Structure of the two promoters of the human lck gene: differential accumulation of two classes of lck transcripts in T cells

NF-κB Signaling and IL-4 Signaling Regulate SATB1 Expression via Alternative Promoter Usage During Th2 Differentiation

SATB1 is a genome organizer protein that is expressed in a lineage specific manner in CD4⁺ T-cells. SATB1 plays a crucial role in expression of multiple genes throughout the thymic development and peripheral differentiation of T cells. Although SATB1 function has been subjected to intense investigation, regulation of SATB1 gene expression remains poorly understood. Analysis of RNA-seq data revealed multiple transcription start sites at the upstream regulatory region of SATB1. We further demonstrated that SATB1 gene is expressed via alternative promoters during T-helper (Th) cell differentiation. The proximal promoter “P1” is used more by the naïve and activated CD4⁺ T-cells whereas the middle “P2” and the distal “P3” promoters are used at a significantly higher level by polarized T-helper cells. Cytokine and TCR signaling play crucial roles toward SATB1 alternative promoter usage. Under Th2 polarization conditions, transcription factor STAT6, which operates downstream of the cytokine signaling binds to the P2 and P3 promoters. Genetic perturbation by knockout and chemical inhibition of STAT6 activation resulted in the loss of P2 and P3 promoter activity. Moreover, chemical inhibition of activation of NF-κB, a transcription factor that operates downstream of the TCR signaling, also resulted in reduced P2 and P3 promoter usage. Furthermore, usage of the P1 promoter correlated with lower SATB1 protein expression whereas P2 and P3 promoter usage correlated with higher SATB1 protein expression. Thus, the promoter switch might play a crucial role in fine-tuning of SATB1 protein expression in a cell type specific manner.

Sequence determinants of DNA binding by the hematopoietic helix-loop-helix transcription factor TAL1: importance of sequences flanking the E-box core

TAL1 is a helix-loop-helix transcription factor that is essential for hematopoiesis. In vitro DNA binding site selection experiments have previously identified the preferred binding site for TAL1 heterodimers as AACAGATGGT. TAL1 homodimers do not bind DNA with significant affinity. A subset of other E-box sequences is also bound by TAL1 heterodimers. Here, we present an analysis of TAL1 heterodimer DNA binding specificity, using E-boxes derived from genomic clones, which were isolated by immunoadsorption of K562 erythroleukemia cell chromatin with a TAL1 antibody. We show that TAL1 heterodimer binding to a CAGATG E-box is strongly modulated by nucleotides flanking the E-box. A 10 base pair element consisting of the CAGATG E-box and two flanking nucleotides in both the 5' and 3' direction is sufficient for high-affinity binding. Certain mutations of nucleotides in either the 5' (-1 and -2) or 3' (+1 and +2) direction strongly inhibit binding. The importance of flanking nucleotides also exists in the context of nonpreferred E-boxes recognized by TAL1 heterodimers. Although there are no known target genes for TAL1, the regulatory regions of several genes involved in hematopoiesis contain the preferred E-box CAGATG. However, based on our results, the E-boxes in these potential target genes contain flanking sequences that would be expected to significantly reduce TAL1 heterodimer binding in vitro. Thus, additional stabilizing forces, such as protein-protein interactions between TAL1 heterodimers and accessory factors, may be required to confer high-affinity TAL1 heterodimer binding to such sequences.

Regulatory patterns of differentially expressed genes in Ebola and related viruses are critical for viral screening and diagnosis

Background Viral detection techniques and applications are a critical first step to pathogen detection within a given population, especially during outbreaks. Common viral tests currently used are direct specimen examination, indirect examination and serological tests. Serological tests have gained intense interest because they are rapidly performed with patient blood samples for quick diagnosis and treatment. The diagnostic techniques developed around serology are often expensive, require expertise to use and cannot be afforded by developing countries with recurrent viral outbreaks. Therefore exploiting the huge amount of viral data available in various databases is critical to develop affordable and easy-to-use diagnostic tools. Methods This study obtained viral sample data from Gene Expression Omnibus database with focus on use of viral glycoprotein for host penetration. Gene relative mean across 34 obtained viral samples were extracted into data tables and used with edgeR statistical software in R version 3.3.1. Results Three clusters previously known to be LCK specific (Ebola virus relative viral cluster, EBOVC), CD209 specific (Mean differentiation cluster, MDC) and both LCK and CD209 specific (Kurtosis group cluster, KGC), expressed unique patterns of four proteins of interest (CD209, LCK, IL-2 and MYB). Differential expression analysis showed two cluster patterns on heatmaps, with differentially expressed proteins down-regulated in MDC but up-regulated in KGC and EBOVC for all pairwise cluster comparative analyses performed. Heatmaps showed two distinct immune related patterns, identifying MDC as B-lymphotropic while KGC and EBOVC as T-lymphotropic. Identified pathways were dominantly involved with homeostasis of immune cells and viral cell surface receptors involved in protein kinase activities. Conclusions Regulatory proteomic variants identified in clusters suggest transcription repression of HLA class I alleles. This study identified viral expression patterns with screening and therapeutic applications. Given that the viral pathogenetic pathway for Ebola has not been clearly identified yet, assembling its components is vital for vaccine development.

