Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells

KLF4: a multifunctional nexus connecting tumor progression and immune regulation

Krüppel-like factors (KLFs) regulate various biological processes such as cell proliferation, migration, invasion, and differentiation as gene transcription factors. Signaling pathways which mediated by KLF4 and KLF4 have a sophisticated role in tumors due to multiple factors, including the types or stage of tumors. KLF4 plays a promoter role in tumorigenesis and development, or tumor suppressor as a context-dependent anti- and pro-inflammatory factor. KLF4 over-expression increases CD8+T cell differentiation and enhances the antitumor immunity. This review aims to provide information about the relationship of KLF4 in immunity with tumors and to guide the future study.

Use of Nuclear Factor of Activated T Cell-Regulated Gene Expression for Monitoring Immunosuppression with Extended-Release Tacrolimus after Liver Transplantation-A Proof of Concept

BACKGROUND

There is a narrow therapeutic window for immunosuppression using calcineurin inhibitors. Drug trough levels do not reflect immunosuppression and should be replaced by pharmacodynamic monitoring. This prospective cohort study was designed to evaluate the effect of an extended-release formulation of tacrolimus (LCP Tac) on the nuclear factor of activated T cell-regulated gene expression (NFAT-RGE).

METHODS

The expression of interleukin-2, interferon-γ, granulocyte-macrophage colony-stimulating factor, and three reference genes was measured. Samples from 23 patients at defined time points in the first year after liver transplantation were analyzed using a droplet digital polymerase chain reaction.

RESULTS

All samples were within the targeted trough levels of LCP Tac, and their LCP Tac peak levels and residual NFAT-RGE showed a strong inverse correlation (r = -0.8). Most importantly, there was an individual immunosuppressive response to the LCP Tac. The mean individual trough effect of LCP Tac on the three target genes when all time points were pooled was 33% (26-56%) in patients without infection and 81% (53-95%) in those with infection (p < 0.011). The mean individual peak effect was 48% (44-64%) in patients without infection and 91% (90-94%) in those with infection (p < 0.001).

CONCLUSIONS

Thus, tailored immunosuppression based on residual NFAT-RGE could prevent infections associated with over-immunosuppression early after liver transplantation.

Naringin as a natural candidate for anti-autoimmune hepatitis: Inhibitory potency and hepatoprotective mechanism

BACKGROUND

Autoimmune hepatitis (AIH), primarily mediated by T cells, is characterized by liver inflammation. Despite the advancements in understanding its pathogenesis, effective therapeutic options are limited. Naringin, a flavonoid abundant in citrus fruits, is recognized for its anti-inflammatory properties and ability to protect against various inflammatory diseases, including drug-induced liver injury. However, the exact effects of naringin on AIH and the mechanisms involved remain poorly understood.

PURPOSE

We aim to determine the role of naringin in AIH, exploring its targets and actions in this disease.

METHODS

Network pharmacology, molecular docking, and molecular dynamics simulations were utilized to predict the HUB targets connecting naringin, T cell-mediated autoimmune disorders, and AIH. Cellular thermal shift assays were used to determine the binding abilities of naringin with the HUB targets. An in vivo experiment confirmed the impact of naringin treatment on AIH development and underlying mechanisms.

RESULTS

Naringin demonstrated therapeutic effects on ConA-induced AIH. There were 455 shared targets between naringin, T cell-mediated autoimmune diseases, and AIH. Ten HUB genes (AKT1, ALB, IL-6, IL-1β, CTNNB1, TNF, TP53, MAPK3, VEGFA, and JUN) were identified through the PPI network. Gene ontology analysis revealed involvement in gene expression regulation, lipopolysaccharide-mediated signaling, and I-kappa kinase/NFκB signaling. Pathway analysis suggested TNF, Th1/Th2 cell differentiation, and Toll-like receptor pathways, with favorable naringin-HUB gene binding. Molecular docking confirmed albumin (ALB), IL-1β, IL-6, and TNF as primary targets for naringin. Molecular dynamics simulations showed stable binding in ALB-naringin, TNF-naringin, and IL-1β-naringin complexes. Naringin's hepatoprotective effect on AIH was supported by increased serum ALB and decreased hepatic inflammatory cytokines including IL-1β, IL-6, and TNF-α.

CONCLUSION

Our data underscore the potential of naringin as a preventive or therapeutical agent in T cell-mediated autoimmune diseases including AIH.

Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells

Exhausted CD8 T cells during chronic inflammatory responses against viral infections and cancer are phenotypically and functionally heterogeneous. In particular, CD8 T cells with cytolytic effector function have been recently identified among the exhausted CD8 T cell subsets. However, the regulation of their differentiation and function remains largely unknown. Here, we report that Krüppel-like factor 4 (KLF4) is a critical regulator of the exhaustion process, promoting the cytolytic effector function of exhausted CD8 T cells. KLF4-expressing CD8 T cells in exhaustion contexts showed the features of transitory effector CD8 T cells. Enforced KLF4 expression increased CD8 T cell differentiation into transitory effector subsets and enhanced their antitumor immunity. We further demonstrated that KLF4 also showed a capacity of reinvigorating exhausted CD8 T cells. Last, high KLF4 expression was positively correlated with a favorable prognosis in human patients with cancer. Our study highlights the potential impacts of KLF4 on CD8 T cell exhaustion and antitumor immune therapy.

