Segment Of Exon Research Articles

SMaRT Technology Enables Gene Expression Repair in Skin Gene Therapy

In this issue, Wally et al. (2008) report successful gene expression repair by spliceosome-mediated RNA trans-splicing (SMaRT), a novel achievement in molecular medicine. In their model, SMaRT was able to replace a mutation of the plectin gene in epidermolysis bullosa simplex with muscular dystrophy. This approach is particularly attractive for skin gene therapy of dominant-negative mutations present in a number of blistering genodermatoses.

5′ Trans-Splicing Repair of the PLEC1 Gene

The efficient treatment of hereditary disorders, especially of those caused by dominant-negative mutations still remains an obstacle to be overcome. Allele specificity is a critical aspect that must be addressed by silencing therapies such as small interfering RNA, which has the potential risk of also reducing expression of the normal allele. To overcome this hurdle, we used spliceosome-mediated RNA trans-splicing (SMaRT) to replace mRNA exon segments in an in vitro disease model. In this model, a heterozygous insertion of a leucine codon into exon 9 of the plectin gene (PLEC1) leads to aggregation of plectin peptide chains and subsequent protein degradation recapitulating, together with a nonsense mutation on the other allele, the blistering skin disease epidermolysis bullosa simplex with muscular dystrophy (EBS-MD). Transient transfection of EBS-MD fibroblasts with a 5' pre-trans-splicing molecule encoding wild-type exons 2-9 led to specific replacement of the mutated 5' portion of the endogenous PLEC1 transcript through trans-splicing. This treatment reduced the levels of mutant mRNA and restored a wild-type pattern of plectin expression as revealed by immunofluorescence microscopy. When EBS-MD fibroblasts were transfected with retroviral constructs, the level of full-length plectin protein in the corrected fibroblasts increased by 58.7%. Thus, SMaRT may be a promising new tool for treatment of autosomal-dominant genetic diseases.

Reduction of human chorionic gonadotropin beta subunit expression by modified U1 snRNA caused apoptosis in cervical cancer cells

BackgroundSecretion of human chorionic gonadotropin, especially its beta subunit by malignant trophoblastic tumors and varieties of tumors of different origin is now well documented; however the role of hCG in tumorogenesis is still unknown.ResultsThis study documents the molecular presence of human chorionic gonadotropin beta subunit in uterine cervix cancer tissues and investigates a novel technique to reduce hCGβ levels based on expression of a modified U1 snRNA as a method to study the hormone's role in biology of human cervical cancer cells cultured in vitro. The property of U1 snRNA to block the accumulation of specific RNA transcript when it binds to its donor sequence within the 3' terminal exon was used. The first 10 nucleotides of the human U1 snRNA gene, which normally binds to the 5'ss in pre-mRNA were replaced by a sequence complementary to a 10-nt segment in the terminal exon of the hCGβ mRNA. Three different 5' end-mutated U1 snRNA expression plasmids were tested, each targeting a different sequence in the hCGβ mRNA, and we found each one blocked the expression of hCGβ in HeLa cells, a cervix carcinoma cell line, as shown by immunohistochemistry and qRT-PCR. Reduction of hCGβ levels resulted in a significantly increased apoptosis rate with almost 90% of cells transfected with modified anti-hCGβ U1 snRNAs showing morphological changes characteristic of the apoptotic process.ConclusionThese data suggest that human chorionic gonadotropin beta subunit may act as a tumor growth-stimulating factor.

Small Nuclear RNAs U11 and U12 Modulate Expression of TNR-CFTR mRNA in Mammalian Kidneys

TNR-CFTR, discovered as a splice variant of CFTR (Cystic Fibrosis Transmembrane conductance Regulator), is distributed in different tissues such as human and rat kidney, trachea, lungs etc and is a functional chloride channel. In Kidneys, our findings show TNR-CFTR to have an unique distribution pattern with low levels of expression in renal cortex and high levels of expression in renal medulla. As shown by us previously, TNR-CFTR mRNA lacks 145 bp corresponding to segments of exons 13 and 14. This deletion causes a frame shift mutation leading to reading of a premature termination codon in exon 14. Premature termination of translation produces a functional half molecule of CFTR; TNR-CFTR. Our analysis of TNR mRNA has shown that the putative alternatively spliced intron has in its 5'' and 3'' conserved element CT and AC, respectively, that can be recognized by snRNAs U11 and U12. With these findings, we hypothesize that TNR-CFTR mRNA alternative splicing is probably mediate by splicing pathways utilizing U11 and U12 snRNAs. In this study, we have determined sequences of snRNAs U11 and U12 derived from rat kidney, which show significant homology to human U11 and U12 snRNAs. We show that there is significantly lower expression of U11 and U12 snRNAs in renal cortex compared to renal medulla in both humans and rats. This renal pattern of distribution of U11 and U12 snRNAs in both humans and rats closely follows distribution pattern of renal TNR-CFTR. Further, we have shown that blocking U11 and/or U12 mRNAs, by using antisense probes transfected in Immortalized Rat Proximal Tubule Cell line (IRPTC), decreases TNR-CFTR mRNA expression but not wild-type CFTR mRNA expression. Our results suggest that expression of U11 and/or U12 snRNAs is important for non-conventional alternative splicing process that gives rise to mRNA transcript coding for TNR-CFTR.

