Segment Of Exon Research Articles

VHL mutation as a cause of three generations familial pheochromocytoma

BackgroundPheochromocytoma is a rare disease, and its familial occurrence is quite uncommon. The aim of this paper is to report a three-generation phenotypical expression of a case familial occurrence of pheochromocytoma.Case presentationA 25-year-old female, with a history of adrenalectomy for pheochromocytoma, arrived at the shock room during her third pregnancy with an adrenergic crisis and hypoglycemia. To prevent perinatal complications, the patient was stabilized and the newborn was delivered through a Kerr-type cesarean section. A detailed history revealed that the paternal grandfather of the patient had an unilateral pheochromocytoma, whereas her paternal uncle had a bilateral pheochromocytoma. Additionally, a brother of the patient presented a unilateral pheochromocytoma. Amplicons for PCR assays were designed to span the protein-coding segments of the three Von Hippel–Lindau (VHL) exons, and the PCR products were sequenced using the Sanger method. In the trace of exon 3, we detected in the sample of the proband a heterozygous guanine to adenine transition (NM_000551.4 c. 552G > A) within the protein-coding segment of exon 3 of the VHL gene, which leads to a substitution of the arginine residue at position 161 by a glutamine residue in the encoded peptide (NP_000542.1p.R161Q). This mutation was absent in two unaffected daughters.ConclusionA VHL mutation was suspected and confirmed in this family that was not transmitted to a fourth generation. This case illustrates the importance of molecular genetics methodologies to assist genetic counseling in cases of pheochromocytoma where familial aggregation is presumed.

Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases

The DEL phenotype represents an intriguing and challenging aspect of blood group serology. This condition is characterized by an extremely weak expression of the D antigen on red blood cells, to the extent that it often eludes detection through routine serological methods. Identifying the DEL phenotype necessitates more specialized techniques, such as adsorption and elution tests, to reveal the presence of the D antigen. This distinctive phenotype underscores the complexity and subtlety of blood group genetics and highlights the importance of using advanced methods to accurately classify individuals with this condition, as their ability to form anti-D antibodies can have clinical implications during transfusion and pregnancy scenarios. There is a paucity of data for the DEL phenotype in the Indian population, and the molecular basis has not been elucidated yet. Our investigation delves into the genetic underpinnings of two distinct DEL phenotype cases that pose challenges for resolution through conventional serological techniques. We employ next-generation amplicon sequencing to unravel the intricate genetic landscape underlying these cases. In the D-negative donor, the DEL phenotype was first identified serologically, which was subsequently confirmed by molecular analysis. In the second case, it was associated with an anti-D antibody in a D-positive patient. Initial data analysis unveiled a substantial reduction in coverage across the exonic segments of the RHD gene in both samples, suggesting the potential presence of RHD exon deletions. On both occasions, we identified a homozygous intronic RHD polymorphism that is well established to be linked to the RHD* 01EL.32/RHD*DEL32 variant.

Detecting Polymorphisms of Mutation (C519T) Sit 112480 of Gene Foxo3 and its Associations with Reproductive Performance of Awassi Sheep