Proteomic study on the lymphocytes from pregnant Wistar rat females treated with immunosuppressive regimen

Kidney transplantation remains the therapeutic option for patients with end-stage kidney disease. Current immunosuppressive regimens are efficient in combating acute kidney rejection. However, insights into chronic kidney allograft injury remains limited. Simultaneously, pregnancy is more common after kidney transplantation than during dialysis treatment. Due to ethical issues, comprehensive studies on the impact of immunosuppressive regimens on pregnancy are challenging. The study aimed to investigate the proteomic status of lymphocytes obtained from pregnant female rats under immunosuppressive treatment. The experiment involved a group of 10 female, pregnant Wistar rats, five of which were treated with tacrolimus, mofetil mycophenolate, and glucocorticosteroids; five were used as control. The lymphocytes were obtained and analyzed with mass spectrometry. Measurements were processed by a database search in the ProteinPilot software with a cutoff of 1% false discovery rate. The outcomes were verified statistically by a t-test (p value < 0.05) regarding proteins up- and downregulation. A total of 2082 proteins were identified in all experiments. Eight hundred five proteins were quantified in an absolute manner in a data-independent acquisition-total protein approach analysis. Ninety-five proteins were recognized as present at different concentrations in analyzed groups and were annotated to intracellular pathways. The proteins involved in nonsense-mediated decay and L13a-mediated translational silencing of ceruloplasmin expression were recognized as downregulated. The set of proteins clinically identified as acute phase proteins was upregulated. Despite the blockade of adaptive cellular immunity, the lymphocytes in the analyzed group reveal sustained proinflammatory status with decreased ability to regulate translation. This potentially affects pregnancy and immunity.

Monitoring of gene expression in tacrolimus-treated de novo renal allograft recipients facilitates individualized immunosuppression: Results of the IMAGEN study

AIMS

Calcineurin inhibitors (CNI) have a small therapeutic window, and drug monitoring is required. Pharmacokinetic monitoring does not correlate sufficiently with clinical outcome. Therefore, the expression of nuclear factor of activated T cells (NFAT)-regulated genes in the peripheral blood has been suggested as a potentially useful immune monitoring tool to optimize CNI therapy. NFAT-regulated gene expression (RGE) was evaluated in renal allograft recipients as predictive biomarker to detect patients at risk of acute rejection or infections.

METHODS

NFAT-RGE (interleukin-2, interferon-γ, granular-macrophage colony-stimulating factor) was evaluated by quantitative real-time polymerase chain reaction in whole blood samples at day 7, day 14, month 1, 3, and 6 after transplantation in 64 de novo renal allograft recipients from 3 European centres. Immunosuppression consisted of tacrolimus (Tac), mycophenolic acid, and corticosteroids.

RESULTS

Tac concentrations (C0 and C1.5) correlated inversely with NFAT-RGE (P < .01). NFAT-RGE showed a high interindividual variability (1-61%). Patients with high residual gene expression (NFAT-RGE ≥30%) were at the increased risk of acute rejection in the following months (35 vs. 5%, P = .02), whereas patients with low residual gene expression (NFAT-RGE <30%) showed a higher incidence of viral complications, especially cytomegalovirus and BK virus replication (52.5 vs. 10%, P = .01).

CONCLUSIONS

NFAT-RGE was confirmed as a potential noninvasive early predictive biomarker in the immediate post-transplant period to detect patients at risk of acute rejection and infectious complications in Tac-treated renal allograft recipients. Monitoring of NFAT-RGE may provide additional useful information for physicians to achieve individualized Tac treatment.

The Multifaceted Output of c-Jun Biological Activity: Focus at the Junction of CD8 T Cell Activation and Exhaustion

c-Jun is a major component of the dimeric transcription factor activator protein-1 (AP-1), a paradigm for transcriptional response to extracellular signaling, whose components are basic-Leucine Zipper (bZIP) transcription factors of the Jun, Fos, activating transcription factor (ATF), ATF-like (BATF) and Jun dimerization protein 2 (JDP2) gene families. Extracellular signals regulate c-Jun/AP-1 activity at multiple levels, including transcriptional and posttranscriptional regulation of c-Jun expression and transactivity, in turn, establishing the magnitude and the duration of c-Jun/AP-1 activation. Another important level of c-Jun/AP-1 regulation is due to the capability of Jun family members to bind DNA as a heterodimer with every other member of the AP-1 family, and to interact with other classes of transcription factors, thereby acquiring the potential to integrate diverse extrinsic and intrinsic signals into combinatorial regulation of gene expression. Here, we review how these features of c-Jun/AP-1 regulation underlie the multifaceted output of c-Jun biological activity, eliciting quite distinct cellular responses, such as neoplastic transformation, differentiation and apoptosis, in different cell types. In particular, we focus on the current understanding of the role of c-Jun/AP-1 in the response of CD8 T cells to acute infection and cancer. We highlight the transcriptional and epigenetic regulatory mechanisms through which c-Jun/AP-1 participates in the productive immune response of CD8 T cells, and how its downregulation may contribute to the dysfunctional state of tumor infiltrating CD8 T cells. Additionally, we discuss recent insights pointing at c-Jun as a suitable target for immunotherapy-based combination approaches to reinvigorate anti-tumor immune functions.

From experiment-driven database analyses to database-driven experiments in Arabidopsis thaliana transcription factor research

Experiment-driven database analysis is employed in forward genetics to predict the function of genes assocíated with a mutant phenotype. These analyses subsequently lead to database-driven experiments involving reverse genetics to verify functional predictions based on bioinformatic analyses. Genomic transcription factors (TFs) are key regulators of gene expression by binding to short regulatory sequences and by interacting with other TFs. Currently more than 2400 TFs are predicted for A. thaliana. As DNA-binding proteins they are particularly amenable to database-driven experiments, especially when their binding site specificities are known. Databases are available for predicting binding sites for specific TFs in regulatory sequences. Since most of these bioinformatically identified binding sites may not be functional, additional experiments for identifying the actual in vivo binding sites for TFs are required. Recently, large scale approaches were employed to determine binding sites for many A. thaliana TFs. With these approaches binding sites for 984 unique TFs were determined experimentally. An area deserving further research is proposed for interacting TFs. Most of the A. thaliana genes are under combinatorial control, and in vivo interacting TFs, similar to mammalian TFs, may bind to combinatorial elements in which the binding sites vary from those detected with the single TFs.

Transcriptome activity of isochores during preimplantation process in human and mouse

This work investigates the role of isochores during preimplantation process. Using RNA-seq data from human and mouse preimplantation stages, we created the spatio-temporal transcriptional profiles of the isochores during preimplantation. We found that from early to late stages, GC-rich isochores increase their expression while GC-poor ones decrease it. Network analysis revealed that modules with few coexpressed isochores are GC-poorer than medium-large ones, characterized by an opposite expression as preimplantation advances, decreasing and increasing respectively. Our results reveal a functional contribution of the isochores, supporting the presence of structural-functional interactions during maturation and early-embryonic development.