Power law exponents characterizing human DNA

The size distributions of all known coding and noncoding DNA sequences are studied in all human chromosomes. In a unified approach, both introns and intergenic regions are treated as noncoding regions. The distributions of noncoding segments Pnc(S) of size S present long tails Pnc(S) approximately S(-1-mu nc) , with exponents mu nc ranging between 0.71 (for chromosome 13) and 1.2 (for chromosome 19). On the contrary, the exponential, short-range decay terms dominate in the distributions of coding (exon) segments Pc(S) in all chromosomes. Aiming to address the emergence of these statistical features, minimal, stochastic, mean-field models are proposed, based on randomly aggregating DNA strings with duplication, influx and outflux of genomic segments. These minimal models produce both the short-range statistics in the coding and the observed power law and fractal statistics in the noncoding DNA. The minimal models also demonstrate that although the two systems (coding and noncoding) coexist, alternating on the same linear chain, they act independently: the coding as a closed, equilibrium system and the noncoding as an open, out-of-equilibrium one.

A comparative study of voltage‐gated sodium channels in the Insecta: implications for pyrethroid resistance in Anopheline and other Neopteran species

We report the complete cDNA sequence of the Anopheles gambiae voltage-gated sodium channel (VGSC) alpha-subunit isolated from mature adult mosquitoes. The genomic DNA contains 35 deduced exons with a predicted translation of <or= 2139 amino acid cDNAs. The transcription of the gene is, however, complex, alternate splicing being evident for at least five optional exons (or exon segments) and two sets of mutually exclusive exons. Overall gene organization was also compared with that of other VGSCs within the Insecta. Several insecticides used in mosquito control (including DDT and synthetic pyrethroids) target the VGSC. Isolation of the sodium channel cDNA for An. gambiae: (1) allows prediction of likely single nucleotide polymorphisms that may arise at residue L1014 to cause resistance to insecticides; (2) defines An. gambiae exon usage in key areas of the VGSC protein that are known (from previous studies in a range of different pest species) to have roles in altering insecticide susceptibility and in generating resistance; and (3) is a critical first step towards development of refined malarial control strategies and of new diagnostics for resistance monitoring.

Identification ofN-Acetyltransferase 2 (NAT2) Transcription Start Sites and Quantitation ofNAT2-Specific mRNA in Human Tissues

Human N-acetyltransferase 2 (NAT2) genetic polymorphism is associated with drug toxicity and/or carcinogenesis in various tissues. Knowledge of NAT2 gene structure and expression is critical for understanding these associations. Previous findings suggest that human NAT2 expression is highest in liver and gut but expressed at functional levels in other tissues. A sensitive and specific TaqMan reverse transcriptase-polymerase chain reaction (RT-PCR) assay with intron-spanning primers was developed and used, together with a second TaqMan RT-PCR assay based on amplification of a NAT2 open reading frame (ORF) exon segment, to measure NAT2 mRNA in 29 different human tissues. Cap-dependent amplification of mRNA 5' termini and review of public database information were done to more precisely define the NAT2 promoter(s) and to validate the quantitative RT-PCR assay design. The great majority (40/41) of NAT2 liver cDNAs had 5' termini between 8682 and 8752 nucleotides upstream of the NAT2 ORF exon, and 34 of 40 5' termini were at the -8711 and -8716 adenines. All 59 NAT2 cDNAs with 5' termini in this vicinity, including 40 of the liver isolates and 19 cDNAs in public databases from liver and other sources, showed direct splicing to the ORF exon, with no other noncoding exon detected. NAT2 mRNA was highest in liver, small intestine, and colon and was readily detected in most other tissues, albeit at much lower levels. NAT2 expression in diverse human tissues provides further mechanistic support underlying associations between NAT2 genetic polymorphism, drug toxicity, and/or chemical carcinogenesis.