The current study was conducted on a sample of 45 local Awassi ewe, with ages ranging from 2-4 years. These ewes produced 54 newborns, and the ages and weights of these newborns were monitored from birth until the sixth month of life for the period from 1/5/2022 to 6/25/2022 at Al-Fayhaa Sheep Station / Babylon Agricultural Directorate / Ministry of Agriculture. As for laboratory analyzes, they were conducted in the laboratories of the Scientific Advancement Company for Molecular Genetics for the period from 1/5/2022 to 6/25/2022. For the purpose of extracting DNA material, and determining the genotypes of the Foxo3 gene through the genotype of the mutation (Sit 112480)) T519C and studying the effect of this mutation on the studied characteristics, which are daily milk production (DMY), milk components, growth characteristics of lambs (different weights and ages), the rate of weight gain between weights mentioned above, growth rate, live mothers’ weights, mothers’ body dimensions, type of delivery (twins or singles). This formed mutation, which was found in the second segment of exon No. 2 of the Foxo3 gene, was amplified with a size of 420 bp N-hall using the nucleotide sequencing technique. This mutation produced three genotypes (TT, TC, and CC), and the ratios of genotypes were (0.00, 53.66, 46.34), sequentially. The variance between these ratios was highly significant (p≤0.01), and the allelic frequency was 0.27, 0.73 for both the T and C alleles. It was clear from the results that the effect of the different genotypes of the Foxo3 gene was not significant for the characteristic of daily milk production, and some other components of milk except for the percentage of fat were significant (p≤0.05). Weight between birth weight and weaning weight, and the results also show that there are significant differences for the type of birth characteristic (P≤0.05). There were no significant differences in the different genotypes of the Foxo3 gene for the characteristics represented by the body dimensions of the mothers and the live weight of the mothers, as well as the growth characteristics of the lambs, which are represented by the weight for the first three months of life and the rate of weight gain between them. It can be concluded from the previous results of this study the possibility of adopting the distinct genotypes of the Foxo3 gene for this genotype in the genetic improvement programs of the studied Awassi sheep to obtain the best economic return by selecting and cross-crossing the distinct genotypes in the characteristics that achieved the best ratios as well as the weight rates.

Counting pseudoalignments to novel splicing events.

Alternative splicing (AS) of introns from pre-mRNA produces diverse sets of transcripts across cell types and tissues, but is also dysregulated in many diseases. Alignment-free computational methods have greatly accelerated the quantification of mRNA transcripts from short RNA-seq reads, but they inherently rely on a catalog of known transcripts and might miss novel, disease-specific splicing events. By contrast, alignment of reads to the genome can effectively identify novel exonic segments and introns. Event-based methods then count how many reads align to predefined features. However, an alignment is more expensive to compute and constitutes a bottleneck in many AS analysis methods. Here, we propose fortuna, a method that guesses novel combinations of annotated splice sites to create transcript fragments. It then pseudoaligns reads to fragments using kallisto and efficiently derives counts of the most elementary splicing units from kallisto's equivalence classes. These counts can be directly used for AS analysis or summarized to larger units as used by other widely applied methods. In experiments on synthetic and real data, fortuna was around 7× faster than traditional align and count approaches, and was able to analyze almost 300 million reads in just 15 min when using four threads. It mapped reads containing mismatches more accurately across novel junctions and found more reads supporting aberrant splicing events in patients with autism spectrum disorder than existing methods. We further used fortuna to identify novel, tissue-specific splicing events in Drosophila. fortuna source code is available at https://github.com/canzarlab/fortuna.

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing.

Alternative splicing (AS) is an important mechanism in the development of many cancers, as novel or aberrant AS patterns play an important role as an independent onco-driver. In addition, cancer-specific AS is potentially an effective target of personalized cancer therapeutics. However, detecting AS events remains a challenging task, especially if these AS events are novel. This is exacerbated by the fact that existing transcriptome annotation databases are far from being comprehensive, especially with regard to cancer-specific AS. Additionally, traditional sequencing technologies are severely limited by the short length of the generated reads, which rarely spans more than a single splice junction site. Given these challenges, transcriptomic long-read (LR) sequencing presents a promising potential for the detection and discovery of AS. We present Freddie, a computational annotation-independent isoform discovery and detection tool. Freddie takes as input transcriptomic LR sequencing of a sample alongside its genomic split alignment and computes a set of isoforms for the given sample. It then partitions the input reads into sets that can be processed independently and in parallel. For each partition, Freddie segments the genomic alignment of the reads into canonical exon segments. The goal of this segmentation is to be able to represent any potential isoform as a subset of these canonical exons. This segmentation is formulated as an optimization problem and is solved with a dynamic programming algorithm. Then, Freddie reconstructs the isoforms by jointly clustering and error-correcting the reads using the canonical segmentation as a succinct representation. The clustering and error-correcting step is formulated as an optimization problem-the Minimum Error Clustering into Isoforms (MErCi) problem-and is solved using integer linear programming (ILP). We compare the performance of Freddie on simulated datasets with other isoform detection tools with varying dependence on annotation databases. We show that Freddie outperforms the other tools in its accuracy, including those given the complete ground truth annotation. We also run Freddie on a transcriptomic LR dataset generated in-house from a prostate cancer cell line with a matched short-read RNA-seq dataset. Freddie results in isoforms with a higher short-read cross-validation rate than the other tested tools. Freddie is open source and available at https://github.com/vpc-ccg/freddie/.