Effects of fermented soybean meal on innate immunity-related gene expressions in nursery pigs acutely challenged with lipopolysaccharides

This experiment was to determine if replacing soybean meal with fermented soybean meal (FSBM) would reduce the innate immune response after lipopolysaccharide challenge and the changes of gene expression profiles associated with this response. Forty-eight 21 day-old pigs were housed individually and fed three diets for 15 days: CON (a diet without FSBM or spray-dried plasma protein; SDPP), PP7 (a diet with 7% SDPP), and FS10 (a diet with 10% FSBM). Pigs were fitted with a jugular vein catheters receiving lipopolysaccharide challenge (25 μg/kg body weight (BW)) on day 15. Blood was collected for 5 h at 30-min intervals to measure cortisol. Expressions of gene transcripts in total RNA from leukocytes were compared using an oligonucleotide microarray at 210 min after lipopolysaccharides injection. Cortisol of FS10 was lower (P < 0.05) than CON after lipopolysaccharides challenge. The expression levels of 17 transcripts, including cytosolic glutathione peroxidase and glutathione S-transferase A4-4 were increased (P < 0.05), whereas 23 genes including adiponectin, neonatal Fc receptor and tumor necrosis factor ligand superfamily member 5 were decreased (P < 0.05) in FS10. This study suggests that FSBM-fed pigs can modulate expression of genes related to inflammatory response and anti-oxidant activity which can be a potential reason for reduced serum cortisol.

The Calcineurin Inhibitor-Sparing (CIS) Trial - individualised calcineurin-inhibitor treatment by immunomonitoring in renal allograft recipients: protocol for a randomised controlled trial

Background

Adequate monitoring tools are required to optimise the immunosuppressive therapy of an individual patient. Particularly, in calcineurin inhibitors, as critical dose drugs with a narrow therapeutic range, the optimal monitoring strategies are discussed in terms of safety and efficacy. Nevertheless, no pharmacokinetic monitoring markers reflect the biological activity of the drug. A new quantitative analysis of gene expression was employed to directly measure the functional effects of calcineurin inhibition: the transcriptional activities of the nuclear factor of activated T-cell (NFAT)-regulated genes in the peripheral blood.

Methods/Design

The CIS study is a randomised prospective controlled trial, comparing a ciclosporin A (CsA)-based immunosuppressive regimen monitored by CsA trough levels to a CsA-based immunosuppressive regimen monitored by residual NFAT-regulated gene expression. Pulse wave velocity as an accepted surrogate marker of the cardiovascular risk is assessed in both study groups. Our hypothesis is that an individualised CsA therapy monitored by residual NFAT-regulated gene expression results in a significantly lower cardiovascular risk compared to CsA therapy monitored by CsA trough levels.

Discussion

There is a lack of evidence in individualising standard immunosuppression in renal allograft recipients. The CIS study will consider the feasibility of individualised ciclosporin A immunosuppression by pharmacodynamic monitoring and evaluate the opportunity to reduce cardiovascular risk while maintaining sufficient immunosuppression.

Trial registration

EudraCT identifier 2011-003547-21, registration date 18 July 2011

https://www.clinicaltrialsregister.eu

NF-κB factors control the induction of NFATc1 in B lymphocytes

In peripheral lymphocytes, the transcription factors (TFs) NF-κB, NFAT, and AP-1 are the prime targets of signals that emerge from immune receptors. Upon activation, these TFs induce gene networks that orchestrate the growth, expansion, and effector function of peripheral lymphocytes. NFAT and NF-κB factors share several properties, such as a similar mode of induction and architecture in their DNA-binding domain, and there is a subgroup of κB-like DNA promoter motifs that are bound by both types of TFs. However, unlike NFAT and AP-1 factors that interact and collaborate in binding to DNA, NFAT, and NF-κB seem neither to interact nor to collaborate. We show here that NF-κB1/p50 and c-Rel, the most prominent NF-κB proteins in BCR-induced splenic B cells, control the induction of NFATc1/αA, a prominent short NFATc1 isoform. In part, this is mediated through two composite κB/NFAT-binding sites in the inducible Nfatc1 P1 promoter that directs the induction of NFATc1/αA by BCR signals. In concert with coreceptor signals that induce NF-κB factors, BCR signaling induces a persistent generation of NFATc1/αA. These data suggest a tight connection between NFATc1 and NF-κB induction in B lymphocytes contributing to the effector function of peripheral B cells.

MatrixCatch--a novel tool for the recognition of composite regulatory elements in promoters

BACKGROUND

Accurate recognition of regulatory elements in promoters is an essential prerequisite for understanding the mechanisms of gene regulation at the level of transcription. Composite regulatory elements represent a particular type of such transcriptional regulatory elements consisting of pairs of individual DNA motifs. In contrast to the present approach, most available recognition techniques are based purely on statistical evaluation of the occurrence of single motifs. Such methods are limited in application, since the accuracy of recognition is greatly dependent on the size and quality of the sequence dataset. Methods that exploit available knowledge and have broad applicability are evidently needed.

RESULTS

We developed a novel method to identify composite regulatory elements in promoters using a library of known examples. In depth investigation of regularities encoded in known composite elements allowed us to introduce a new characteristic measure and to improve the specificity compared with other methods. Tests on an established benchmark and real genomic data show that our method outperforms other available methods based either on known examples or statistical evaluations. In addition to better recognition, a practical advantage of this method is first the ability to detect a high number of different types of composite elements, and second direct biological interpretation of the identified results. The program is available at http://gnaweb.helmholtz-hzi.de/cgi-bin/MCatch/MatrixCatch.pl and includes an option to extend the provided library by user supplied data.

CONCLUSIONS

The novel algorithm for the identification of composite regulatory elements presented in this paper was proved to be superior to existing methods. Its application to tissue specific promoters identified several highly specific composite elements with relevance to their biological function. This approach together with other methods will further advance the understanding of transcriptional regulation of genes.

