Novel muscle-specific enhancer sequences upstream of the cardiac actin gene

Variable cardiac α-actin (Actc1) expression in early adult skeletal muscle correlates with promoter methylation

Different genes encode the α-actin isoforms that are predominantly expressed in heart and skeletal muscle. Mutations in the skeletal muscle α-actin gene (ACTA1) cause muscle diseases that are mostly lethal in the early postnatal period. We previously demonstrated that the disease phenotype of ACTA1 mouse models could be rescued by transgenic over-expression of cardiac α-actin (ACTC1). ACTC1 is the predominant striated α-actin isoform in the heart but is also expressed in developing skeletal muscle. To develop a translatable therapy, we investigated the genetic regulation of Actc1 expression. Using strains from The Collaborative Cross (CC) genetic resource, we found that Actc1 varies in expression by up to 24-fold in skeletal muscle. We defined significant expression quantitative trait loci (eQTL) associated with early adult Actc1 expression in soleus and heart. eQTL in both heart and soleus mapped to the Actc1 locus and replicate an eQTL mapped for Actc1 in BXD heart and quadriceps. We built on this previous work by analysing genes within the eQTL peak regions to prioritise likely candidates for modifying Actc1 expression. Additionally we interrogated the CC founder haplotype contributions to enable prioritisation of genetic variants for functional analyses. Methylation around the Actc1 transcriptional start site in early adult skeletal muscle negatively correlated with Actc1 expression in a strain-dependent manner, while other marks of regulatory potential (histone modification and chromatin accessibility) were unaltered. This study provides novel insights into the complex genetic regulation of Actc1 expression in early adult skeletal muscles.

Cis and trans regulation of hepcidin expression by upstream stimulatory factor

Hepcidin is the presumed negative regulator of systemic iron levels; its expression is induced in iron overload, infection, and inflammation, and by cytokines, but is suppressed in hypoxia and anemia. Although the gene is exquisitely sensitive to changes in iron status in vivo, its mRNA is devoid of prototypical iron-response elements, and it is therefore not obvious how it may be regulated by iron flux. The multiplicity of effectors of its expression also suggests that the transcriptional circuitry controlling the gene may be very complex indeed. In delineating enhancer elements within both the human and mouse hepcidin gene promoters, we show here that members of the basic helix-loop-helix leucine zipper (bHLH-ZIP) family of transcriptional regulators control hepcidin expression. The upstream stimulatory factor 2 (USF2), previously linked to hepcidin through gene ablation in inbred mice, appears to exert a polar or cis-acting effect, while USF1 may act in trans to control hepcidin expression. In mice, we found variation in expression of both hepcidin genes, driven by these transcription factors. In addition, c-Myc and Max synergize to control the expression of this hormone, supporting previous findings for the role of this couple in regulating iron metabolism. Transcriptional activation by both USF1/USF2 and c-Myc/Max heterodimers occurs through E-boxes within the promoter. Site-directed mutagenesis of these elements rendered the promoter unresponsive to USF1/USF2 or c-Myc/Max. Dominant-negative mutants of USF1 and USF2 reciprocally attenuated promoter transactivation by both wild-type USF1 and USF2. Promoter occupancy by the transcription factors was confirmed by DNA-binding and chromatin immunoprecipitation assays. Taken together, it would appear that synergy between these members of the bHLH-ZIP family of transcriptional regulators may subserve an important role in iron metabolism as well as other pathways in which hepcidin may be involved.

Characterization of a cardiac-specific enhancer, which directs {alpha}-cardiac actin gene transcription in the mouse adult heart

Expression of the mouse alpha-cardiac actin gene in skeletal and cardiac muscle is regulated by enhancers lying 5' to the proximal promoter. Here we report the characterization of a cardiac-specific enhancer located within -2.354/-1.36 kbp of the gene, which is active in cardiocytes but not in C2 skeletal muscle cells. In vivo it directs reporter gene expression to the adult heart, where the proximal promoter alone is inactive. An 85-bp region within the enhancer is highly conserved between human and mouse and contains a central AT-rich site, which is essential for enhancer activity. This site binds myocyte enhancer factor (MEF)2 factors, principally MEF2D and MEF2A in cardiocyte nuclear extracts. These results are discussed in the context of MEF2 activity and of the regulation of the alpha-cardiac actin locus.