Identification of genetic pathways driving Ebola virus disease in humans and targets for therapeutic intervention

Introduction: LCK gene, also known as lymphocyte-specific proto-oncogene, is expressed in lymphocytes, and associated with coordinated expression of MHC class I and II in response to physiological stimuli, mediated through a combined interaction of promoters, suppressors, and enhancers. Differential usage of LCK promoters, transcribes dysfunctional transcript variants leading to leukemogenesis and non-induction of MHC class I gene variants. Viruses use C-type lectins, like CD209, to penetrate the cell, and inhibit Pattern Recognition Receptors (PRR), hence evading immune destruction. Given that Ebolavirus (EBOV) disease burden could result from a dysfunctional LCK pathway, identification of the genetic pathway leading to proper immune induction is a major priority. Methods: Data for EBOV related virus samples were obtained from Gene Expression Omnibus database and RMEAN information per gene per sample were entered into a table of values. R software v.3.3.1 was used to process differential expression patterns across samples for LCK, CD209 and immune-related genes. Principal component analysis (PCA) using ggbiplot v.0.55 was used to explain the variance across samples. Results: Data analyses identified three viral clusters based on transmission patterns as follows: LCK-CD209 dependent, LCK-dependent specific to EBOV, and CD209 dependent. Compared to HLA class II gene variants, HLA class I (A, B and C) variants were <2 fold expressed, especially for EBOV samples. PCA analyses classified TYRO3, TBK1 and LCK genes independent of the data, leading to identification of a possible pathway involving LCK, IL2, PI3k, TBK1, TYRO3 and MYB genes with downstream induction of immune T-cells. Discussion: This is the first study undertaken to understand the non-functional immune pathway, leading to EBOV disease pathogenesis and high fatality rates. Our lab currently exploits, through cutting edge genetic technology to understand the interplay of identified genes required for proper immune induction. This will guide antiviral therapy and possible markers for viral disease identification during outbreaks.

Molecular cloning and characterization of lymphocyte cell kinase from humphead snapper (Lutjanus sanguineus)

Lymphocyte cell kinase (LCK) belongs to the Src family of tyrosine kinases, which involves in the proliferation control of lymphocytes. In this study, we cloned the LCK gene of humphead snapper (Lutjanus sanguineus) (designed as LsLCK). Sequence analysis showed that the full-length cDNA of LsLCK was 2279 bp, contained a 1506-bp open reading frame (ORF), encoding a polypeptide of 501 amino acids. The deduced amino acid possessed the typical structural features of known LCK proteins, including four Src homology (SH) domains arranged as the SH1 domain followed by a regulatory C-terminal tail (COOH-domain), SH2 and SH3 adapter domains and SH4 domain which required for membrane attachment and CD4/CD8 binding. Fluorescent quantitative real-time PCR analysis indicated that LsLCK transcripts were expressed mainly in thymus, spleen and head kidney in healthy fish. Moreover, the mRNA expressions in these tissues were significantly up-regulated after challenge with Vibrio harveyi. The results of immunohistochemistry showed that LsLCK protein localized distinctly in cytoplasm of cell in thymus, spleen and head kidney. Taken together, these findings indicated that LsLCK may play an important role in the immune response of humphead snapper against bacterial infection.

Molecular and biochemical analysis of rainbow trout LCK suggests a conserved mechanism for T-cell signaling in gnathostomes

Two genes were identified in rainbow trout that display high sequence identity to vertebrate Lck. Both of the trout Lck transcripts are associated with lymphoid tissues and were found to be highly expressed in IgM-negative lymphocytes. In vitro analysis of trout lymphocytes indicates that trout Lck mRNA is up-regulated by T-cell mitogens, supporting an evolutionarily conserved function for Lck in the signaling pathways of T-lymphocytes. Here, we describe the generation and characterization of a specific monoclonal antibody raised against the N-terminal domains of recombinant trout Lck that can recognize Lck protein(s) from trout thymocyte lysates that are similar in size ( approximately 57kDa) to mammalian Lck. This antibody also reacted with permeabilized lymphocytes during FACS analysis, indicating its potential usage for cellular analyses of trout lymphocytes, thus representing an important tool for investigations of salmonid T-cell function.

