Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences

Another family of repetitive sequences, designated the EcoRI family, was found in the DNA of the chicken W chromosome by hybridization with the W chromosome-specific XhoI family probe under conditions of low stringency. A 1.2 kb EcoRI fragment, the major repeating unit of the family, was cloned and sequenced. The 1.2 kb unit showed an overall sequence similarity of about 68% to the 0.7 kb XhoI family repeating unit and it consisted of tandem repeats of average length 21 bp, most of which contained (A)_3–5 and (T)_3–4 clusters separated by 6–8 G+C-rich sequences. These features and its behavior as a strongly bent molecule in solution were very similar to those found for other W chromosome-specific repetitive sequences in the order Galliformes: XhoI family of chicken, PstI family of turkey and TaqI family of pheasant. The cloned 1.2 kb unit contained 78 CpG dinucleotide sequences and those that were in HapII, HhaI and BstUI sites were shown to be extensively methylated in the genomic DNA. Repetition frequencies of the 1.2 kb unit among the female population of chicken fell into high- and low-level classes, which accounted for about 30% and 10%, respectively, of the DNa in the W chromosome. Thus, 70% to 90% of the DNA in the chicken W chromosome was shown to be occupied by bent-repetitive sequences. The EcoRI and XhoI family sequences were not intermingled over the short range but each family formed a unique domain ranging from one to several million base pairs.by H.C. Macgregor     

Presence of female-specific bent-repetitive DNA sequences in the genomes of turkey and pheasant and their interactions with W-protein of chicken

Two female-specific repetitive DNA units, the 0.4 kb PstI and 0.5 kb TaqI sequences, were detected in the genomic DNA of turkey and pheasant, respectively, by Southern blot hybridization under non-stringent conditions with the W chromosome-specific 0.7 kb XhoI repetitive unit of chicken as a probe. Cloning and sequencing of these two repetitive units revealed that they shared features with the XhoI family repetitive unit of chicken although the overall similarities of the nucleotide sequences were less than 60%. In common with the chicken XhoI family they consisted of tandem repeats of about 21 bp, the majority of which contained (A)_3–5 and (T)_3–5 clusters separated by six or seven relatively G+C-rich sequences, and they behaved as bent DNA molecules on polyacrylamide gel electrophoresis at room temperature. W-protein, purified from chicken liver nuclei and shown to bind with high affinity to the XhoI family repetitive unit, also bound with the cloned repetitive units from turkey and pheasant. DNase I footprint analysis suggested that the mode of interaction of W-protein with these units was similar to that with the 0.7 kb XhoI sequence. On the other hand, W-protein did not bind to the female-specific 0.4 kb BamHI repetitive unit from the Bobwhite quail. The 0.4 kb BamHI sequence contained some A and T clusters but these clusters did not appear in phase with the pitch of DNA helix and the repetitive unit did not show DNA bending.     

The intragenomic polymorphism of a partially inverted repeat (PIR) in Gallus gallus domesticus, potential role of inverted repeats in satellite DNAs evolution

We report here the molecular characterization of the basic repeating unit of a novel repetitive family, partially inverted repeat (PIR), previously identified from chicken genome. This repetitive DNA family shares a close evolutionary relationship with XhoI/EcoRI repeats and chicken nuclear-membrane-associated (CNM) repeat. Sequence analyses reveal the 1430 bp basic repeating unit can be divided into two regions: the central region ( approximately 1000 bp) and the flanking region ( approximately 430 bp). Within the central region, a pair of repeats (86 bp) flanks the central core ( approximately 828 bp) in inversed orientation. Due to the tandem array feature shared by the repeating units, the inverted repeats fall between the central core and flanking region. Southern blot analyses further reveal the intragenomic polymorphism of PIR, and the molecular size of repeating units ranges from 1.1 kb to 1.6 kb. The identified monomer variants may result from multiple crossing-over events, implying the potential roles of inverted repeats in satellite DNAs variation.     