An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein

Human genome sequencing has resulted in a great body of data, including a stunningly large number of single nucleotide polymorphisms (SNPs) with unknown phenotypic manifestations. Identification and comprehensive analysis of regulatory SNPs in human gene promoters will help quantify the effects of these SNPs on human health. Based on our experimental and computer-aided study of SNPs in TATA boxes and the use of literature data, we have derived an equation for TBP/TATA equilibrium binding in three successive steps: TATA-binding protein (TBP) sliding along DNA due to their nonspecific affinity for each other ↔ recognition of the TATA box ↔ stabilization of the TBP/TATA complex. Using this equation, we have analyzed TATA boxes containing SNPs associated with human diseases and made in silico predictions of changes in TBP/TATA affinity. An electrophoretic mobility shift assay (EMSA)-based experimental study performed under the most standardized conditions demonstrates that the experimentally measured values are highly correlated with the predicted values: the coefficient of linear correlation, r, was 0.822 at a significance level of α<10⁻⁷ for equilibrium K(D) values, (-ln K(D)), and 0.785 at a significance level of α<10⁻³ for changes in equilibrium K(D) (δ) due to SNPs in the TATA boxes (δ= -ln[K(D,TATAMut)]-(-ln[K(D,TATAMut)])). It has been demonstrated that the SNPs associated with increased risk of human diseases such as α-, β- and δ-thalassemia, myocardial infarction and thrombophlebitis, changes in immune response, amyotrophic lateral sclerosis, lung cancer and hemophilia B Leyden cause 2-4-fold changes in TBP/TATA affinity in most cases. The results obtained strongly suggest that the TBP/TATA equilibrium binding equation derived can be used for analysis of TATA-box sequences and identification of SNPs with a potential of being functionally important.

Transcriptome map of mouse isochores in embryonic and neonatal cortex

Several studies on adult tissues agree on the presence of a positive effect of the genomic and genic base composition on mammalian gene expression. Recent literature supports the idea that during developmental processes GC-poor genomic regions are preferentially implicated. We investigate the relationship between the compositional properties of the isochores and of the genes with their respective expression activity during developmental processes. Using RNA-seq data from two distinct developmental stages of the mouse cortex, embryonic day 18 (E18) and postnatal day 7 (P7), we established for the first time a developmental-related transcriptome map of the mouse isochores. Additionally, for each stage we estimated the correlation between isochores' GC level and their expression activity, and the genes' expression patterns for each isochore family. Our analyses add evidence supporting the idea that during development GC-poor isochores are preferentially implicated, and confirm the positive effect of genes' GC level on their expression activity.

3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations

We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein–DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein–DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.

Isochores and the regulation of gene expression in the human genome

It is well established that changes in the phenotype depend much more on changes in gene expression than on changes in protein-coding genes, and that cis-regulatory sequences and chromatin structure are two major factors influencing gene expression. Here, we investigated these factors at the genome-wide level by focusing on the trinucleotide patterns in the 0.1- to 25-kb regions flanking the human genes that are present in the GC-poorest L1 and GC-richest H3 isochore families, the other families exhibiting intermediate patterns. We could show 1) that the trinucleotide patterns of the 25-kb gene-flanking regions are representative of the very different patterns already reported for the whole isochores from the L1 and H3 families and, expectedly, identical in upstream and downstream locations; 2) that the patterns of the 0.1- to 0.5-kb regions in the L1 and H3 isochores are remarkably more divergent and more specific when compared with those of the 25-kb regions, as well as different in the upstream and downstream locations; and 3) that these patterns fade into the 25-kb patterns around 5kb in both upstream and downstream locations. The 25-kb findings indicate differences in nucleosome positioning and density in different isochore families, those of the 0.1- to 0.5-kb sequences indicate differences in the transcription factors that bind upstream and downstream of genes. These results indicate differences in the regulation of genes located in different isochore families, a point of functional and evolutionary relevance.

Compositional perspectives on human brain aging

Using publicly available microarray data from the frontal cortex of 30 individuals, spanning the ages of 26-106 years old, we investigate the expression patterns of compositionally distinct genes during human brain aging. Our analyses revealed that at advance ages, GC-poor genes appear to be induced while GC-rich genes are repressed. Interestingly, investigations upon two different types of genes, named pivotal (permanently expressed genes) and non-pivotal (on-off regulated genes), revealed an induction of the GC-poor pivotal genes and a repression of the GC-richer non-pivotal genes at advanced ages. Summarizing, this study shows that genes with different compositional properties have opposite age-related expression patterns, suggesting an implication of different regulation mechanisms related to their localization in different chromatin structure, which correlates with the GC level. Finally, an innovative approach on investigating human aging process is suggested, which involves the base composition of genes.

Conservation of the ST6Gal I gene and its expression in the mammary gland

Milk sialoglycoconjugates can protect the gastrointestinal tract of the suckling neonate by competitively binding to invading pathogens and promoting growth of beneficial flora, and their potential role in postnatal brain development is of particular interest in human infant nutrition. Although the concentration and the distribution of sialoglycoconjugates have been extensively studied in the milk of various species, the investigation of sialyltransferase gene expression in the mammary gland, in the context of lactation, has been limited. The sialyltransferase enzyme ST6Gal I transfers sialic acid from CMP-sialic acid to type 2 (Galβ1,4GlcNAc) free disaccharides or the termini of N- or O-linked oligosaccharides using an α2,6-linkage. Expression of the ST6Gal I gene is primarily regulated at the level of transcription through the use of several cell and development-specific promoters, producing transcripts with divergent 5' untranslated regions (UTR). In the mouse mammary gland, the novel 5'UTR exon (L) appears to be associated with a drastic increase in ST6Gal I gene expression during lactation. We find that rats also possess an exon (L), suggesting conservation of this regulatory mechanism in rodents. In contrast, an exon (L)-containing transcript was not detected in the lactating bovine or human mammary gland. We also observed a trend of increasing ST6Gal I gene expression in the bovine mammary gland, culminating in involution. This is in contrast to species such as mice where the greatest change in ST6Gal I gene expression occurs between pregnancy and lactation, suggesting different roles in rodents vs. other mammals for α2,6-sialylated oligosaccharides present in milk.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

The genetic code-the binding specificity of all transfer-RNAs--defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the approximately 1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.

