Linkage between the beta B2 and beta B3 crystallin genes in man and rat: a remnant of an ancient beta-crystallin gene cluster

Analysis of copy number variation in the normal human population within a region containing complex segmental duplications on 22q11 using high-resolution array-CGH

A previously detected copy number polymorphism (Ep CNP) in patients affected with neuroectodermal tumors led us to investigate its frequency and length in the normal population. For this purpose, a program called Sequence Allocator was developed and applied for the construction of an array that consisted of unique and duplicated fragments, allowing the assessment of copy number variation within regions of segmental duplications. The average resolution of this array was 11 kb and we determined the size of the Ep CNP to be 290 kb. Analysis of normal controls identified 7.7 and 7.1% gains in peripheral blood and lymphoblastoid cell line (LCL) DNA, respectively, while deletions were found only in the LCL group (7.1%). This array platform allows the detection of DNA copy number variation within regions of pronounced genomic complexity, which constitutes an improvement over available technologies.

The cooperation between two silencers creates an enhancer element that controls both the lens-preferred and the differentiation stage-specific expression of the rat beta B2-crystallin gene

The rat beta B2-crystallin gene is active only during a specific stage of the differentiation of rat lens fibre cells directed by basic fibroblast growth factor. The regulatory elements that determine the transient activity of this gene are located in the -750/-123 region and in the first intron. Singly, these elements act as silencers, together they constitute an enhancer that is active only during the specific differentiation stage. An additional silencer is found between -123 and -77. The proximal promoter region contains a Pax-6 binding site at -65/-51. In vitro, binding to this site could be detected but, according to in vivo footprinting experiments, this site is not occupied in the endogenous gene. Furthermore, co-expression of Pax-6 did not enhance promoter activity. Finally, mutation or deletion of this site did not affect promoter activity: the region -37/+10 sufficed for basal promoter activity. The cooperation between the -750/ -123 region and the first intron of the beta B2-crystallin gene not only determines the differentiation stage-specific activity of the gene, but also contributes to the highly increased expression in lens cells compared with non-lens cells.

The chicken beta A4- and beta B1-crystallin-encoding genes are tightly linked

Analysis of the 5' flanking region of the chicken beta B1-crystallin-encoding gene (beta B1-cry) revealed regions of sequence homology with the bovine beta A4-crystallin-encoding gene (beta A4-cry). Subsequently, the chicken beta A4-cry cDNA sequence was determined, and it was demonstrated that beta A4- and beta B1-cry are linked head to head in the chicken chromosome with 2147 nucleotides (nt) of intergenic spacer. Chicken beta A4-cry contains six exons, with the first exon being noncoding. Chicken beta A4-cry is the smallest beta-cry ever described, due to the small size of its introns which range in length from 68 to 96 nt. While three polymorphisms were noted between some cDNA clones and the genomic sequence, Southern blot analysis demonstrated that beta A4-cry exists as a single copy in the chicken genome. Northern blot analysis indicated that beta A4-cry is a lens-specific transcript which is expressed at higher levels in the embryo than in the adult. The beta A4-cry mRNA is present at 400-fold lower levels than the beta B1-cry mRNA in the 14-day embryonic chicken lens, and at 2000-fold lower levels than the beta B1-cry mRNA in the adult lens. These results are consistent with the idea that the beta-cry family was once clustered in the chromosome as the gamma-cry family is today, and raises the possibility that the relatively low expression of beta A4-cry is mechanistically linked to the high expression of beta B1-cry in the chicken lens.

The t(11;22)(p15.5;q11.23) in a retroperitoneal rhabdoid tumor also includes a regional deletion distal to CRYBB2 on 22q

Translocations and deletions involving chromosomal band 22q11 are common genetic aberrations in malignant rhabdoid tumors. Previous molecular analyses of a t(11;22) in the malignant rhabdoid tumor cell line TM87-16 localized the breakpoint distal to BCR on 22q11. In the present report, we have further refined the map position of this breakpoint between CRYBB2 and D22S258. Moreover, the D22S258, CRYBA4, D22S300, D22S1, and D22S310 loci, which lie between CRYBB2 and D22S42, were found to be deleted, presumably as a result of the translocation event. The identification of this deletion of at least 2 Mb on the long arm of chromosome 22 should be helpful for mapping the gene(s) in the region involved in the development of malignant rhabdoid tumors as well as providing insights into the mechanisms of chromosomal translocation in human solid tumors.

The beta crystallin genes on human chromosome 22 define a new region of homology with mouse chromosome 5

The human beta crystallin genes CRYBB2, CRYBB2P1, CRYBB3, and CRYBA4 are located in 22q11.2. Using interspecific backcross analysis, we mapped the mouse homologues of CRYBB2, CRYBB3, and CRYBA4 (i.e., Crybb2, Crybb3, and Cryba4) to the central region of mouse chromosome 5. The homologue of human CRYBB2P1 is absent in mouse. These assignments define a new region of homology in human and mouse.

