Construction of I-Deletion-Correcting Ternary Codes

Finding large deletion correcting codes is an important issue in coding theory. Many researchers have studied this topic over the years. Varshamov and Tenegolts constructed the Varshamov-Tenengolts codes (VT codes) and Levenshtein showed the Varshamov-Tenengolts codes are perfect binary one-deletion correcting codes in 1992. Tenegolts constructed T codes to handle the non-binary cases. However the T codes are neither optimal nor perfect, which means some progress can be established. Latterly, Bours showed that perfect deletion-correcting codes have a close relationship with design theory. By this approach, Wang and Yin constructed perfect 5-deletion correcting codes of length 7 for large alphabet size. For our research, we focus on how to extend or combinatorially construct large codes with longer length, few deletions and small but non-binary alphabet especially ternary. After a brief study, we discovered some properties of T codes and produced some large codes by 3 different ways of extending some existing good codes.

Detection of classical 17p11.2 deletions, an atypical deletion and RAI1 alterations in patients with features suggestive of Smith-Magenis syndrome

Smith-Magenis syndrome (SMS) is a complex disorder whose clinical features include mild to severe intellectual disability with speech delay, growth failure, brachycephaly, flat midface, short broad hands, and behavioral problems. SMS is typically caused by a large deletion on 17p11.2 that encompasses multiple genes including the retinoic acid induced 1, RAI1, gene or a mutation in the RAI1 gene. Here we have evaluated 30 patients with suspected SMS and identified SMS-associated classical 17p11.2 deletions in six patients, an atypical deletion of ∼139 kb that partially deletes the RAI1 gene in one patient, and RAI1 gene nonsynonymous alterations of unknown significance in two unrelated patients. The RAI1 mutant proteins showed no significant alterations in molecular weight, subcellular localization and transcriptional activity. Clinical features of patients with or without 17p11.2 deletions and mutations involving the RAI1 gene were compared to identify phenotypes that may be useful in diagnosing patients with SMS. © 2012 Macmillan Publishers Limited All rights reserved.

Large deletions in the CFTR gene: clinics and genetics in Swiss patients with CF

Cystic fibrosis (CF) is the most common life-shortening autosomal recessive disorder in Caucasians, and is associated with at least one mutation on each CF transmembrane conductance regulator (CFTR) allele. Some patients, however, with only one identifiable point mutation carry on the other allele, a large deletion that is not detected by conventional screening methods. The overall frequency of large deletions in patients with CF is estimated to be 1-3%. Using the CFTR Multiplex Ligation dependent Probe Amplification Kit (MRC-Holland, Amsterdam, Netherlands) that allows the exact detection of copy numbers from all 27 exons in the CFTR gene, we screened 50 patients with only one identified mutation for large deletions in the CFTR gene. Each detected deletion was confirmed using our real-time polymerase chain reaction (PCR) assay and deletion-specific PCR reactions using junction fragment primers. We detected large deletions in eight patients (16%). These eight CF alleles belong to four different deletion types (CFTRindel2, CFTRdele14b-17b, CFTRdele17a-17b and CFTRdele 2-9) whereof the last is novel. Comparing detailed clinical data of all these patients with CF and the molecular genetic findings, we were able to elaborate criteria for deletion screenings and possible genotype-phenotype associations. In conclusion, we agree with other authors that deletion screenings should be implemented in routine genetic diagnostics of CF.

