Differential functions for the transcription factor E2A in positive and negative gene regulation in pre-B lymphocytes

Transcription factor 3 is dysregulated in megakaryocytes in myelofibrosis

Transcription factor 3 (TCF3) is a DNA transcription factor that modulates megakaryocyte development. Although abnormal TCF3 expression has been identified in a range of hematological malignancies, to date, it has not been investigated in myelofibrosis (MF). MF is a Philadelphia-negative myeloproliferative neoplasm (MPN) that can arise de novo or progress from essential thrombocythemia [ET] and polycythemia vera [PV] and where dysfunctional megakaryocytes have a role in driving the fibrotic progression. We aimed to examine whether TCF3 is dysregulated in megakaryocytes in MPN, and specifically in MF. We first assessed TCF3 protein expression in megakaryocytes using an immunohistochemical approach analyses and showed that TCF3 was reduced in MF compared with ET and PV. Further, the TCF3-negative megakaryocytes were primarily located near trabecular bone and had the typical "MF-like" morphology as described by the WHO. Genomic analysis of isolated megakaryocytes showed three mutations, all predicted to result in a loss of function, in patients with MF; none were seen in megakaryocytes isolated from ET or PV marrow samples. We then progressed to transcriptomic sequencing of platelets which showed loss of TCF3 in MF. These proteomic, genomic and transcriptomic analyses appear to indicate that TCF3 is downregulated in megakaryocytes in MF. This infers aberrations in megakaryopoiesis occur in this progressive phase of MPN. Further exploration of this pathway could provide insights into TCF3 and the evolution of fibrosis and potentially lead to new preventative therapeutic targets.

Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma

BACKGROUND

The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences on pediatric asthma, are not well understood. We investigated whether ambient levels of fine PM with aerodynamic diameter ≤2.5 microns (PM_2.5 ) are associated with alterations in circulating monocytes in children with or without asthma.

METHODS

Monocyte phenotyping was performed by cytometry time-of-flight (CyTOF). Cytokines were measured using cytometric bead array and Luminex assay. ChIP-Seq was utilized to address histone modifications in monocytes.

RESULTS

Increased exposure to ambient PM_2.5 was linked to specific monocyte subtypes, particularly in children with asthma. Mechanistically, we hypothesized that innate trained immunity is evoked by a primary exposure to fine PM and accounts for an enhanced inflammatory response after secondary stimulation in vitro. We determined that the trained immunity was induced in circulating monocytes by fine particulate pollutants, and it was characterized by the upregulation of proinflammatory mediators, such as TNF, IL-6, and IL-8, upon stimulation with house dust mite or lipopolysaccharide. This phenotype was epigenetically controlled by enhanced H3K27ac marks in circulating monocytes.

CONCLUSION

The specific alterations of monocytes after ambient pollution exposure suggest a possible prognostic immune signature for pediatric asthma, and pollution-induced trained immunity may provide a potential therapeutic target for asthmatic children living in areas with increased air pollution.

The transcription factor E2A can bind to and cleave single-stranded immunoglobulin heavy chain locus DNA

Class switch recombination (CSR) changes the constant region of the immunoglobulin heavy chain (IgH), and somatic hypermutation (SH) introduces point mutations in the variable regions of the antibody genes. Both these processes that optimize antibody responses of B lymphocytes are initiated by the enzyme Activation Induced cytidine Deaminase (AID). Here we have searched for CSR or SH coupled activities of the transcription factor E2A, since E2A is in a complex with AID and the transcription factors PAX5, ETS1 and IRF4 on key sequences of the Igh locus in B lymphocytes activated to CSR and SH. We report that E2A in contrast to other described transcription factors binds sequence specifically also to single-stranded DNA. The binding of E2A to single-stranded DNA has a strong sequence preference for one strand of a site in the intronic enhancer of the Igh locus. Furthermore, E2A was also found to cleave single-stranded DNA. The sequence profile of substrates cleaved by E2A is coupled to the sequences of substrates and products of AID, suggesting that E2A has a role not only in targeting of AID to switch regions and SH parts of antibody genes but also in cleavage of DNA at these sites.

Identification of the transcriptional regulators by expression profiling infected with hepatitis B virus

BACKGROUND

The molecular pathogenesis of infection by hepatitis B virus with human is extremely complex and heterogeneous. To date the molecular information is not clearly defined despite intensive research efforts. Thus, studies aimed at transcription and regulation during virus infection or combined researches of those already known to be beneficial are needed.

AIMS

With the purpose of identifying the transcriptional regulators related to infection of hepatitis B virus in gene level, the gene expression profiles from some normal individuals and hepatitis B patients were analyzed in our study.