Src family kinase members have a common response to histone deacetylase inhibitors in human colon cancer cells

Histone deacetylase inhibitors (HDIs) induce cell cycle arrest, differentiation and/or apoptosis in numerous cancer cell types and have shown promise in clinical trials. These agents are particularly novel, given their ability to selectively influence gene expression. Previously, we demonstrated that the HDIs butyrate and trichostatin A (TSA) directly repress c-Src proto-oncogene expression in many cancer cell lines. Activation and/or overexpression of c-Src have been frequently observed in numerous malignancies, especially of the colon. Therefore, our observation was particularly interesting since butyrate is a naturally abundant component of the large intestine and has been suggested to be a cancer-preventive agent. However, c-Src is not the only Src family kinase (SFK) member to be implicated in the development of human cancers, including those of the colon. Therefore, the relative expression levels of known SFKs were examined in a panel of human colon cancer cell lines. We found a surprisingly diverse expression pattern but noted that most cell lines expressed relatively high levels of at least 2 SFKs. When the effects of butyrate and TSA were examined in representative cell lines, the expression of all SFKs was repressed in a dose- and time-dependent manner. Further, detailed examination of Lck, Yes and Lyn demonstrated that this repression had a direct effect on transcription and was independent of new protein synthesis. These results mirror our earlier data obtained with c-Src and suggest that SFKs are a major target of HDIs and likely account in part for the anticancer effects of these promising new drugs.

A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene with intron B retention and exon 7 skipping encodes a putative protein with altered SH3-dependent molecular interactions

A rare mRNA variant of the human lymphocyte-specific protein tyrosine kinase LCK gene that retains intron B and excludes exon 7 (B+7-) due to alternative splicing of the canonical LCK transcripts was identified and characterized. LCK B+7- mRNA is detected in all tested peripheral blood T lymphocytes total RNA samples but is apparently sequestered in the nucleus. The presence of intron B sequence does not disrupt the reading frame and results in the insertion of 58 aminoacids, containing a proline-rich region just upstream of p56lck SH3 domain. This putative isoform encodes an unstable 516 aminoacids protein (LckB+7-) which can be expressed in transfected COS-7 cells. Furthermore in Jurkat T cell extracts, a recombinant intron B plus SH3 p56lck domain fails to interact with some TCR-induced tyrosine phosphorylated polypeptides and known p56lck partners such as Sam68 and c-Cbl. The biological function of this rare messenger remains to be elucidated.

Molecular structure and transcriptional regulation by nuclear factor-κB of the mouse kinin B1 receptor gene

Kinins are important mediators in cardiovascular homeostasis, inflammation, and nociception. Two kinin receptors have been described, B 1 and B 2 . The B 1 receptor is normally absent in healthy tissues, but is highly induced under pathological conditions. To understand the molecular mechanism of B 1 receptor up-regulation, we determined the mouse B 1 receptor gene structure, isolated and characterized the promoter region and studied its transcriptional regulation. The mouse B 1 receptor gene contains two exons (with the entire coding region located in the second exon) and a TATA-less promoter with multiple transcription start sites. A 7.7-kbp portion of the 5'-flanking region was examined for promoter activity in vascular smooth muscle cells (VSMCs). A minimal 92-bp fragment, located immediately upstream of the transcription start region, exerted basal and lipopolysaccharide (LPS)-inducible transcription activity in the sense and antisense orientation, and was thereby identified as an enhancer element. Nuclear extracts from VSMCs showed basal and LPS-inducible binding activity of nuclear factor (NF)-kappaB at this sequence. B 1 receptor transcription activation in response to LPS was abolished by cotransfection with IkappaBalphaDeltaN, an NF-kappaB repressor. In summary, our results reveal the structure of the mouse B 1 receptor gene and the involvement of NF-kappaB in the inducible mouse kinin B 1 receptor expression under pathological conditions.

Identification of upstream cis-acting regulatory elements controlling lineage-specific expression of the mouse NK cell activation receptor, NKR-P1C

Mouse NKR-P1C (NK1.1) is a homodimeric type II transmembrane protein expressed on natural killer (NK) cells, NKT cells, and on CD117+ progenitor thymocytes capable of giving rise to cells of the T and NK lineages. Although its physiological ligands remain unknown, NKR-P1C engagement with a monoclonal antibody (mAb) leads to interferon-gamma (IFN-gamma) production and the directed release of cytotoxic granules from NK cells. We have cloned and sequenced a approximately 10-kb genomic fragment corresponding to the 5'-flanking region of the C57Bl/6 mouse NKR-P1C gene. A transcriptional initiation site has been mapped in NK cells and an NK1.1+ T cell line by primer extension and rapid amplification of 5'-cDNA ends (5'-RACE) techniques. Although the 5'-flanking region of NKR-P1C is TATA-less, we have identified an initiator region and a downstream promoter element, which together constitute the principal minimal functional promoter. Computational analysis of the 10-kb 5'-flanking region revealed potential regulatory factor binding sites. DNaseI hypersensitivity assays identified a single hypersensitive site (HS) about a 9-kb upstream of the transcriptional initiation site. This site, termed HS1, was able to act as a transcriptional enhancer element in an NK cell line, while minimally affecting transcription in non-NK cell lines. Moreover, the HS1 element was shown to function as a promoter, with a transcript detected only in fetal NK1.1+ cells. An additional promoter and two non-coding exons were also characterized. These results identify the minimal upstream cis-acting elements, and point to a complex regulatory mechanism involved in the lineage-specific control of NKR-P1C expression in NK lymphocytes.

