Structural and functional characterization of the human PAX7 5'-flanking regulatory region

'Enhancing' skeletal muscle and stem cells in three-dimensions: genome regulation of skeletal muscle in development and disease

The noncoding genome imparts important regulatory control over gene expression. In particular, gene enhancers represent a critical layer of control that integrates developmental and differentiation signals outside the cell into transcriptional outputs inside the cell. Recently, there has been an explosion in genomic techniques to probe enhancer control, function, and regulation. How enhancers are regulated and integrate signals in stem cell development and differentiation is largely an open question. In this review, we focus on the role gene enhancers play in muscle stem cell specification, differentiation, and progression. We pay specific attention toward the identification of muscle-specific enhancers, the binding of transcription factors to these enhancers, and how enhancers communicate to their target genes via three-dimensional looping.

A novel PAX7 10-bp indel variant modulates promoter activity, gene expression and contributes to different phenotypes of Chinese cattle

Paired box 7 (PAX7) gene regulates the conversion of muscle satellite cells into myogenic cells and participates in multi-step processes in myogenesis. Expression levels of PAX7 are decisive for its regulatory function. Previous reports revealed that PAX7 were responsible for the developmental traits of muscle. The relationship of the PAX7 promoter variants and livestock phenotypic traits has not been fully elucidated. We detected a novel 10-bp insertion/deletion (indel) polymorphism in the bovine PAX7 promoter and revealed that the indel altered the binding of the transcriptional factor ZNF219. Luciferase reporter assay showed that deletion-deletion (Del-Del) genotype of the PAX7 gene showed 2.79-fold higher promoter activity than the insertion-insertion (Ins-Ins) genotype (P < 0.05), and ZNF219 overexpression significantly diminished the luciferase activity in Ins-Ins groups. Moreover, the expression of PAX7 and its down-stream genes were detected in fetal skeletal muscle of cattle with different PAX7 genotypes, where the Del-Del genotype also displayed high expression levels. Statistical association analysis demonstrated that this indel had significant effects on early growth traits in cattle. These findings provide a complete overview of the function of the PAX7 10-bp variant, which may have potential as a genetic marker for marker-assisted selection in improving economically significant traits of cattle.

A polymorphic (GA/CT)n- SSR influences promoter activity of Tryptophan decarboxylase gene in Catharanthus roseus L. Don

Simple Sequence Repeats (SSRs) of polypurine-polypyrimidine type motifs occur very frequently in the 5' flanks of genes in plants and have recently been implicated to have a role in regulation of gene expression. In this study, 2 accessions of Catharanthus roseus having (CT)8 and (CT)21 varying motifs in the 5'UTR of Tryptophan decarboxylase (Tdc) gene, were investigated for its role in regulation of gene expression. Extensive Tdc gene expression analysis in the 2 accessions was carried out both at the level of transcription and translation. Transcript abundance was estimated using Northern analysis and qRT-PCR, whereas the rate of Tdc gene transcription was assessed using in-situ nuclear run-on transcription assay. Translation status of Tdc gene was monitored by quantification of polysome associated Tdc mRNA using qRT-PCR. These observations were validated through transient expression analysis using the fusion construct [CaM35S:(CT)8-21:GUS]. Our study demonstrated that not only does the length of (CT)n -SSRs influences the promoter activity, but the presence of SSRs per se in the 5'-UTR significantly enhances the level of gene expression. We termed this phenomenon as "microsatellite mediated enhancement" (MME) of gene expression. Results presented here will provide leads for engineering plants with enhanced amounts of medicinally important alkaloids.

Neuropathology and Cellular Pathogenesis of Spinocerebellar Ataxia Type 12

OBJECTIVE

SCA12 is a progressive autosomal-dominant disorder, caused by a CAG/CTG repeat expansion in PPP2R2B on chromosome 5q32, and characterized by tremor, gait ataxia, hyperreflexia, dysmetria, abnormal eye movements, anxiety, depression, and sometimes cognitive impairment. Neuroimaging has demonstrated cerebellar and cortical atrophy. We now present the neuropathology of the first autopsied SCA12 brain and utilize cell models to characterize potential mechanisms of SCA12 neurodegeneration.

METHODS

A fixed SCA12 brain was examined using gross, microscopic, and immunohistochemical methods. The effect of the repeat expansion on PPP2R2B Bβ1 expression was examined in multiple cell types by transient transfection of constructs containing the PPP2R2B Bβ1 promoter region attached to a luciferase reporter. The neurotoxic effect of PPP2R2B overexpression was examined in transfected rat primary neurons.