METHODS

In this work, the differential expressed genes were selected primarily. The several genes among those were validated in an independent set by qRT-PCR. Then the differentially co-expression analysis was conducted to identify differentially co-expressed links and differential co-expressed genes. Next, the analysis of the regulatory impact factors was performed through mapping the links and regulatory data. In order to give a further insight to these regulators, the co-expression gene modules were identified using a threshold-based hierarchical clustering method. Incidentally, the construction of the regulatory network was generated using the computer software.

RESULTS

A total of 137,284 differentially co-expressed links and 780 differential co-expressed genes were identified. These co-expressed genes were significantly enriched inflammatory response. The results of regulatory impact factors revealed several crucial regulators related to hepatocellular carcinoma and other high-rank regulators. Meanwhile, more than one hundred co-expression gene modules were identified using clustering method.

CONCLUSIONS

In our study, some important transcriptional regulators were identified using a computational method, which may enhance the understanding of disease mechanisms and lead to an improved treatment of hepatitis B. However, further experimental studies are required to confirm these findings.

Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells

Complement receptor 2 (CR2/CD21) is predominantly expressed on the surface of mature B cells where it forms part of a coreceptor complex that functions, in part, to modulate B-cell receptor signal strength. CR2/CD21 expression is tightly regulated throughout B-cell development such that CR2/CD21 cannot be detected on pre-B or terminally differentiated plasma cells. CR2/CD21 expression is upregulated at B-cell maturation and can be induced by IL-4 and CD40 signaling pathways. We have previously characterized elements in the proximal promoter and first intron of CR2/CD21 that are involved in regulating basal and tissue-specific expression. We now extend these analyses to the CR2/CD21 core promoter. We show that in mature B cells, CR2/CD21 transcription proceeds from a focused TSS regulated by a non-consensus TATA box, an initiator element and a downstream promoter element. Furthermore, occupancy of the general transcriptional machinery in pre-B versus mature B-cell lines correlate with CR2/CD21 expression level and indicate that promoter accessibility must switch from inactive to active during the transitional B-cell window.

E proteins in lymphocyte development and lymphoid diseases

As members of the basic helix-loop-helix (bHLH) family of transcription factors, E proteins function in the immune system by directing and maintaining a vast transcriptional network that regulates cell survival, proliferation, differentiation, and function. Proper activity of this network is essential to the functionality of the immune system. Aberrations in E protein expression or function can cause numerous defects, ranging from impaired lymphocyte development and immunodeficiency to aberrant function, cancer, and autoimmunity. Additionally, disruption of inhibitor of DNA-binding (Id) proteins, natural inhibitors of E proteins, can induce additional defects in development and function. Although E proteins have been investigated for several decades, their study continues to yield novel and exciting insights into the workings of the immune system. The goal of this chapter is to discuss the various classical roles of E proteins in lymphocyte development and highlight new and ongoing research into how these roles, if compromised, can lead to disease.

A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation

The p53 transcription factor participates in diverse cellular responses to stress, including cell-cycle arrest, apoptosis, senescence, and autophagy. The molecular mechanisms defining the ultimate outcome of p53 activation remain poorly characterized. We performed a genome-wide genetic screen in human cells to identify pathway-specific coregulators of the p53 target gene CDKN1A (p21), an inhibitor of cell-cycle progression, versus BBC3 (PUMA), a key mediator of apoptosis. Our screen identified numerous factors whose depletion creates an imbalance in the p21:PUMA ratio upon p53 activation. The transcription factor TCF3, also known as E2A, drives p21 expression while repressing PUMA across cancer cell types of multiple origins. Accordingly, TCF3/E2A depletion impairs the cell-cycle-arrest response and promotes apoptosis upon p53 activation by chemotherapeutic agents. In contrast, TRIAP1 is a specific repressor of p21 whose depletion slows down cell-cycle progression. Our results reveal strategies for driving cells toward specific p53-dependent responses.

The interacting MYB75 and KNAT7 transcription factors modulate secondary cell wall deposition both in stems and seed coat in Arabidopsis

The Arabidopsis thaliana KNAT7 (KNOX family) and MYB75 (MYB family) transcription factors were each shown earlier to interact in yeast two-hybrid assays, and to modulate secondary cell wall formation in inflorescence stems. We demonstrate here that their interaction also occurs in vivo, and that specific domains of each protein mediate this process. The participation of these interacting transcription factors in secondary cell wall formation was then extended to the developing seed coat through the use of targeted transcript analysis and SEM in single loss-of-function mutants. Novel genetic and protein-protein interactions of MYB75 and KNAT7 with other transcription factors known to be involved in seed coat regulation were also identified. We propose that a MYB75-associated protein complex is likely to be involved in modulating secondary cell wall biosynthesis in both the Arabidopsis inflorescence stem and seed coat, and that at least some parts of the transcriptional regulatory network in the two tissues are functionally conserved.

