Direct Targets Of Transcription Factors Research Articles

The TARGET System: Rapid Identification of Direct Targets of Transcription Factors by Gene Regulation in Plant Cells.

The TARGET system allows for the rapid identification of direct regulated gene targets of transcription factors (TFs). It employs the transient transformation of plant protoplasts with inducible nuclear entry of the TF and subsequent transcriptomic and/or ChIP-seq analysis. The ability to separate direct TF-target gene regulatory interactions from indirect downstream responses and the significantly shorter amount of time required to perform the assay, compared to the generation of transgenics, make this plant cell-based approach a valuable tool for a higher throughput approach to identify the genome-wide targets of multiple TFs, to build validated transcriptional networks in plants. Here, we describe the use of the TARGET system in Arabidopsis seedling root protoplasts to map the gene regulatory network downstream of transcription factors-of-interest.

The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus

Filamentous fungi, such as Neurospora crassa, are very efficient in deconstructing plant biomass by the secretion of an arsenal of plant cell wall-degrading enzymes, by remodeling metabolism to accommodate production of secreted enzymes, and by enabling transport and intracellular utilization of plant biomass components. Although a number of enzymes and transcriptional regulators involved in plant biomass utilization have been identified, how filamentous fungi sense and integrate nutritional information encoded in the plant cell wall into a regulatory hierarchy for optimal utilization of complex carbon sources is not understood. Here, we performed transcriptional profiling of N. crassa on 40 different carbon sources, including plant biomass, to provide data on how fungi sense simple to complex carbohydrates. From these data, we identified regulatory factors in N. crassa and characterized one (PDR-2) associated with pectin utilization and one with pectin/hemicellulose utilization (ARA-1). Using in vitro DNA affinity purification sequencing (DAP-seq), we identified direct targets of transcription factors involved in regulating genes encoding plant cell wall-degrading enzymes. In particular, our data clarified the role of the transcription factor VIB-1 in the regulation of genes encoding plant cell wall-degrading enzymes and nutrient scavenging and revealed a major role of the carbon catabolite repressor CRE-1 in regulating the expression of major facilitator transporter genes. These data contribute to a more complete understanding of cross talk between transcription factors and their target genes, which are involved in regulating nutrient sensing and plant biomass utilization on a global level.

Identification of direct targets of plant transcription factors using the GR fusion technique.

The glucocorticoid receptor-dependent activation of plant transcription factors has proven to be a powerful tool for the identification of their direct target genes. In the absence of the synthetic steroid hormone dexamethasone (dex), transcription factors fused to the hormone-binding domain of the glucocorticoid receptor (TF-GR) are held in an inactive state, due to their cytoplasmic localization. This requires physical interaction with the heat shock protein 90 (HSP90) complex. Hormone binding leads to disruption of the interaction between GR and HSP90 and allows TF-GR fusion proteins to enter the nucleus. Once inside the nucleus, they bind to specific DNA sequences and immediately activate or repress expression of their targets. This system is well suited for the identification of direct target genes of transcription factors in plants, as (A) there is little basal protein activity in the absence of dex, (B) steroid application leads to rapid transcription factor activation, (C) no side effects of dex treatment are observed on the physiology of the plant, and (D) secondary effects of transcription factor activity can be eliminated by simultaneous application of an inhibitor of protein biosynthesis, cycloheximide (cyc). In this chapter, we describe detailed protocols for the preparation of plant material, for dex and cyc treatment, for RNA extraction, and for the PCR-based or genome-wide identification of direct targets of transcription factors fused to GR.

Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana

Short noncoding RNAs have been demonstrated to play important roles in regulation of gene expression and stress responses, but the repertoire and functions of long noncoding RNAs (lncRNAs) remain largely unexplored, particularly in plants. To explore the role of lncRNAs in disease resistance, we used a strand-specific RNA-sequencing approach to identify lncRNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. Antisense transcription was found in c. 20% of the annotated A. thaliana genes. Several noncoding natural antisense transcripts responsive to F. oxysporum infection were found in genes implicated in disease defense. While the majority of the novel transcriptionally active regions (TARs) were adjacent to annotated genes and could be an extension of the annotated transcripts, 159 novel intergenic TARs, including 20 F. oxysporum-responsive lncTARs, were identified. Ten F. oxysporum-induced lncTARs were functionally characterized using T-DNA insertion or RNA-interference knockdown lines, and five were demonstrated to be related to disease development. Promoter analysis suggests that some of the F. oxysporum-induced lncTARs are direct targets of transcription factor(s) responsive to pathogen attack. Our results demonstrated that strand-specific RNA sequencing is a powerful tool for uncovering hidden levels of transcriptome and that IncRNAs are important components of the antifungal networks in A. thaliana.

Abstract 3058: miRNA networks mediate the tumor suppressive function of FOXO proteins.