The CCAAT/enhancer binding protein beta (C/EBPbeta) cooperates with NFAT to control expression of the calcineurin regulatory protein RCAN1-4

Regulator of calcineurin 1 (RCAN1) inhibits the protein phosphatase calcineurin and is required for appropriate immune responses, synaptic plasticity, vascular tone, angiogenesis, and cardiac remodeling. Expression of the RCAN1-4 isoform is under the control of the calcineurin-responsive transcription factor NFAT. Typically, NFATs act in cooperation with other transcription factors to achieve maximal activation of gene expression. In this study, we identify the CCAAT/enhancer binding protein beta (C/EBPbeta) as an NFAT binding partner that cooperates with NFAT to regulate RCAN1-4 expression. Numerous C/EBPbeta binding sites are conserved in the RCAN1-4 proximal promoter. Overexpression of C/EBPbeta increased activity of both the endogenous mouse Rcan1-4 gene and a human RCAN1-4 luciferase reporter. Binding of C/EBPbeta to multiple sites in the promoter was verified using electrophoretic mobility shift assays and chromatin immunoprecipitation. A direct interaction between C/EBPbeta and NFAT was demonstrated by co-immunoprecipitation of proteins and complex formation at NFAT-C/EBPbeta composite sites. Depletion of endogenous C/EBPbeta decreased maximal activation of RCAN1-4 expression by calcineurin, whereas inhibition of calcineurin did not alter the ability of C/EBPbeta to activate RCAN1-4 expression. Together, these findings suggest that calcineurin/NFAT activation of RCAN1-4 expression is in part dependent upon C/EBPbeta, whereas activation by C/EBPbeta is not dependent on calcineurin and may provide a calcineurin-independent pathway for regulating RCAN1-4 expression. Importantly, nuclear localization, C/EBPbeta DNA binding activity and occupancy of the Rcan1-4 promoter increased in mouse models of heart failure demonstrating in vivo activation of this pathway to regulate Rcan1-4 expression and ultimately shape the dynamics of calcineurin-dependent signaling.

Identification of promoter regions and regulatory sites

Promoter sequences are the main regulatory elements of gene expression. Their recognition by computer algorithms is fundamental for understanding gene expression patterns, cell specificity and development. This chapter describes the advanced approaches to identify promoters in animal, plant and bacterial sequences. Also, we discuss an approach to identify statistically significant regulatory motifs in genomic sequences.

SSMBS: a web server to locate sequentially separated motifs in biological sequences

The identification of sequence (amino acids or nucleotides) motifs in a particular order in biological sequences has proved to be of interest. This paper describes a computing server,SSMBS, which can locate and display the occurrences of user-defined biologically important sequence motifs (a maximum of five) present in a specific order in protein and nucleotide sequences. While the server can efficiently locate motifs specified using regular expressions, it can also find occurrences of long and complex motifs. The computation is carried out by an algorithm developed using the concepts of quantifiers in regular expressions. The web server is available to users around the clock at http://dicsoft1.physics.iisc.ernet.in/ssmbs/.

FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1

The mechanisms of blood vessel maturation into distinct parts of the blood vasculature such as arteries, veins, and capillaries have been the subject of intense investigation over recent years. In contrast, our knowledge of lymphatic vessel maturation is still fragmentary. In this study, we provide a molecular and morphological characterization of the major steps in the maturation of the primary lymphatic capillary plexus into collecting lymphatic vessels during development and show that forkhead transcription factor Foxc2 controls this process. We further identify transcription factor NFATc1 as a novel regulator of lymphatic development and describe a previously unsuspected link between NFATc1 and Foxc2 in the regulation of lymphatic maturation. We also provide a genome-wide map of FOXC2-binding sites in lymphatic endothelial cells, identify a novel consensus FOXC2 sequence, and show that NFATc1 physically interacts with FOXC2-binding enhancers. As damage to collecting vessels is a major cause of lymphatic dysfunction in humans, our results suggest that FOXC2 and NFATc1 are potential targets for therapeutic intervention.

Evolutionary computation for discovery of composite transcription factor binding sites

Previous research demonstrated the use of evolutionary computation for the discovery of transcription factor binding sites (TFBS) in promoter regions upstream of coexpressed genes. However, it remained unclear whether or not composite TFBS elements, commonly found in higher organisms where two or more TFBSs form functional complexes, could also be identified by using this approach. Here, we present an important refinement of our previous algorithm and test the identification of composite elements using NFAT/AP-1 as an example. We demonstrate that by using appropriate existing parameters such as window size, novel-scoring methods such as central bonusing and methods of self-adaptation to automatically adjust the variation operators during the evolutionary search, TFBSs of different sizes and complexity can be identified as top solutions. Some of these solutions have known experimental relationships with NFAT/AP-1. We also indicate that even after properly tuning the model parameters, the choice of the appropriate window size has a significant effect on algorithm performance. We believe that this improved algorithm will greatly augment TFBS discovery.

Identification and analysis of co-occurrence networks with NetCutter

Background

Co-occurrence analysis is a technique often applied in text mining, comparative genomics, and promoter analysis. The methodologies and statistical models used to evaluate the significance of association between co-occurring entities are quite diverse, however.