Mutation screening and genotype:phenotype correlation in familial hypercholesterolaemia

The aim of this study was to develop a mutation screening protocol for familial hypercholesterolaemia (FH) patients and to assess genotype/phenotype effects in terms of pre-treatment lipid profiles and presentation of tendon xanthomata (TX). A total of 158 families with clinical definitions of possible (120) or definite (38) FH were studied using a tiered screening protocol. Mutations were identified in 52 families, 44 families showing 23 different LDLR gene defects and eight families showing the common Apo B100 gene defect R3500Q. LDLR defects were detected in various regions of the gene with 56% in the LDL binding domain (exons 2-6) and 37% in the EGF precursor homology domain (exons 7-14). The most common mutations were D461N(7), C210X(5), 932delA(5), and C163Y(4). Frameshift mutations accounted for 20% with nonsense 13%, mis-sense 35%, splice 3%, Apo B 13% and 2% large deletion, 13% of clinically definite FH remained undefined. In conclusion, DNA based diagnosis is possible in 79% (30/38) of clinically definite FH families and of the 120 possible FH families at the start of the screening program, 18% (22/120) now have defined mutations. Overall 60 families from the original 158 meet the clinical and/or genetic criteria for definite FH. Tendon xanthomata were present in only 58% (30/52) of genetically defined FH families, thus limiting its use as a strict diagnostic criteria. Families with low density lipoprotein receptor (LDLR) defects present with higher total and LDL cholesterol levels and a higher incidence of TX than do those with the common Apo B variant, and frameshift mutations appear to have the most severe presentation. Copyright (C) 1999 Elsevier Science Ireland Ltd.