Abstract FOXO transcription factors, as regulators of a variety of cellular functions, including promotion of apoptotic cell death, are negatively regulated by various oncogenic signaling cascades and have emerged as bona fide tumor suppressors. Indeed, studies by others and us have shown that the suppression of FOXO function is critical in promoting evasion of apoptosis and is a significant occurrence in several hematological malignancies. Consequently, FOXO proteins signify an important therapeutic target in hematopoietic malignancies as well as other types of cancer, where repression of FOXO plays a key role in malignancy. Since transcription factors are not yet easily “druggable," it is vital to identify mediators of FOXO function that can be readily targeted. It is now apparent that aberrant miRNA expression plays a major role in cell and tissue-specific manner in the pathogenesis of various types of cancers including hematological malignancies. Both miRNA loss of function and miRNA overexpression have been shown to target key cellular proteins and contribute to cancer pathogenesis. Conversely, miRNA genes themselves have been shown to be direct targets of transcription factors that are known as important tumor suppressors or oncogenic proteins. Through a systematic screening approach, we have identified members of three miRNA clusters that are dependent on FOXO transcription factors for expression. We have observed that the level of these miRNAs is dependent on BCR-ABL status of hematopoeitc cells and they their levels are changed in specimens from Leukemia patients. Our studies indicates a mechanism of action for FOXO tumor suppressors whereby members of two miRNA families are direct transcriptional targets of FOXO3. Moreover, these miRNAs target and reduce the expression of two key oncogenic factors, the serine/threonine kinase mTOR, and proto-onocogene c-myc, to keep cell growth at bay and prevent tumorigenesis. Our investigations have unraveled the miRNA arm of the FOXO tumor suppression network. Citation Format: Monica Nadler, Robin Zabolian, Kenneth Ndebele, thierry bertomeu, Octavian Bucur, Bodvael Pennarun, Roya Khosravi-Far. miRNA networks mediate the tumor suppressive function of FOXO proteins. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3058. doi:10.1158/1538-7445.AM2013-3058 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Combined Gene Expression and DNA Occupancy Profiling as a Strategy to Identify Therapeutic Target(s) in t(8;21) Acute Myeloid Leukemia

Microarray technology has contributed valuable information to gene expression signatures of leukemia and other types of cancers and helped to identify biological markers and potential therapeutic targets for treating these diseases. Acute myeloid leukemia (AML) is often caused by aberrant fusion transcription factors resulting from chromosomal translocations, and the dysregulated genes detected by microarray include both direct and indirect targets of the oncogenic transcription factors. The ChIP-chip technology enables the identification of direct targets of a transcription factor based on its promoter occupancy and cellular context. Using AML1-ETO9a-induced AML as a cancer model and using a combined gene expression and promoter occupancy profiling approach, we recently identified CD45 as a direct down-regulated target of t(8;21) fusion proteins. This finding subsequently led us to discover the enhanced Janus activated kinase (JAK)/signal transducer and activator of transcription (STAT) signaling pathway, which is negatively regulated by CD45, in t(8;21) AML. This review summarizes the background of t(8;21) leukemia, structural features of the translocation fusion proteins, and the merits of combining gene discovery technologies for the identification of therapeutic targets in t(8;21) leukemia.

Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

BackgroundPathway databases are becoming increasingly important and almost omnipresent in most types of biological and translational research. However, little is known about the quality and completeness of pathways stored in these databases. The present study conducts a comprehensive assessment of transcriptional regulatory pathways in humans for seven well-studied transcription factors: MYC, NOTCH1, BCL6, TP53, AR, STAT1, and RELA. The employed benchmarking methodology first involves integrating genome-wide binding with functional gene expression data to derive direct targets of transcription factors. Then the lists of experimentally obtained direct targets are compared with relevant lists of transcriptional targets from 10 commonly used pathway databases.ResultsThe results of this study show that for the majority of pathway databases, the overlap between experimentally obtained target genes and targets reported in transcriptional regulatory pathway databases is surprisingly small and often is not statistically significant. The only exception is MetaCore pathway database which yields statistically significant intersection with experimental results in 84% cases. Additionally, we suggest that the lists of experimentally derived direct targets obtained in this study can be used to reveal new biological insight in transcriptional regulation and suggest novel putative therapeutic targets in cancer.ConclusionsOur study opens a debate on validity of using many popular pathway databases to obtain transcriptional regulatory targets. We conclude that the choice of pathway databases should be informed by solid scientific evidence and rigorous empirical evaluation.ReviewersThis article was reviewed by Prof. Wing Hung Wong, Dr. Thiago Motta Venancio (nominated by Dr. L Aravind), and Prof. Geoff J McLachlan.

