Overall and allele-specific expression of the SMC1A gene in female Cornelia de Lange syndrome patients and healthy controls

Cornelia de Lange syndrome (CdLS) is a rare multisystem disorder characterized by facial dysmorphisms, limb anomalies, and growth and cognitive deficits. Mutations in genes encoding subunits (SMC1A, SMC3, RAD21) or regulators (NIPBL, HDAC8) of the cohesin complex account for approximately 65% of clinically diagnosed CdLS cases. The SMC1A gene (Xp11.22), responsible for 5% of CdLS cases, partially escapes X chromosome inactivation in humans and the allele on the inactive X chromosome is variably expressed. In this study, we evaluated overall and allele-specific SMC1A expression. Real-time PCR analysis conducted on 17 controls showed that SMC1A expression in females is 50% higher than in males. Immunoblotting experiments confirmed a 44% higher protein level in healthy females than in males, and showed no significant differences in SMC1A protein levels between controls and patients. Pyrosequencing was used to assess the reciprocal level of allelic expression in six female carriers of different SMC1A mutations and 15 controls who were heterozygous at a polymorphic transcribed SMC1A locus. The two alleles were expressed at a 1:1 ratio in the control group and at a 2:1 ratio in favor of the wild type allele in the test group. Since a dominant negative effect is considered the pathogenic mechanism in SMC1A-defective female patients, the level of allelic preferential expression might be one of the factors contributing to the wide phenotypic variability observed in these patients. An extension of this study to a larger cohort containing mild to borderline cases could enhance our understanding of the clinical spectrum of SMC1A-linked CdLS.     

Nucleotide sequence analysis of NIPBL gene in Indian Cornelia de Lange syndrome cases

BACKGROUND:

Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder in children. The disorder is caused mainly due to mutations in Nipped-B-like protein. The molecular data for CdLS is available from developed countries, but not available in developing countries like India. In the present study, the hotspot region of NIPBL gene was screened by Polymerase Chain Reaction which includes exon 2, 22, 42, and a biggest exon 10, in six CdLS patients and ten controls.

MATERIALS AND METHODS:

The method adopted in present study was amplification of the target exon by using polymerase chain reaction, qualitative confirmation of amplicons by Agarose Gel Electrophoresis and use of amplicons for Conformation Sensitive Gel Electrophoresis to find heteroduplex formation followed by sequencing.

RESULTS:

We report two polymorphisms in the studied region of gene NIPBL. The polymorphisms are in the region of intron 1 and in exon 10. The polymorphism C/A is present in intron 1 region and polymorphism T/G in exon 10.

CONCLUSION:

The intronic region polymorphism may have a role in intron splicing whereas the polymorphism in exon 10 results in amino acid change (Val to Gly). These polymorphisms are disease associated as these are found in CdLS patients only and not in controls.     

Cornelia de Lange Syndrome: NIPBL haploinsufficiency downregulates canonical Wnt pathway in zebrafish embryos and patients fibroblasts

Cornelia de Lange Syndrome is a severe genetic disorder characterized by malformations affecting multiple systems, with a common feature of severe mental retardation. Genetic variants within four genes (NIPBL (Nipped-B-like), SMC1A, SMC3, and HDAC8) are believed to be responsible for the majority of cases; all these genes encode proteins that are part of the ‘cohesin complex''. Cohesins exhibit two temporally separated major roles in cells: one controlling the cell cycle and the other involved in regulating the gene expression. The present study focuses on the role of the zebrafish nipblb paralog during neural development, examining its expression in the central nervous system, and analyzing the consequences of nipblb loss of function. Neural development was impaired by the knockdown of nipblb in zebrafish. nipblb-loss-of-function embryos presented with increased apoptosis in the developing neural tissues, downregulation of canonical Wnt pathway genes, and subsequent decreased Cyclin D1 (Ccnd1) levels. Importantly, the same pattern of canonical WNT pathway and CCND1 downregulation was observed in NIPBL-mutated patient-specific fibroblasts. Finally, chemical activation of the pathway in nipblb-loss-of-function embryos rescued the adverse phenotype and restored the physiological levels of cell death.     