Identification and characterization of a transcriptional regulator for the lck proximal promoter

The lck gene encodes a protein-tyrosine kinase that plays a key role in signaling mediated through T cell receptor (TCR) and pre-TCR complexes. Transcription of the lck gene is regulated by two independent promoter elements: the proximal and distal promoters. Previous studies employing transgenic mice demonstrated that the sequence between -584 and -240 from the transcription start site in the mouse lck proximal promoter is required for its tissue-specific expression in the thymus. In this study, we demonstrate that a Krüppel-like zinc finger protein, mtbeta (BFCOL1, BERF-1, ZBP-89, ZNF148), previously cloned as a protein that binds to the CD3delta gene enhancer, binds to the -365 to -328 region of the lck proximal promoter. mtbeta is ubiquitously expressed in various cell lines and mouse tissues. Overexpressed mtbeta is more active in T-lineage cells than B-lineage cells for transactivating an artificial promoter consisting of the mtbeta binding site and a TATA box. Activity of the lck proximal promoter was significantly impaired by mutating the mtbeta binding site or by reducing mtbeta protein expression level by using antisense mRNA. Our results indicate that mtbeta activity is regulated in a tissue-specific manner and that mtbeta is a critical transactivator for the lck proximal promoter.

Progression of T cell lineage restriction in the earliest subpopulation of murine adult thymus visualized by the expression of lck proximal promoter activity

The proximal promoter of lck directs gene expression exclusively in T cells. To investigate the developmental regulation of the lck proximal promoter activity and its relationship to T cell lineage commitment, a green fluorescence protein (GFP) transgenic (Tg) mouse in which the GFP expression is under the control of the proximal promoter of lck was created. In the adult GFP-Tg mice, >90% of CD4(+)CD8(+) and CD4(+)CD8(-) thymocytes, and the majority of CD4(-)CD8(+) and CD4(-)CD8(-) [double-negative (DN)] thymocytes were highly positive for GFP. Slightly lower but substantial levels of expression of GFP was also observed in mature splenic T cells. No GFP(+) cells was detected in non-T lineage subsets, including mature and immature B cells, CD5(+) B cells, and NK cells, indicating a preserved tissue specificity of the promoter. The earliest GFP(+) cells detected were found in the CD44(+)CD25(-) DN thymocyte subpopulation. The developmental potential of GFP(-) and GFP(+) cells in the CD44(+)CD25(-) DN fraction was examined using in vitro culture systems. The generation of substantial numbers of alphabeta and gammadelta T cells as well as NK cells was demonstrated from both GFP(-) and GFP(+) cells. However, no development of B cells or dendritic cells was detected from GFP(+) CD44(+)CD25(-) DN thymocytes. These results suggest that the progenitors expressing lck proximal promoter activity in the CD44(+)CD25(-) DN thymocyte subset have lost most of the progenitor potential for the B and dendritic cell lineage. Thus, progression of T cell lineage restriction in the earliest thymic population can be visualized by lck proximal promoter activity, suggesting a potential role of Lck in the T cell lineage commitment.

Specific deficiency of p56lck expression in T lymphocytes from type 1 diabetic patients

Peripheral T lymphocyte activation in response to TCR/CD3 stimulation is reduced in type 1 diabetic patients. To explore the basis of this deficiency, a comprehensive analysis of the signal transduction pathway downstream of the TCR/CD3 complex was performed for a cohort of patients (n = 38). The main result of the study shows that T cell hyporesponsiveness is positively correlated with a reduced amount of p56(lck) in resting T lymphocytes. Upon CD3-mediated activation, this defect leads to a hypophosphorylation of the CD3zeta-chain and few other polypeptides without affecting the recruitment of ZAP70. Other downstream effectors of the TCR/CD3 transduction machinery, such as phosphatidylinositol 3-kinase p85alpha, p59(fyn), linker for activation of T cells (LAT), and phospholipase C-gamma1, are not affected. In some patients, the severity of this phenotypic deficit could be linked to low levels of p56(lck) mRNA and resulted in the failure to efficiently induce the expression of the CD69 early activation marker. We propose that a primary deficiency in human type 1 diabetes is a defect in TCR/CD3-mediated T cell activation due to the abnormal expression of the p56(lck) tyrosine kinase.