Evolution of NLR resistance genes with noncanonical N-terminal domains in wild tomato species.

Nucleotide-binding and leucine-rich repeat immune receptors (NLRs) provide resistance against diverse pathogens. To create comparative NLR resources, we conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real-time sequencing of PacBio for 18 accessions in Solanaceae, including 15 accessions of five wild tomato species. We investigated the evolution of a class of NLRs, CNLs with extended N-terminal sequences previously named Solanaceae Domain. Through comparative genomic analysis, we revealed that the extended CNLs (exCNLs) anciently emerged in the most recent common ancestor between Asterids and Amaranthaceae, far predating the Solanaceae family. In tomatoes, the exCNLs display exceptional modes of evolution in a clade-specific manner. In the clade G3, exCNLs have substantially elongated their N-termini through tandem duplications of exon segments. In the clade G1, exCNLs have evolved through recent proliferation and sequence diversification. In the clade G6, an ancestral exCNL has lost its N-terminal domains in the course of evolution. Our study provides high-quality NLR gene models for close relatives of domesticated tomatoes that can serve as a useful resource for breeding and molecular engineering for disease resistance. Our findings regarding the exCNLs offer unique backgrounds and insights for future functional studies of the NLRs.

Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing.

Recognition of highly degenerate mammalian splice sites by the core spliceosomal machinery is regulated by several protein factors that predominantly bind exonic splicing motifs. These are postulated to be single-stranded in order to be functional, yet knowledge of secondary structural features that regulate the exposure of exonic splicing motifs across the transcriptome is not currently available. Using transcriptome-wide RNA structural information we show that retained introns in mouse are commonly flanked by a short (≲70 nucleotide), highly base-paired segment upstream and a predominantly single-stranded exonic segment downstream. Splicing assays with select pre-mRNA substrates demonstrate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, the substitution or hybridization of which impedes splicing. Additionally, the exonic segments flanking the retained introns appeared to be more enriched in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to their spliced counterparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a means for occlusion of ESEs. The upstream exonic loops of the test substrate promoted recruitment of splicing factors and consequent pre-mRNA structural remodeling, leading up to assembly of the early spliceosome. These results suggest that disruption of exonic stem–loop structures immediately upstream (but not downstream) of the introns regulate alternative splicing events, likely through modulating accessibility of splicing factors.

Sequencing the exon 1 of MSTN in Mongolian horse (Equus caballus)

Myostatin (MSTN) is a protein responsible for muscular tissue differentiation, development, and growth in mammals. Studies on cattle, mice, pig, and dog have provided sample demonstrations of mutations on myostatin, which strongly affected animal Ankole93200phenotype, particularly muscle development. In horse, myostatin gene is usually studied with respect to racing performance. Most Mongolian native horses do race for long distance and such racing is a very popular sport in Mongolia. On the other hand, the MSTN gene also affects meat yield and quality. We partially sequenced of MSTN gene to explore its polymorphic features in Mongolian horse. A 238 bp long segment of exon 1 was sequenced, using 3130 Genetic Analyser and MEGAX. The sequence was registered with accession number LC216412 in the Gene bank database of NCBI and aligned to four reference sequences (GQ183900.1, KC708233.1, AY840554.2, NM 001081817) from this database. The nucleotide diversity was 0.0084, Tajima test statistic was -1.12. so that there were 233 invariable (monomorphic) sites and 5 variable (polymorphic) sites, in the group of animals compared. The Mongolian horse differed from the reference sequence at 3 sites. There was an amino acid difference in the partial sequence, in which isoleucine in the reference sequence was converted into valine. The results of the study indicate that the Mongolian horse seems to differ substantially from the reference genome of equus caballus. Sequencing of the full length of exon 1 or even the whole MSTN gene, including introns, is strongly advised, to get more insights with regard to the identification and characterization of variants at the myostatin locus in Mongolian horses.