Nucleotide sequences and unusual electrophoretic behavior of the W chromosome-specific repeating DNA units of the domestic fowl,Gallus gallus domesticus

Nucleotide sequences of three independently cloned repeating units of the W chromosome-specific repettive DNA sequences (XhoI family) of the chicken were determined. All three units are 717 bp long with XhoI sites at both ends. There are only 21 sites out of 717 bases where a single base change occurs in one of the three clones. Each of these repeating units consists of 34 tandem repeats of about 21 bp. Sequences of some members of these internal repeats are not well conserved, but the majority of the repeats are characterized by the presence of (A)_3–5 and (T)_3–5 clusters separated by 6–7 relatively G+C-rich base pairs. One striking feature of the cloned 717 bp repeating units is that they migrate unusually slowly on electrophoresis in polyacrylamide gels. The same feature is also shown by a genomic population of the 0.7 kb repeating units recovered from XhoI digests of the genomic DNA of the female chicken. This anomalous behavior is attributed to the occurrence of DNA curvatures because of the above sequence characteristics and partial recovery of the electrophoretic mobility in the presence of distamycin A. Another feature of the 717 bp repeating unit is the presence of 438 and 159 nucleotide-long open reading frames (ORFs) at each end of the unit. A possible function of the XhoI family sequences in the heterochromatization of the W chromosome and the significance of the ORFs are discussed.     

Microdissection of and microcloning from the short arm of human chromosome 2.

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.     

Physical mapping of unique nucleotide sequences on identified rice chromosomes

A physical mapping method for unique nucleotide sequences on specific chromosomal regions was developed combining objective chromosome identification and highly sensitive fluorescence in situ hybridisation (FISH). Four unique nucleotide sequences cloned from rice genomic DNAs, varying in size from 1.3 to 400 kb, were mapped on a rice chromosome map. A yeast artificial chromosome (YAC) clone with a 399 kb insert of rice genomic DNA was localised at the distal end of the long arm of rice chromosome (1q2.1) and a bacterial artificial chromosome (BAC) clone (180 kb) containing the rice leaf blast-resistant gene (Pi-b) was shown to occur at the distal end of the long arm of chromosome 2 (2q2.1). A cosmid (35 kb) with the resistance gene (Xa-21) against bacterial leaf blight was mapped on the interstitial region of the long arm on chromosome 11 (11q1.3). Furthermore a single RFLP marker, 1.29 kb in size, was mapped successfully to the distal region of the long arm of rice chromosome 4 (4q2.1). For precise localisation of the nucleotide sequences within the chromosome region, image analyses were effective. The BAC clone was localised to the specific region, 2q2.1:96.16, by image analysis. The result was compared with the known location of the BAC clone on the genetic map and the consistency was confirmed. The effectiveness and reliability in physically mapping nucleotide sequences on small plant chromosomes achieved by the FISH method using a variety of probes was unequivocally demonstrated.     

Structure and organization of the highly repeated and interspersed 1.3 kb EcoRI-Bg1II sequence family in mice.

EcoRI digestion of total mouse DNA yields a prominant 1.3 kb fragment amounting to between 1 and 2% of the mouse genome. The majority of the 1.3 kb EcoRI fragments have a single Bg1II site 800 bp from one end. This EcoRI-Bg1II sequence family shows HindIII and HaeIII sequence heterogeneity. We have cloned representatives of the EcoRI-Bg1II gene family in Charon 16A and studied their structure and organization within the genome. The cloned 1.3 kb fragments show the expected restriction enzyme patterns as well as additional heterogeneity. Representatives of the EcoRI-Bg1II sequence family were found to be interspersed throughout the mouse genome as judged by CsCl density gradient centrifugation experiments. Family members were also found to be organized in higher order repeating units. Homologous sequences were also found in other rodent species including rat and Chinese hamster. Cross hybridization between a cloned 1.3 kb mouse fragment and a cloned CHO repeated sequence is of special interest since the latter has been shown to contain sequences homologous to the Human A1uI family by nucleotide sequencing.     

Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome.