Dysregulation of the protein tyrosine kinase LCK in lymphoproliferative disorders and in other neoplasias

Initially identified as a T-cell specific member of the Src family of protein tyrosine kinases, Lck has become the object of intensive investigations which have revealed a key role for this kinase in the central processes controlling T-cell development, activation, proliferation and survival. Experimental evidence of the oncogenic potential of Lck, together with the identification of defects in the regulation of Lck expression or activity in T-cell leukemias, suggests that dysregulation of Lck might play a role in neoplastic transformation. Here we review the data documenting a potential role for this kinase in the initiation and maintenance of the transformed state in human cancers.

Regulation of Src-family protein tyrosine kinase transcription during lymphocyte ontogeny

The distribution and quantity of cellular signaling elements influence response patterns to a variety of stimuli. As protein tyrosine phosphorylation is a requisite event induced by a majority of surface receptors, and protein tyrosine kinases of the src-family (src-PTKs) act as proximal transducers for many hematopoietic receptors, we have designed a quantitative RT-PCR assay to measure src-family PTK expression during critical stages of lymphocyte ontogeny. With this assay we demonstrate that the distal promoter element regulating expression of lck, a src-PTK essential for T-cell development and activation, is similarly regulated during ontogeny of T and B cells. However, lck transcript abundance is drastically reduced in B lineage cells, suggesting that transcriptional elements influencing lck promoter activity are modulated in these cells. Moreover, although transcripts encoding the src-PTK fyn accumulate at 0.1% of lck mRNA levels in thymocytes, diminished activity of the lck distal promoter in the B-cell background brings lck and fyn transcript levels to near equivalence in this population. Importantly, transcripts arising from the lck distal promoter element and the fyn locus are similarly upregulated during developmental transitions associated with antigen-receptor expression in both B and T cells. These findings suggest that although the magnitude of lck and fyn expression is differentially regulated in B and T cells, expression at these loci is similarly developmentally programmed during ontogeny of both lymphocyte lineages.

A single base mutation in the 5' splice site of intron 7 of the lck gene is responsible for the deletion of exon 7 in lck mRNA of the JCaM1 cell line

The failure of signal transduction in the JCaM1 cell line was associated with the presence of an abnormal lck mRNA deleted of the exon 7 encoding for an inactive p56lck kinase. Our study of the lck mRNA from various T cell lines and from peripheral blood lymphocytes of healthy donors has revealed the presence of both complete and exon 7-deleted lck transcripts. Thus the exon 7-deleted lck transcript initially described in the JCaM1 mutant cell line, arises from an alternative splicing event occurring in each cells expressing the lck gene. Genomic DNA sequencing of the lck exons 6-8 portion from both the mutant JCaM1 and its parental Jurkat cell lines revealed as the only difference, the presence of a A to G mutation within the 5' splice site of intron 7 in the JCaM1 cell line DNA. To demonstrate the role of this point mutation in the lck pre-mRNA maturation, COS cells were transfected by lck minigenes from the Jurkat and JCaM1 cell lines. In COS cells transfected with minigene from the Jurkat cell line both lck transcripts (with and without exon 7) were observed whereas only the exon 7-spliced lck transcript was observed in COS cells transfected with minigene from the JCaM1 cell line. Thus the mutation is per se responsible for the deletion of exon 7 and the absence of complete lck mRNA in the JCaM1 cell line. Presence of a restriction site (HphI) in the 5' splice site of lck intron 7 from Jurkat DNA allowed to confirm the presence of the mutation on both alleles in the JCaM1 cell line.

Induction of interferon-gamma production in Th1 CD4+ T cells: evidence for two distinct pathways for promoter activation

IFN-gamma produced by CD4+ T helper 1 (Th1) cells promotes protection against intracellular pathogens. Antigen activation of Th1 cells is an important mode of IFN-gamma induction, but here we analyze a second, antigen-nonspecific pathway capable of inducing full IFN-gamma transcription. IL-12 or IL-18 alone do not induce IFN-gamma mRNA, and only modestly augment antigen-induced IFN-gamma mRNA from Th1 cells. However, IL-12 and IL-18 together fully induce IFN-gamma transcription independently of TCR-activated signals, by a mechanism that does not simply involve Stat4 and NF-kappaB activation, but requires additional protein synthesis. Cyclosporin A inhibits TCR-induced IFN-gamma production, but not IL-12/IL-18-induced IFN-gamma production, biochemically discriminating between these pathways. These results suggest that the two pathways induce IFN-gamma production through functionally segregated but spatially overlapping cis-acting elements, similar to other genes under the control of two or more promoters.