Heteroplasmy in mammal mitochondrial deoxyribonucleic acid

La nature a développé diverses stratégies afin d’assurer le commencement de la vie dans des conditions d’homoplasmie, c’est-à-dire des conditions telles que les cellules sont dotées du même ADN mitochondrial. Toutefois, des nouveaux haplotypes de l’acide désoxyribonucléique mitochondrial (ADNmt) peuvent apparaitre et croître de plusieurs façons tout au long de la durée d’une vie menant à l’hétéroplasmie. Par exemple, l’hétéroplasmie de l’ADNmt peut être créée artificiellement par des technologies reproductives assistées, ainsi que naturellement par le processus de vieillissement. De ce fait, la thèse de ce doctorat fut divisée en deux principaux objectifs. Le premier étant celui d’analyser les changements survenus dans l’hétéroplasmie de l’ADNmt produit par le transfert nucléaire des cellules somatiques (SCNT) lors du développement de l’embryon jusqu’au fœtus et aux tissus adultes de bovins clonés. En ce qui concerne le second objectif, il s’agit d’analyser les changements survenus dans l’hétéroplasmie de l’ADNmt causés par le vieillissement dans une cellule somatique adulte et dans des tissus germinaux durant l’ovogénèse, ainsi qu’au début de l’embryogenèse et dans la procédure de culture in vitro sur des souris. Dans la première série d’expériences sur des bovins, des fibroblastes fœtaux transportant une mutation d’ADNmt (insertion de 66 pb) furent fusionnés avec des ovocytes receveurs transportant l’ADNmt du type sauvage. La présence d’ADNmt venant de la cellule donneuse a été analysée à différents stades de développement, soit sur des embryons âgés de 17 jours (n=17), des fœtus âgés de 40 jours (n=3), des fœtus âgés de 60 jours (n=3), un fœtus âgé de 240 jours et 3 clones post-nataux âgés de 18 à 24 mois. Chaque individu s’est avéré être hétéroplasmique et 99 % (103/104) des échantillons de tissus analysés étaient également hétéroplasmiques. Cependant, l’ovaire venant du fœtus de 240 jours fut le seul à être homoplasmique pour l’ADNmt de l’ovocyte receveur. Dans la plupart des échantillons analysés (95,2 %, soit 99/104) la moyenne d’hétéroplasmie était de 1,46 %. Par contre, un fœtus âgé de 40 jours a présenté un niveau élevé d’hétéroplasmie (20,9 %), indiquant ainsi que des évènements rares d’augmentation de l’ADNmt des cellules donneuses peuvent survenir. Étant donné que la majorité des clones SCNT montrait de l’hétéroplasmie de l’ADNmt à des proportions comparables à celles des cellules donneuses au moment de la reconstruction de l’embryon, on a pu conclure que l’hétéroplasmie produite par des techniques de transfert nucléaire utilisant des cellules somatiques est due à une ségrégation neutre de l’ADNmt. Dans la seconde série d’expériences sur des souris, des femelles de différents âges, c.à.d. jeunes (0 – 8 mois), moyennes (8 – 16 mois) et vieilles (16 – 24 mois), ont été synchronisées (gonadotrophines) et sacrifiées dans le but d’obtenir des ovocytes au stade de vésicule germinal, et des ovocytes au stade métaphase-II produits in vivo et in vitro. De plus, des embryons in vivo et in vitro au stade de deux-cellules et des embryons au stade de blastocystes ont été obtenus de femelles jeunes. Différents tissus somatiques, venant de femelles des trois stades d’âge ont été obtenus : cerveau, foie, muscle et du cumulus ovocytaire. De plus, l’effet du vieillissement a été mesuré selon la fertilité de la femelle. En effet, les effets sur l’hétéroplasmie du vieillissement, du stade de développement et de la culture in vitro ont été mesurés dans des ovocytes et dans des embryons. Les effets du vieillissement sur les mitochondries ont été mesurés par rapport au nombre total de copies de l’ADNmt, au pourcentage des délétions communes et sur l’expression de trois gènes : Ndufs4, Mt-nd2 and Mt-nd4. Il a été possible d’observer que la fertilité des femelles dans la colonie de souris diminuait avec l’âge. En fait, le vieillissement affectait l’ADNmt dans les tissus somatiques, cependant il n’avait pas d’effet sur le cumulus, les ovocytes et les embryons. Le nombre de délétions de l’ADNmt augmentait pendant la reprise de la méiose et celui-ci diminuait au début du développement embryonnaire. La culture in vitro n’affectait pas la quantité d’ADNmt dans la plupart des tissus germinaux. Puisque nous n’avons pas trouvé d’effet de l’âge dans la majorité des paramètres mitochondriaux analysés dans les ovocytes et les embryons, il est suggéré que la délétion commune de l’ADNmt dans les tissus germinaux est davantage reliée au statut cellulaire de la production d’énergie qu’au processus de vieillissement. Deux sources différentes de mutations de l’ADNmt produites dans les ovocytes normaux ou reconstitués ont produit différents résultats d’hétéroplasmie au début de l’embryogénèse. Chez les bovins, l’hétéroplasmie artificielle impliquant une petite insertion (66 pb) dans la région non codante (D-loop) de l’ADNmt a été vraisemblablement non nocive pour l’embryon, tolérant la persistance de l’ADNmt étranger pendant les différents stades du développement des clones. Chez les souris, l’hétéroplasmie naturelle produite par une grande délétion (4974 pb délétion commune) dans la région codante de l’ADNmt a été vraisemblablement nocive pour l’embryon et par conséquent éliminée pour assurer l’homoplasmie au début du développement embryonnaire.

Prevalence of GJB2 (Connexin-26) and GJB6 (Connexin-30) Mutations in a Cohort of 300 Brazilian Hearing-Impaired Individuals: Implications for Diagnosis and Genetic Counseling

