scholarly journals Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework

2019 ◽  
Author(s):  
Patrick C.N. Martin ◽  
Nicolae Radu Zabet

AbstractTranscription Factors (TFs) bind to DNA and control activity of target genes. Here, we present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs. We focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). While CTCF preferentially binds only to a subset of high affinity sites located mainly in open chromatin, BEAF-32 binds to most of its high affinity binding sites available in open chromatin. In contrast, su(Hw) binds to both open chromatin and also partially closed chromatin. Most importantly, differences in TF binding profiles between cell lines for these TFs are mainly driven by differences in DNA accessibility and not by differences in TF concentrations between cell lines. Finally, we investigated binding of Hox TFs in Drosophila and found that Ubx binds only in open chromatin, while Abd-B and Dfd are capable to bind in both open and partially closed chromatin. Overall, our results show that TFs display different binding mechanisms and that our model is able to recapitulate this diverse repertoire of mechanisms.

2019 ◽  
Author(s):  
Qiong Zhang

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of Chromatin immunoprecipitation sequencing (ChIP-Seq) provides great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7,190 ChIP-Seq samples of 659 TFs and high confident TF binding sites of 699 TFs) and epigenetic modification information to predict accurate TF-target regulations. hTFtarget offers the following functions for users to explore TF-target regulations: 1) Browse or search general targets of a query TF across datasets; 2) Browse TF-target regulations for a query TF in a specific dataset or tissue; 3) Search potential TFs for a given target gene or ncRNA; 4) Investigate co-association between TFs in cell lines; 5) Explore potential co-regulations for given target genes or TFs; 6) Predict candidate TFBSs on given DNA sequences; 7) View ChIP-Seq peaks for different TFs and conditions in genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF-target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 819-819
Author(s):  
Maciej Szydlowski ◽  
Monika Prochorec-Sobieszek ◽  
Anna Szumera-Cieckiewicz ◽  
Grazyna Hoser ◽  
Ewa Jablonska ◽  
...  

Abstract The classical Hodgkin lymphoma (cHL) is characterized by a presence of rare malignant Reed-Sternberg (RS) cells surrounded by abundant reactive infiltrate. Tumor RS cells express multiple cytokines, chemokines and immunoregulatory proteins, such as PD-L1 or galectin-1, that enhance recruitment of the infiltrating cells and allow malignant cells to escape from host immune surveillance. Since targeting these immunomodulatory molecules is a highly promising therapeutic strategy in cHL, identification of pathways and mechanisms orchestrating tumor immune evasion and supporting RS cell survival can further reveal targetable vulnerabilities of cHL. Expression of immunoregulatory proteins in cHL is modulated by tumor-specific activity of certain pro-survival transcription factors, such as NFκB and STATs. Since the activity of these transcription factors is modulated by oncogenic PIM1/2/3 serine/threonine kinases, we hypothesized that PIMs may support RS cell survival and foster their immune privilege. For these reasons, we investigated PIM1/2/3 expression in cHL and determined mechanisms underlying their expression. Furthermore, we assessed impact of PIM inhibition on expression of key factors engaged in development of the immunosuppressive microenvironment and HRS cell survival. Our analyses revealed that PIM1/2/3 are ubiquitously expressed in primary and cultured RS cell lines. At least one PIM isoform was expressed in each cell line and in 97% of 67 primary cHL biopsies. RS cells treated with JAK1/2/3 inhibitor exhibited reduced PIM1 and PIM2 levels. Genetic inhibition of canonical NFkB activity with IkB super-repressor or shRNA-mediated ablation of alternative NFkB pathway led to decrease of PIM2 and PIM3, suggesting that PIM-1/2/3 expresion in cHL depends at least in part on JAK-STAT and NFkB activity. To assess the role of PIM kinases in cell viability, we silenced expression of each PIM isoform (individually or simultaneously) in HDLM-2 cells. Knockdowns of individual PIM isoforms were associated with marked increased in remaining isoforms expression and were not associated with toxicity. In marked contrast, downregulation of all three isoforms increased cellular apoptosis by 17%. For this reason, for subsequent studies we used a newly developed pan-PIM inhibitor (SEL24-B489). The inhibitor was toxic to all cells with IC50 ranging from 3-5 µM. To determine mechanisms underlying toxicity, we assessed the activities of specific PIM substrates: 4EBP1, S6, and p65 (RelA). SEL24-B489 rapidly decreased PIM-dependent phosphorylation of these molecules in all tested cell lines. Furthermore, it reduced DNA binding activity of the NFκB-p65 complexes, indicating that PIM kinases modulate NFκB activity in cHL. For this reason, we next assessed the consequences of PIM inhibition on NFκB-dependent transcription. SEL24-B489 significantly downregulated mRNA of NFkB target genes associated with HRS cell survival and proliferation, such as Bfl-1, RelB and CD40. In cells treated with PIM inhibitor SEL24-B489 we also found markedly decreased expression NFkB-dependent cytokines and chemokines specifically shaping pro-tumoral microenvironment, such as IL-8, CCL5 and IL-13. In addition, cell lines exposed to SEL24-B489 treatment exhibited decreased expression of immunomodulatory PD-L1 and Gal-1 proteins. Finally, we investigated the efficacy of SEL24-B489 in vivo in the murine xenograft model using HDLM-2 cells. In contrast to animals exposed to vehicle alone, we observed inhibition of tumor growth by 95,8% in SEL24-B489-treated animals (p=0,0002). Consistent with the in vitro data, we observed strong downregulation of phospho-S6, GAL-1 and PD-L1 proteins in tumor sections from PIM inhibitor-treated animals. Taken together, we demonstrated that the oncogenic PIM-1/2/3 kinases are expressed in RS cells and their activity can be specifically blocked using a pan-PIM inhibitor SEL24-B489. PIM inhibition significantly reduced activity of specific PIM substrates and decreased the expression of NFκB-dependent pro-survival genes and key immunomodulatory proteins. These results highlight the pleiotropic activity of SEL24-B489 and indicate that PIM kinases are promising therapeutic targets in cHL. Disclosures Czardybon: Selvita S.A.: Employment. Galezowski:Selvita S.A.: Employment. Windak:Selvita S.A.: Employment. Brzozka:Selvita S.A.: Employment.