Two novel RAD21 mutations in patients with mild Cornelia de Lange syndrome-like presentation and report of the first familial case

Cornelia de Lange syndrome (CdLS) is a developmental disorder characterized by limb reduction defects, characteristic facial features and impaired cognitive development. Mutations in the NIPBL gene predominate; however, mutations in other cohesin complex genes have also been implicated, particularly in atypical and mild CdLS cases. Missense mutations and whole gene deletions in RAD21 have been identified in children with growth retardation, minor skeletal anomalies and facial features that overlap findings in individuals with CdLS. We report the first intragenic deletion and frameshift mutations identified in RAD21 in two patients presenting with atypical CdLS. One patient had an in-frame deletion of exon 13, while the second patient had a c.592_593dup frameshift mutation. The first patient presented with developmental delay, hypospadias, inguinal hernia and dysmorphic features while, the second patient presented with developmental delay, characteristic facial features, hirsutism, and hand and feet anomalies, with the first patient being milder than the second. The in-frame deletion mutation was found to be inherited from the mother who had a history of melanoma and other unspecified medical problems.     

Effects of clinorotation on COL1A1-EGFP gene expression

Bone-formation related gene plays a critical role in bone loss induced by space microgravity, however the exact mechanism is unclear. In this study, we aim to investigate the effect of microgravity on the activity of α 1(I) collagen (COL1A1) gene promoter and the expression of osteoblast-related genes. COL1A1 promoter was digested by restriction enzymes resulting in three DNA fragments. The fragments were ligated with the enhanced green fluorescent protein report gene, and subcloned into expression vectors. ROS17/2.8 cells transfected by these vectors were screened by G418, and enhanced green fluorescent protein (EGFP) positive colonies were isolated and cultured under clinostat condition. EGFP and Collagen type I expression level were detected by fluorescence intensity analysis and immunocytochemistry methods respectively. The results showed that the expression of EGFP and collagen type I was increased 24 h, 48 h after the cells were cultured under stimulated microgravity, illustrating that the activity of COL1A1 promoter might be increased. In conclusion, osteoblasts can compensatively increase the expression of type I collagen by enhancing the activity of COL1A1 promoter under short-term simulated microgravity conditions.     

The brain 5-HT1A receptor gene expression in hibernation

Hibernation is a unique physiological state characterized by profound reversible sleep-like state, depression in body temperature and metabolism. The serotonin 5-hydroxytryptamine_1A (5-HT_1A) receptor gene sequence in typical seasonal hibernator, ground squirrel ( Spermophilus undulatus ), was specified. It was found that the fragment encoding the fifth transmembrane domain showed 93.6% of homology with the analogous fragment of the mouse and rat genes and displayed 88.5% homology with the human 5-HT_1A receptor gene. Using primers designed on the basis of obtained sequence, the expression of 5-HT_1A receptor gene in the brain regions in active, entering into hibernation, hibernating and coming out of hibernation ground squirrels was investigated. Significant structure-specific changes were revealed in the 5-HT_1A messenger RNA (mRNA) level in entry into hibernation and in arousal. An increase in the 5-HT_1A gene expression was found in the hippocampus during the prehibernation period and in ground squirrels coming out of hibernation, thus confirming the idea of the hippocampus trigger role in the hibernation. Significant decrease in 5-HT_1A receptor mRNA level in the midbrain was found in animals coming out of hibernation. There was no considerable changes in 5-HT_1A receptor mRNA level in different stages of sleep–wake cycle in the frontal cortex. Despite drastically decreased body temperature in hibernating animals (about 37°C in active and 4–5°C in hibernation), 5-HT_1A receptor mRNA level in all examined brain regions remained relatively high, suggesting the essential role of this 5-HT receptor subtype in the regulation of hibernation and associated hypothermia.     