E2A proteins enhance the histone acetyltransferase activity of the transcriptional co-activators CBP and p300

The E2A gene encodes the E-protein transcription factors E12 and E47 that play critical roles in B-lymphopoiesis. A somatic chromosomal translocation detectable in 5% of cases of acute lymphoblastic leukemia (ALL) involves E2A and results in expression of the oncogenic transcription factor E2A-PBX1. CREB binding protein (CBP) and its close paralog p300 are transcriptional co-activators with intrinsic histone acetyltransferase (HAT) activity. We and others have shown that direct binding of an N-terminal transcriptional activation domain present in E12/E47 and E2A-PBX1 to the KIX domain of CBP/p300 contributes to E2A protein function. In the current work we show for the first time that the catalytic HAT activity of CBP/p300 is increased in the presence of residues 1-483 of E2A (i.e., the portion present in E2A-PBX1). The addition of purified, recombinant E2A protein to in vitro assays results in a two-fold augmentation of CBP/p300 HAT activity, whereas in vivo assays show a ten-fold augmentation of HAT-dependent transcriptional induction and a five-fold augmentation of acetylation of reporter plasmid-associated histone by CBP in response to co-transfected E2A. Our results indicate that the HAT-enhancing effect is independent of the well-documented E2A-CBP interaction involving the KIX domain and suggest a role for direct, perhaps low affinity binding of E2A to a portion of CBP that includes the HAT domain and flanking elements. Our findings add to a growing body of literature indicating that interactions between CBP/p300 and transcription factors can function in a specific manner to modulate HAT catalytic activity.

Repression of the DNA-binding inhibitor Id3 by Blimp-1 limits the formation of memory CD8+ T cells

Blimp-1 is a transcriptional repressor that promotes the differentiation of CD8⁺ T cells into short-lived KLRG-1⁺ effector cells (SLEC), but how it operates remains poorly defined. Here we show that Blimp-1 binds and represses the Id3 promoter in SLEC. Repression of Id3 by Blimp-1 was dispensable for SLEC development but limited their capacity to persist as memory cells. Enforced expression of Id3 was sufficient to rescue SLEC survival and enhanced recall responses. Id3 function was mediated in part through inhibition of E2a transcriptional activity and induction of genes regulating genome stability. These findings identify a Blimp-1-Id3-E2a axis as a key molecular switch that determines whether effector CD8⁺ T cells are programmed to die or enter the memory pool.

E proteins and the regulation of early lymphocyte development

Lymphopoiesis generates mature B, T, and NK lymphocytes from hematopoietic stem cells via a series of increasingly restricted developmental intermediates. The transcriptional networks that regulate these fate choices are composed of both common and lineage-specific components, which combine to create a cellular context that informs the developmental response to external signals. E proteins are an important factor during lymphopoiesis, and E2A in particular is required for normal T- and B-cell development. Although the other E proteins, HEB and E2-2, are expressed during lymphopoiesis and can compensate for some of E2A's activity, E2A proteins have non-redundant functions during early T-cell development and at multiple checkpoints throughout B lymphopoiesis. More recently, a role for E2A has been demonstrated in the generation of lymphoid-primed multipotent progenitors and shown to favor their specification toward lymphoid over myeloid lineages. This review summarizes both our current understanding of the wide-ranging functions of E proteins during the development of adaptive lymphocytes and the novel functions of E2A in orchestrating a lymphoid-biased cellular context in early multipotent progenitors.

Gene expression analysis in clear cell renal cell carcinoma using gene set enrichment analysis for biostatistical management

OBJECTIVE

To improve the workflow for standardizing the statistical interpretation provides an opportunity for the analysis of gene expression in clear cell renal cell carcinoma (ccRCC). RCC as a solid tumour entity represents a very suitable tumour model for such investigations. Although it is possible to investigate expression profiles by microarray technologies, the main problem is how to adequately interpret the accumulated mass of data derived from microarray technologies. There is a clear lack of a defined, consistent and comparable biostatistical analysis system, with no specific biostatistical standard methodology being available to compare the results of microarray analyses. We used the gene set enrichment analysis (GSEA) method to analyze microarray data from RCC tissue. The present study aimed to analyze differential expression profiles and establish biomarkers suitable for prognostication at the time of renal surgery by comparing RCC patients with long-term survival data against RCC samples of patients with poorly differentiated (grade 3) RCC, concomitant metastatic disease and short survival.