2005 ◽  
Vol 25 (20) ◽  
pp. 8960-8970 ◽  
Author(s):  
Andreas Fischer ◽  
Jürgen Klattig ◽  
Burkhard Kneitz ◽  
Holger Diez ◽  
Manfred Maier ◽  
...  

ABSTRACT The Hey basic helix-loop-helix transcription factors are downstream effectors of Notch signaling in the cardiovascular system. Mice lacking Hey2 develop cardiac hypertrophy, often associated with congenital heart defects, whereas combined Hey1/Hey2 deficiency leads to severe vascular defects and embryonic lethality around embryonic day E9.5. The molecular basis of these disorders is poorly understood, however, since target genes of Hey transcription factors in the affected tissues remain elusive. To identify genes regulated by Hey factors we have generated a conditional Hey1 knockout mouse. This strain was used to generate paired Hey2- and Hey1/2-deficient embryonic stem cell lines. Comparison of these cell lines by microarray analysis identified GATA4 and GATA6 as differentially expressed genes. Loss of Hey1/2 leads to elevated GATA4/6 and ANF mRNA levels in embryoid bodies, while forced expression of Hey factors strongly represses expression of the GATA4 and GATA6 promoter in various cell lines. In addition, the promoter activity of the GATA4/6 target gene ANF was inhibited by Hey1, Hey2, and HeyL. Protein interaction and mutation analyses suggest that repression is due to direct binding of Hey proteins to GATA4 and GATA6, blocking their transcriptional activity. In Hey2-deficient fetal hearts we observed elevated mRNA levels of ANF and CARP. Expression of ANF and Hey2 is normally restricted to the trabecular and compact myocardial layer, respectively. Intriguingly, loss of Hey2 leads to ectopic ANF expression in the compact layer, suggesting a direct role for Hey2 in limiting ANF expression in this cardiac compartment.


Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5668
Author(s):  
Laura García-García ◽  
Enrique Fernández-Tabanera ◽  
Saint T. Cervera ◽  
Raquel M. Melero-Fernández de Mera ◽  
Santiago Josa ◽  
...  