Genome-wide Analysis of CDX2 Binding in Intestinal Epithelial Cells (Caco-2)

The CDX2 transcription factor is known to play a crucial role in inhibiting proliferation, promoting differentiation and the expression of intestinal specific genes in intestinal cells. The overall effect of CDX2 in intestinal cells has previously been investigated in conditional knock-out mice, revealing a critical role of CDX2 in the formation of the normal intestinal identity. The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. The ChIP-seq technique combines chromatin immunoprecipitation (ChIP) with next generation sequencing resulting in a high throughput experimental method of identifying direct targets of specific transcription factors. The method was applied to CDX2, leading to the identification of the direct binding of CDX2 to several known and novel target genes in the intestinal cell. Examination of the transcript levels of selected genes verified the regulatory role of CDX2 binding. The results place CDX2 as a key node in a transcription factor network controlling the proliferation and differentiation of intestinal cells.

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3

The identification of direct targets of transcription factors is a key problem in the study of gene regulatory networks. However, the use of high throughput experimental methods, such as ChIP-chip and ChIP-sequencing, is limited by their high cost and strong dependence on cellular type and context. We developed a computational method for the genome-wide identification of functional transcription factor binding sites based on positional weight matrices, comparative genomics, and gene expression profiling. The method was applied to Stat3, a transcription factor playing crucial roles in inflammation, immunity and oncogenesis, and able to induce distinct subsets of target genes in different cell types or conditions. A newly generated positional weight matrix enabled us to assign affinity scores of high specificity, as measured by EMSA competition assays. Phylogenetic conservation with 7 vertebrate species was used to select the binding sites most likely to be functional. Validation was carried out on predicted sites within genes identified as differentially expressed in the presence or absence of Stat3 by microarray analysis. Twelve of the fourteen sites tested were bound by Stat3 in vivo, as assessed by Chromatin Immunoprecipitation, allowing us to identify 9 Stat3 transcriptional targets. Given its high validation rate, and the availability of large transcription factor-dependent gene expression datasets obtained under diverse experimental conditions, our approach appears to be a valid alternative to high-throughput experimental assays for the discovery of novel direct targets of transcription factors.

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

Genome-wide identification of bona-fide targets of transcription factors in mammalian cells is still a challenge. We present a novel integrated computational and experimental approach to identify direct targets of a transcription factor. This consists of measuring time-course (dynamic) gene expression profiles upon perturbation of the transcription factor under study, and in applying a novel "reverse-engineering" algorithm (TSNI) to rank genes according to their probability of being direct targets. Using primary keratinocytes as a model system, we identified novel transcriptional target genes of TRP63, a crucial regulator of skin development. TSNI-predicted TRP63 target genes were validated by Trp63 knockdown and by ChIP-chip to identify TRP63-bound regions in vivo. Our study revealed that short sampling times, in the order of minutes, are needed to capture the dynamics of gene expression in mammalian cells. We show that TRP63 transiently regulates a subset of its direct targets, thus highlighting the importance of considering temporal dynamics when identifying transcriptional targets. Using this approach, we uncovered a previously unsuspected transient regulation of the AP-1 complex by TRP63 through direct regulation of a subset of AP-1 components. The integrated experimental and computational approach described here is readily applicable to other transcription factors in mammalian systems and is complementary to genome-wide identification of transcription-factor binding sites.

Cis-regulatory element-based genome-wide identification of DREB1/CBF targets in Arabidopsis

Microarray analysis is used to identify transcriptional targets. However, the direct targets of transcription factors cannot be distinguished from indirect ones; further, genes with low-expression levels cannot be identified by this method. In the present study, we exploit the cis-element dehydration-responsive element (DRE) that is known to be responsible for the transcription of DRE binding factor 1 (DREB1) targets in the promoter region of all Arabidopsis genes. Putative targets whose promoters contain the elements were verified by both microarray and reverse transcription-polymerase chain reaction (RT-PCR) analysis. Five new DREB1/CBF direct targets were identified. Compared with traditional microarray analysis, our method is convenient and cost-effective for identifying the downstream targets of transcription factors.

Transcription Factor Target Practice

In this issue of Cell, Hallikas et al. (2006) and Wei et al. (2006) describe different ways of identifying direct targets of transcription factors and their corresponding regulatory sequences in the genome. Although still under development, these studies provide an efficient way to decipher regulatory networks.

BEARR: Batch Extraction and Analysis of cis-Regulatory Regions.

Transcription factors play important roles in regulating biological and disease processes. Microarray technology has enabled researchers to simultaneously monitor changes in the expression of thousands of transcripts. By identifying specific transcription factor binding sites in the cis-regulatory regions of differentially expressed genes, it is then possible to identify direct targets of transcription factors, model transcriptional regulatory networks and mine the dataset for relevant targets for experimental and clinical manipulation. We have developed web-based software to assist biologists in efficiently carrying out the analysis of microarray data from studies of specific transcription factors. Batch Extraction and Analysis of cis-Regulatory Regions, or BEARR, accepts gene identifier lists from microarray data analysis tools and facilitates identification, extraction and analysis of regulatory regions from the large amount of data that is typically generated in these types of studies. The software is publicly available at http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/.