RESULTS

Neuropathological investigation revealed enlarged ventricles, marked cerebral cortical atrophy and Purkinje cell loss, less-prominent cerebellar and pontine atrophy, and neuronal intranuclear ubiquitin-positive inclusions, consistent with Marinesco bodies, which did not stain for long polyglutamine tracts, alpha-synuclein, tau, or transactive response DNA-binding protein 43. Reporter assays demonstrated that the region of PPP2R2B containing the repeat functions as a promoter, and that promoter activity increases with longer repeat length and is dependent on cell type, repeat sequence, and sequence flanking the repeat. Overexpression of PPP2R2B in primary cortical neurons disrupted normal morphology.

CONCLUSIONS

SCA12 involves extensive, but selective, neurodegeneration distinct from Alzheimer's disease, synucleinopathies, tauopathies, and glutamine expansion diseases. SCA12 neuropathology may arise from the neurotoxic effect of repeat-expansion-induced overexpression of PPP2R2B.

Pax7 is regulated by cMyb during early neural crest development through a novel enhancer

The neural crest (NC) is a migratory population of cells unique to vertebrates that generates many diverse derivatives. NC cells arise during gastrulation at the neural plate border (NPB), which is later elevated as the neural folds (NFs) form and fuse in the dorsal region of the closed neural tube, from where NC cells emigrate. In chick embryos, Pax7 is an early marker, and necessary component of NC development. Unlike other early NPB markers, which are co-expressed in lateral ectoderm, medial neural plate or posterior-lateral mesoderm, Pax7 early expression seems more restricted to the NPB. However, the molecular mechanisms controlling early Pax7 expression remain poorly understood. Here, we identify a novel enhancer of Pax7 in avian embryos that replicates the expression of Pax7 associated with early NC development. Expression from this enhancer is found in early NPB, NFs and early emigrating NC, but unlike Pax7, which is also expressed in mesodermal derivatives, this enhancer is not active in somites. Further analysis demonstrates that cMyb is able to interact with this enhancer and modulates reporter and endogenous early Pax7 expression; thus, cMyb is identified as a novel regulator of Pax7 in early NC development.

A GAG trinucleotide-repeat polymorphism in the gene for glutathione biosynthetic enzyme, GCLC, affects gene expression through translation

A guanine-adenine-guanine (GAG) repeat polymorphism with 5 different alleles (4, 7, 8, 9, and 10 repeats) in the 5' untranslated region (UTR) of GCLC has been associated with altered GCL activity and glutathione (GSH) levels. We investigated whether this polymorphism affects either transcription or translation using luciferase reporter constructs containing variant GCLC 5' UTRs. Higher luciferase activity was observed in HepG2 and human embryonic kidney 293 (HEK293) cells transfected with constructs containing either 8 or 9 repeats than in constructs containing 4, 7, or 10 repeats (P<0.05). In cell-free lysates, GAG repeat number had no effect on luciferase mRNA yield. In vitro translation of mRNAs from luciferase constructs resulted in differences similar to those found in cell cultures (P<0.05). A similar association of GAG repeat with GCLC phenotype was observed in vivo in healthy adults, as individuals with GAG-7/7 genotype had lower GCL activity and GSH levels in lymphocytes compared to those with GAG-9/9 (P<0.05). Higher GCL activity and GSH levels observed in red blood cells (RBCs) from individuals with GAG-7/7 compared to GAG-9/9 are likely due to differences in GCL regulation in RBCs. Altogether, these results suggest that GAG polymorphism affects GCLC expression via translation, and thus may be associated with altered risk for GSH-related diseases and toxicities.

Over-expression of the transcription factor, ZBP-89, leads to enhancement of the C2C12 myogenic program