The in vivo form of the murine class VI POU protein Emb is larger than that encoded by previously described transcripts

The class VI POU domain family member known as Emb in the mouse (rat Brn5 or human mPOU/TCFbeta1) is present in vivo as a protein migrating at about 80 kDa on western blots, considerably larger than that predicted (about 42 kDa) from previously cloned coding sequences. By RT-PCR and 5' RACE strategies a full-length Emb sequence, Emb FL, is now identified. Shorter sequences encoding the -COOH terminal, and an -NH(2) terminal isoform, EmbN, were also isolated. Comparisons of Emb coding sequences between species, including the full-length zebra fish, POU(c), are presented, together with a compilation of the multiple transcripts produced by alternative splicing and the presence of different transcriptional start and stop sites, from the Emb gene.

An enhancer directs differential expression of the linked Mrf4 and Myf5 myogenic regulatory genes in the mouse

The myogenic regulatory factors, Mrf4 and Myf5, play a key role in skeletal muscle formation. An enhancer trap approach, devised to isolate positive-acting elements from a 200-kb YAC covering the mouse Mrf4-Myf5 locus in a C2 myoblast assay, yielded an enhancer, A17, which mapped at -8 kb 5' of Mrf4 and -17 kb 5' of Myf5. An E-box bound by complexes containing the USF transcription factor is critical for enhancer activity. In transgenic mice, A17 gave two distinct and mutually exclusive expression profiles before birth, which correspond to two phases of Mrf4 transcription. Linked to the Tk or Mrf4 minimal promoters, the nlacZ reporter was expressed either in embryonic myotomes, or later in fetal muscle, with the majority of Mrf4 lines showing embryonic expression. When linked to the Myf5 minimal promoter, only fetal muscle expression was detected. These observations identify A17 as a sequence that targets sites of myogenesis in vivo and raise questions about the mutually exclusive modes of expression and possible promoter/enhancer interactions at the Mrf4-Myf5 locus.

Cell history determines the maintenance of transcriptional differences between left and right ventricular cardiomyocytes in the developing mouse heart

The molecular mechanisms that establish and maintain transcriptional differences between cardiomyocytes in the left and right ventricular chambers are unkown. We have previously analysed a myosin light chain 3f transgene containing an nlacZ reporter gene, which is transcribed in left but not right ventricular cardiomyocytes. In this report we examine the mechanisms involved in maintaining regionalised transgene expression. Primary cardiomyocytes prepared from left and right ventricular walls of transgenic mice were found to maintain transgene expression status in culture. However, similar cultures prepared from nontransgenic mice or rats show uniform expression after transient transfection of Mlc3f constructs, suggesting that the mechanism responsible for differential expression of the transgene between left and right ventricular cells does not operate on transiently introduced molecules. These data suggest that developmental cell history determines transgene expression status. Maintenance of transgene expression status is regulated by a cell-autonomous mechanism that is independent of DNA methylation, trichostatin A-sensitive histone deacetylation and miss-expression of transcription factors that are expressed in the left or right ventricles of the embryonic heart. Parallels between Mlc3f transgene repression in right ventricular cardiomyocytes and polycomb-mediated silencing in Drosophila suggest that Mlc3f regulatory sequences included on the transgene may contain a cellular memory module that is switched into an on or off state during early cardiogenesis. Epigenetic mechanisms may therefore be involved in maintaining patterning of the mammalian myocardium.

The circadian E-box: when perfect is not good enough

Life on earth has evolved on a photic carousel, spinning through alternating periods of light and darkness. This playful image belies the fact that only those organisms that learned how to benefit from the recurring features in their environment were allowed to ride on. This selection process has engendered many daily rhythms in our biosphere, most of which rely on the anticipatory power of an endogenously generated marker of phase: the biological clock. The basic mechanisms driving this remarkable device have been really tough to decode but are finally beginning to unravel as chronobiologists probe deeper and wider in and around the recently discovered gears of the clock. Like its chemical predecessors, biological circadian oscillators are characterized by interlaced positive and negative feedback loops, but with constants and variables carefully balanced to achieve an approximately 24h period. The loops at the heart of these biological oscillators are sustained by specific patterns of gene expression and precisely tuned posttranscriptional modifications. It follows that a molecular understanding of the biological clock hinges, in no small measure, on a better understanding of the cis-acting elements that bestow a given gene with its circadian properties. The present review summarizes what is known about these elements and what remains to be elucidated.