Effects of clinorotation on COL1A1- EGFP gene expression

Itisnowwellestablishedthatspaceflightin-ducesbonelossafterlong-termexposuretomicro-gravity.Biochemicalstudiesshowedthatcontinuousboneloss[1,2]andmineralredistribution[3]inducedbyspaceflightwereassociatedwiththedecreasedos-teoblasticactivityanddifferentialfunction[4—6].Recentfindingssuggestthechangeintheexpressionofbone-formationrelatedgeneplaysanimportantroleintheprocessofdecreasedosteoblasticfunctionsin-ducedbyspaceflight.CollagentypeIexpressedthroughouttheprocessofosteoblasticproliferationa…     

Analysis of the porcine APOA2 gene expression in liver,polymorphism identification and association with fatty acid composition traits

APOA2 is a protein implicated in triglyceride, fatty acid and glucose metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4) in a QTL region affecting fatty acid composition, fatness and growth traits. In this study, we evaluated APOA2 as a candidate gene for meat quality traits in an Iberian × Landrace backcross population. The APOA2:c.131T>A polymorphism, located in exon 3 of APOA2 and determining a missense mutation, was associated with the percentage of hexadecenoic acid [C16:1(n–9)], linoleic acid [C18:2(n–6)], α‐linolenic acid [C18:3(n–3)], dihomo‐gamma‐linolenic acid [C20:3(n–6)] and polyunsaturated fatty acids (PUFAs) in backfat. Furthermore, this SNP was associated with the global mRNA expression levels of APOA2 in liver and was used as a marker to determine allelic expression imbalance by pyrosequencing. We determined an overexpression of the T allele in heterozygous samples with a mean ratio of 2.8 (T/A), observing a high variability in the allelic expression among individuals. This result suggests that complex regulatory mechanisms, beyond a single polymorphism (e.g. epigenetic effects or multiple cis‐acting polymorphisms), may be regulating APOA2 gene expression.     

Mutations in cohesin complex members SMC3 and SMC1A cause a mild variant of cornelia de Lange syndrome with predominant mental retardation

Mutations in the cohesin regulators NIPBL and ESCO2 are causative of the Cornelia de Lange syndrome (CdLS) and Roberts or SC phocomelia syndrome, respectively. Recently, mutations in the cohesin complex structural component SMC1A have been identified in two probands with features of CdLS. Here, we report the identification of a mutation in the gene encoding the complementary subunit of the cohesin heterodimer, SMC3, and 14 additional SMC1A mutations. All mutations are predicted to retain an open reading frame, and no truncating mutations were identified. Structural analysis of the mutant SMC3 and SMC1A proteins indicate that all are likely to produce functional cohesin complexes, but we posit that they may alter their chromosome binding dynamics. Our data indicate that SMC3 and SMC1A mutations (1) contribute to approximately 5% of cases of CdLS, (2) result in a consistently mild phenotype with absence of major structural anomalies typically associated with CdLS, and (3) in some instances, result in a phenotype that approaches that of apparently nonsyndromic mental retardation.     

An as-1-like motif controls the level of expression of the gene for the pathogenesis-related protein 1a from tobacco

Pathogenesis-related proteins of group 1 (PR-1) are strongly induced in plants by pathogen attack, exposure of the plants to (acetyl)salicylic acid (ASA, SA), and by developmental cues. Functional analysis of the PR-1a promoter identified a region of 139 bp (from -691 to -553) mediating expression of the GUS reporter gene in response to ASA. Inspection of this region revealed two TGACG elements reminiscent of activation sequence-1 (as-1). Recently, as-1 has been reported to be responsive to SA in the context of the CaMV 35S RNA promoter. To address the question of whether the as-1-like sequence may be of functional significance for the expression of the PR-1a gene, gel shift assays were performed with TGA1a, a protein been shown to interact with as-1 in vitro. TGA1a was found to bind to the PR-1a as-1-like sequence with similar specificity and affinity as to as-1. Furthermore, mutations were introduced in the as-1-like sequence in the context of the inducible 906 bp PR-1a promoter which are impaired in binding TGA1a in vitro. Significantly reduced levels of GUS reporter gene activity were obtained with the mutant promoter regions as compared to the wild-type PR-1a promoter in response to all stimuli in transgenic tobacco plants. Yet, mutation of the as-1-like sequence did not abolish induction of reporter gene expression. Taken together, these results suggest that the level of expression of the tobacco PR-1a gene is controlled by an as-1-like sequence motif in the PR-1a upstream region, possibly interacting with a factor related to TGA1a.     