Endonuclease G modulates the alternative splicing of deoxyribonuclease 1 mRNA in human CD4+ T lymphocytes and prevents the progression of apoptosis

Apoptotic endonucleases act cooperatively to fragment DNA and ensure the irreversibility of apoptosis. However, very little is known regarding the potential regulatory links between endonucleases. Deoxyribonuclease 1 (DNase I) inactivation is caused by alternative splicing (AS) of DNase I pre-mRNA skipping exon 4, which occurs in response to EndoG overexpression in cells. The current study aimed to determine the role of EndoG in the regulation of DNase I mRNA AS and the modulation of its enzymatic activity. A strong correlation was identified between the EndoG expression levels and DNase I splice variants in human lymphocytes. EndoG overexpression in CD4+ T cells down-regulated the mRNA levels of the active full-length DNase I variant and up-regulated the levels of the non-active spliced variant, which acts in a dominant-negative fashion. DNase I AS was induced by the translocation of EndoG from mitochondria into nuclei during the development of apoptosis. The DNase I spliced variant was induced by recombinant EndoG or by incubation with EndoG-digested cellular RNA in an in vitro system with isolated cell nuclei. Using antisense DNA oligonucleotides, we identified a 72-base segment that spans the adjacent segments of exon 4 and intron 4 and appears to be responsible for the AS. DNase I-positive CD4+ T cells overexpressing EndoG demonstrated decreased progression towards bleomycin-induced apoptosis. Therefore, EndoG is an endonuclease with the unique ability to inactivate another endonuclease, DNase I, and to modulate the development of apoptosis.

Kiss1 and its receptor: molecular characterization and immunolocalization in the hypothalamus and corpus luteum of the buffalo

ABSTARCTThe neuropeptide kisspeptin (Kp) through its receptor Kiss1r regulates the HPG axis by controlling GnRH release. Since buffalo is a seasonal breeder with problems of delayed puberty and postpartum anestrus, we characterized the Kiss1 and Kiss1r and investigated the immunolocalization in the hypothalamus and corpus luteum (CL). Kiss1 and Kiss1r genes were amplified from gDNA covering the coding region, cloned and sequenced with accession numbers MF168937 and MG820539, respectively. The Kiss1 DNA sequence had two exonic segment contained coding sequence (cds); 408 bp encoding a predicted protein of 136 aa with conservation of Kp-10 and shared 94.5–98.3% identity with ruminants. Kiss1r DNA sequence consisted of five exons with a cds of 1134 bp encoding a protein of 378 aa. Phylogenetic analysis of Kiss1 and Kiss1r revealed that it formed a monophyletic clade with cattle, which branched from sheep and goat. Immunofluorescence study revealed the presence of Kiss1 and Kiss1r in the neuronal soma and perinuclear area of preoptic and arcuate regions of the hypothalamus and luteal cells of the CL. This is the first report on molecular characterization of bubaline Kiss1 and Kiss1r genes that confirmed the presence of conserved Kp-10 like other ruminants and kisspeptinergic system is present in the hypothalamus and CL.