Fragile X syndrome is the most frequent form of inherited mental retardation and is associated with a fragile site at Xq27.3. We identified human YAC clones that span fragile X site-induced translocation breakpoints coincident with the fragile X site. A gene (FMR-1) was identified within a four cosmid contig of YAC DNA that expresses a 4.8 kb message in human brain. Within a 7.4 kb EcoRI genomic fragment, containing FMR-1 exonic sequences distal to a CpG island previously shown to be hypermethylated in fragile X patients, is a fragile X site-induced breakpoint cluster region that exhibits length variation in fragile X chromosomes. This fragment contains a lengthy CGG repeat that is 250 bp distal of the CpG island and maps within a FMR-1 exon. Localization of the brain-expressed FMR-1 gene to this EcoRI fragment suggests the involvement of this gene in the phenotypic expression of the fragile X syndrome.     

Construction of new cloning vehicles with genes of the tryptophan operon of Escherichia coli as genetic markers

In vitro recombination techniques were used to construct a series of new cloning vehicles with genes of the tryptophan (trp) operon of Escherichia coli as selective marker. To construct these plasmids we have made a restriction cleavage map of the trp operon for the enzymes AosI, AvaI, BglI, BglII, HindIII, HpaI, PvuII, SalI, SstI and XhoI. The constructed plasmids pHP39, pEP392, pEP3921 and pEP3923 are derived from the amplifiable plasmid pBR345 and carry two or more genes of the trp operon, which are controlled by the trp regulatory elements. Plasmid pEP3921 (7.0 kb) carries intact trpE and trpA genes and contains single BglII and SstI sites in trpE, a single HindIII site located between trpE and trpA, and single EcoRI, SalI and XhoI sites located outside the trp genes. Plasmid pEP121 (12 kb) is similar to pEP3921, but has an extra selective marker conferring bacterial resistance to ampicillin. Plasmid pEP3923 (7.4 kb) comprises intact trpB and trpA genes and single BglII, HindIII, EcoRI, SalI and XhoI sites. Plasmids pHP39 (9.8 kb) and pEP392 (9.8 kb) carry an intact trp operon and have two and one EcoRI site, respectively. Plasmid pHP3 (18 kb) carries an intact trp operon and markers for tetracycline and ampicillin resistance.     

斜纹夜蛾核型多角体病毒p74基因的克隆和序列分析

用ＡｃＮＰＶｐ７４基因３’端的１．４ｋｂ片段,通过Ｓｏｕｔｈｅｒｎｂｌｏｔｔｉｎｇ将ＳｐｌｔＮＰＶ的ｐ７４基因定位于ＸｈｏＩ（４．９ｋｂ）、ＥｃｏＲＩ（４．４ｋｂ）、ＢａｍＨＩ（３．０ｋｂ）片段上。进一步用ＥｘｏⅢ和构建亚克隆测序法,对长２５４５ｂｐ的ｐ７４基因进行,其中１９７４ｂｐ的编码编码６５８个氨基酸,蛋白分子量约７５．８７ｋＤ,其编码蛋白与ＡｃＭＮＰＶ和ＣｆＭＮＰＶｐ７４蛋白的氨基酸序列同     

Independent chromosomal localization of two different size 5S rDNA of Allium victorialis var. platyphyllum by sequential fluorescence in situ hybridization in accordance with sequence polymorphism

5S rRNA gene repeat units in a species are usually organized as either one relatively close size with numbers of intraspecific variations in NTS region or two different sizes with completely different sequence in NTS. Allium victorialis var. platyphyllum revealed two different size products of approximately 0.39 kb and 0.51 kb with highly conserved coding region of 120 bp. However, an extra sequences of approximately 120 bp between at 324 and 443 bp in long NTS region revealed, besides the remaining sequences of two NTS regions of short and long size were highly conserved giving the identity of 94.9%. To identify whether two different size 5S rDNA are occupied by a mixed state as random repeat or an independent group by each size in a particular locus, two rounds of FISH was sequentially performed using two probes of independent different size 5S rDNA and additional probe of only extra sequences of 120 bp in long NTS. Due to the highly conserved coding regions of both 5S rDNA, two different size 5S rDNA were detected in 3 loci in short arm of chromosome 6, however, extra sequences of long NTS was shown only in one locus within detected 5S rDNA from all examined chromosomes and interphase cells. This independent localization of two different size 5S rDNA suggests that 5S rDNA may be organized as a tandem repeat with random positions in a molecular level, but of cytogenetic view in chromosomes and interphase cells, they are organized as an independent group in a significant loci consisting of own size by the patterns of nucleotide variations.     