Flashback to the 1960s: Utility of archived sera to explore the origin and evolution of Plasmodium falciparum chloroquine resistance in the Pacific

The increasing frequencies of Plasmodium falciparum strains that are resistant to chloroquine (CQ) and other antimalarials are resulting in a global resurgence of malaria morbidity and mortality. CQ resistance (CQR) is associated with multiple mutations in the P. falciparum chloroquine resistance transporter ( pfcrt) gene. The mode and tempo of the accumulation of substitutions leading to these complex CQR haplotypes remain speculative due to the dearth of samples temporally spanning the evolution of drug resistance. The origin and evolution of the CQR alleles of Papua New Guinea (PNG) is particularly ambiguous. It remains unclear whether the pfcrt haplotype in PNG resulted from an independent origin of a CQR haplotype identical in sequence to the South American haplotype, or if this haplotype originated in South America and recombined into a Southeast Asian-derived genome. We sequenced a segment of pfcrt exon 2 from 398 plasmid clones derived from archival human sera collected in the Pacific before and after the first reported cases of CQ treatment failure ( n = 251) and modern samples ( n = 147). None of the 251 pfcrt plasmid clones from nine archival samples displayed the C72S or the K76T mutations that are characteristic of CQR strains. In contrast, these two amino acid substitutions were present in all 147 pfcrt plasmid clones from five samples collected between 2001 and 2003; thus, the archival samples represent the baseline parasite genetic diversity before the evolution of CQR strains. We are currently expanding our analyses to include additional samples from the series described here and from series collected in the 1970s and the 1980s to evaluate the geographic origin of CQR strains in the Pacific and the validity of the sequential point mutation accumulation model of CQR evolution.

Patterns of variation among distinct alleles of the Flag silk gene from Nephila clavipes

Spider silk proteins and their genes are very attractive to researchers in a wide range of disciplines because they permit linking many levels of organization. However, hypotheses of silk gene evolution have been built primarily upon single sequences of each gene each species, and little is known about allelic variation within a species. Silk genes are known for their repeat structure with high levels of homogenization of nucleotide and amino acid sequence among repeated units. One common explanation for this homogeneity is gene convergence. To test this model, we sequenced multiple alleles of one intron–exon segment from the Flag gene from four populations of the spider Nephila clavipes and compared the new sequences to a published sequence. Our analysis revealed very high levels of heterozygosity in this gene, with no pattern of population differentiation. There was no evidence of gene convergence within any of these alleles, with high levels of nucleotide and amino acid substitution among the repeating motifs. Our data suggest that minimally, there is relaxed selection on mutations in this gene and that there may actually be positive selection for heterozygosity.

β‐Catenin splice variants and downstream targets as markers for neoplastic progression of esophageal cancer

This study characterizes the frequency of exon 3 CTNNB1 mutations and compares the expression of CTNNB1 transcript variants and downstream targets MYC and WAF1 (p21) across the neoplastic progression of esophageal squamous cell carcinomas (ESCCs). Mutational analysis was performed on 56 tumors and corresponding germline DNA, using primers to exon 3 of CTNNB1 and SSCP DNA sequencing gels. Quantitative Real Time RT-PCR was performed on 45 foci representing the histological spectrum from normal to invasive cancer, using specific primer sets for alternative splice variants that differ by the presence (16A) or absence (16B) of a 159-bp noncoding segment of exon 16 of CTNNB1, in conjunction with downstream targets MYC and WAF1. Two unique mutations were identified, S37F in the SxxxS repeat region, and a germline polymorphism, T59A. Thus, mutation of CTNNB1 exon 3 is a rare event in this population. RT-PCR analysis successfully confirmed the presence of both beta-catenin splice variants in histologically normal and preneoplastic squamous epithelium, and invasive tumors of the esophagus, and identified a significant reduction in the 16A/16B ratio (P = 0.014) and an accompanying significant increase in the MYC/WAF1 expression ratio (P = 0.001) with progression from normal mucosa to dysplasia. This represents the first identification of two CTNNB1 transcripts in histologically "normal" esophageal squamous cells, squamous dysplasia, and invasive ESCC. These results show an increase in the minor mRNA (16B) isoform and changes in the expression of downstream markers consistent with increased transcription during the histological progression from normal to squamous dysplasia.