Ewing sarcoma is a rare pediatric tumor characterized by chromosomal translocations that give rise to aberrant chimeric transcription factors (e.g., EWSR1-FLI1). EWSR1-FLI1 promotes a specific cellular transcriptional program. Therefore, the study of EWSR1-FLI1 target genes is important to identify critical pathways involved in Ewing sarcoma tumorigenesis. In this work, we focused on the transcription factors regulated by EWSR1-FLI1 in Ewing sarcoma. Transcriptomic analysis of the Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in neural cell identity. The functional characterization of FEZF1 was performed in three Ewing sarcoma cell lines (A673, SK-N-MC, SK-ES-1) through an shRNA-directed silencing approach. FEZF1 knockdown inhibited clonogenicity and cell proliferation. Finally, the analysis of the FEZF1-dependent expression profile in A673 cells showed several neural genes regulated by FEZF1 and concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is transcriptionally regulated by EWSR1-FLI1 in Ewing sarcoma cells and is involved in the regulation of neural-specific genes, which could explain the neural-like phenotype observed in several Ewing sarcoma tumors and cell lines.


2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Kalina Andreeva ◽  
Nigel G. F. Cooper

The health and function of the visual system rely on a collaborative interaction between diverse classes of molecular regulators. One of these classes consists of transcription factors, which are known to bind to DNA and control the transcription activities of their target genes. For a long time, it was thought that the transcription factors were the only regulators of gene expression. More recently, however, a novel class of regulators emerged. This class consists of a large number of small noncoding endogenous RNAs, namely, miRNAs. The miRNAs compose an essential component of posttranscriptional gene regulation, since they ultimately control the fate of gene transcripts. The retina, as a part of the central nervous system, is a well-established model for unraveling the molecular mechanisms underlying neuronal and glial functions. Numerous recent efforts have been made towards identification of miRNAs and their inferred roles in the visual pathway. In this review, we summarize the current state of our knowledge regarding the expression and function of miRNA in the neural retina and we discuss their potential uses as biomarkers for some retinal disorders.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Timothy Warwick ◽  
Marcel H. Schulz ◽  
Stefan Günther ◽  
Ralf Gilsbach ◽  
Antonio Neme ◽  
...  

AbstractThe transcription factor vitamin D receptor (VDR) is the high affinity nuclear target of the biologically active form of vitamin D3 (1,25(OH)2D3). In order to identify pure genomic transcriptional effects of 1,25(OH)2D3, we used VDR cistrome, transcriptome and open chromatin data, obtained from the human monocytic cell line THP-1, for a novel hierarchical analysis applying three bioinformatics approaches. We predicted 75.6% of all early 1,25(OH)2D3-responding (2.5 or 4 h) and 57.4% of the late differentially expressed genes (24 h) to be primary VDR target genes. VDR knockout led to a complete loss of 1,25(OH)2D3–induced genome-wide gene regulation. Thus, there was no indication of any VDR-independent non-genomic actions of 1,25(OH)2D3 modulating its transcriptional response. Among the predicted primary VDR target genes, 47 were coding for transcription factors and thus may mediate secondary 1,25(OH)2D3 responses. CEBPA and ETS1 ChIP-seq data and RNA-seq following CEBPA knockdown were used to validate the predicted regulation of secondary vitamin D target genes by both transcription factors. In conclusion, a directional network containing 47 partly novel primary VDR target transcription factors describes secondary responses in a highly complex vitamin D signaling cascade. The central transcription factor VDR is indispensable for all transcriptome-wide effects of the nuclear hormone.


2003 ◽  
Vol 23 (21) ◽  
pp. 7460-7474 ◽  
Author(s):  
Natasha Rekhtman ◽  
Kevin S. Choe ◽  
Igor Matushansky ◽  
Stuart Murray ◽  
Tomas Stopka ◽  
...  