Efficient Adaptive Exon Prediction for DNA study using Proportionate LMS Variants

In the field of Bio-informatics, locating the exon fragments in a deoxyribonucleic acid (DNA) sequence is an important and vital work. Study of protein coding regions is a wide phenomenon in identification of diseases and design of drugs. The regions of DNA that have the protein coding information are termed as exons. Hence identifying the exon segments in a genomic sequence is a crucial job in bio-informatics. Three base periodicity (TBP) has been observed in the regions of DNA sequences can be easily determined by applying signal processing methods. Adaptive signal processing techniques found to be useful than other available methods. This is due to their unique capability to alter weight coefficients based on genomic sequence. We propose efficient adaptive exon predictors (AEPs) based on these considerations using Proportionate Normalized LMS (PNLMS) algorithm and Maximum Proportionate Normalized LMS (MPNLMS) algorithm to improve exon locating ability and better convergence. To ease the complexity of computations in the denominator during filtering process, proposed AEPs using PNLMS and its maximum variants are combined with signature algorithms. Hybrid variants of proposed AEPs include PNLMS, DCPNLMS, ECPNLMS, SSPNLMS, MPNLMS, MDCPNLMS, MECPNLMS and MSSPNLMS algorithms. It was shown that the AEP based on MDCPNLMS is superior in applications of exon identification depending on performance measures with Sensitivity 0.7346, Specificity 0.7483 and precision 0.7325 for a genomic sequence with accession AF009962 at a threshold of 0.8. Finally the capability of several AEPs in predicting exon locations is verified using different DNA sequences found in National Center for Biotechnology Information (NCBI) gene database.

Expression of succinate dehydrogenase subunit protein in succinate dehydrogenase-deficient gastrointestinal stromal tumors

Objective: To investigate the expression of succinate dehydrogenase complex subunit protein in succinate dehydrogenase-deficient gastrointestinal stromal tumors (SDH-deficient GISTs). Methods: Three hundred fifty-two cases of GISTs were collected from January 2003 to January 2017 at the Affiliated Hospital of Guizhou Medical University and West China Hospital of Sichuan University.The expression of succinate dehydrogenase subunit protein was detected by immunohistochemical EnVision technique in 352 cases of GISTs, and the negative cases were analyzed for clinicopathologic features and outcome. The gene segments of CKIT exons 9, 11, 13 and 17 and PDGFRA exons 12 and 18 were amplified and detected in SDH-deficient (negative) cases. Results: A total of 15 SDHB-deficient (negative) GISTs (4.3%, 15/352) were found among 352 cases of GISTs. Six patients were male and nine were female. The age of initial diagnosis ranged from 15 to 84 years (median=53 years, mean=47 years). The tumor involved stomach (14 cases) and mesentery (1 case). The tumor sizes varied from 0.5 cm to 15.0 cm (mean=6.9 cm). There were six, six and three cases of epithelioid, mixed and spindle cell types respectively. Eight cases showed multi-nodularity in the wall of stomach. Metastasis to lymph node was noted in four cases, one case showed intraperitoneal implantation metastasis. Metastases to liver, pancreas and lymph node were found in one case, and one case showed vascular invasion. Among SDHB-deficient GISTs, two SDHA-deficient (negative) cases were found (0.6%, 2/352), but there were no SDHC and SDHD deficient (negative) cases. Five of the fifteen SDH-deficient GISTs had follow-up data: one patient died 8 months after surgery from unknown cause, four had no recurrences or metastases, and there was no history of paraganglioma and pulmonary chondroma found in patients and their families. No mutation in CKIT and PDGFRA gene was identified in 15 cases of SDH-deficient GISTs. Conclusion: SDH-deficient GISTs have unique clinicopathologic features and a favorable prognosis, and a small proportion of cases are SDHA-deficient.

Conformational Change in the Ligand-Binding Pocket via a KISS1R Mutation (P147L) Leads to Isolated Gonadotropin-Releasing Hormone Deficiency.