Objective: Hereditary nonsyndromic deafness is an autosomal recessive condition in about 80% of cases, and point mutations in the GJB2 gene (connexin 26) and two deletions in the GJB6 gene (connexin 30), del(GJB6-D13S1830) and del(GJB6-D13S1854), are reported to account for 50% of recessive deafness, Aiming at establishing the frequencies of GJB2 mutations and GJB6 deletions in the Brazilian population, we screened 300 unrelated individuals with hearing impairment, who were not affected by known deafness related syndromes. Methods: We firstly screened the most frequently reported mutations, c.35delG and c.167delT in the GJB2 gene, and del(GJB6-D13S1830) and del(GJB6-D13S1854) in the GJB6 gene, through specific techniques. The detected c.35delG and c.167delT mutations were validated by sequencing. Other mutations in the GJB2 gene were screened by single-strand conformation polymorphism and the coding region was sequenced when abnormal patterns were found. Results: Pathogenic mutations in GJB2 and GJB6 genes were detected in 41 individuals (13.7%), and 80.5% (33/41) presented these mutations in homozygosis or compound heterozygosis, thus explaining their hearing defect. The c.35delG in the GJB2 gene was the most frequent mutation (37/300; 12.4%), detected in 23% familial and 6.2% the sporadic cases. The second most frequent mutation (1%; 3/300) was the del(GJB6- D13S1830), always found associated with the c.35delG mutation. Nineteen different sequence variations were found in the GJB2 gene. In addition to the c.35delG mutation, nine known pathogenic alterations were detected 0 67delT, p.Trp24X, p.Val37lle, c.176_191del16, c.235delC, p.Leu90Pro, p.Arg127His, c.509insA, and p.Arg184Pro, Five substitutions had been previously considered benign polymorphisms: c.-15C>T, p.Val27lle, p.Met34hr, p.Ala40Ala, and p.Gly160Ser. Two previously reported Mutations of unknown pathogenicity were found (p.Lys168Arg, and c.684C>A), and two novel substitutions, p.Leu81Val (c.G241C) and p.Met195Val (c.A583G), both in heterozygosis without an accompanying mutation in the other allele. None of these latter four variants of undefined status was present in a sample of 100 hearing controls. Conclusions: The present study demonstrates that Mutations in the GJB2 gene and del(GJB6 D13S1830) are important causes of hearing impairment in Brazil, thus justifying their screening in a routine basis. The diversity of variants in our sample reflects the ethnic heterogeneity of the Brazilian population.

Genomic alterations in patients showing multiple primary tumors and family history of cancer

Multiple primary tumors (MPT) are a major cause of mortality and morbidity among patients that have survived after the treatment of a first cancer. It has been proposed that after the first primary tumor, high risk of a subsequent tumor could be associated with radiotherapy used as treatment for the first cancer. Other potential risk factors include unhealthy lifestyle, genetic predisposition, aging, environmental determinants or an interaction between these factors. However, an association between the presence of MPT and family history of cancer in cases without clinical and molecular evidence of a known hereditary cancer syndrome is rarely described. Genomic DNA from 12 patients with at least two primary tumors and without mutations on TP53 was evaluated by CytoScan HD Array (Affymetrix). Chromosome Analysis Suite (ChAS) software v.2.0.1 was used considering at least 50 markers for gains; 25 for losses and a minimum of 5Mb for cnLOHs. Data from 1038 phenotypically healthy individuals (Affymetrix) and from Database of Genomic Variants were used as reference. Only alterations found in <1% (rare) or never described (new rare) in the reference population were considered. All cases, except one, presented a family history of cancer. Five cases developed MTP after radiotherapy and only one was located in the same treated area. It was detected 67 rare and 15 new rare genomic alterations encompassing 5.906 genes: 17 losses, 29 gains, and 36 cnLOH. X chromosome presented the higher number of alterations. Two patients with breast cancer presented a large deletion/cnLOH on 7q21. Enrichment analysis revealed 1275 genes associated with breast cancer (p= 0.001), which was diagnosed in 6 patients and their family members (all negative for BRCA1/2 or TP53 mutations). cnLOHs accounted for 44% of all the alterations. A significant proportion of cases (11/12) presented family history of cancer and the patients were not submitted to radiotherapy (7/12). We demonstrated the presence of rare genomic alterations in patients with MPT suggesting their involvement in the MPT development. cnLOH may arise as a new mechanism associated with the risk to develop MPT. All authors have declared no conflicts of interest.