PATIENTS AND METHODS

In the present study, a total of 29 ccRCC fresh-frozen tissue samples were used; 14 samples from grade 1 (G1) RCC patients without metastatic disease and 15 from grade 3 (G3) RCC patients with synchronous metastatic disease. Expression profiling was performed with the Human Genome U133 Plus 2.0 Array (Affymetrix Corp., Santa Clara, CA, USA). Clinical data and long-term follow-up were obtained for all patients. The primary probe level analysis was performed using the Affymetrix MAS 5 algorithm. Further statistical processing was carried out by GSEA, using the Molecular Signatures Database, MSigDB (http://www.broad.mit.edu/gsea/msigdb/index.jsp). After selecting gene sets with the highest leading edge subsets, a cluster and a further analyses based on MSigDB data bank analysis was performed.

RESULTS

In total, 15 poorly G3 ccRCC, 14 well differentiated G1 ccRCC and 14 normal renal tissue samples were analyzed for comparative gene expression profiling. There were 12 of 15 G3 ccRCC patients who had synchronous metastatic disease at the time of surgery (pN+ and/or distant metastases: pN+ only = 4, M+ only = 11 and pN+M+ = 3). The GSEA identified 700 gene sets. Out of these, 120 sets with the highest leading edge subset were selected monitored by hierarchical clustering G1 vs G3. Comparative analysis using the the MSigDB data bank for pathway network identified 16 gene sets that were differentially strongly over- or underexpressed in G3 vs G1 tumours and are involved in various aspects of tumour physiology, such as metastases and cell motility, signalling and cell proliferation, as well as gene products that are involved in the building of the extracellular matrix and as cell surface markers.

CONCLUSIONS

We analyzed microarray data of gene expression in ccRCC comparing poorly differentiated and well differentiated tumour tissue samples. Using GSEA, we found a number of genes set candidates relevant to biological network processes with high complexity; conspicuously, these comprised members of the interleukin- and chemokine-family, cyclin-dependent kinases, angiogenic growth factors and transcriptional factors. This suggests that, in poorly differentiated aggressive ccRCC, there may be a limited number of gene sets that are responsible for the very aggressive biological behaviour. This comparison performed at a gene set level enables the identification of such congruency between different gene sets and whole data sets with respect to a specific biological question. GSEA embedded in the statistical workflow procedure for the suitable preparation of expression data may improve the analysis and avoid missing changes at the molecular level. A systematic approach such as GSEA is clearly needed to analyze raw data from microarray analyses, although these data can only be descriptive and the mass of raw data is derived from a relatively small number of tissue samples. However, consistent alterations of gene expression found in specific tumour entities may allow a better understanding of certain aspects of specific tumour biology. Therefore, the molecular characterization of individual tumours may potentially be useful for the better individual assessment of prognosis and, finally, the identification of biomarkers and targets of specific treatments may eventually help to improve treatment.

Patients with drug-free long-term graft function display increased numbers of peripheral B cells with a memory and inhibitory phenotype

Several transplant patients maintain stable kidney graft function in the absence of immunosuppression. Here we compared the characteristics of their peripheral B cells to that of others who had stable graft function but were under pharmacologic immunosuppression, to patients with chronic rejection and to healthy volunteers. In drug-free long-term graft function (DF) there was a significant increase in both absolute cell number and frequency of total B cells; particularly activated, memory and early memory B cells. These increased B-cell numbers were associated with a significantly enriched transcriptional B-cell profile. Costimulatory/migratory molecules (B7-2/CD80, CD40, and CD62L) were upregulated in B cells; particularly in memory CD19(+)IgD(-)CD38(+/-)CD27(+) B cells in these patients. Their purified B cells, however, responded normally to a polyclonal stimulation and did not have cytokine polarization. This phenotype was associated with the following specific characteristics which include an inhibitory signal (decreased FcgammaRIIA/FcgammaRIIB ratio); a preventive signal of hyperactive B-cell response (an increase in BANK1, which negatively modulates CD40-mediated AKT activation); an increased number of B cells expressing CD1d and CD5; an increased BAFF-R/BAFF ratio that could explain why these patients have more peripheral B cells; and a specific autoantibody profile. Thus, our findings show that patients with DF have a particular blood B-cell phenotype that may contribute to the maintenance of long-term graft function.