Context:Kisspeptin receptor (KISS1R) is expressed in hypothalamic gonadotropin-releasing hormone neurons and responsible for pubertal onset and reproductive functions. KISS1R mutations remain a rare cause of congenital hypogonadotropic hypogonadism (CHH).Objective:The aim of this study was to identify the genetic cause of CHH in a patient and to functionally characterize a KISS1R mutation.Design:The patient was a 47-year-old Japanese man whose parents were first cousins. He lacked secondary sexual characteristics owing to normosmic CHH. Exon segments for the KISS1R gene in this patient were screened for mutations. Functional analyses were performed using HEK293 cells expressing KISS1R mutants. Molecular dynamics simulations were performed to compare the ligand-KISS1R mutant complex with those of wild-type KISS1R variants.Results:A homozygous mutation (c.440C>T, p.P147L) in KISS1R was identified. The P147L mutation did not affect either receptor expression level or subcellular localization in the recombinant expression system. Intracellular calcium measurements and cellular dielectric spectroscopy demonstrated that the P147L mutation impaired receptor function to an extent more severe than that of a previously reported L148S mutation. A receptor-ligand binding assay showed the P147L mutation causes a substantial loss of ligand-binding affinity. Molecular dynamics simulations revealed the P147L mutation decreases the contact surface area of the ligand-receptor complex in an expanded ligand-binding pocket.Conclusion:We identified a loss-of-function mutation in KISS1R associated with CHH. Our results demonstrated that the P147L mutation causes a severe phenotype and functional impairment resulting from the loss of ligand-binding affinity due to an expanded ligand-binding pocket.

Age-associated chromatin relaxation is enhanced in Huntington's disease mice.

Expansion of polyglutamine stretch in the huntingtin (HTT) protein is a major cause of Huntington's disease (HD). The polyglutamine part in HTT interacts with various proteins implicated in epigenetic regulation of genes, suggesting that mutant HTT may disturb the integrity of the epigenetic system. Here, we used a PCRseq-based method to examine expression profile of 395 exonic segments from 260 “epi-driver” genes in splenic T lymphocytes from aged HD mice. We identified 67 exonic segments differentially expressed between young and aged HD mice, most of them upregulated in the aged. Polycomb-repressive complex (PRC)-regulated genes (PRGs) were markedly upregulated in aged HD mice, consistent with downregulation of PRC genes. Epi-driver gene categories of lysine-methylation, lysine-demethylation, arginine-methylation, and PRG showed differential age-associated changes between HD and control. Analyzing the pattern of change in epi-driver gene expressions hinted at an enhanced shift in HD chromatin to a more accessible state with age, which was experimentally demonstrated by DNase-I-hypersensitivity sequencing showing increased chromatin accessibility in HD cells compared to control. We suggest the global change can potentially relieve chromatin-induced repression of many genes, and the unintended expressions of some detrimental proteins could alter T cell function to a greater degree in aged HD mice.

Altered Expression of Human Smooth Muscle Myosin Phosphatase Targeting (MYPT) Isovariants with Pregnancy and Labor.