Detection of exon deletions within an entire gene (CFTR) by relative quantification on the LightCycler

BACKGROUND: Cystic fibrosis (CF) is associated with at least 1 pathogen point sequence variant on each CFTR allele. Some symptomatic patients, however, have only 1 detectable pathogen sequence variant and carry, on the other allele, a large deletion that is not detected by conventional screening methods. METHODS: For relative quantitative real-time PCR detection of large deletions in the CFTR gene, we designed DNA-specific primers for each exon of the gene and primers for a reference gene (beta2-microglobulin). For PCR we used a LightCycler system (Roche) and calculated the gene-dosage ratio of CFTR to beta2-microglobulin. We tested the method by screening all 27 exons in 3 healthy individuals and 2 patients with only 1 pathogen sequence variant. We then performed specific deletion screenings in 10 CF patients with known large deletions and a blinded analysis in which we screened 24 individuals for large deletions by testing 8 of 27 exons. RESULTS: None of the ratios for control samples were false positive (for deletions or duplications); moreover, for all samples from patients with known large deletions, the calculated ratios for deleted exons were close to 0.5. In addition, the results from the blinded analysis demonstrated that our method can also be used for the screening of single individuals. CONCLUSIONS: The LightCycler assay allows reliable and rapid screening for large deletions in the CFTR gene and detects the copy number of all 27 exons.

Phenotype-genotype correlation in eight Polish patients with inherited Factor XIII deficiency: identification of three novel mutations

Inherited factor XIII (FXIII) deficiency is known as one of the most rare blood coagulation disorder in humans. In the present study, phenotype and genotype of eight FXIII deficient Polish patients from five unrelated families were compared. The patients presented with a severe phenotype demonstrated by a high incidence of intracerebral haemorrhages (seven of eight patients), haemarthrosis (six patients) and bleeding due to trauma (five patients). Introduction of regular substitution with FXIII concentrate prevented spontaneous bleeding in seven patients. In all patients, mutations within the F13A gene have been identified revealing four missense mutations (Arg77Cys, Arg260Cys, Ala378Pro, Gly420Ser), one nonsense mutation (Arg661X), one splice site mutation (IVS5-1 G>A) and one small deletion (c.499-512del). One homozygous large deletion involving exon 15 was detected by failure of PCR product. The corresponding mutations resulted in severely reduced FXIII activity and FXIII A-subunit antigen concentration, while FXIII B-subunit antigen remained normal or mildly decreased. Structural analysis demonstrated that the novel Ala378Pro mutation may cause a disruption of the FXIII catalytic triad leading to a non-functional protein which presumably undergoes premature degradation. In conclusion, the severe phenotype with high incidence of intracranial bleeding and haemarthrosis was in accordance with laboratory findings on FXIII and with severe molecular defects of the F13A gene.

Haematologic data, iron parameters and molecular findings in two new cases of iron-refractory iron deficiency anaemia

Matriptase-2 (Tmprss6), a type II transmembrane serine protease, has an essential role in iron homoeostasis as a hepcidin regulator. Recently, patients with TMPRSS6 mutations and suffering from iron-refractory iron deficiency anaemia (IRIDA) have been reported. We describe two new cases of IRIDA, one patient of Swiss origin and the second of Italian origin. The first case results from a large deletion of 1054 nucleotides corresponding to an in frame deletion of 30 amino acid residues in the low-density lipoprotein receptor-1/-2 (LDLR-1/-2) domains and from a missense mutation in CUB1 (S304L). In the second case, a homozygous G-->C mutation in the last nucleotide of exon 15 and which modified the consensus sequence of the 5' splice donor site of intron 15 (AGgt-->ACgt) was identified. Both patients had a high hepcidin level and low serum iron and transferrin saturation compared to age-matched controls. Continuous perfusion of i.v. iron 4 h/d x 5 d in the first case resulted in a significant rise in haemoglobin. These new cases of IRIDA illustrate the importance of LDLR-1/-2 and CUB1 domains in matriptase-2 function as well as the role of matriptase-2 in hepcidin regulation. Furthermore a deletional form of TMPRSS6 (in LDLR-1/-2 domains) resulting in IRIDA is described for the first time. These cases reinforce the belief that patients suffering from IRIDA have no specific geographical or ethnic distribution and are sporadic secondary to different mutations of the matriptase-2 gene.