A Brassica napus skp1-like gene promoter drives GUS expression in Arabidopsis thaliana male and female gametophytes

We isolated a gene, BnSKP1γ1, expressed in rapeseed (Brassica napus) microspores, which encodes a protein closely related to the Saccharomyces cerevisiae Skp1p protein previously shown to play a role in cell cycle regulation. Twelve SKP1-related genes have already been identified in the Arabidopsis thaliana genome. Using a PCR-based strategy, we isolated three other genes. To date, most data available concerning the function of the SKP1-related genes in plants are indirect. Studies on transgenic A. thaliana plants showthat a 1100-bp BnSKP1γ1 promoter fragment can direct GUS expression in female gametophytes soon after the first haploid mitosis and in male gametophytes from the tetrade stage. No GUS expression can be detected in sporophytic tissues. RT-PCR experiments suggest that this gene is expressed in a similar way in rapeseed. This is the first reported case of a gene exhibiting such an expression pattern in angiosperms. Received: 5 October 1999 / Revision accepted: 28 March 2000     

Normalization and quantification of differential expression in gene expression microarrays

Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a number of technical and statistical problems. Possible remedies on the level of computational analysis lie in appropriate preprocessing steps, proper normalization of the data and application of statistical testing procedures in the derivation of differentially expressed genes. This review summarizes methods that are available for these purposes and provides a brief overview of the available software tools.     

The myocardial protein S100A1 plays a role in the maintenance of normal gene expression in the adult heart

S100A1 and S100B are members of a family of 20 kDa Ca²⁺⁺-binding homodimers that play a role in signal transduction in mammalian cells. S100A1 is the major isoform in normal heart and S100B, normally a brain protein, is induced in hypertrophic myocardium and functions as an intrinsic negative modulator of the hypertrophic response. In order to examine the function of S100A1, we first showed that, in contrast to S100B, S100A1 was downregulated in rat experimental models of myocardial hypertrophy following myocardial infarction or pressure overload. Second, in co-transfection experiments in cultured neonatal rat cardiac myocytes, S100A1 inhibited the ₁-adrenergic activation of promoters of genes induced during the hypertrophic response including the fetal genes skeletal actin (skACT), and -myosin heavy chain (MHC) and S100B, but not the triiodothyronine (T3) activation of the promoter of the -MHC gene, that is normally expressed in adult myocardium. These results suggest that S100A1 is involved in the maintenance of the genetic program that defines normal myocardial function and that its downregulation is permissive for the induction of genes that underlie myocardial hypertrophy.     

Analysis of the fibrillin-1 gene (FBN1) in patients with Marfan syndrome

Thirty exons of the fibrillin-1 gene (FBN1) were screened in patients with Marfan syndrome (MFS), and eleven point mutations, insertions, and deletions were detected. These included two missense mutations resulting in conformational changes of the calcium-binding EGF-like domains of FBN1 and nine polymorphisms located in both coding and noncoding regions of FBN1. Three intragenic polymorphic microsatellite loci—MTS-1, MTS-2, and MTS-4—were analyzed in MFS patients and unrelated healthy controls, and significant differences between these two groups were found for the MTS-2 and MTS-4 allele frequency distributions. Haplotype frequency distributions on wild-type and mutant chromosomes of MFS patients were also significantly different. The predominant haplotype was 2-11-8 on wild-type chromosomes, and 2-2-8 on mutant chromosomes. These data are a prerequisite to working out DNA diagnosis of MFS.     

Cloning and expression of streptococcal pyrogenic exotoxin A and staphylococcal toxic shock syndrome toxin-1 in Bacillus subtilis

Summary The genes encoding streptococcal pyrogenic exotoxin type A (SPE A) and staphylococcal toxic shock syndrome toxin-1 (TSST-1) were stably cloned and expressed in Bacillus subtilis. In the non-pathogenic Bacillus background, the recombinant speA clone expressed 32-fold more SPE A than the native streptococcus, and similarly, the recombinant plasmid harboring tst expressed 4-fold more TSST-1 in Bacillus than in the native Staphylococcus aureus. The Bacillus-derived products were secreted into the culture fluid, were resistant to proteolytic degradation and their biological activites mimicked native preparations.