Identification of the promoters for the human and murine protective protein/cathepsin A genes

Protective protein/cathepsin A (PPCA) is a lysosomal serine carboxypeptidase that forms a complex with beta-galactosidase and neuraminidase. Its deficiency in humans leads to the lysosomal storage disorder galactosialidosis (GS). The pathologic manifestations in patients relate primarily to the severe deficiency of neuraminidase, and the physiological significance of cathepsin A activity remains unclear. The mouse model of GS, which closely resembles the human phenotype, shows that cells from numerous tissues, especially the central nervous system (CNS), are affected by this disease. To study the site and level of expression of PPCA mRNA in murine and human tissues, we analyzed the promoter regions of the corresponding genes. Their 5' genomic regions were strikingly similar in both organization and sequence. A single 1.8-kb PPCA transcript is present in humans, whereas mouse tissues have a major 1.8-kb and a minor 2.0-kb transcript, both of which are differentially expressed. These two mouse mRNA species differ only in their 5' untranslated region (UTR). The larger mRNA, unique to mouse, is transcribed from an upstream TATA-box-containing promoter, which is absent in the human gene. The downstream promoter, which transcribes the 1.8-kb mRNA common to human and mouse, has characteristics of housekeeping gene promoters and contains putative Sp1 binding sites and three USF/MLTF sequences. In vitro studies demonstrated that expression from the downstream promoter is higher than that from the upstream murine-specific promoter. In situ hybridization of mouse tissue sections identified regions of the brain that preferentially express the 2.0-kb transcript. Our results imply that PPCA mRNA distribution and regulation in murine tissues differs from that in human tissues.

Expression of the RT6 mono(ADP-ribosyl)transferases is regulated by two promoter regions

The structure of the RT6 mono(ADP-ribosyl)transferase gene was studied. Analysis of cDNA clones revealed eight exons and suggested two independent transcriptional start sites. The existence of the downstream initiation site was confirmed by S1-nuclease protection and localized to position +29 of exon 2. The corresponding 5' flanking regions were found to contain typical promoter structures such as TATA- and CCAAT-boxes. Comparison with sequences deposited in the TRANSFAC database of transcription factor binding sites revealed few putative regulatory elements in the region associated with exon 1 (promoter 1). In contrast, several elements contained in the regulatory regions of other T cell-specific genes, such as ets, lyf-1 and ikaros were found in in promoter 2. Analysis of RT6-transcripts showed this region to be the most active promoter in spleen cells of adult rats. Finally, transient transfection assays with reporter gene constructs showed promoter 2 to mediate T-cell specific transcription.

Augmented expression of LCK message directed from the downstream promoter in human colorectal cancer specimens

Lck protein is expressed in some colon carcinoma cell lines but its expression in colon cancer cells in vivo has not been clarified. LCK transcription is regulated from two distinct promoters and initiated exclusively from the downstream promoter in colon carcinoma cell lines in contrast to peripheral lymphocytes. We investigated the expression of the downstream promoter-initiated LCK transcript in 18 colorectal primary cancer and normal mucosae, and two hepatic metastases, using a RNase protection assay with the EcoRI-BglII fragment of human LCK cDNA, YT16. In normal tissues, only traces of the LCK transcript were detected. The expression of the LCK transcript was augmented in 3/18 cancer specimens. The relative level of the LCK transcript in the cancer tissue compared to the average value of normal adjacent tissue was 10-60 in 3 cases, and 3-10 in 7 cases. One hepatic metastasis expressed more LCK message than the primary lesion. Our results indicate that the LCK message is strongly expressed in some colorectal cancers.

A conserved downstream element defines a new class of RNA polymerase II promoters

Although many TATA-less promoters transcribed by RNA polymerase II initiate transcription at multiple sites, the regulation of multiple start site utilization is not understood. Beginning with the prediction that multiple start site promoters may share regulatory features and using the P-glycoprotein promoter (which can utilize either a single or multiple transcription start site(s)) as a model, several promoters with analogous transcription windows were grouped and searched for the presence of a common DNA element. A downstream protein-binding sequence, MED-1 (Multiple start site Element Downstream), was found in the majority of promoters analyzed. Mutation of this element within the P-glycoprotein promoter reduced transcription by selectively decreasing utilization of downstream start sites. We propose that a new class of RNA polymerase II promoters, those that can utilize a distinctive window of multiple start sites, is defined by the presence of a downstream MED-1 element.