Impact of female cigarette smoking on circulating B cells in vivo: the suppressed ICOSLG, TCF3, and VCAM1 gene functional network may inhibit normal cell function

As pivotal immune guardians, B cells were found to be directly associated with the onset and development of many smoking-induced diseases. However, the in vivo molecular response of B cells underlying the female cigarette smoking remains unknown. Using the genome-wide Affymetrix HG-133A GeneChip microarray, we firstly compared the gene expression profiles of peripheral circulating B cells between 39 smoking and 40 non-smoking healthy US white women. A total of 125 differential expressed genes were identified in our study, and 75.2% of them were down-regulated in smokers. We further obtained genotypes of 702 single nucleotide polymorphisms in those promising genes and assessed their associations with smoking status. Using a novel multicriteria evaluation model integrating information from microarray and the association studies, several genes were further revealed to play important roles in the response of smoking, including ICOSLG (CD275, inducible T-cell co-stimulator ligand), TCF3 (E2A immunoglobulin enhancer binding factors E12/E47), VCAM1 (CD106, vascular cell adhesion molecule 1), CCR1 (CD191, chemokine C-C motif receptor 1) and IL13 (interleukin 13). The differential expression of ICOSLG (p = 0.0130) and TCF3 (p = 0.0125) genes between the two groups were confirmed by real-time reverse transcription PCR experiment. Our findings support the functional importance of the identified genes in response to the smoking stimulus. This is the first in vivo genome-wide expression study on B cells at today's context of high prevalence rate of smoking for women. Our results highlight the potential usage of integrated analyses for unveiling the novel pathogenesis mechanism and emphasized the significance of B cells in the etiology of smoking-induced disease.

A tamoxifen inducible knock-in allele for investigation of E2A function

Background

E-proteins are transcription factors important for the development of a variety of cell types, including neural, muscle and lymphocytes of the immune system. E2A, the best characterized E-protein family member in mammals, has been shown to have stage specific roles in cell differentiation, lineage commitment, proliferation, and survival. However, due to the complexity of E2A function, it is often difficult to separate these roles using conventional genetic approaches. Here, we have developed a new genetic model for reversible control of E2A protein activity at physiological levels. This system was created by inserting a tamoxifen-responsive region of the estrogen receptor (ER) at the carboxyl end of the tcfe2a gene to generate E2AER fusion proteins. We have characterized and analyzed the efficiency and kinetics of this inducible E2A^ER system in the context of B cell development.

Results

B cell development has been shown previously to be blocked at an early stage in E2A deficient animals. Our E2A^ER/ER mice demonstrated this predicted block in B cell development, and E2AER DNA binding activity was not detected in the absence of ligand. In vitro studies verified rapid induction of E2AER DNA binding activity upon tamoxifen treatment. While tamoxifen treatment of E2A^ER/ER mice showed inefficient rescue of B cell development in live animals, direct exposure of bone marrow cells to tamoxifen in an ex vivo culture was sufficient to rescue and support early B cell development from the pre-proB cell stage.

Conclusion

The E2A^ER system provides inducible and reversible regulation of E2A function at the protein level. Many previous studies have utilized over-expression systems to induce E2A function, which are complicated by the toxicity often resulting from high levels of E2A. The E2A^ER model instead restores E2A activity at an endogenous level and in addition, allows for tight regulation of the timing of induction. These features make our E2A^ER ex vivo culture system attractive to study both immediate and gradual downstream E2A-mediated events.

Regulation of V(D)J recombination by E-protein transcription factors

Extensive study of the E-proteins E2A and HEB duringlymphocyte development has revealed various functions for these bHLH transcription factors in regulating V(D)J recombination in both B- and T-cells. The study of E-proteins in mammals began with the identification of E2A by its ability to bind immunoglobulin heavy and light chain enhancers. Subsequent analysis has identified numerous roles for E2A and HEB at the immunoglobulin and T-cell receptor loci. E-protein targets also include the rag genes and other factors critical for recombination and for regulation of the developmental windows when cells undergo recombination. E-proteins appear to be master regulators that coordinate antigen receptor gene rearrangement and expression. This chapter focuses on how E-proteins regulate V(D)J recombination by activating transcription, initiating rearrangement and driving differentiation during B- and T-cell development.

Balance between Id and E proteins regulates myeloid-versus-lymphoid lineage decisions

Hematopoiesis consists of a series of lineage decisions controlled by specific gene expression that is regulated by transcription factors and intracellular signaling events in response to environmental cues. Here, we demonstrate that the balance between E-protein transcription factors and their inhibitors, Id proteins, is important for the myeloid-versus-lymphoid fate choice. Using Id1-GFP knockin mice, we show that transcription of the Id1 gene begins to be up-regulated at the granulocyte-macrophage progenitor stage and continues throughout myelopoiesis. Id1 expression is also stimulated by cytokines favoring myeloid differentiation. Forced expression of Id1 in multipotent progenitors promotes myeloid development and suppresses B-cell formation. Conversely, enhancing E-protein activity by expressing a variant of E47 resistant to Id-mediated inhibition prevents the myeloid cell fate while driving B-cell differentiation from lymphoid-primed multipotent progenitors. Together, these results suggest a crucial function for E proteins in the myeloid-versus-lymphoid lineage decision.