Investigation of APC Mutations in a Turkish Familial Adenomatous Polyposis Family by Heterodublex Analysis

Familial adenomatous polyposis is an autosomal dominant disease characterized by the presence of 100 or more colorectal adenomatous polyps. Mutations in the adenomatous polyposis coli gene are primarily responsible for the development of this disease. This study was designed to investigation of adenomatous polyposis coli (APC) gene mutations in members of familial adenomatous polyposis family to identify individuals at risk of the disease. We examined one patient with familial adenomatous polyposis and 21 family members including one affected person from familial adenomatous polyposis and 20 nonsymptomatic persons. We studied E, D, F, and G segments of exon 15 of the adenomatous polyposis coli gene by heteroduplex analysis. We used silver staining method for staining. We found a mutation for five persons at segment F of exon 15 of the adenomatous polyposis coli gene. Two of them were affected by colorectal cancer, one of whom was the proband, and the other three were nonsymptomatic family members. The pathogenetic mutation was a T deletion at codon 1172, causing a frameshift in the adenomatous polyposis coli gene, as a result of the sequencing analysis of these cases. Investigation of adenomatous polyposis coli gene mutations is very important for the identification of genetic susceptibility to colorectal cancer and for the definition of tumor developing at an early stage. Furthermore, the identification of this mutation for the first time in a Turkish family will be useful to foster further studies on familial adenomatous polyposis in Turkey.

A cautionary note: false homozygosity for BRCA2 6174delT mutation resulting from a single nucleotide polymorphism masking the wt allele.

Sequencing an amplification product of the terminal segment of BRCA2 exon 11 showed apparent homozygosity for the 6174delT mutation in two healthy sisters. Subsequent sequencing of an alternate overlapping amplicon revealed the presence of the 5972C >T polymorphism, which is within the standard upstream amplification primer. This mismatch was responsible for the failure to amplify the normal (5972T) allele in both sisters who were heterozygous for the 6174delT mutation. Though the unexpected finding of apparent homozygosity for the 6174delT mutation prompted re-evaluation of the assay, the potential for false negative results due to masking of a mutation-bearing allele by such a circumstance should be a cautionary note for the testing and also in the interpretation of the results published under such assay conditions.

Multiple Messenger Ribonucleic Acid Transcripts and Revised Gene Organization of the Human TSH Receptor.

Northern blot analysis of human TSH receptor (hTSHR) messenger ribonucleic acid (mRNA) expression has previously demonstrated multiple species of transcripts in the thyroid gland, suggesting the presence of multiple transcription initiation sites, alternatively spliced forms or alternate polyadenylation (poly(A)) sites. The first two have already been reported elsewhere. To clarify alternate poly(A) sites in the hTSHR gene, the present study was designed to characterize three full-length hTSHR cDNAs with distinct poly(A) signals that we have previously cloned. The comparison of the nucleotide sequencing data on the 3'UTR of these three clones to the Draft Human Genome in NCBI database revealed that the 3' segment of exon 10 of hTSHR gene contains three tandem repeats of the poly(A) sites, from which are expressed three full-length TSHR mRNAs with distinct 3'UTR length. The longest one appears to be a predominant transcript. From these data, together with (i) the previously reported organization of hTSHR genome and (ii) use of the Draft Human Genome to localize the unidentified sequence in the alternatively spliced form of truncated hTSHR, we propose the complete structure of hTSHR gene. Rather than 10 exons, our analysis suggests that hTSHR gene seems to contain 13 exons and 12 introns. At least three full-length TSHR mRNAs with distinct poly(A) sites and five alternatively spliced forms of TSHR mRNAs are expressed from the single hTSHR gene.

Exon 5 encoding the transmembrane region of HLA-A contains a transitional region for the induction of nonsense-mediated mRNA decay.

HLA class I alleles containing premature termination codons (PTCs) are increasingly being found. To understand their effects on MHC class I expression, HLA-A*2402 mutants containing PTCs were transfected into class I-deficient cells, and expression of HLA-A mRNA and protein was determined. In exons 2, 3, and 4, and in the 5' part of exon 5, PTCs reduced mRNA levels by up to 90%, whereas in the 3' part of exon 5 and in exons 6 and 7 they had little effect. Transition in the extent of nonsense-mediated mRNA decay occurred within a 48-nt segment of exon 5, placed 58 nt upstream from the exon 5/exon 6 junction. This transition did not conform to the positional rule obeyed by other genes, which predicted it to be approximately 50-55 nt upstream of the exon 7/exon 8 junction and thus placing it in exon 6. Mutants containing extra gene segments showed the difference is caused by the small size of exons 5 and 6, which renders them invisible to the surveillance machinery. For the protein, a transition from secretion to membrane association occurs within a 26-nt segment of exon 5, 17 nt upstream of the exon 5/exon 6 junction. Premature termination in exon 5 can produce secreted and membrane-associated HLA-A variants expressed at high levels.

