the largest TF family.

Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription.

Eukaryotic transcription factors (TFs) activate gene expression by recruiting cofactors to promoters. However, the relationships between TFs, promoters and their associated cofactors remain poorly understood. Here we combine GAL4-transactivation assays with comparative CRISPR-Cas9 screens to identify the cofactors used by nine different TFs and core promoters in human cells. Using this dataset, we associate TFs with cofactors, classify cofactors as ubiquitous or specific and discover transcriptional co-dependencies. Through a reductionistic, comparative approach, we demonstrate that TFs do not display discrete mechanisms of activation. Instead, each TF depends on a unique combination of cofactors, which influences distinct steps in transcription. By contrast, the influence of core promoters appears relatively discrete. Different promoter classes are constrained by either initiation or pause-release, which influences their dynamic range and compatibility with cofactors. Overall, our comparative cofactor screens characterize the interplay between TFs, cofactors and core promoters, identifying general principles by which they influence transcription.

DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues.

Homeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.

Growth hormone resistance induced by amino acid deprivation in fao cells is independent of FGF21

Adequate dietary intake of amino acids is imperative for normal animal growth. Our previous work using rat hepatocarcinoma Fao cells demonstrated that growth hormone (GH) resistance, coupled with a concurrent reduction in insulin-like growth factor 1 (Igf1) mRNA levels, may underlie the growth retardation associated with a low-protein diet (LPD). In this study, we investigated whether FGF21 contributes to liver GH resistance in Fao rat hepatoma cells under amino acid deprivation conditions. Mice subjected to an LPD exhibited growth retardation, compromised GH signaling in the liver, and decreased blood IGF-1 levels compared with those on a control diet. To assess the potential involvement of fibroblast growth factor (FGF) 21, produced in response to amino acid deficiency, in the development of GH resistance, we examined GH signaling and Igf1 mRNA levels in Fao cells cultured in amino acid-deprived medium. Despite the inhibition of Fgf21 expression by the integrated stress response inhibitor, an inhibitor of the eukaryotic initiation factor 2-activating transcription factor 4 pathway, GH resistance persisted in response to amino acid deprivation. Additionally, the introduction of FGF21 into the control medium did not impair either GH signaling or GH-induced Igf1 transcription. These data suggest that, in Fao cells, amino acid deprivation induces GH resistance independently of FGF21 activity. By shedding light on the mechanisms behind growth retardation-associated GH resistance linked to amino acid deficiencies, our findings provide valuable insights for clinicians in formulating effective treatment strategies for individuals facing these challenges.

Structural and dynamical aspect of DNA motif sequence specific binding of AP-1 transcription factor.

Activator protein-1 (AP-1) comprises one of the largest and most evolutionary conserved families of ubiquitous eukaryotic transcription factors that act as a pioneer factor. Diversity in DNA binding interaction of AP-1 through a conserved basic-zipper (bZIP) domain directs in-depth understanding of how AP-1 achieves its DNA binding selectivity and consequently gene regulation specificity. Here, we address the structural and dynamical aspects of the DNA target recognition process of AP-1 using microsecond-long atomistic simulations based on the structure of the human AP-1 FosB/JunD bZIP-DNA complex. Our results show the unique role of DNA shape features in selective base specific interactions, characteristic ion population, and solvation properties of DNA grooves to form the motif sequence specific AP-1-DNA complex. The TpG step at the two terminals of the AP-1 site plays an important role in the structural adjustment of DNA by modifying the helical twist in the AP-1 bound state. We addressed the role of intrinsic motion of the bZIP domain in terms of opening and closing gripper motions of DNA binding helices, in target site recognition and binding of AP-1 factors. Our observations suggest that binding to the cognate motif in DNA is mainly accompanied with the precise adjustment of closing gripper motion of DNA binding helices of the bZIP domain.

Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors.

Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.

Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors

Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation, occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the early Drosophila embryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high-concentration clusters within nuclei. Here, we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in the Drosophila proteome, we generated a library of IDRs from transcription factors expressed in the early Drosophila embryo. We used this library to perform a high-throughput imaging screen in Drosophila Schneider-2 (S2) cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full-length transcription factors. These results are consistent in live Drosophila embryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.

Protein-Protein Interaction via Two-Hybrid Assay in Yeast.

The yeast two-hybrid assay enables detecting interactions between proteins, which makes this tool of particular interest for plant-virus interaction studies. Basically, the reporter gene expression (HIS3) is activated by the binding of a transcription factor GAL4, which, like eukaryotic transcription factors, is modular in nature and consists of two structurally independent domains: DNA-binding (DB) and activation (AD) domains. The two proteins under investigation are expressed separately, one fused to the BD domain and the other to the AD domain. In the yeast strain AH109, activation of the reporter gene occurs only in cells that contain interacting proteins, reconstituting the transcription factor GAL4 which then binds to the responsive promoter and results in yeast colony growth.