ABSTRACT PU.1 and GATA-1 are two hematopoietic specific transcription factors that play key roles in development of the myeloid and erythroid lineages, respectively. The two proteins bind to one another and inhibit each other's function in transcriptional activation and promotion of their respective differentiation programs. This mutual antagonism may be an important aspect of lineage commitment decisions. PU.1 can also act as an oncoprotein since deregulated expression of PU.1 in erythroid precursors causes erythroleukemias in mice. Studies of cultured mouse erythroleukemia cell lines indicate that one aspect of PU.1 function in erythroleukemogenesis is its ability to block erythroid differentiation by repressing GATA-1 (N. Rekhtman, F. Radparvar, T. Evans, and A. I. Skoultchi, Genes Dev. 13:1398-1411, 1999). We have investigated the mechanism of PU.1-mediated repression of GATA-1. We report here that PU.1 binds to GATA-1 on DNA. We localized the repression activity of PU.1 to a small acidic N-terminal domain that interacts with the C pocket of pRB, a well-known transcriptional corepressor. Repression of GATA-1 by PU.1 requires pRB, and pRB colocalizes with PU.1 and GATA-1 at repressed GATA-1 target genes. PU.1 and pRB also cooperate to block erythroid differentiation. Our results suggest that one of the mechanisms by which PU.1 antagonizes GATA-1 is by binding to it at GATA-1 target genes and tethering to these sites a corepressor that blocks transcriptional activity and thereby erythroid differentiation.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1436-1436
Author(s):  
Tomasz Sewastianik ◽  
Patryk Gorniak ◽  
Przemyslaw Kiliszek ◽  
Anna Polak ◽  
Emilia Bialopiotrowicz ◽  
...  

Abstract Precursor B-cell lymphoblastic leukemia (B-ALL) in adults remains a challenging clinical problem due to higher relapse rate and worse prognosis than in children. Although most of adult patients respond to standard induction therapy and complete remissions (CR) are typically achieved in 90% of patients, the majority of them eventually relapse. Our previous studies indicate that the minimal residual disease (MRD) status after induction therapy is the most important risk factor of relapse in adult B-ALL patients [Br J Haematol 2008;142:227-37]. We hypothesized that the survival of B-ALL blasts after induction therapy is a result of intrinsic characteristics of the tumor cells that determine resistance to chemotherapeutics. Therefore, we sought to identify the molecular background of B-ALL cells resistance to daunorubicin. To identify potential mechanisms responsible for drug-resistant phenotype, we utilized gene expression data from previous studies that assessed transcriptional profiles of drug-sensitive and drug-resistant cells. Using gene set enrichment analysis (GSEA) of daunorubicin-sensitive versus -resistant phenotypes of B-ALL cells we identified differential expression HIF1α and MYC transcription factors target genes (p=0.002, FDR=0.144; p<0.001; FDR=0.171, respectively). To verify these in silico findings, we compared the expression of a panel of MYC and HIF1α target genes in 41 newly diagnosed adult B-ALL patients who subsequently underwent standard induction therapy according to Polish Adult Leukemia Group PALG-ALL6 protocol. Expression of MYC and HIF1α signature genes was significantly higher in patients with positive (>0.1%) MRD status after completion of the induction therapy. Among studied HIF1α and MYC targets, lactate dehydrogenase A (LDHA) expression was the best predictor differentiating MRD+ versus MRD- patients (p=0.0019, FDR=0.005). It was of particular interest, since tumor stem cells are typically characterized by MYC and HIF1α transcriptional signatures, which rewire cellular metabolism towards aerobic glycolysis. We next assessed the effect of LDHA inhibition with a small molecule inhibitor, GSK2837808A, on proliferation and clonogenicity of human B-ALL cell lines. GSK2837808A markedly reduced lactate production in B-ALL cell lines (RS4;11, SEM-K2 and NALM-6) and decreased proliferation and colony formation in semi-solid medium in a dose-dependent fashion. Taken together, we show that adult B-ALL patients with positive MRD status after induction therapy exhibit concordant upregulation of HIF1α and MYC signature genes. Expression of LDHA, a target gene regulated by both HIF1α and MYC transcription factors was significantly higher in MRD-positive patients. Finally, inhibition of LDHA markedly decreased proliferation and clonogenicity of B-ALL cell lines, indicating that LDHA might be a therapeutic target in B-ALL. Disclosures No relevant conflicts of interest to declare.


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