Prevalence, phenotypic spectrum, and modes of inheritance of gonadotropin-releasing hormone receptor mutations in idiopathic hypogonadotropic hypogonadism.

Mutations in the GnRH receptor (GNRHR) have been described as a cause of reproductive failure in a subset of patients with idiopathic hypogonadotropic hypogonadism (IHH). Given the apparent rarity of these mutations, we set out to determine the frequency and distribution of GNRHR mutations in a heterogeneous population of patients with IHH who were well characterized with respect to diagnosis, phenotype, and mode of inheritance and to define their distribution within the receptor protein. One hundred and eight probands with IHH were screened for mutations in the coding sequence of GNRHR. Forty-eight of the 108 patients had a normal sense of smell, whereas the remaining 60 had anosmia or hyposmia (Kallmann syndrome). Exon segments in the GNRHR were screened for mutations using temperature gradient gel electrophoresis, and all mutations were confirmed by direct sequencing. Five unrelated probands (3 men and 2 women), all normosmic, were documented to have changes in the coding sequence of the GNRHR. Two of these probands were from a subgroup of 5 kindreds consistent with a recessive mode of inheritance, establishing a GNRHR mutation frequency of 2 of 5 (40%) in patients with normosmic, autosomal recessive IHH. The remaining 3 probands with GNRHR mutations were from a subgroup of 18 patients without evidence of familial involvement, indicating a prevalence of 3 of 18 (16.7%) in patients with sporadic IHH and a normal sense of smell. Among the five individuals bearing GNRHR mutations, a broad spectrum of phenotypes was noted, including testicular sizes in the male that varied from prepubertal to the normal adult male range. Three probands had compound heterozygous mutations, and two had homozygous mutations. Of the eight DNA sequence changes identified, four were novel: Thr(32)Ile, Cys(200)Tyr, Leu(266)Arg, and Cys(279)TYR: COS-7 cells transiently transfected with complementary DNAs encoding the human GNRHR containing each of these four novel mutations failed to respond to GnRH agonist stimulation. We conclude that 1) the spectrum of phenotypes in patients with GNRHR mutations is much broader than originally anticipated; 2) the frequency of GNRHR mutations may be more common than previously appreciated in familial cases of normosmic IHH and infrequent in sporadic cases; and 3) functional mutations of the GNRHR are distributed widely throughout the protein.

12. The search for the genetic lesion in Ashkenazi Jews with classic Tay-Sachs disease

Publisher Summary This chapter gives an overview on the search for the genetic lesion in Askenazi Jews with Classic Tay-Sachs diseases (TSD). Elucidation of the mutation underlying classic TSD in the Ashkenazi Jewish population posed more of a challenge. Restriction enzyme digestion patterns of the mutant α-chain gene were identical to those of the normal gene, indicating that the mutation involved a small deletion or single base change. Amplification of the region encompassing the mutation by polymerase chain reaction followed by digestion of the amplified product with Dde1, then Southern analysis of the sample, reveals a 120-base-pair DNA (deoxyribonucleic acid) fragment from the normal allele in contrast to an 85-base pair piece from the mutant. It has generally been assumed that only one mutation gives rise to the classic form of TSD in the Ashkenazi Jewish population. PCR-based assay for the insertion mutation which involved amplification of a segment of exon 11 inclusive of the region of insertion and detection of the lesion by probing duplicate samples of the amplified product with oligonucleotides specific for either the normal or mutant sequence was developed.

Analysis of KIT Mutation and Protein Expression in Fine Needle Aspirates of Gastrointestinal Stromal/Smooth Muscle Tumors