Myogenesis involves the complex interplay between the down-regulation of non-muscle genes and the up-regulation of muscle-specific genes. This interplay is controlled by the myogenic regulatory factors Myf5, MRF4, MyoD and myogenin. To trigger the up-regulation of these muscle-specific factors, certain environmental cues, such as the removal of serum, signal C2C12 myoblast cells to withdraw from cell cycle, fuse and activate muscle-specific genes. Here, the level of ZBP-89 (zfp148), a Krüppel-like transcription factor, has been shown to increase during myogenesis. Over-expression of ZBP-89, via adenoviral infection, led to the enhancement of the myogenic program without requiring the removal of serum. Quantitative real-time PCR and ChIP assays documented that ZBP-89 promoted the down-regulation of Pax7 coupled with the up-regulation of MRF4 and MyoD to regulate C2C12 differentiation in vitro. In addition, ZBP-89 over-expression up-regulated p21 and Rb while promoting the down-regulation of cyclinA and cyclinD1. In converse, the diminution of ZBP-89 by siRNA promoted the retention of myogenic and cell cycle regulators at myoblast levels resulting in a concomitant delay of the myogenic program. From these studies we conclude that the transcription factor ZBP-89 plays an important role in the timing of the myogenic program.

Quantitative differences in chromatin accessibility across regulatory regions can be directly compared in distinct cell-types

Transcriptional activation in eukaryotes is often accompanied by alterations to chromatin structure at specific regulatory sites while other genomic regions may remain unchanged. In this study, we have examined the correlation between expression and chromatin accessibility of the human CR2 gene in a panel of cell lines (U937, REH, Ramos, and Raji) using the CHART-PCR assay with the accessibility agent micrococcal nuclease (MNase). To validate the use of this assay for comparing multiple cell-types, we first tested a series of genomic regions to determine if we could observe consistent, site-specific levels of MNase chromatin accessibility. Promoter regions of the ubiquitously expressed genes GAPDH and beta-actin were similar and showed high accessibility to MNase digestion in each of the cell lines, while on the other hand, promoter regions of developmentally restricted genes PAX-7 and SP-A2 showed consistently reduced chromatin accessibility. Since CHART-PCR detected site-specific differences in chromatin accessibility in a manner that could be compared between cell-types, we next examined chromatin accessibility over the CR2 core promoter in the panel of cell lines representing either CR2 expressing or CR2 non-expressing cell-types. Our data revealed significantly enhanced accessibility over the -289 to -101 and the -115 to -12 regions of the CR2 promoter in expressing B-cells (Ramos, Raji) compared to non-expressing cells (U937, REH). Thus, CHART-PCR assays detected a correlation between chromatin accessibility and expression of the human CR2 gene, while the accessibility of other genomic regions was site-specific, but not altered between cell-types.

Comparison of the proximal promoter regions of the PAX3 and PAX7 genes

Translocations t(2;13)(q35;q14) and t(1;13)(p36;q14), which fuse PAX3 and PAX7, respectively, to FOXO1A, characterize alveolar rhabdomyosarcoma. Previous studies have suggested that the expression of PAX7-FOXO1A is copy-number dependent, but that of PAX3-FOXO1A is not, which may be due to a weaker PAX7 than PAX3 promoter. The aim of the present study was to compare the transcriptional activities of the PAX3 and PAX7 proximal promoter regions, using the dual-luciferase reporter assay with three vector systems in eight cell lines. The PAX3 promoter was found to have higher transcriptional activity than that of PAX7 irrespective of the vector system or cell line used. These findings are consistent with the idea that an amplification event is required for the PAX7-FOXO1A chimeric transcript to reach a critical expression level.

HSF1 down-regulates XAF1 through transcriptional regulation

Studies have indicated the role of HSF1 (heat-shock transcription factor 1) in repressing the transcription of some nonheat shock genes. XAF1 (XIAP-associated factor 1) was an inhibitor of apoptosis-interacting protein with the effect of antagonizing the cytoprotective role of XIAP. XAF1 expression was lower in gastrointestinal cancers than in normal tissues with the mechanism unclear. Here we showed that gastrointestinal cancer tissues expressed higher levels of HSF1 than matched normal tissues. The expression of XAF1 and HSF1 was negatively correlated in gastrointestinal cancer cell lines. Stress stimuli, including heat, hypo-osmolarity, and H2O2, significantly suppressed the expression of XAF1, whereas the alteration of HSF1 expression negatively correlated with XAF1 expression. We cloned varying lengths of the 5'-flanking region of the XAF1 gene into luciferase reporter vectors, and we evaluated their promoter activities. A transcription silencer was found between the -592- and -1414-nucleotide region that was rich in nGAAn/nT-TCn elements (where n indicates G, A, T, or C). A high affinity and functional HSF1-binding element within the -862/-821-nucleotide region was determined by electrophoretic mobility shift assay and chromatin immunoprecipitation assay. Inactivation of this "heat-shock element" by either site-directed mutation or an HSF1 inhibitor, pifithrin-alpha, restored the promoter activity of the silencer structure. Moreover, pretreatment with antioxidants suppressed HSF1 binding activity and increased the transcriptional activity and expression of XAF1. These findings suggested that endogenous stress pressure in cancer cells sustained the high level expression of HSF1 and subsequently suppressed XAF1 expression, implicating the synergized effect of two anti-apoptotic protein families, HSP and inhibitors of apoptosis, in cytoprotection under stress circumstances.