Stable length polymorphism of up to 260 kb at the tip of the short arm of human chromosome 16

We have completed a long-range restriction map of the terminal region of the short arm of human chromosome 16 (16p13.3) by physically linking a distal genetic locus (alpha-globin) with two recently isolated probes to telomere-associated repeats (TelBam3.4 and TelBam-11). Comparison of 47 chromosomes has revealed major polymorphic length variation in this region: we have identified three alleles in which the alpha-globin genes lie 170 kb, 350 kb, or 430 kb from the telemere. The two most common alleles contain different terminal segments, starting 145 kb distal to the alpha-globin genes. Beyond this boundary these alleles are nonhomologous, yet each contains sequences related to other (different) chromosome termini. This chromosome size polymorphism has probably arisen by occasional exchanges between the subtelomeric regions of nonhomologous chromosomes; analogous length variation is likely to be present at other human telomeres.     

Analysis of intergenic spacer regions in the nuclear rDNA of Pharbitis nil.

The nucleotide sequence of a 4.2-kb EcoRI fragment from the intergenic region between the genes for 25S and 18S ribosomal RNA of Pharbitis nil Choisy was determined. The region contained a unique repetitive family of DNA sequences, called the RsaI family, composed of 32-bp units. The 32-bp unit was tandemly repeated in the intergenic region, and four subfamilies of repeating units were clustered as discrete blocks. The RsaI family of repeats was shown to be specific to the genus Pharbitis by Southern blot hybridization.     

Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome.

There are several copies of related sequences on the distal short arm of the human X chromosome and the proximal long arm of the Y chromosome which were originally detected by cross hybridization with a genomic DNA clone, CRI-S232. Recombination between two S232-like sequences flanking the steroid sulfatase locus has been shown to cause frequent deletions in the X chromosome short arm, resulting in steroid sulfatase deficiency. We now report the characterization of several S232-like sequences. Restriction mapping and sequence analysis show that each S232 unit contains 5 kb of unique sequence in addition to two elements, RU1 and RU2, composed of a variable number of tandem repeats. RU1 consists of 30 bp repeating units and its length shows minimal variation between individuals. The RU2 elements in the hypervariable S232 loci on the X chromosome consist of repeating sequences which are highly asymmetric, with about 90% purines and no C's on one strand. The X-derived RU2 elements range from 0.6 kb to over 23 kb among different individuals, accounting entirely for the observed polymorphism at the S232 loci. Although the repeating units of the RU2 elements in the nonpolymorphic S232 loci on the Y chromosome share high sequence homology with those on the X chromosome, they exhibit much higher intrarepeat sequence variation. S232 homologous sequences are found in great apes, old world and new world monkeys. In chimpanzees and gorillas the S232-like sequences are polymorphic in length.     

Human ribosomal RNA gene spacer sequences are found interspersed elsewhere in the genome

A cloned EcoRI fragment containing human 18 S rRNA gene sequences was used to screen a gene library to obtain a set of 8 overlapping cloned DNA segments extending into the non-transcribed spacer region of the human ribosomal RNA gene cluster. 19.4 kb of the approx. 43-kb rDNA repeat was obtained in cloned form and mapped with restriction endonucleases. None of the clones obtained extended into 28 S rRNA sequences. A 7-kb region of non-transcribed spacer DNA shared in common between five independent clones was subjected to comparative restriction digests. It was estimated that sequences among the five different spacer isolated varied by not more than 1.0%, if all the observed differences are assumed due to point mutation. HaeII-restriction fragments from within this same 7-kb region contain sequences carried not only within the tandem repeats of the gene cluster but interspersed elsewhere in the genome. Some of these sequences correspond to the Alu family of highly repeated interspersed sequences.     

A method of identifying and isolating a unique member of a multigene family: application to a trypanosome surface antigen gene.