Methodology/Principal Findings

We present a general framework for co-occurrence analysis based on a bipartite graph representation of the data, a novel co-occurrence statistic, and software performing co-occurrence analysis as well as generation and analysis of co-occurrence networks. We show that the overall stringency of co-occurrence analysis depends critically on the choice of the null-model used to evaluate the significance of co-occurrence and find that random sampling from a complete permutation set of the bipartite graph permits co-occurrence analysis with optimal stringency. We show that the Poisson-binomial distribution is the most natural co-occurrence probability distribution when vertex degrees of the bipartite graph are variable, which is usually the case. Calculation of Poisson-binomial P-values is difficult, however. Therefore, we propose a fast bi-binomial approximation for calculation of P-values and show that this statistic is superior to other measures of association such as the Jaccard coefficient and the uncertainty coefficient. Furthermore, co-occurrence analysis of more than two entities can be performed using the same statistical model, which leads to increased signal-to-noise ratios, robustness towards noise, and the identification of implicit relationships between co-occurring entities. Using NetCutter, we identify a novel protein biosynthesis related set of genes that are frequently coordinately deregulated in human cancer related gene expression studies. NetCutter is available at http://bio.ifom-ieo-campus.it/NetCutter/).

Conclusion

Our approach can be applied to any set of categorical data where co-occurrence analysis might reveal functional relationships such as clinical parameters associated with cancer subtypes or SNPs associated with disease phenotypes. The stringency of our approach is expected to offer an advantage in a variety of applications.

Cyclic AMP-induced chromatin changes support the NFATc-mediated recruitment of GATA-3 to the interleukin 5 promoter

Elevated intracellular cyclic AMP levels, which suppress the proliferation of naive T cells and type 1 T helper (Th1) cells are a property of T helper 2 (Th2) cells and regulatory T cells. While cyclic AMP signals interfere with the IL-2 promoter induction, they support the induction of Th2-type genes, in particular of il-5 gene. We show here that cyclic AMP signals support the generation of three inducible DNase I hypersensitive chromatin sites over the il-5 locus, including its promoter region. In addition, cyclic AMP signals enhance histone H3 acetylation at the IL-5 promoter and the concerted binding of GATA-3 and NFATc to the promoter. This is facilitated by direct protein-protein interactions involving the C-terminal Zn(2+)-finger of GATA-3 and the C-terminal region of the NFATc1 DNA binding domain. Because inhibition of NFATc binding to the IL-5 promoter in vivo also affects the binding of GATA-3, one may conclude that upon induction of Th2 effector cells NFATc recruits GATA-3 to Th2-type genes. These data demonstrate the functional importance of cyclic AMP signals for the interplay between GATA-3 and NFATc factors in the transcriptional control of lymphokine expression in Th2 effector cells.

Novel high-throughput profiling of human transcription factors and its use for systematic pathway mapping

Transcription factors (TFs) are crucial components of regulatory networks that control gene transcription. Current TF assays are limited to the analysis of a single TF or require TF-specific antibodies. Here we report the Single Primer Amplification assisted Oligonucleotide Array-based Transcription Factor Assay (SPA-OATFA) which can directly analyze the binding activities of 240 human TFs simultaneously. Examining early events during serum-stimulation of HeLa cells as a model, we demonstrated the utility of SPA-OATFA combined with whole genome gene expression to systematically map the temporal activation of signaling pathways. Both TFs known to function in this stimulation response such as EGR1 and AP1 and new TFs such as HSF1 were identified. This information, combined with mRNA profiling, provided novel insights into the activities of regulatory pathways, and illustrates the potential of SPA-OATFA in detailed systems biology analysis of cell responses.

Genome wide prediction of HNF4alpha functional binding sites by the use of local and global sequence context

An application of machine learning algorithms enables prediction of the functional context of transcription factor binding sites in the human genome.

We report an application of machine learning algorithms that enables prediction of the functional context of transcription factor binding sites in the human genome. We demonstrate that our method allowed de novo identification of hepatic nuclear factor (HNF)4α binding sites and significantly improved an overall recognition of faithful HNF4α targets. When applied to published findings, an unprecedented high number of false positives were identified. The technique can be applied to any transcription factor.

Predicting combinatorial binding of transcription factors to regulatory elements in the human genome by association rule mining

Background

Cis-acting transcriptional regulatory elements in mammalian genomes typically contain specific combinations of binding sites for various transcription factors. Although some cis-regulatory elements have been well studied, the combinations of transcription factors that regulate normal expression levels for the vast majority of the 20,000 genes in the human genome are unknown. We hypothesized that it should be possible to discover transcription factor combinations that regulate gene expression in concert by identifying over-represented combinations of sequence motifs that occur together in the genome. In order to detect combinations of transcription factor binding motifs, we developed a data mining approach based on the use of association rules, which are typically used in market basket analysis. We scored each segment of the genome for the presence or absence of each of 83 transcription factor binding motifs, then used association rule mining algorithms to mine this dataset, thus identifying frequently occurring pairs of distinct motifs within a segment.

Results

Support for most pairs of transcription factor binding motifs was highly correlated across different chromosomes although pair significance varied. Known true positive motif pairs showed higher association rule support, confidence, and significance than background. Our subsets of high-confidence, high-significance mined pairs of transcription factors showed enrichment for co-citation in PubMed abstracts relative to all pairs, and the predicted associations were often readily verifiable in the literature.

Conclusion

Functional elements in the genome where transcription factors bind to regulate expression in a combinatorial manner are more likely to be predicted by identifying statistically and biologically significant combinations of transcription factor binding motifs than by simply scanning the genome for the occurrence of binding sites for a single transcription factor.

NFAT in lymphocytes: a factor for all events?

A typical immune response to infection by a microbe results in rapid amplification and subsequent differentiation of a few antigen-specific naïve lymphocytes into many effector lymphocytes. Upon antigen exposure, these effector T or B cells rapidly secrete large amounts of either lymphokines (cytokines produced by lymphocytes) or soluble antibodies, respectively. Although the vast majority of these effector cells die after antigen clearance, some cells survive as memory cells and give lifelong protection to the host against a second infection by the same microbe. It has been appreciated for years that memory cells respond more rapidly than do naïve lymphocytes; however, the molecular mechanisms controlling memory cells remain largely unknown. A study now shows that abundance of the transcription factors nuclear factor of activated T cells c1 and c2 (NFATc1 and NFATc2) is much higher in memory (and effector) T cells than in naïve T cells. This suggests that NFATs have an important function in memory T cells but leaves open the questions of which transcription factors control interleukin-2 (IL-2) synthesis in naïve T cells and which mechanisms generate the high abundance of NFAT in memory T cells.

Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters

To explore the global mechanisms of estrogen-regulated transcription, we used chromatin immunoprecipitation coupled with DNA microarrays to determine the localization of RNA polymerase II (Pol II), estrogen receptor alpha (ERalpha), steroid receptor coactivator proteins (SRC), and acetylated histones H3/H4 (AcH) at estrogen-regulated promoters in MCF-7 cells with or without estradiol (E2) treatment. In addition, we correlated factor occupancy with gene expression and the presence of transcription factor binding elements. Using this integrative approach, we defined a set of 58 direct E2 target genes based on E2-regulated Pol II occupancy and classified their promoters based on factor binding, histone modification, and transcriptional output. Many of these direct E2 target genes exhibit interesting modes of regulation and biological activities, some of which may be relevant to the onset and proliferation of breast cancers. Our studies indicate that about one-third of these direct E2 target genes contain promoter-proximal ERalpha-binding sites, which is considerably more than previous estimates. Some of these genes represent possible novel targets for regulation through the ERalpha/AP-1 tethering pathway. Our studies have also revealed several previously uncharacterized global features of E2-regulated gene expression, including strong positive correlations between Pol II occupancy and AcH levels, as well as between the E2-dependent recruitment of ERalpha and SRC at the promoters of E2-stimulated genes. Furthermore, our studies have revealed new mechanistic insights into E2-regulated gene expression, including the absence of SRC binding at E2-repressed genes and the presence of constitutively bound, promoter-proximally paused Pol IIs at some E2-regulated promoters. These mechanistic insights are likely to be relevant for understanding gene regulation by a wide variety of nuclear receptors.

Integrative content-driven concepts for bioinformatics “beyond the cell”

Bioinformatics has delivered great contributions to genome and genomics research, without which the world-wide success of this and other global ('omics') approaches would not have been possible. More recently, it has developed further towards the analysis of different kinds of networks thus laying the foundation for comprehensive description, analysis and manipulation of whole living systems in modern "systems biology". The next step which is necessary for developing a systems biology that deals with systemic phenomena is to expand the existing and develop new methodologies that are appropriate to characterize intercellular processes and interactions without omitting the causal underlying molecular mechanisms. Modelling the processes on the different levels of complexity involved requires a comprehensive integration of information on gene regulatory events, signal transduction pathways, protein interaction and metabolic networks as well as cellular functions in the respective tissues / organs.

NFAT transcription factors in control of peripheral T cell tolerance

The Ca++-regulated calcineurin/NFAT cascade is one of the crucial signalling pathways that controls adaptive immunity. However, a number of novel experimental data suggest that, in addition to their role in T cell activation, NFATc transcription factors play also a decisive role in the generation of peripheral tolerance against self-antigens. This function of NFATc factors is mediated by controlling activation-induced cell death and clonal anergy of T helper cells and the activity of regulatory T cells. The multi-functional role of NFATc proteins characterize these transcription factors as key regulators of immunological tolerance and, if dysregulated, of development of autoimmune diseases.

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm

Composite Module Analyst (CMA) is a novel software tool aiming to identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs. CMA is closely interconnected with the TRANSFAC database. In particular, CMA uses the positional weight matrix (PWM) library collected in TRANSFAC and therefore provides the possibility to search for a large variety of different TF binding sites. We model the structure of the long gene regulatory regions by a Boolean function that joins several local modules, each consisting of co-localized TF binding sites. Having as an input a set of co-regulated genes, CMA builds the promoter model and optimizes the parameters of the model automatically by applying a genetic-regression algorithm. We use a multicomponent fitness function of the algorithm which includes several statistical criteria in a weighted linear function. We show examples of successful application of CMA to a microarray data on transcription profiling of TNF-alpha stimulated primary human endothelial cells. The CMA web server is freely accessible at http://www.gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlaintrade mark (www.biobase.de) designed for causal analysis of gene expression data.

NFATc1 autoregulation: a crucial step for cell-fate determination

Nuclear factor of activated T cell c (NFATc) transcription factors appeared in evolution with the emergence of lymphocytes in jawed fish. They have decisive roles in the development of the immune system and adaptive immune responses. Following immunoreceptor stimulation, NFAT factors control the expression of a large set of genes and thereby the fate of peripheral lymphocytes. NFATc1 and NFATc2 are the most prominent NFAT factors in peripheral T cells; they overlap in their function but differ remarkably in the mode of expression. NFATc2 is constitutively synthesized in T cells, whereas the expression of NFATc1/alphaA, the most prominent of six NFATc1 isoforms in peripheral T cells, is strongly induced following T-cell receptor and co-receptor stimulation and maintained by positive autoregulation. Findings concerning NFATc1 autoregulation in peripheral T lymphocytes and other cells suggest that positive autoregulation of NFATc1 is a crucial step in cell-fate determination.

CardioSignal: a database of transcriptional regulation in cardiac development and hypertrophy

BACKGROUND

Although extensive research has characterized intricate genetic programs in heart system, the information generated is highly fragmented. Here we have developed a new database called CardioSignal, which was designed for integration of regulatory information on the transcriptional regulation involved in heart development and cardiac hypertrophy.

METHODS

Data about sequences, positions and functional annotation of transcription binding sites, cis-regulatory modules as well as promoters were collected from scientific literature. Genes involved in both processes were also manually gathered, particularly those preferentially expressed in the heart. Data was stored in MySQL database and Perl was used as the server-side programming language.

RESULTS

Currently, CardioSignal contains 677 cardiac genes from twenty species. Among them are 128 cardiac transcription factors. Of the approximately 179 individual promoters from six species, the database also documented 247 experimentally verified binding sites and 64 cis-regulatory modules. CardioSignal may be searched for the promoter of a specific gene by specifying a gene name, Entrez geneID, swissProt accession number and so on. Downstream targets of transcriptional factors and cardiac regulatory modules can also be retrieved through a user-friendly web interface. Also available is experimental supporting evidence. Computational analysis tools were implemented for on-the-fly motif finding and comparative genomic analysis respectively.