The processing of human pro-tumor necrosis factor

Human pro-TNF-$\alpha$ is a 26 kd type II transmembrane protein, and it is the precursor of 17 kd mature TNF. Pro-TNF release mature from its extracellular domain by proteolytic cleavage between resideu Ava ($-$1) and Val (+1). Both forms of TNF are biologically active and the native form of mature TNF is a bell-shaped trimer. The structure of pro-TNF was studied both in intact cell system and in an in vitro translation system by chemical crosslinking. We found that human pro-TNF protein exist as a trimer in intact cells (LPS-induced THP-1 cells and TNF cDNA transfected COS-3 cells) and this trimeric structure is assembled intracellularly, possibly in the ER. By analysis several deletion mutants, we observed a correlation between expression of pro-TNF cytotoxicity in a juxtacrine fashion and detection of the trimer, suggesting the trimeric structure is very important for its biologic activity. With a series of deletion mutants in the linking domain, we found that the small deletion did not block the cleavage and large deletion did regardless of the presence or absence of the native cleavage site, suggesting that the length of the residues between the plasma membrane and the base of the trimer determines the rate of the cleavage, possibly by blocking the accessibility of the cleavage enzyme to its action site. Our data also suggest that the native cleavage site is not sufficient for the release of mature TNF and alternative cleavage site(s) exists. ^

Control of pre-mRNA accumulation by the essential yeast protein Nrd1 requires high-affinity transcript binding and a domain implicated in RNA polymerase II association

Nrd1 is an essential yeast protein of unknown function that has an RNA recognition motif (RRM) in its carboxyl half and a putative RNA polymerase II-binding domain, the CTD-binding motif, at its amino terminus. Nrd1 mediates a severe reduction in pre-mRNA production from a reporter gene bearing an exogenous sequence element in its intron. The effect of the inserted element is highly sequence-specific and is accompanied by the appearance of 3′-truncated transcripts. We have proposed that Nrd1 binds to the exogenous sequence element in the nascent pre-mRNA during transcription, aided by the CTD-binding motif, and directs 3′-end formation a short distance downstream. Here we show that highly purified Nrd1 carboxyl half binds tightly to the RNA element in vitro with sequence specificity that correlates with the efficiency of cis-element-directed down-regulation in vivo. A large deletion in the CTD-binding motif blocks down-regulation but does not affect the essential function of Nrd1. Furthermore, a nonsense mutant allele that produces truncated Nrd1 protein lacking the RRM has a dominant-negative effect on down-regulation but not on cell growth. Viability of this and several other nonsense alleles of Nrd1 appears to require translational readthrough, which in one case is extremely efficient. Thus the CTD-binding motif of Nrd1 is important for pre-mRNA down-regulation but is not required for the essential function of Nrd1. In contrast, the RNA-binding activity of Nrd1 appears to be required both for down-regulation and for its essential function.

The ATPase Domain but Not the Acidic Region of Cockayne Syndrome Group B Gene Product Is Essential for DNA Repair