Identification of a novel repressive element in the proximal lck promoter

The T-cell-specific protooncogene lck, a src-related tyrosine kinase, is under the control of two promoters that give rise to transcripts differing only in their 5'-untranslated regions. The distal promoter is transcriptionally active in both peripheral and thymic T-cells, whereas expression of the proximal promoter is highest in developing thymocytes. The proximal promoter has also been shown to be selectively activated in a number of colon carcinoma cell lines. Approximately 570 base pairs of proximal promoter sequence is required for expression in both T-cells and colon carcinoma cell lines. Protein binding studies were initiated with an oligonucleotide homologous to a region that, when deleted, causes an increase in promoter activity in transgenic animals. Two proteins with approximate molecular masses of 35 and 75 kDa were found to bind to this region as determined by UV cross-linking studies. Absence of specific protein binding is correlated with a high level of proximal promoter expression. Competitive gel retardation analysis identified a 9-base pair binding site within the proximal lck promoter that is necessary for repression of transcription in cells that contain specific binding activity. Mutants of this binding site do not repress transcription. Repression does not occur in a cell line that expresses lck and lacks this activity. These data support the hypothesis that activation of lck transcription in colon carcinoma is due, at least in part, to the loss of a transcriptional repressor.

Transcription of the blk gene in human B lymphocytes is controlled by two promoters

Genomic DNA containing the first exon and 5'-flanking region of the human protein tyrosine kinase, blk, was isolated. Sequence analysis identified a TG repeat element in this region with enhancer activity, but no TATA or CCAAT sequences were found. Two blk transcripts of 2.2 and 2.5 kilobases were identified in various B-cell lines by Northern blot analyses, and primer extension experiments demonstrated two clusters of multiple transcription start sites. Subsequent promoter analyses by transient transfection assays with a reporter gene identified two promoter elements in the human blk gene. Promoter P1 contains sequences that have been shown to regulate the expression of immunoglobulin genes and promoter P2 contains elements that are highly conserved in the promoter of major histocompatibility complex class II genes, as well as a B-cell-specific activator protein- (BSAP) binding site. Electrophoretic mobility shift assays demonstrated that the binding of a protein to the BSAP-binding site was correlated with the presence of the 2.5-kilobase blk transcript. These data suggest that the two human blk RNAs arise from the transcription of the blk gene by two distinct promoters and that these promoters may be subject to regulation by different trans-acting factors.

Identification of a duplication of the mouse Lyn gene

The Lyn gene encodes a PTK that is believed to participate in the transduction of signals from a variety of cell membrane receptors. Here we report the genomic organisation of the mouse Lyn gene and show that, while the promoter and exons 11-13 are present in single copy, sequences corresponding to the first coding exon are duplicated and this duplication extends into intron 10. Two sets of genomic clones representing the duplicated regions have been isolated and characterised. Nucleotide sequence analysis of these clones has revealed minimal sequence divergence between the two, suggesting that the duplication is a recent event. This is supported by Southern blot analysis of DNA from other mammalian species showing that the duplication is confined to the mouse. Aside from the duplicated sequences, the overall structure of the mouse Lyn gene is similar to that of other Src family members. These data suggest that the process of duplication which generated the Src family of PTK is an ongoing process and provide an insight into the molecular evolution of this group of genes.

The genomic locus of the human hemopoietic-specific cell protein tyrosine kinase (PTK)-encoding gene (HCK) confirms conservation of exon-intron structure among human PTKs of the src family

Protein tyrosine kinases (PTKs) are implicated in the control of cell growth by virtue of their frequent appearance as products of retroviral oncogenes, as intracellular signal transducers, and as growth factor receptors or components thereof. The knowledge of the structure and sequence of family genes encoding PTKs is still limited. To date, the complete genomic structure of human src family members is only available for the C-FGR gene (encoding p55 Fgr, PTK). Sequence analysis and characterization of the intron/exon organization of the human HCK gene, encoding a hemopoietic-specific cell PTK of the src-related family, revealed a length of over 16 kb for the seven 3'-exons. All intron/exon splice junctions agree with the GT/AG rule. In each case where a boundary occurs at a Gly codon, GGG or GGA, the triplet is split between the first and second nucleotide (nt). A total of eight complete and one partial Alu repeats were identified within the introns. The nt sequence of the genomic clones resolves existing discrepancies among two published sequences of HCK cDNAs. Human HCK, C-SRC (encoding p60 Src PTK), C-FGR and LCK (encoding p56 Lck, PTK) genes thus share very similar exon/intron structures for the conserved exons. These results provide additional evidence that the different PTKs of the src-like family most likely arose by duplication of an ancestral src-like gene.