Sequence of the human lens beta B2-crystallin-encoding cDNA

This study reports the nucleotide (nt) sequence of the human beta B2-crystallin (h beta B2-Cry)-encoding cDNA (h beta B2-cry). The h beta B2-cry gene encodes a major structural protein in the lens of the vertebrate eye. Sequence information obtained from mouse genomic clones and the mouse beta B2-cry cDNA (m beta B2-cry) sequence was used to design oligodeoxyribonucleotide primers, corresponding to exon 1, transcription start points, and termination and polyadenylation sites, that were used in the polymerase chain reaction (PCR) to generate full-length cDNA clones from total human lens RNA. In addition, cDNA libraries were made with lambda gt11 from both human fetal and adult lens tissue RNAs, and screened with a m beta B2-cry cDNA clone. The full-length h beta B2-cry cDNA is 721 bp and contains an open reading frame of 612 nt. It codes for a 23-kDa protein of 205 amino acid residues. Comparison of the overall nt and deduced aa sequences shows a greater similarity of h beta B2-cry to bovine beta B2-cry than to m beta B2-cry or rat beta B2-cry.

Regional fine mapping of the beta crystallin genes on chromosome 22 excludes these genes as physically linked markers for neurofibromatosis type 2

Neurofibromatosis type 2 (NF2) is a rare autosomal dominant disease, characterized by the development of bilateral vestibular schwannomas. The NF2 gene has been assigned to chromosome 22. Cataract and other eye abnormalities are frequently seen in NF2 patients. The specific association of eye abnormalities and NF2 might be caused by a genetic change on chromosome 22 that affects both the NF2 gene and a physically linked crystallin gene. In order to test this hypothesis, we regionally localized the known crystallin genes (i.e. CRYBB2, CRYBB2P1, CRYBB3, and CRYBA4) on chromosome 22. Crystallin gene-specific probes were hybridized to an extended panel of human x rodent somatic cell hybrids containing various portions of chromosome 22. It was found that all crystallin genes map to a very small region on chromosome 22 that is physically separate from the NF2 gene region by at least 160 kb of DNA. In addition, we found that the beta B crystallin genes (CRYBB2, CRYBB2P1, and CRYBB3) are clustered on a 300 kb SacII fragment and that the beta A4 crystallin gene (CRYBA4) is not part of this cluster. We conclude that the ocular manifestations in many NF2 patients are probably not the primary consequence of rearrangements on chromosome 22 that involve both the NF2 gene and a nearby beta crystallin gene.

A panel of human chromosome 22-specific sequence tagged sites

A panel of 29 sequence tagged sites (STSs) covering the long arm of chromosome 22 has been assembled. STS primer pairs were synthesized using available chromosome 22 sequence derived from the GenBank and EMBL DNA sequence databases, as well as published cDNA and genomic sequence, or from previously published and communicated primer pairs. Each STS was optimized for the polymerase chain reaction using a chromosome 22-only hybrid and human genomic DNA. Further STS content analysis on a panel of somatic cell hybrids that incorporated two chromosome 22 translocations resulted in the mapping of the X-box binding protein (XBP), D22S156, and transcobalamin II (TCN2) genes to 22q11-q13.1. The panel of STSs was used for the rapid determination of the STS content and thus the chromosomal DNA content of a new irradiation hybrid.

The second human beta B2-crystallin gene is a pseudogene

Comparison of the partial sequences of the human beta B2-1- and beta B2-2-crystallin genes with orthologous rat or calf sequences shows that the fourth exon sequence of the human beta B2-2 gene contains a one triplet deletion and a mutated splice acceptor site. No transcripts from the beta B2-2-crystallin gene could be detected in the human lens. These data suggest that the human beta B2-2-crystallin gene is a pseudogene.

Gene mapping of ocular diseases

Increasing awareness of the role of genetic factors in the causation of many human eye diseases has made ocular genetics one of the fastest growing areas of ophthalmology. The objective of this paper is to present the basic principles of gene mapping and their application to ophthalmology. The techniques used to map the genome are reviewed with emphasis placed on molecular genetics. The advances in this area have already provided the major impetus to the areas of diagnosis and prevention of some genetic eye disorders. Tables are presented that list the autosomal, X-linked and mitochondrial assignment of eye genes and disorders with ocular involvement.