Circadian Transcription. Thinking outside the E-Box

The E-Box is a widely used DNA control element. Despite its brevity and broad distribution the E-Box is a remarkably versatile sequence that affects many different genetic programs, including proliferation, differentiation, tissue-specific responses, and cell death. The circadian clock is one of the latest pathways shown to employ this element. In this context, E-Boxes are likely to play a key role in establishing the robust waves of gene expression characteristic of circadian transcription. The regulatory flexibility of the E-Box hinges on the sequence ambiguity allowed at its core, the strong influence of the surrounding sequences, and the recruitment of spatially and temporally regulated E-Box-binding factors. Therefore, understanding how a particular E-Box can accomplish a specific task entails the identification and systematic analysis of these cis- and trans-acting E-Box modifiers. In the present study we compared the E-Box-containing minimal promoters of vasopressin and cyclin B1, two genes that can respond to the transcriptional oscillators driving the circadian clock and cell cycle, respectively. Results of this comparison will help elucidate the manner in which discreet DNA modules associate to either augment or restrain the activation of potential circadian E-Boxes in response to competing regulatory signals.

Analysis of ferrochelatase expression during hematopoietic development of embryonic stem cells

Ferrochelatase, the last enzyme in the heme pathway, chelates protoporphyrin IX and iron to form heme and is mutated in protoporphyria. The ferrochelatase gene is expressed in all tissues at low levels to provide heme for essential heme-containing proteins and is up-regulated during erythropoiesis for the synthesis of hemoglobin. The human ferrochelatase promoter contains 2 Sp1 cis-elements and GATA and NF–E2 sites, all of which bind their cognatetrans-acting factors in vitro. To investigate the role of these elements during erythropoiesis, we introduced expression of the green fluorescent protein (EGFP) transgenes driven by various ferrochelatase promoter fragments into a single locus in mouse embryonic stem cells. EGFP expression was monitored during hematopoietic differentiation in vitro using flow cytometry. We show that a promoter fragment containing the Sp1 sites, the NF–E2 and GATA elements, was sufficient to confer developmental-specific expression of the EGFP transgene, with an expression profile identical to that of the endogenous gene. In this system the −0.275 kb NF–E2 cis-element is required for erythroid-enhanced expression, the GATA cis-element functions as a stage-specific repressor and enhancer, and elements located between −0.375kb and −1.1kb are necessary for optimal levels of expression. Ferrochelatase mRNA increased before the primitive erythroid-cell stage without a concomitant increase in ferrochelatase protein, suggesting the presence of a translational control mechanism. Because of the sensitivity of this system, we were able to assess the effect of an A-to-G polymorphism identified in the promoters of patients with protoporphyria. There was no effect of the G haplotype on transcriptional activity of the −1.1 kb transgene.

Analysis of ferrochelatase expression during hematopoietic development of embryonic stem cells

Ferrochelatase, the last enzyme in the heme pathway, chelates protoporphyrin IX and iron to form heme and is mutated in protoporphyria. The ferrochelatase gene is expressed in all tissues at low levels to provide heme for essential heme-containing proteins and is up-regulated during erythropoiesis for the synthesis of hemoglobin. The human ferrochelatase promoter contains 2 Sp1 cis-elements and GATA and NF–E2 sites, all of which bind their cognatetrans-acting factors in vitro. To investigate the role of these elements during erythropoiesis, we introduced expression of the green fluorescent protein (EGFP) transgenes driven by various ferrochelatase promoter fragments into a single locus in mouse embryonic stem cells. EGFP expression was monitored during hematopoietic differentiation in vitro using flow cytometry. We show that a promoter fragment containing the Sp1 sites, the NF–E2 and GATA elements, was sufficient to confer developmental-specific expression of the EGFP transgene, with an expression profile identical to that of the endogenous gene. In this system the −0.275 kb NF–E2 cis-element is required for erythroid-enhanced expression, the GATA cis-element functions as a stage-specific repressor and enhancer, and elements located between −0.375kb and −1.1kb are necessary for optimal levels of expression. Ferrochelatase mRNA increased before the primitive erythroid-cell stage without a concomitant increase in ferrochelatase protein, suggesting the presence of a translational control mechanism. Because of the sensitivity of this system, we were able to assess the effect of an A-to-G polymorphism identified in the promoters of patients with protoporphyria. There was no effect of the G haplotype on transcriptional activity of the −1.1 kb transgene.