The LCK gene is involved in the t(1;7)(p34;q34) in the T-cell acute lymphoblastic leukemia derived cell line, HSB-2

HSB-2 is a cell line derived from a patient who had T-cell acute lymphoblastic leukemia (T-cell ALL) with a t(1;7)(p34;q34). We used a genomic probe from the T-cell receptor beta (TCR beta) locus (7q34) to identify DNA rearrangements in HSB-2. Two rearranged BglII DNA fragments were cloned, and one of these clones was shown to contain the translocation breakpoint on the derivative chromosome I [der(I)]. We used a probe derived from this clone to isolate an unrearranged phage clone encompassing the breakpoint at Ip34. The restriction map of this clone was compared to the published maps of known protooncogenes located at Ip32-34. By restriction mapping, Southern blot analysis, and DNA sequencing we showed that the translocation breakpoint on chromosome I is located within the first intron of the LCK gene. The LCK gene codes for p56lck, a member of the SRC family of cytoplasmic tyrosine protein kinases. There are two classes of LCK transcripts (type I and type II), each expressed from a distinct promoter, and each having a unique 5' untranslated region (UTR); the protein coding regions of the two classes are identical. The breakpoint in the t(1;7) separates the two LCK promoters and juxtaposes the constant region of the TCR beta locus with the proximal promoter and with the protein-coding region of the LCK gene on the der(I) chromosome.

Differential expression of two classes of lck transcripts upon phorbol ester treatment of human leukemic T cells

The human lymphocyte-specific tyrosine kinase gene, lck, is transcribed from two distinct promoters, resulting in two classes of transcripts (type I and II) differing in their 5' untranslated regions. The steady-state levels of the type I and II lck transcripts were measured in a variety of lymphoid and non-lymphoid human tumor cell lines by S1 nuclease mapping and by a sensitive assay system using the polymerase chain reaction. Human thymocytes and all the leukemic T cell lines tested express both type I and II lck transcripts, albeit at different relative levels. Peripheral blood T cells express mainly type II lck transcripts, whereas two colonic carcinoma lines, COLO 201 and COLO 205, express exclusively type I lck transcripts. Treatment of the leukemic T cell lines, P30/OKUBO and Jurkat, by the phorbol esters tetradecanoylphorbol acetate (TPA) or phorbol dibutyrate (PDB) results in the down-regulation of the type I, and the up-regulation of the type II, lck transcript levels. The effect of PDB on the in vitro differentiation of Jurkat cells, and the expression of lck transcripts, is reversible. The modulation of lck transcript levels in TPA-treated Jurkat cells is not due to differential RNA stability, suggesting that the two lck promoters are utilized differentially during T cell differentiation. The leukemic T cell line, Jurkat, may thus serve as a model for the elucidation of molecular mechanisms that regulate lck transcription and T cell differentiation.

Differential expression of two lck transcripts directed from the distinct promoters in HTLV-I+ and HTLV-I- T-cells

The lck gene encodes a lymphocyte-specific tyrosine protein kinase, p56lck, the expression of which is almost exclusive in T-cells. The expression of lck in human T-cell leukemia virus type I (HTLV-I)-transformed T-cell lines is closely associated with interleukin-2 (IL-2) dependence for their growth. That is, IL-2-dependent HTLV-I-transformed cell lines contain the lck message abundantly as HTLV-I-negative T-cell lines, whereas IL-2-independent HTLV-I-transformed cell lines express either no or little lck mRNA, although they are derived from T-cells. The lck gene contains 2 distinct promoters which direct 2 types of lck transcript with different 5' untranslated regions. In this study, we show that HTLV-I-transformed IL-2-dependent T-cell lines contain the upstream promoter-initiated lck transcript exclusively, in contrast to HTLV-I-negative transformed T-cell lines which express the down-stream promoter- as well as the upstream promoter-initiated lck transcript. In addition, lck mRNA disappears transiently in IL-2-dependent HTLV-I-transformed T-cell lines after stimulation for T-cell activation, which is also observed in peripheral blood T lymphocytes. These results indicate that the disappearance of lck mRNA in HTLV-I-transformed, IL-2-independent cell lines is caused by a mechanism which down-regulates the upstream promoter-initiated lck transcript and this IL-2-independent state may represent a further "activated" condition of the IL-2-dependent state by the stimulation which mediates T-cell activation.

Human T-cell leukemia virus type-I-infected T-cell lines scarcely produce p56lck, whether or not they express lck mRNA

We have previously reported that lck mRNA (a lymphocyte-specific protein tyrosine kinase gene) is absent in human T-cell leukemia virus type I (HTLV-I)-infected interleukin-2(IL-2)-independent T-cell lines, while HTLV-I-negative T-cell lines and HTLV-I-positive IL-2-dependent ones express a large amount of lck mRNA. To further investigate the levels of lck expression, we prepared rabbit anti-Lck antiserum directed against the synthetic oligopeptide of 32 amino acids corresponding to the carboxy terminus of this gene product, p56lck. Using this antiserum, we show that HTLV-I-positive T-cell lines, whether they are IL-2-dependent or not, scarcely express p56lck. In other words, IL-2-dependent HTLV-I-positive T-cell lines seldom produce p56lck in spite of high expression of lck mRNA. Absence of p56lck is suspected of playing an important role in malignant transformation of HTLV-I-infected T-cells.