Sesquiterpene Lactones as Potential G1/S Phase Cell Cycle Inhibitors: A Molecular Docking Study

Cell cycle checkpoints play a crucial role in cell division by monitoring the orderly progression of each phase, ensuring accurate completion before advancing to the next stage. They act as quality control mechanisms, pausing the cell cycle when optimal conditions are not met, thereby preventing errors during cell division. Objective: To discover Sesquiterpene Lactones (SLs) as inhibitory compounds targeting Cyclin D1/Cyclin Dependent Kinase 4 (CDK4)- Cyclin Dependent kinase 6 (CDK6) complex and Eukaryotic Transcription Factor 2 protein (E2F-2). Methods: The inhibitory potential of SLs, namely ilicol, eucalyptone, and ascleposide E, was investigated using molecular docking analysis. The docking and visualization of ligand-protein complexes were performed using MGL Tools version 1.5.7, BIOVIA Discovery Studio version 21.1.0, and PyMol version 2.5.2. Additionally, drug likeness and pharmacokinetic properties of SLs were assessed via pkCSM and ADMET analysis. Results: Findings demonstrate that ilicol exhibit most favourable complex with CDK6 having binding energy of –7.8 kCal/mol and inhibition constant 1.81 μM. The visualization of ligand-receptor complexes reveals substantial hydrogen bonding interactions. Conclusions: Current study revealed that novel SLs show favourable drug likeness and promising ADMET profile along with strong inhibitory effect on G1/S regulatory proteins. The potency of SLs is in order of ilicol&gt; ascleposide E&gt;eucalyptone. To further validate the inhibitory effect of ilicol, implementation of comprehensive in vitro and in vivo investigations must be employed for progression of its development as a novel anti-cancer therapeutic.

Dimerization choice and alternative functions of ZBTB transcription factors.

Zinc Finger DNA-binding domain-containing proteins are the most populous family among eukaryotic transcription factors. Among these, members of the BTB domain-containing ZBTB sub-family are mostly known for their transcriptional repressive functions. In this Viewpoint article, we explore molecular mechanisms that potentially diversify the function of ZBTB proteins based on their homo and heterodimerization, alternative splicing and post-translational modifications. We describe how the BTB domain is as much a scaffold for the assembly of co-repressors, as a domain that regulates protein stability. We highlight another mechanism that regulates ZBTB protein stability: phosphorylation in the zinc finger domain. We explore the non-transcriptional, structural roles of ZBTB proteins and highlight novel findings that describe the ability of ZBTB proteins to associate with poly adenosine ribose in the nucleus during the DNA damage response. Herein, we discuss the contribution of BTB domain scaffolds to the formation of transcriptional repressive complexes, to chromosome compartmentalization and their non-transcriptional, purely structural functions in the nucleus.

Genome-Wide Identification, Classification and Expression Analyses of MADS-Box Genes Reveal Their Role in Stem Gall Formation and Expansion of Zizania latifolia

MADS-box genes are important transcription factors in eukaryotes that are involved in regulating the growth and development of many plants. Jiaobai is a special aquatic vegetable formed through the stem expansion of Zizania latifolia infected by Ustilago esculenta and is wildly cultivated in Southeast Asia. To date, the biological function of MADS-box genes in Z. latifolia remains largely unknown. In this study, a genome-wide search for MADS-box genes in Z. latifolia was performed, and 87 MADS-box genes were identified. According to the phylogenetic analysis, there were 27 type I genes and 60 type II genes. The type I genes were mainly distributed in the Mα, Mβ and Mγ subfamilies, and the type II genes were divided into 14 subfamilies and unevenly distributed across 17 chromosomes. The encoded protein sequences ranged from 91 to 433 amino acids, the number of exons was 1~14, and most type I genes did not contain introns. The promoter region contained a large number of functional domains related to light response, plant hormones, stress and the meristem. An analysis of the expression patterns showed that there were massive differences in the expression of the MADS-box genes in different tissues, with six genes highly expressed in leaves and eight genes highly expressed in the stem apical meristem. Photoperiod and temperature were found to regulate the formation of the stem gall (SG) of Z. latifolia, and short-day (SD) conditions had an obvious promoting effect. ZlMADS57 and ZlMADS85 were significantly increased in SG under SD. Further analysis of the expression levels of MADS-box genes during the developmental stages of Z. latifolia found that the ZlMADS45, ZlMADS57, ZlMADS81 and ZlMADS85 were highly expressed 10 days before the SG formation, and ZlMADS66 reached its highest value on the day when the SG began forming. ZlMADS14, ZlMADS15, ZlMADS32, ZlMADS36, ZlMADS59 and ZlMADS71 were highly expressed after SG expansion, indicating that the MADS-box gene may play an important role in regulating SG formation and the subsequent expansion of Jiaobai. This study provides a reference for the functional identification of the MADS-box gene family and establishes a foundation for regulating the maturity of Z. latifolia.