Cockayne syndrome (CS) is a human genetic disorder characterized by UV sensitivity, developmental abnormalities, and premature aging. Two of the genes involved, CSA and CSB, are required for transcription-coupled repair (TCR), a subpathway of nucleotide excision repair that removes certain lesions rapidly and efficiently from the transcribed strand of active genes. CS proteins have also been implicated in the recovery of transcription after certain types of DNA damage such as those lesions induced by UV light. In this study, site-directed mutations have been introduced to the human CSB gene to investigate the functional significance of the conserved ATPase domain and of a highly acidic region of the protein. The CSB mutant alleles were tested for genetic complementation of UV-sensitive phenotypes in the human CS-B homologue of hamster UV61. In addition, the CSB mutant alleles were tested for their ability to complement the sensitivity of UV61 cells to the carcinogen 4-nitroquinoline-1-oxide (4-NQO), which introduces bulky DNA adducts repaired by global genome repair. Point mutation of a highly conserved glutamic acid residue in ATPase motif II abolished the ability of CSB protein to complement the UV-sensitive phenotypes of survival, RNA synthesis recovery, and gene-specific repair. These data indicate that the integrity of the ATPase domain is critical for CSB function in vivo. Likewise, the CSB ATPase point mutant failed to confer cellular resistance to 4-NQO, suggesting that ATP hydrolysis is required for CSB function in a TCR-independent pathway. On the contrary, a large deletion of the acidic region of CSB protein did not impair the genetic function in the processing of either UV- or 4-NQO-induced DNA damage. Thus the acidic region of CSB is likely to be dispensable for DNA repair, whereas the ATPase domain is essential for CSB function in both TCR-dependent and -independent pathways.

Respiratory syncytial virus (RSV) SH and G proteins are not essential for viral replication in vitro: Clinical evaluation and molecular characterization of a cold-passaged, attenuated RSV subgroup B mutant

A live, cold-passaged (cp) candidate vaccine virus, designated respiratory syncytial virus (RSV) B1 cp-52/2B5 (cp-52), replicated efficiently in Vero cells, but was found to be overattenuated for RSV-seronegative infants and children. Sequence analysis of reverse-transcription–PCR-amplified fragments of this mutant revealed a large deletion spanning most of the coding sequences for the small hydrophobic (SH) and attachment (G) proteins. Northern blot analysis of cp-52 detected multiple unique read-through mRNAs containing SH and G sequences, consistent with a deletion mutation spanning the SH:G gene junction. Immunological studies confirmed that an intact G glycoprotein was not produced by the cp-52 virus. Nonetheless, cp-52 was infectious and replicated to high titer in tissue culture despite the absence of the viral surface SH and G glycoproteins. Thus, our characterization of this negative-strand RNA virus identified a novel replication-competent deletion mutant lacking two of its three surface glycoproteins. The requirement of SH and G for efficient replication in vivo suggests that selective deletion of one or both of these RSV genes may provide an alternative or additive strategy for developing an optimally attenuated vaccine candidate.

Fate of a redundant gamma-globin gene in the atelid clade of New World monkeys: implications concerning fetal globin gene expression.

Conclusive evidence was provided that gamma 1, the upstream of the two linked simian gamma-globin loci (5'-gamma 1-gamma 2-3'), is a pseudogene in a major group of New World monkeys. Sequence analysis of PCR-amplified genomic fragments of predicted sizes revealed that all extant genera of the platyrrhine family Atelidae [Lagothrix (woolly monkeys), Brachyteles (woolly spider monkeys), Ateles (spider monkeys), and Alouatta (howler monkeys)] share a large deletion that removed most of exon 2, all of intron 2 and exon 3, and much of the 3' flanking sequence of gamma 1. The fact that two functional gamma-globin genes were not present in early ancestors of the Atelidae (and that gamma 1 was the dispensible gene) suggests that for much or even all of their evolution, platyrrhines have had gamma 2 as the primary fetally expressed gamma-globin gene, in contrast to catarrhines (e.g., humans and chimpanzees) that have gamma 1 as the primary fetally expressed gamma-globin gene. Results from promoter sequences further suggest that all three platyrrhine families (Atelidae, Cebidae, and Pitheciidae) have gamma 2 rather than gamma 1 as their primary fetally expressed gamma-globin gene. The implications of this suggestion were explored in terms of how gene redundancy, regulatory mutations, and distance of each gamma-globin gene from the locus control region were possibly involved in the acquisition and maintenance of fetal, rather than embryonic, expression.