Detecting reliable gene interactions by a hierarchy of Bayesian network classifiers

The main purpose of a gene interaction network is to map the relationships of the genes that are out of sight when a genomic study is tackled. DNA microarrays allow the measure of gene expression of thousands of genes at the same time. These data constitute the numeric seed for the induction of the gene networks. In this paper, we propose a new approach to build gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling. The interactions induced by the Bayesian classifiers are based both on the expression levels and on the phenotype information of the supervised variable. Feature selection and bootstrap resampling add reliability and robustness to the overall process removing the false positive findings. The consensus among all the induced models produces a hierarchy of dependences and, thus, of variables. Biologists can define the depth level of the model hierarchy so the set of interactions and genes involved can vary from a sparse to a dense set. Experimental results show how these networks perform well on classification tasks. The biological validation matches previous biological findings and opens new hypothesis for future studies.

Instructive role of the transcription factor E2A in early B lymphopoiesis and germinal center B cell development

The transcription factor E2A controls the initiation of B lymphopoiesis, which is arrested at the pre-pro-B cell stage in E2A-deficient mice. Here, we demonstrate by conditional mutagenesis that E2A is essential for the development of pro-B, pre-B, and immature B cells in the bone marrow. E2A is, however, dispensable for the generation of mature B cells and plasma cells in peripheral lymphoid organs. In contrast, germinal center B cell development is impaired in the absence of E2A despite normal AID expression and class-switch recombination. Molecular analysis revealed that E2A is required not only for initiating but also for maintaining the expression of Ebf1, Pax5, and the B cell gene program in pro-B cells. Notably, precocious Pax5 transcription from the Ikzf1 locus promotes pro-B cell development in E2A-deficient mice, demonstrating that ectopic Pax5 expression is sufficient to activate the B lymphoid transcription program in vivo in the absence of E2A.

Subcellular localization of the Schlafen protein family

Although the first members of the Schlafen gene family were first described almost 10 years ago, the precise molecular/biochemical functions of the proteins they encode still remain largely unknown. Roles in cell growth, haematopoietic cell differentiation, and T cell development/maturation have, with some experimental support, been postulated, but none have been conclusively verified. Here, we have determined the subcellular localization of Schlafens 1, 2, 4, 5, 8, and 9, representing all three of the murine subgroups. We show that the proteins from subgroups I and II localize to the cytoplasm, while the longer forms in subgroup III localize exclusively to the nuclear compartment. We also demonstrate upregulation of Schlafen2 upon differentiation of haematopoietic cells and show this endogenous protein localizes to the cytoplasm. Thus, we propose the different subgroups of Schlafen proteins are likely to have functionally distinct roles, reflecting their differing localizations within the cell.

HDAC2 controls IgM H- and L-chain gene expressions via EBF1, Pax5, Ikaros, Aiolos and E2A gene expressions

We previously reported that histone deacetylase-2 (HDAC2) controls the amount of IgM H-chain at the steps of transcription of its gene and alternative processing of its pre-mRNA in DT40 cells. Here, we showed not only that the HDAC2-deficiency caused repressions of gene expressions for HDAC7, EBF1, Pax5, Aiolos and Ikaros, and elevations of gene expressions for HDAC4, HDAC5, PCAF and E2A, but also that it caused altered acetylation levels of several Lys residues of core histones. Using gene targeting techniques, we generated three homozygous DT40 mutants: EBF1(-/-), Aiolos(-/-) and E2A(-/-), devoid of EBF1, Aiolos and E2A genes, respectively. Semiquantitative RT-PCR analysis of the resultant mutants revealed not only that EBF1 and Aiolos down-regulate expressions of IgM H- and L-chain genes, but also that E2A up-regulates expressions of these two genes. These results, together with others, indicate that HDAC2 controls indirectly expressions of IgM H- and L-chain genes through opposite transcriptional regulations of EBF1, Pax5, Aiolos plus Ikaros and E2A genes.

E2A promotes the survival of precursor and mature B lymphocytes

The basic helix-loop-helix transcription factor E2A is an essential regulator of B lymphocyte lineage commitment and is required to activate the expression of numerous B lineage-specific genes. Studies involving ectopic expression of Id proteins, which inhibit E2A as well as other basic helix-loop-helix proteins such as HEB, suggest additional roles of E2A at later stages of B cell development. We use E2A-deficient and E2A and HEB double-deficient pre-B cell lines to directly assess the function of E2A and HEB in B cell development after lineage commitment. We show that, in contrast to the established role of E2A in lineage commitment, elimination of E2A and HEB in pre-B cell lines has only a modest negative impact on B lineage gene expression. However, E2A single and E2A and HEB double-deficient but not HEB single-deficient cell lines show dramatically enhanced apoptosis upon growth arrest. To address the possible role of E2A in the regulation of B cell survival in vivo, we crossed IFN-inducible Cre-transgenic mice to E2A conditional mice. Cre-mediated E2A deletion resulted in a block in bone marrow B cell development and a significant reduction in the proportion and total number of splenic B cells in these mice. We show that Cre-mediated deletion of E2A in adoptively transferred mature B cells results in the rapid depletion of the transferred population within 24 h of Cre induction. These results reveal that E2A is not required to maintain B cell fate but is essential in promoting pre-B and B cell survival.