Target-responsive DNA translator for amplified and sensitive sensing of Myc-Max transcription factor dimer

Myc-Max is a central eukaryotic transcription factor dimer that plays key roles in regulating cellular activities such as cell growth, proliferation, and differentiation. Selective and sensitive quantification of Myc-Max thus has valuable significances for biological studies and disease diagnosis. On the basis of a new DNA translator probe, we construct an amplified FRET sensing strategy for sensitively detecting Myc-Max in human serums via DNAzyme and clamped hybridization chain reaction (cHCR)-integrated signal amplifications. Myc-Max binds the DNA translator and switches its conformation to activate the DNAzyme and trigger cHCR for the assembly generation of DNA networks from two respective dye-labeled dual stem-loop and palindromic sequence-containing hairpin structures. Such DNA networks pull the two dyes into proximity position to exhibit highly magnified FRET responses for sensitively detecting Myc-Max with a 1.2 pM low detection limit in the dynamic range between 10 pM and 1 nM. Besides, sensitive discrimination of low levels of Myc-Max in diluted human serums has been verified by the developed method. Moreover, the sequence of the DNA translator can be tuned to accommodate different biomolecules, making the developed sensing strategy a versatile tool for detecting various trace biomarkers for diagnosing diseases at their early stages.

Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors

Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.

Evolution and diversification of the ACT-like domain associated with plant basic helix–loop–helix transcription factors

Basic helix-loop-helix (bHLH) proteins are one of the largest families of transcription factor (TF) in eukaryotes, and ~30% of all flowering plants' bHLH TFs contain the aspartate kinase, chorismate mutase, and TyrA (ACT)-like domain at variable distances C-terminal from the bHLH. However, the evolutionary history and functional consequences of the bHLH/ACT-like domain association remain unknown. Here, we show that this domain association is unique to the plantae kingdom with green algae (chlorophytes) harboring a small number of bHLH genes with variable frequency of ACT-like domain's presence. bHLH-associated ACT-like domains form a monophyletic group, indicating a common origin. Indeed, phylogenetic analysis results suggest that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. We determined the functional significance of this association by showing that Chlamydomonas reinhardtii ACT-like domains mediate homodimer formation and negatively affect DNA binding of the associated bHLH domains. We show that, while ACT-like domains have experienced faster selection than the associated bHLH domain, their rates of evolution are strongly and positively correlated, suggesting that the evolution of the ACT-like domains was constrained by the bHLH domains. This study proposes an evolutionary trajectory for the association of ACT-like and bHLH domains with the experimental characterization of the functional consequence in the regulation of plant-specific processes, highlighting the impacts of functional domain coevolution.

Frontispiece: Multifunctional Intrinsically Disordered Regions in Transcription Factors

Eukaryotic transcription factors (TFs) are the final integrators of a complex molecular feedback mechanism that interfaces with the genome, consolidating information for transcriptional regulation. TFs consist of both structured DNA-binding domains and long intrinsically disordered regions (IDRs) embedded with motifs linked to transcriptional control. These IDRs endow transcription factors with structural plasticity which is central to their functions in the nucleus. More information can be found in the Review article by P. O. Heidarsson and co-workers. (DOI: 10.1002/chem.202203369)

Global analysis of basic leucine zipper transcription factors in trifoliate orange and the function identification of PtbZIP49 in salt tolerance

As one of the most widely distributed and highly conserved transcription factors in eukaryotes, basic leucine zipper proteins (bZIPs) are involved in a variety of biological processes in plants, but they are largely unknown in citrus. In this study, 56 bZIP family members were identified genome-wide from an important citrus rootstock, namely trifoliate orange (Poncirus trifoliata L. Raf.), and these putative bZIPs were named PtbZIP1–PtbZIP56. All PtbZIPs were classified into 13 subgroups by phylogenetic comparison with Arabidopsis thaliana bZIPs (AtbZIPs), and they were randomly distributed on nine known (50 genes) chromosomes and one unknown (6 genes) chromosome. Sequence analysis revealed the detailed characteristics of PtPZIPs, including their amino acid length, isoelectric point (pI), molecular weight (MW), predicted subcellular localization, gene structure, and conserved motifs. Prediction of promoter elements suggested the presence of drought, low-temperature, wound, and defense and stress responsive elements, as well as multiple hormone-responsive cis-acting elements. Spatiotemporal expression analysis showed the transcriptional patterns of PtbZIPs in different tissues and under dehydration, high salt, ABA, and IAA treatments. In addition, 21 PtbZIPs were predicted to have direct or indirect protein–protein interactions. Among these, PtbZIP49 was experimentally proven to interact with PtbZIP1 or PtbZIP11 by using a yeast two-hybrid assay and bimolecular fluorescence complementation (BiFC). Subcellular localization analysis further revealed that PtbZIP1, PtbZIP11, and PtbZIP49 were localized in the nucleus. Moreover, PtbZIP49 was functionally identified as having an important role in salt stress via ectopic expression in A. thaliana and silenced in trifoliate orange using virus-induced gene silencing (VIGS). This study provided comprehensive information on PtbZIP transcription factors in citrus and highlights their potential functions in abiotic stress.