A chimeric oligonucleotide was constructed using DNA sequences from two distal regions of a cDNA which encodes a major surface antigen (TSA-1) of Trypanosoma cruzi. Conditions were found that allowed the chimeric oligonucleotide to hybridize only to a 5.4 kb EcoRI fragment in a Southern blot of total genomic DNA. The 5.4 kb EcoRI genomic DNA fragment has previously been shown to be located at a telomeric site, thus the studies described here directly demonstrate that the TSA-1 gene is telomeric in location. It is also shown that the chimeric oligonucleotide can be used to selectively identify recombinant lambda phage which harbor the TSA-1 gene using standard library screening procedures. Since these studies demonstrate that a chimeric oligonucleotide can be used to identify in both Southern blots and library screens a single member among the more than sixty members of the TSA-1 gene family, it seems likely that chimeric oligonucleotides may be of general use in studies involving repetitive DNA sequence families.     

The structure of the phi 80d3 ilv+ Su+7 transducing phage and the origin of its Su+7 tRNA-gene containing fragment.

Summary The Bam HI, XhoI, and EcoRI sites of the transducing phage 80d₃Su⁺ 7ilv⁺ are located. The 1.2×10⁶ MD EcoRI fragment which, when cloned, contains tRNA^Asp and expresses the mutant tRNA^Try gene, Su⁺7, and which also relaxes control of stable RNA synthesis is found immediately adjacent to the rrnC region. Its tRNA genes, tRNA^Asp and tRNA^Try, are transcribed in the same direction as the ribosomal RNA genes, though no mature rRNA sequences are on the fragment. This fragment also exists as such in another F-prime factor derived from the same Hfr host, and therefore presumably also in the Hfr chromosome itself. It is composed of about half ordinary chromosomal and half F DNA sequences, the latter from the - region of F.The advantages of a novel mapping method used are discussed.Abbreviations MD megadaltons. Expressions of the form XhoI: 5.5 refers to a DNA fragment produced by the indicated enzyme, and characterized by the indicated molecular weight in MD     

A small mobilizable IncP group plasmid vector packageable into bacteriophage lambda capsids in vitro

A mobilizable cosmid derivative of an IncP group plasmid was constructed by cloning the oriT region of RK2, a wide host-range plasmid, and the minimal DNA sequence of bacteriophage lambda required for efficient packaging in vitro. This cosmid is 13 kb in size and has unique restriction sites for EcoRI, XhoI, HindIII, and SalI. The XhoI and HindIII sites are within the kanamycin-resistance gene and the SalI site is in the tetracycline-resistance gene. This plasmid was mobilizable from an Escherichia coli donor to a number of diverse gram-negative bacteria at a frequency of 0.8 to 10 per 100 donors. This vector is one of the smallest of all wide host-range cosmids described in the literature. As part of this study, another mobilizable IncP group plasmid vector has also been constructed which, in addition to the sites listed above, has a unique BglII site, but which lacks the packager sequence.     

Organization of delta-crystallin genes in the chicken.

Double-stranded DNA was synthesized from delta-crystallin mRNA prepared from lens fibers of 15-day-old chick embryos and cloned at the Pst I site of the plasmid pBR322. Using the cloned cDNA and single-stranded cDNA as hybridization probes, a number of genomic DNA fragments containing delta-crystallin gene sequences have been cloned from the partial and complete EcoRI digests of chick brain DNA. One of the clones from the partial digests contains a DNA fragment that consists of four EcoRI fragments of 7.6 kb, 4.0 kb, 2.6 kb, and 0.8 kb. The gene sequences reside in the (5')7.6 kb - 0.8 kb - 4.0 kb (3') fragments. Electron microscopy has provided evidence that the cloned DNA fragment includes the entire gene sequences complementary to delta-crystallin mRNA except for the 3' terminal poly(A) tail, and that the delta-crystallin gene is interrupted by at least 13 intervening sequences. Another clone contains a genomic fragment that consists of two EcoRI fragments of 3.0 kb and 11 kb. The DNA fragment in the latter clone represents a different delta-crystallin gene, as judged by restriction endonuclease mapping and by electron microscopy.