E2A and IRF-4/Pip promote chromatin modification and transcription of the immunoglobulin kappa locus in pre-B cells

The immunoglobulin kappa light chain (Igkappa) locus is regulated in a lineage- and stage-specific manner during B-cell development. The highly restricted timing of V to J gene recombination at the pre-B-cell stage is under the control of two enhancers, the intronic enhancer (kappaEi) and the 3' enhancer (kappaE3'), flanking the constant exon. E2A transcription factors have been indicated to be directly involved in the regulation of Igkappa locus activation. In this study, we utilize E2A-deficient pre-B cells to directly investigate the mechanism of E2A-mediated Igkappa activation. We demonstrate that Igkappa germ line transcription is severely impaired and recombination is blocked in the absence of E2A. Reconstitution of E2A-/- pre-B cells with inducible human E2A (E47R) is sufficient to promote chromatin modification of Igkappa and rescue Igkappa germ line transcription and Jkappa gene recombinase accessibility. Furthermore, we show that increased E2A recruitment to kappaEi and kappaE3' correlates with activation of Igkappa in pre-B cells and that recruitment of E2A to kappaE3' is in part dependent on the transcription factor IRF-4. Inhibition of IRF-4 expression in pre-B cells leads to a significant reduction of Igkappa germ line transcription and enhancer acetylation. In the absence of E2A, increased IRF-4 expression is not sufficient to promote Igkappa enhancer chromatin modification or transcription, suggesting that the sequential involvement of IRF-4 and E2A is necessary for the activation of the Igkappa locus. Finally, we provide genetic evidence in the mouse that E2A gene dosage can influence the development of pre-B cells during the phase of Igkappa gene activation.

At the crossroads: diverse roles of early thymocyte transcriptional regulators

Transcriptional regulation of T-cell development involves successive interactions between complexes of transcriptional regulators and their binding sites within the regulatory regions of each gene. The regulatory modules that control expression of T-lineage genes frequently include binding sites for a core set of regulators that set the T-cell-specific background for signal-dependent control, including GATA-3, Notch/CSL, c-myb, TCF-1, Ikaros, HEB/E2A, Ets, and Runx factors. Additional regulators in early thymocytes include PU.1, Id-2, SCL, Spi-B, Erg, Gfi-1, and Gli. Many of these factors are involved in simultaneous regulation of non-T-lineage genes, T-lineage genes, and genes involved in cell cycle control, apoptosis, or survival. Potential and known interactions between early thymic transcription factors such as GATA-3, SCL, PU.1, Erg, and Spi-B are explored. Regulatory modules involved in the expression of several critical T-lineage genes are described, and models are presented for shifting occupancy of the DNA-binding sites in the regulatory modules of pre-Talpha, T-cell receptor beta (TCRbeta), recombinase activating genes 1 and 2 (Rag-1/2), and CD4 during T-cell development. Finally, evidence is presented that c-kit, Erg, Hes-1, and HEBAlt are expressed differently in Rag-2(-/-) thymocytes versus normal early thymocytes, which provide insight into potential regulatory interactions that occur during normal T-cell development.

Id3 induces growth arrest and caspase-2-dependent apoptosis in B lymphocyte progenitors

The E-protein transcription factors E2A, HEB, and E2-2 play an essential role in the differentiation, proliferation, and survival of B lymphocyte progenitors (BLPs). In this study, we show that the E-protein antagonist Id3 induces apoptosis of both primary and transformed BLPs through a caspase-2-dependent mechanism that does not require p53 and is not inhibited by bcl-2. Id3 expressing B lineage cells show reduced expression of known E-protein target genes as well as multiple genes involved in cell proliferation. We hypothesize that Id3 induces activation of caspase-2 as a consequence of severe or "catastrophic" growth arrest. In support of this hypothesis, we show that chemical-induced growth arrest is sufficient to activate caspase-2 and induce apoptosis in BLPs. Our data suggest that E-proteins function in the control of differentiation and proliferation and that diminished E-protein activity results in apoptosis as a consequence of growth arrest.