Presence of hybridizing DNA sequences homologous to bovine acidic and basic beta-crystallins in all classes of vertebrates

The eye lens beta-crystallins in cow and chicken are encoded by a family of at least six genes. In order to assess the distribution of the corresponding genes among other vertebrates we hybridized beta-crystallin sequences (beta A2, beta A3/A1, beta A4, beta B1, beta B2, beta B3), isolated from a bovine lens cDNA library, to Southern blots on which EcoR1-digested chromosomal DNA was blotted from different vertebrate species. These included human, chimpanzee, calf, rat, pigeon, duck, monitor lizard, toad, trout, and lamprey. Positive hybridization signals were found in the representatives of virtually all classes of vertebrates. The basic beta B-crystallins gave hybridization signals in more species than the acidic beta A ones. In monitor lizard and toad the weakest hybridization signals for basic crystallin probes were found. For acidic crystallin probes the distribution pattern was more simple; among cold-blooded vertebrates a signal for beta A2 was found in trout and lamprey, for beta A4 in trout, and for beta A3/A1 only in toad. The results demonstrate that the duplications leading to the beta-crystallin gene family occurred before or during the earliest stages of vertebrate evolution.

Isolation and characterization of cDNAs encoding beta A2- and beta A4-crystallins: heterologous interactions in the predicted beta A4-beta B2 heterodimer

Except for the two acidic chains, beta A2 and beta A4, the primary structures of all bovine beta-crystallins have previously been elucidated, either by direct protein sequencing or prediction from cDNA sequencing. Both beta A2 and beta A4 were found to be synthesized in half-year-old calf lenses and are therefore likely to be present in a cDNA bovine library constructed from mRNA isolated from lenses of that age. A large number of cDNA clones was screened with all available crystallin, actin, vimentin and lens membrane protein MP26 probes and finally with a randomly primed mRNA probe. Clones positive for the latter, but negative for known lens proteins, were isolated and sequenced. beta A2, comprising 197 aa, and beta A4, comprising 209 aa, were identified. Both proteins have a conserved two-domain structure and an N-terminal extension which is variable. A three-dimensional model of the structure of beta A4 was made based on the coordinates of one subunit from the beta B2 dimer which has recently been solved using x-ray diffraction techniques. The resulting heterodimer structure, together with the compiled bovine beta-crystallin sequences, was used to indicate those regions of the sequences which distinguish acidic from basic beta-crystallins with a view to defining structural features necessary for subunit recognition in beta-crystallin aggregates. With the aid of the present data, the complete evolutionary tree of the bovine beta-crystallin family has been constructed, which confirms the early separation of the genes encoding the three acidic and the three basic beta-crystallins.

Crystallin gene expression during rat lens development

The analysis of the developmental pattern of the alpha A-, alpha B-, beta B1-, beta B2-, beta B3-, beta A3/A1-, and beta s-crystallin genes during fetal and postnatal development of the rat shows that the differential regulation of crystallin synthesis relies on differential gene shutdown rather than differential gene activation; that is, all crystallin genes are active during early development but turn off at different stages. The only two exceptions to this rule are the alpha B- and beta s-crystallin genes. The alpha B-crystallin gene transcript becomes first detectable at 18 days of fetal development, while the beta s-crystallin gene appears to be active only in the postnatal period. We also determined the absolute numbers of the alpha A-, alpha B-, beta B1-, beta B2-, beta B3-, beta A3/A1-, beta s-, and gamma-crystallin gene transcripts present in the lens at various times after birth. Comparison of these RNA data with the published protein data shows that the alpha B- and beta B2-crystallin RNAs are relatively overrepresented, suggesting the possibility that these two RNA species are not used as efficiently as other crystallin mRNAs. Examination of the known (hamster) alpha B-crystallin sequence and elucidation of the (rat) beta B2-crystallin sequence yielded no evidence for aberrant codon usage. These two RNAs have one sequence motif in common: they are the only crystallin mRNAs in which the translation initiation codon is preceded by CCACC.

Different evolution rates within the lens-specific beta-crystallin gene family

We have determined the sequence of a rat beta A3/A1-crystallin complementary DNA (cDNA) clone and the (partial) sequence of the human beta B3-crystallin gene. Calculation of the ratio of silent to nonsynonymous substitution between orthologous beta A3/A1-, beta B3-, and other beta- and gamma-crystallin sequences revealed that the region encoding the two globular domains of the beta A3/A1-crystallin sequence is the best conserved during evolution, much better than the corresponding region of the beta B1-, beta B3-, or the gamma-crystallin sequences, and even better (at least in the rodent/frog comparison) than the well-conserved alpha A-crystallin sequence. Remarkably, the rate of change of the beta A3/A1-crystallin coding sequence does not differ in the rodent and primate lineages, in contrast with previous findings concerning the evolution rates of the alpha A- or gamma-crystallin sequences in these two lineages. Comparison of the regions that encode the four motifs of the beta-crystallin between orthologous mammalian sequences showed that the extent of nonsynonymous substitution in each of these four homologous motif regions is the same. However, when the orthologous beta-crystallin genes of more distantly related species (mammals vs chicken or frog) are compared, the extent of non-synonymous substitution is higher in the regions encoding the external motifs I and III than in the regions encoding the internal motifs II and IV. This phenomenon is also observed when paralogous members of the beta/gamma-crystallin supergene family are compared.