Enhancer and promoter chimeras in plasmids designed for intramuscular injection: a comparative in vivo and in vitro study

Enhancers and promoters from various muscle-specific genes were substituted for or combined with the enhancer/promoter of the human cytomegalovirus (CMV) IE gene in a luciferase reporter gene plasmid in an effort to identify new promoter chimeras with increased expression activity after direct intramuscular injection. The regulatory sequence substitutions or additions varied in content, location, and orientation relative to the CMV regulatory sequences. The expression activities of the derivative and parent plasmids were compared quantitatively in vivo using a standard mouse intramuscular injection assay, and in vitro by transfection of differentiated C2C12 mouse myoblasts and BHK hamster kidney cells, to test whether cultured cell transfection could substitute for at least some animal experimentation. In vivo, 1 of 19 of the enhancer/promoter chimeras increased expression levels. In vitro, some chimeras showed significant expression augmentation in C2C12 cells, but not in BHK cells. We conclude that because of differences in plasmid expression profiles, these cell culture systems cannot readily substitute for in vivo testing of new plasmid constructs.

A novel site, Mt, in the human desmin enhancer is necessary for maximal expression in skeletal muscle

Previous investigations have shown that expression of the muscle-specific intermediate filament desmin gene in skeletal muscle is controlled in part by a 5' muscle-specific enhancer. This enhancer activity can be divided into myoblast-specific and myotube-specific activation domains. The myotube-specific region contains a MyoD and MEF2 sites, whereas the myoblast-specific region contains Sp1, Krox, and Mb sites. In the present study, we designed mutations in the conserved portion of the myotube-specific region; transfection analysis of these mutations showed that a novel site located between the MyoD and MEF2 sites, named Mt (GGTATTT), is required for full transcriptional activity of the desmin enhancer in skeletal muscle. Although gel mobility shift assays demonstrate that myotube, myoblast, fibroblast, and HeLa nuclear extracts contain a nuclear factor that binds specifically to Mt, four copies of the Mt site function as the native enhancer only in myotubes. Functional synergism among the MyoD, MEF2, and Mt sites in myotubes has been demonstrated. These results show that the novel Mt site cooperates with MyoD and MEF2 to give maximal expression of the desmin gene.

Embryonic and fetal myogenic programs act through separate enhancers at the MLC1F/3F locus

Embryonic and fetal stages of skeletal muscle development are characterized by the differential expression of a number of muscle-specific genes. These include the products of independent promoters at the fast myosin light chain 1F/3F locus. In the mouse embryo MLC1F transcripts accumulate in embryonic skeletal muscle from E9, 4-5 days before high-level accumulation of MLC3F transcripts. A 3' enhancer can activate MLC1F and MLC3F promoters in differentiated muscle cells in vitro and in transgenic mice; both promoters, however, are activated at the time of MLC1F transcript accumulation. We now demonstrate the presence of a second muscle-specific enhancer at this locus, located in the intron separating the MLC1F and MLC3F promoters. Transgenic mice containing the intronic, but lacking the 3' enhancer, express high levels of an nlacZ reporter gene from the MLC3F promoter in adult fast skeletal muscle fibers. In contrast to the 3' enhancer, the intronic element is inactive both in embryonic muscle cells in vivo and in embryonic myocyte cultures. The intronic enhancer is activated at the onset of fetal development in both primary and secondary muscle fibers, at the time of endogenous MLC3F transcript accumulation. Late-activated MLC3F transgenes thus provide a novel in toto marker of fetal myogenesis. These results suggest that temporal regulation of transcription at the MLC1F/3F locus is controlled by separate enhancers which are differentially activated during embryonic and fetal development.

An E-box motif conveys inhibitory activity on the atrial natriuretic peptide gene