CSX/Nkx2.5 modulates differentiation of skeletal myoblasts and promotes differentiation into neuronal cells in vitro

CSX/Nkx2.5 transcription factor plays a pivotal role in cardiac development; however, its role in development and differentiation of other organs has not been investigated. In this study, we used C2C12 myoblasts and human fetal primary myoblasts to investigate the function of Nkx2.5 in skeletal myogenesis. The expression levels of Nkx2.5 decreased as C2C12 myoblasts elongated and fused to form myotubes. The expression of human NKX2.5 in C2C12 myoblasts inhibited myocyte differentiation and myotube formation, and up-regulated Gata4 and Tbx5 expression. The expression of NKX2.5 in terminally differentiated C2C12 myotubes resulted in a change in morphology and breakdown into smaller myotubes. Furthermore, overexpression of NKX2.5 in C2C12 cells and primary cultures of human fetal myoblasts led to differentiation of myoblasts into neuron-like cells and expression of neuronal markers. This study sheds light on the previously unknown non-cardiac functions of Nkx2.5 transcription factor.

Some microsatellites may act as novel polymorphic cis-regulatory elements through transcription factor binding

Although microsatellites with functional effects have been described, generally, these repeats are considered as "junk" DNA in the same way as other repetitive sequences. Our aim was to investigate if certain microsatellites can have a functional role as cis-regulatory elements. A database was created of all short tandem repeats, from 2 to 10 bases, located in the first 10-kb 5' of the transcription start sites of all annotated genes of the human genome. Of 114 microsatellites selected based on their size and location in the promoter, 51 were found to be polymorphic. Using electrophoretic mobility shift assay (EMSA), we studied five repetitive motifs and three displayed specific protein binding which were found in 12 of the polymorphic microsatellites. An interesting microsatellite is the CTC/GAG repeat which, as double-stranded (DS) DNA, bound specificity protein 1 (SP1) with high affinity, formed triplexes in vitro and displayed differences in SP1 binding and triplex formation capacity for repeats with distinct numbers of repeat units. Interestingly, the polypyrimidine strand of the repeat (CTC) bound other proteins such as polypyrimidine tract-binding protein 1 (PTBP1) as single-stranded (SS) DNA, and a model with two alternative DNA conformations is proposed for these repeats. Distinct protein binding to DS DNA was also observed for different numbers of AAACA and AAAAT repeats. Our results suggest that certain microsatellites may act as cis-regulatory elements, controlling gene expression through transcription factor binding and/or secondary DNA structure formation. Due to their high polymorphism and abundance, they might represent an important source of quantitative genetic variation.

Chromatin immunoprecipitation (ChIP) on chip experiments uncover a widespread distribution of NF-Y binding CCAAT sites outside of core promoters

The CCAAT box is a prototypical promoter element, almost invariably found between -60 and -100 upstream of the major transcription start site. It is bound and activated by the histone fold trimer NF-Y. We performed chromatin immunoprecipitation (ChIP) on chip experiments on two different CpG islands arrays using chromatin from hepatic HepG2 and pre-B cell leukemia NALM-6 cell lines, with different protocols of probe preparation and labeling. We analyzed and classified 239 known or predicted targets; we validated several by conventional ChIPs with anti-YB and anti-YC antibodies, in vitro EMSAs, and ChIP scanning. The importance of NF-Y binding for gene expression was verified by the use of a dominant negative NF-YA mutant. All but four genes are new NF-Y targets, falling into different functional categories. This analysis reinforces the notion that NF-Y is an important regulator of cell growth, and novel unexpected findings emerged from this unbiased approach. (i) A remarkable proportion of NF-Y targets, 40%, are complex transcriptional units composed of divergent, convergent, and tandem promoters. (ii) 40-50% of NF-Y sites are not in core promoters but are in introns or at distant 3' or 5' locations. The abundance of "unorthodox" CCAAT positions highlights an unexpected complexity of the NF-Y-mediated transcriptional network.