Multifunctional Intrinsically Disordered Regions in Transcription Factors.

Eukaryotic transcription factors (TFs) are the final integrators of a complex molecular feedback mechanism that interfaces with the genome, consolidating information for transcriptional regulation. TFs consist of both structured DNA-binding domains and long intrinsically disordered regions (IDRs) embedded with motifs linked to transcriptional control. It is now well established that the dynamic multifunctionality of IDRs is the basis for a wide spectrum of TF functions necessary to navigate and regulate the human genome. This review dissects the chemical features of TF IDRs that endow them with structural plasticity that is central to their functions in the nucleus. Sequence analysis of a set of over 1600 human TFs through AlphaFold was used to identify key features of their IDRs. Recent studies were then highlighted to illustrate IDR involvement in processes such as protein interactions, DNA binding and specificity, chromatin opening, and phase separation. To expand our understanding of TF functions, future directions are suggested for integrating experiments and simulations, from in vitro to living systems.

Using Restriction Endonuclease, Protection, Selection, and Amplification to Identify Preferred DNA-Binding Sequences of Microbial Transcription Factors.

Regulation of gene expression is a vital component of cellular biology. Transcription factor proteins often bind regulatory DNA sequences upstream of transcription start sites to facilitate the activation or repression of RNA polymerase. Research laboratories have devoted many projects to understanding the transcription regulatory networks for transcription factors, as these regulated genes provide critical insight into the biology of the host organism. Various in vivo and in vitro assays have been developed to elucidate transcription regulatory networks. Several assays, including SELEX-seq and ChIP-seq, capture DNA-bound transcription factors to determine the preferred DNA-binding sequences, which can then be mapped to the host organism's genome to identify candidate regulatory genes. In this protocol, we describe an alternative in vitro, iterative selection approach to ascertaining DNA-binding sequences of a transcription factor of interest using restriction endonuclease, protection, selection, and amplification (REPSA). Contrary to traditional antibody-based capture methods, REPSA selects for transcription factor-bound DNA sequences by challenging binding reactions with a type IIS restriction endonuclease. Cleavage-resistant DNA species are amplified by PCR and then used as inputs for the next round of REPSA. This process is repeated until a protected DNA species is observed by gel electrophoresis, which is an indication of a successful REPSA experiment. Subsequent high-throughput sequencing of REPSA-selected DNAs accompanied by motif discovery and scanning analyses can be used for determining transcription factor consensus binding sequences and potential regulated genes, providing critical first steps in determining organisms' transcription regulatory networks. IMPORTANCE Transcription regulatory proteins are an essential class of proteins that help maintain cellular homeostasis by adapting the transcriptome based on environmental cues. Dysregulation of transcription factors can lead to diseases such as cancer, and many eukaryotic and prokaryotic transcription factors have become enticing therapeutic targets. Additionally, in many understudied organisms, the transcription regulatory networks for uncharacterized transcription factors remain unknown. As such, the need for experimental techniques to establish transcription regulatory networks is paramount. Here, we describe a step-by-step protocol for REPSA, an inexpensive, iterative selection technique to identify transcription factor-binding sequences without the need for antibody-based capture methods.

Expression Pattern and Clinical Significance of E2F Transcription Factors in Skin Cutaneous Melanoma

Introduction: E2F is a group of genes that encodes a family of transcription factors in higher eukaryotes. Although emerging evidence indicates that E2Fs are implicated in various cancer types, the diverse expression patterns and prognostic values of E2F transcription factors in SKCM have yet to be elucidated. The purpose of this study was to enhance our knowledge concerning the role of E2Fs in SKCM patients.. Methods: GEPIA, The Human Protein Atlas, TIMER, cBioPortal, GeneMANIA, DAVID 6.8 and KEGG PATHWAY Database were utilized in this study.