Atrial natriuretic peptide (ANP) is a potent diuretic, natriuretic, and vasorelaxant hormone that is expressed early in ventricular hypertrophy. Expression of human ANP is controlled by a series of regulatory elements located in the 5' flanking sequence of its gene. We generated a series of 5' deletion mutations extending from -2600 to -1150 relative to the transcription start site and linked them to a chloramphenicol acetyltransferase reporter gene. Using transient transfection analysis, we have identified a negative regulatory element between -1206 and -1152 relative to the start site. Each of a series of 5' deletion mutants, when introduced into fibroblast cultures, expressed the reporter function at a level that was significantly less (< 20%) than that seen with the -1152 reporter construct, whereas comparably transfected atrial cardiocytes demonstrated no change in reporter activity, implying that the repressor function is specific to cell type. The critical region (from -1206 to -1152) associates with a soluble protein present in cardiac fibroblast extracts in a sequence-specific fashion. Deoxyribonuclease I footprint analysis demonstrated the presence of several protected regions, including one that overlies an E-box motif (CAACTG), an element that in other systems has been implicated in promoting differentiation in the myocyte lineage. Site-directed mutagenesis of the E-box motif suppressed both the protein-binding and inhibitory activities of the 54-bp fragment. In summary, we have found a region in the 5' flanking sequence of the human ANP gene that represses transcriptional activity in nonmyocardial cells. This element may play an important role in the restriction of ANP gene expression to cardiac myocytes.

Prolonged alteration in E-box binding after a single systemic kainate injection: potential relation to F1/GAP-43 gene expression

The presence in hippocampus of a basic helix-loop-helix (bHLH) family of transcription factors (TFs) specifically binding in an electrophoretic mobility shift assay (EMSA) to the E-box recognition element was established by selective blockade of binding both by cold competition and by an antibody to MyoD1, an E-box TF. Protein source was from a micro-dissected preparation enriched in hippocampal granule cells. Specific E-box binding of hippocampal transcription factors was significantly reduced in kainate acid (KA) treated animals. This was observed at 24 and 72 h, but not before (3, 6 h) or after (96 h). This is the first report to our knowledge to study functional regulation of E-box binding protein in adult hippocampus. To determine the generality of this E-box regulatory event, we studied four other situations, in addition to kainate treatment, where axonal growth is known or has been suggested to increase: NGF treatment of PC12 cells, unilateral hilar lesions, long-term potentiation after 1 h, and postnatal rat hippocampal development. In all four cases, decreased E-box binding was observed. The recent link of F1/GAP-43 mRNA induction in hippocampal granule cells by KA to growth of their axons, the mossy fibers in the adult rat, suggests a potential role for the F1/GAP-43 5' flanking promoter region in regulating neurite outgrowth. Since in all cases decreased E-box binding preceded increased F1/GAP-43 mRNA expression, it is suggested that E-box binding to the F1/GAP-43 promoter in hippocampal granule cells could negatively regulate F1/GAP-43 gene expression. Indeed, analysis of recognition elements on the F1/GAP-43 gene revealed an arrangement, previously described in other genes, of multiple adjacent E-box elements. E-box binding of bHLH transcription factors is likely to occur on several different genes in addition to F1/GAP-43. It is, therefore, attractive to think that E-box binding is regulated by in vivo activation of the adult brain and that this gene regulatory event participates in the orchestration of molecular and cellular responses underlying axonal growth.

Regulation of tissue-specific expression of the skeletal muscle ryanodine receptor gene

The ryanodine receptors (RYR) are a family of calcium release channels that are expressed in a variety of tissues. Three genes, i. e. ryr1, ryr2, and ryr3, have been identified coding for a skeletal muscle, cardiac muscle, and brain isoform, respectively. Although, the skeletal muscle isoform (RYR1) was shown to be expressed predominantly in skeletal muscle, expression was also detected in the esophagus and brain. To analyze the transcriptional regulation of the RYR1 gene, we have constructed chimeric genes composed of the upstream region of the RYR1 gene and the bacterial chloramphenicol acetyltransferase (CAT) gene and transiently transfected them into primary cultured porcine myoblasts, myotubes, and fibroblasts. A 443-base pair region upstream from the transcription start site was sufficient to direct CAT activity without tissue specificity. Deletion of a 61-base pair fragment from the 5'-end of the promoter resulted in a marked reduction of CAT activity in all three tissue types. A similar reduction of expression was observed when using a construct with the first intron in antisense orientation upstream from the promoter. In contrast, the first intron in sense orientation enhanced expression only in myotubes, while expression was repressed in fibroblasts and myoblasts. Gel retardation analyses showed DNA binding activity in nuclear extracts for two upstream DNA sequence elements. Our data suggest that (i) RYR1 gene expression is regulated by at least two novel transcription factors (designated RYREF-1 and RYREF-2), and (ii) tissue specificity results from a transcriptional repression in nonmuscle cells mediated by the first intron.