To determine if sequencing the KIT gene could facilitate more definitive FNA diagnosis. Sixteen cases of gastrointestinal stromal/smooth muscle tumor (GIST) in which fine needle aspiration (FNA) was performed (mean age, 67; M/F = 12/4) were studied. DNA was extracted from cytologic preparations from all patients (15 cell blocks, 1 alcohol-fixed smear) and seven subsequent resection specimens. DNA was amplified by polymerase chain reaction, using primers designed to amplify a segment of the KIT gene exon 11 and sequenced on an ABI Prism 377 DNA sequence analyzer (Applied Biosystems, Indianapolis, Indiana, U.S.A.). Immunocytochemical staining for CD 117 (the KIT gene product) was performed on sections from 12 cell blocks and 7 surgical resections. In-frame deletion of exon 11 was detected in eight cases (7 monoalleic, 1 bialleic); a point mutation was found in one case. Mutation was found only in histologically malignant (6 of 10 cases) and borderline GISTs (3 of 4 cases). No mutation was identified in benign tumors. In three cases, scant cellularity or blood precluded sequencing. CD 117 was expressed in 12 of 15 cases. Immunocytochemical staining for CD 117 is useful in confirming a cytologic diagnosis of GIST but does not facilitate diagnosis of malignancy. FNA biopsy specimens are suitable for KIT gene sequencing; detection of a KIT mutation favors a malignant diagnosis, though absence of mutation does not preclude malignancy.

Discrete mobility of single-stranded DNA in non-denaturing gel electrophoresis.

Gel electrophoresis is the standard method to separate, identify and purify nucleic acids. SSCP detects single base changes by altered mobility of single-stranded segments electrophoresed through non-denaturing polyacrylamide gels. Herein, changes in electrophoretic mobilities due to single base substitutions were measured for single-stranded segments of lengths ranging from 333 to 547 nt. A 484 nt segment in exon H of the human factor IX gene was studied most intensively. After SSCP, mobilities were determined by scanning autoradiograms at very high resolution (1200 d.p.i.), which allowed precise measurement of mobilities. When the mobilities of 46 single base substitutions were characterized, the distribution of mutant segments relative to a wild-type control was found to be discrete, i.e. the observed mobility values occurred in distinct ranges. Discrete mobility distributions were seen at different electrophoretic temperatures, buffer concentrations, segment lengths and segment sequences. In addition: (i) single base substitutions caused discontinuous distributions between highly dispersed and sharp bands; (ii) at least one single-stranded segment produced two sharp bands of similar intensity. These observations suggest that: (i) the single base changes in DNA segments in the size range 333-547 nt result in discrete conformational changes; (ii) individual DNA molecules of the same DNA segment can occasionally adopt two or more discrete conformations.

The γ-Crystallins and Human Cataracts: A Puzzle Made Clearer

Despite the fact that cataracts constitute the leading cause of blindness worldwide, the mechanisms of lens opacification remain unclear. We recently mapped the aculeiform cataract to the gamma-crystallin locus (CRYG) on chromosome 2q33-35, and mutational analysis of the CRYG-genes cluster identified the aculeiform-cataract mutation in exon 2 of gamma-crystallin D (CRYGD). This mutation occurred in a highly conserved amino acid and could be associated with an impaired folding of CRYGD. During our study, we observed that the previously reported Coppock-like-cataract mutation, the first human cataract mutation, in the pseudogene CRYGE represented a polymorphism seen in 23% of our control population. Further analysis of the original Coppock-like-cataract family identified a missense mutation in a highly conserved segment of exon 2 of CRYGC. These mutations were not seen in a large control population. There is no direct evidence, to date, that up-regulation of a pseudogene causes cataracts. To our knowledge, these findings are the first evidence of an involvement of CRYGC and support the role of CRYGD in human cataract formation.

Polymorphism across an exon-intron boundary in an avian Mhc class II B gene.

Twenty-three sequence haplotypes spanning the boundary of the second exon and intron of a red-winged blackbird Mhc class II B gene, Agph-DAB1, are presented. The polymorphism of the exon segment is distributed in two divergent allelic lineages which appear to be maintained by balancing selection. The silent nucleotide diversity of the exon (pi = 0.101) is more than five times that of the intron (pi = 0.018) and decays rapidly across the exon-intron boundary. Additionally, genealogical reconstruction indicates that divergence from a common ancestor in the exon sample is over four times that of the intron. The intron sequences reveal a pattern of polymorphism which is characteristic of directional selection, rather than a pattern expected from linkage to a balanced polymorphism. These results suggest that the evolutionary histories of these two adjacent regions have been disassociated by recombination or gene conversion. The estimated population recombination parameter between the exon and the intron is sufficiently high (4NeC = 8.545) to explain the homogenization of intron sequences. Compatibility analyses estimate that these events primarily occur from the exon-intron boundary to about 20-30 bases into the intron. Additionally, the observation that divergent exon alleles share identical intron sequence supports the conclusion of disassociation of exon and intron evolutionary histories by recombination.