Single-strand recombination signal sequence nicks in vivo: evidence for a capture model of synapsis

Variable (diversity) joining (V(D)J) recombination is initiated by the introduction of single-strand DNA breaks (nicks) at recombination signal sequences (RSSs). The importance and fate of these RSS nicks for the regulation of the V(D)J rearrangement and their potential contribution to genomic instability are poorly understood. Using two new methodologies, we were able to detect and quantify specific RSS nicks introduced into genomic DNA by incubation with recombination-activating gene proteins in vitro. In vivo, however, we found that nicks mediated by recombination-activating gene (RAG) proteins were detectable only in gene segments associated with RSSs containing 12-base pair spacers but not in those containing 23-base pair spacers. These data support a model of capture rather than synapsis for pairwise RSS cleavage during V(D)J recombination.

Helix-loop-helix proteins and lymphocyte development

Helix-loop-helix (HLH) proteins are transcriptional regulators that control a wide variety of developmental pathways in both invertebrate and vertebrate organisms. Results obtained in the past decade have shown that HLH proteins also contribute to the development of lymphoid lineages. A subset of HLH proteins, the 'E proteins', seems to be particularly important for proper lymphoid development. Members of the E protein family include E12, E47, E2-2 and HEB. The E proteins contribute to B lineage- and T lineage-specific gene expression programs, regulate lymphocyte survival and cellular proliferation, activate the rearrangement of antigen receptor genes and control progression through critical developmental checkpoints. This review discusses HLH proteins in lymphocyte development and homeostasis.

New insights into E-protein function in lymphocyte development

Lymphocyte development has long served as an experimental paradigm, revealing fundamental mechanisms of gene regulation and cellular differentiation in mammals. The study of E-protein-mediated transcriptional regulation in lymphocyte development provides a means to address these mechanistic issues. Both genetic and biochemical studies have defined many important regulatory events during lymphocyte development that are mediated by E-proteins. The E2A gene, one of the three known E-protein genes in mammals, has a particularly important role in B-lymphocyte development. Major progress has been made in recent years towards understanding the physiological targets of E2A during B-lymphocyte development. Most notably, new insights have been gained regarding the role of E2A in controlling lineage commitment and V(D)J recombination. This Review focuses primarily on E2A-mediated gene regulation during B-lymphocyte development.

Genetic networks that regulate B lymphopoiesis

PURPOSE OF REVIEW

The B cell developmental pathway represents a leading model within the hematopoietic system for the analysis of genetic networks, which orchestrate cell fate specification and commitment. Considerable progress is being achieved in the characterization of regulatory components that comprise such networks and examining their connectivity. These components include the cytokine receptors Flk2 and IL-7R as well as the transcription factors PU.1, Ikaros, Bcl11a, E2A, EBF, and Pax-5. Based on new experimental evidence, a comprehensive model is proposed that invokes sequentially acting and inter-dependent regulatory modules that instruct the generation of B cell precursors from multipotential hematopoietic progenitors.

RECENT FINDINGS

The transcription factor PU.1 regulates the generation of lymphoid progenitors that express Flk2 and IL-7R. IL-7R receptor signaling appears to function in specification of the B cell fate. The transcription factor EBF can bypass the requirement for PU.1 and E2A in early B cell development. Pax-5 expression and function are contingent on EBF.

SUMMARY

Assembly of gene regulatory networks involved in cell fate specification may facilitate the efficient and directed generation of lineage-specific hematopoietic progenitors from embryonic stem cells for therapeutic purposes.

Regulation of immunoglobulin gene transcription in a teleost fish: identification, expression and functional properties of E2A in the channel catfish

The function of the transcriptional enhancer, Emu3', of the IgH locus of the channel catfish, Ictalurus punctatus, involves the interaction of E-protein and Oct family transcription factors. The E-proteins [class I basic helix-loop-helix (bHLH) family] are encoded in mammals by three genes: E2A (of which E12/E47 are alternatively spliced products), HEB, and E2-2. An E2A homologue has been identified in a catfish B-cell cDNA library and contains regions homologous to the bHLH and activation domains of mammalian and other vertebrate E2A proteins. E2A message is widely expressed, being readily detected in catfish B cells, T cells, kidney, spleen, brain, and muscle. Its expression is lower than that previously observed for TF12/CFEB, the catfish homologue of HEB. E2A strongly activated transcription of a muE5 motif-dependent construct in catfish B cells, and also activated transcription from the core region of the catfish IgH enhancer (Emu3') in a manner dependent on the presence of the muE5 site. Catfish E2A, expressed in vitro, bound the muE5 motif present in the core region of Emu3'. These results document the conservation of structure and function in vertebrate E2A and suggest a potential role of E2A in driving expression of the IgH locus at the phylogenetic level of a teleost fish.