CONCLUSIONS

CardioSignal offers a unique resource as it contains simultaneously the promoter collected while correlating the information of transcription factor binding sites and cis-regulatory modules from heart system. We are hopeful that its implementation will contribute toward the elucidation of the complex processes in cardiac development and hypertrophy.

Human immunodeficiency virus type 1 Tat increases cooperation between AP-1 and NFAT transcription factors in T cells

Human immunodeficiency virus type 1 (HIV-1) Tat affects cellular gene expression through modulation of the activity of different transcription factors. Here, the role of Tat in the cooperation between nuclear factor of activated T cells (NFAT) and activator protein 1 (AP-1) transcription factors was investigated. Constitutive or transient Tat expression in Jurkat T cells enhanced cooperative NFAT/AP-1- but not AP-1-dependent transcription independent of its ability to transactivate the HIV-1 LTR. The enhancing effect of Tat took place after nuclear translocation of NFAT. Furthermore, transactivation of an NFAT/AP-1 reporter by transfection of NFAT and c-Jun was strongly enhanced by simultaneous Tat transfection. Moreover, intracellular Tat expression increased the binding of NFAT/AP-1 complexes to the interleukin 2 promoter without significantly altering NFAT- and AP-1-independent binding. HIV-1 Tat interacted with NFAT but not c-Jun. These results indicate that Tat interacts with NFAT, affecting its cooperation with AP-1, without altering independent binding of these transcription factors to DNA.

Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events

Multiple transcription factors (TFs) coordinately control transcriptional regulation of genes in eukaryotes. Although numerous computational methods focus on the identification of individual TF-binding sites (TFBSs), very few consider the interdependence among these sites. In this article, we studied the relationship between TFBSs and microarray gene expression levels using both family-wise and memberspecific motifs, under various combination of regression models with Bayesian variable selection, as well as motif scoring and sharing conditions, in order to account for the coordination complexity of transcription regulation. We proposed a three-step approach to model the relationship. In the first step, we preprocessed microarray data and used p-values and expression ratios to preselect upregulated and downregulated genes. The second step aimed to identify and score individual TFBSs within DNA sequence of each gene. A method based on the degree of similarity and the number of TFBSs was employed to calculate the score of each TFBS in each gene sequence. In the last step, linear regression and probit regression were used to build a predictive model of gene expression outcomes using these TFBSs as predictors. Given a certain number of predictors to be used, a full search of all possible predictor sets is usually combinatorially prohibitive. Therefore, this article considered the Bayesian variable selection for prediction using either of the regression models. The Bayesian variable selection has been applied in the context of gene selection, missing value estimation, and regulatory motif identification. In our modeling, the regressor was approximated as a linear combination of the TFBSs and a Gibbs sampler was employed to find the strongest TFBSs. We applied these regression models with the Bayesian variable selection on spinal cord injury gene expression data set. These TFs demonstrated intricate regulatory roles either as a family or as individual members in neuroinflammatory events. Our analysis can be applied to create plausible hypotheses for combinatorial regulation by TFBSs and avoiding false-positive candidates in the modeling process at the same time. Such a systematic approach provides the possibility to dissect transcription regulation, from a more comprehensive perspective, through which phenotypical events at cellular and tissue levels are moved forward by molecular events at gene transcription and translation levels.

Ethanol-responsive genes: identification of transcription factors and their role in metabolomics

Transcription factors (TFs) and their combinatorial control on cis-regulatory elements play critical role in the co-expression of genes. This affects the interaction of genes in the transcriptome and thus may affect signals that cascade through cellular pathways. Using a combination of bioinformatic approaches, we sought to identify such common combinations of TFs in a set of ethanol-responsive (ER) genes and assess the role of ethanol in affecting multiple pathways through their co-regulation. Our results show that the metallothionein genes are regulated by TF motifs cAMP responsive element binding protein (CREB) and metal-activated transcription factor 1 and primarily involved in zinc ion homeostasis. We have also identified new target genes, Synaptojanin 1 and tryptophan hydroxylase 1, potentially regulated by this module. Altered arrangement of TF-binding sites in the module may direct the action of these and other target genes in intracellular signaling cascades, cell growth and/or maintenance. In addition to CREB, other key TFs identified are ecotropic viral integration site-1 and SP1. These modulate the contribution of the target ER genes in cell cycle regulation and apoptosis or programmed cell death. Multiple lines of evidence confirm the above findings and indicate that different groups of ER genes are involved in different biological processes and their co-regulation most likely results from different sets of regulatory modules. These findings associate the role of the ER genes studied and their potential TF modules with alcohol response pathways and phenotypes.

Complete Sequence Assembly and Characterization of the C57BL/6 Mouse Ig Heavy Chain V Region

The mechanisms that regulate variable (V) gene selection during the development of the mouse IgH repertoire are not fully understood, due in part to the absence of the complete locus sequence. To better understand these processes, we have assembled the entire 2.5-Mb mouse IgH (Igh) V region sequence of the C57BL/6 strain from public sequences and present the first complete annotated map of the region, including V genes, pseudogenes, repeats, and nonrepetitive intergenic sequences. In so doing, we have discovered a new V gene family, VH16. We have identified clusters of conserved region-specific intergenic sequences and have verified our assembly by genic and intergenic Southern blotting. We have observed that V pseudogenes are not evenly spread throughout the V region, but rather cluster together. The largest J558 family, which spans more than half of the locus, has two strikingly different domains, which suggest points of evolutionary divergence or duplication. The 5' end contains widely spaced J558 genes interspersed with 3609 genes and is pseudogene poor. The 3' end contains closely spaced J558 genes, no 3609 genes, and is pseudogene rich. Each occupies a different branch of the phylogenetic tree. Detailed analysis of 500-bp upstream of all functional genes has revealed several conserved binding sites, general and B cell-specific, as well as key differences between families. This complete and definitive assembly of the mouse Igh V region will facilitate detailed study of promoter function and large-scale mechanisms associated with V(D)J recombination including locus contraction and antisense intergenic transcription.