BackgroundMyosin light-chain phosphatase is a trimeric protein that hydrolyses phosphorylated myosin II light chains (MYLII) to cause relaxation in smooth muscle cells including those of the uterus. A major component of the phosphatase is the myosin targeting subunit (MYPT), which directs a catalytic subunit to dephosphorylate MYLII. There are 5 main MYPT family members (MYPT1 (PPP1R12A), MYPT2 (PPP1R12B), MYPT3 (PPP1R16A), myosin binding subunit 85 MBS85 (PPP1R12C) and TIMAP (TGF-beta-inhibited membrane-associated protein (PPP1R16B)). Nitric oxide (NO)-mediated smooth muscle relaxation has in part been attributed to activation of the phosphatase by PKG binding to a leucine zipper (LZ) dimerization domain located at the carboxyl-terminus of PPP1R12A. In animal studies, alternative splicing of PPP1R12A can lead to the inclusion of a 31-nucleotide exonic segment that generates a LZ negative (LZ-) isovariant rendering the phosphatase less sensitive to NO vasodilators and alterations in PPP1R12ALZ- and LZ+ expression have been linked to phenotypic changes in smooth muscle function. Moreover, PPP1R12B and PPP1R12C, but not PPP1R16A or PPP1R16B, have the potential for LZ+/LZ- alternative splicing. Yet, by comparison to animal studies, the information on human MYPT genomic sequences/mRNA expressions is scant. As uterine smooth muscle undergoes substantial remodeling during pregnancy we were interested in establishing the patterns of expression of human MYPT isovariants during this process and also following labor onset as this could have important implications for determining successful pregnancy outcome.ObjectivesWe used cross-species genome alignment, to infer putative human sequences not available in the public domain, and isovariant-specific quantitative PCR, to analyse the expression of mRNA encoding putative LZ+ and LZ- forms of PPP1R12A, PPP1R12B and PPP1R12C as well as canonical PPP1R16A and PPP1R16B genes in human uterine smooth muscle from non-pregnant, pregnant and in-labor donors.ResultsWe found a reduction in the expression of PPP1R12A, PPP1R12BLZ+, PPP1R16A and PPP1R16B mRNA in late pregnancy (not-in-labor) relative to non-pregnancy. PPP1R12ALZ+ and PPP1R12ALZ- mRNA levels were similar in the non-pregnant and pregnant not in labor groups. There was a further reduction in the uterine expression of PPP1R12ALZ+, PPP1R12CLZ+ and PPP1R12ALZ- mRNA with labor relative to the pregnant not-in-labor group. PPP1R12A, PPP1R12BLZ+, PPP1R16A and PPP1R16B mRNA levels were invariant between the not in labor and in-labor groups.ConclusionsMYPT proteins are crucial determinants of smooth muscle function. Therefore, these alterations in human uterine smooth muscle MYPT isovariant expression during pregnancy and labor may be part of the important molecular physiological transition between uterine quiescence and activation.

P132 Complete nucleotide sequence characterization of DRB5 alleles indicate a homogeneous allele group which is distinct from other DRB genes

Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. More complete sequence assessment can be achieved by the description of the entire common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of only one allele available. The haplotypes bearing DRB5 genes associate with susceptibility and resistance to many diseases; furthermore, the role of DRB5 mismatches in transplantation has not been utterly evaluated. In the present study, we cloned and sequenced DRB genes from 87 individuals including 18 subjects with DRB5 alleles. We developed robust and efficient methods for long range PCR and molecular cloning. Clones were sequenced by NGS and consensus was generated by a novel de novo assembly algorithm. The fragments generated overlapped and span exons 1–2 and 2–6 of DRB genes. We obtained DRB5 sequences spanning 12,638-12,681 of DRB5 ∗ 01:01, 01:02 and 02:01; partial information for the segment exon 2–6 was obtained for DRB5 ∗ 01:03, 01:08N and 02:03. Phylogenetic trees show that DRB5 alleles, group together and have distinctive differences with other DRB loci, with only 65, 73 and 83 percent homology with DRB1 ∗ 15, DRB4 and DRB3 alleles respectively. All DRB5 alleles are similar with at least 97.0 percent homology. Among 7 subjects we identified 4 intron variants of DRB5 ∗ 01:01, 3 differing in length in one intron2 STR and additional allele differing from the others by 1 SNP substitution. We identified 2 intron variants of DRB5 ∗ 01:02; with exception of the known exon substitutions one DRB5 ∗ 01:02 variant is identical to DRB5 ∗ 01:03 and DRB ∗ 01:08N differs in introns from DRB5 ∗ 01:02 by length in one STR. Similarly, we identified two DRB5 ∗ 02:02 variants differing in length at the same STR while DRB5 ∗ 02:03 is identical in the intron sequences to one of these alleles. The DRB5 intron variants of each DRB5 allele were found in subject carrying distinct associations with alleles of DRB1, B and/or ethnicity. Our studies provide useful information that can be applied in NGS based typing. Unexpectedly, we identified intron variation that may shed light on understanding the evolution of the DRB region. Examination of DRB5 variants may also lead to identify the disease susceptibility factors of DRB5 containing haplotypes.

Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase.

The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp) gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.

Polymorphism in the TRP8 gene in Kyrgyz population: Putative association with highland adaptation

The human TRPM8 gene encodes a receptor mediating cold sensitivity, and this points to its putative role in cold adaptation. The structural variability of the TRPM8 gene for five single-nucleotide polymorphisms (SNPs) has been studied in the Kyrgyz population. The SNPs are located in the coding regions of the gene, and three of them are confined to a 20-bp segment in exon 7. The frequencies of minor SNP alleles are as follows: rs13004520 G/C = 0.06; rs28901637 A/T = 0.13; rs11562975 G/C = 0.27; rs7593557 G/A = 0.21; rs11563071 C/G = 0.12. The analyzed sample of Kyrgyz population includes 275 individuals living at different altitudes and under drastically different climatic conditions. The frequency of the minor rs11562975 allele in the highlanders (living above 3200 m ASL and higher) is lower by a factor of 1.5 than in the residents of lower regions (760–3000 m ASL; p < 0.01). This result indicates a selective role of rs11562975 in adapting to cold. A comparison of haplotype frequencies in the Kyrgyz population with Europeans, East Asians, and Africans shows a clear narrowing of genotype variation in Europeans in comparison to all the others. Probably, this phenomenon is related to a decline in the population size (bottleneck effect) during evolution. We consider the exon–intron structure of the TRPM8 gene. The epigenetic markers in the vicinity of the gene have been analyzed. Two strong binding sites for insulator ctcf proteins are present there. They are likely to be associated with chromatin conformation and alternative splicing regulation. A structural–functional characterization of genes for the TRP protein family is provided.

Prevalence and Genetic Profile of Duchene and Becker Muscular Dystrophy in Puerto Rico.

Duchenne and Becker Muscular Dystrophy (DMD and BMD, respectively), are common forms of inherited muscle disease. Information regarding the epidemiology of these conditions, including genotype, is still sparse. To establish the prevalence and genetic profile of DMD and BMD in Puerto Rico. We collected data from medical records in all Muscular Dystrophy Association (MDA) clinics in Puerto Rico in order to estimate the prevalence of DMD and BMD and to describe the genotypic profile of these patients. Patients selected for data analysis matched "definite", "probable" and "possible" case definitions as established by MD STARnet. A total of 141 patients matched the inclusion criteria, with 64.5% and 35.5% being categorized into DMD and BMD, respectively. DMD and BMD prevalence in Puerto Rico was estimated at 5.18 and 2.84 per 100,000 males, respectively. Deletion was the most common form of mutation (66.7%) in the dystrophin gene, with exons in segment 45 to 47 being the most frequently affected. This is the first report of the prevalence and genetic profile characteristics of DMD and BMD in Puerto Rico. Prevalence of DMD was similar to that reported worldwide, while prevalence of BMD was higher. Genetic profile was consistent with that reported in the literature.

αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome.

Alternative splicing (AS) is a robust generator of mammalian transcriptome complexity. Splice site specification is controlled by interactions of cis-acting determinants on a transcript with specific RNA binding proteins. These interactions are frequently localized to the intronic U-rich polypyrimidine tracts (PPT) located 5′ to the majority of splice acceptor junctions. αCPs (also referred to as polyC-binding proteins (PCBPs) and hnRNPEs) comprise a subset of KH-domain proteins with high affinity and specificity for C-rich polypyrimidine motifs. Here, we demonstrate that αCPs promote the splicing of a defined subset of cassette exons via binding to a C-rich subset of polypyrimidine tracts located 5′ to the αCP-enhanced exonic segments. This enhancement of splice acceptor activity is linked to interactions of αCPs with the U2 snRNP complex and may be mediated by cooperative interactions with the canonical polypyrimidine tract binding protein, U2AF65. Analysis of αCP-targeted exons predicts a substantial impact on fundamental cell functions. These findings lead us to conclude that the αCPs play a direct and global role in modulating the splicing activity and inclusion of an array of cassette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptome.