Molecular and cytogenetic analyses of stably and unstably expressed transgene loci in tobacco

To study the influence of genomic context on transgene expression, we have determined the T-DNA structure, flanking DNA sequences, and chromosomal location of four independent transgene loci in tobacco. Two of these loci were stably expressed in the homozygous condition over many generations, whereas the other two loci became unstable after several generations of homozygosity. The stably expressed loci comprised relatively simple T-DNA arrangements that were flanked on at least one side by plant DNA containing AT-rich regions that bind to nuclear matrices in vitro. Of the unstably expressed loci, one consisted of multiple incomplete T-DNA copies, and the second contained a single intact T-DNA; in both cases, however, binary vector sequences were directly contiguous to a right T-DNA border. Fluorescence in situ hybridization demonstrated that the two stably expressed inserts were present in the vicinity of telomeres. The two unstably expressed inserts occupied intercalary and paracentromeric locations, respectively. Results on the stability of transgene expression in F1 progeny obtained by intercrossing the four lines and the sensitivity of the four transgene loci to inactivation in the presence of an unlinked "trans-silencing" locus are also presented. The findings are discussed in the context of repetitive DNA sequences and the allotetraploid nature of the tobacco genome.     

Variegated expression of a globin transgene correlates with chromatin accessibility but not methylation status

There are now many mammalian examples in which single cell assays of transgene activity have revealed variegated patterns of expression. We have previously reported that transgenes in which globin regulatory elements drive the lacZ reporter gene exhibit variegated expression patterns in mouse erythrocytes, with transgene activity detectable in only a sub-population of circulating erythroid cells. In order to elucidate the molecular mechanism responsible for variegated expression in this system, we have compared the chromatin structure and methylation status of the transgene locus in expressing and non-expressing populations of erythrocytes. We find that there is a difference in the chromatin conformation of the transgene locus between the two states. Relative to active transgenes, transgene loci which have been silenced exhibit a reduced sensitivity to general digestion by DNase I, as well as a failure to establish a transgene-specific DNase I hypersensitive site, suggesting that silenced transgenes are situated within less accessible chromatin structures. Surprisingly, the restrictive chromatin structure observed at silenced transgene loci did not correlate with increased methylation, with transgenes from both active and inactive loci appearing largely unmethylated following analysis with methylation-sensitive restriction enzymes and by sequencing PCR products derived from bisulphite-converted genomic DNA.     

Transgenic DNA integrated into the oat genome is frequently interspersed by host DNA

Integration of transgenic DNA into the plant genome was investigated in 13 transgenic oat (Avena sativa L.) lines produced using microprojectile bombardment with one or two cotransformed plasmids. In all transformation events, the transgenic DNA integrated into the plant genome consisted of intact transgene copies that were accompanied by multiple, rearranged, and/or truncated transgene fragments. All fragments of transgenic DNA cosegregated, indicating that they were integrated at single gene loci. Analysis of the structure of the transgenic loci indicated that the transgenic DNA was interspersed by the host genomic DNA. The number of insertions of transgenic DNA within the transgene loci varied from 2 to 12 among the 13 lines. Restriction endonucleases that do not cleave the introduced plasmids produced restriction fragments ranging from 3.6 to about 60 kb in length hybridizing to a probe comprising the introduced plasmids. Although the size of the interspersing host DNA within the transgene locus is unknown, the sizes of the transgene-hybridizing restriction fragments indicated that the entire transgene locus must be at least from 35-280 kb. The observation that all transgenic lines analyzed exhibited genomic interspersion of multiple clustered transgenes suggests a predominating integration mechanism. We propose that transgene integration at multiple clustered DNA replication forks could account for the observed interspersion of transgenic DNA with host genomic DNA within transgenic loci.     

n-3 fatty acids and lipoproteins: comparison of results from human and animal studies

Marker allele-disease association and linkage between a disease locus and a marker locus are two different phenomena. Linkage without evidence of association and association without evidence of linkage are possible observations. Linkage analysis uses marker loci and the phenomenon of recombination to look for disease-related loci which are presumably major contributors to disease expression ("necessary" loci). However, the phenomenon of association is more complex. One explanation for the existence of an association is that there is a "necessary" locus in linkage disequilibrium with a marker locus. Another explanation is that the marker locus itself (or a closely linked locus in linkage disequilibrium with the marker) is a "susceptibility" locus, which increases the probability of contracting the disease but is not necessary for disease expression. Although there are other possible explanations for the existence of an association, these two can lead to different results when family data from a disease showing association are analyzed for linkage between the associated marker and the disease. If the linkage disequilibrium hypothesis is correct, there will be evidence for linkage. If the susceptibility locus hypothesis is correct, there may be strong evidence against linkage. In this work, we explore a method that could indicate whether an association is due to a susceptibility locus or a necessary locus. We show that, by dividing families based on the presence or absence of the associated marker allele in a randomly chosen affected sib, calculating lod scores, and then calculating a heterogeneity statistic, we could distinguish whether linkage data came from a susceptibility locus or a necessary locus.     

A cis-acting element that directs the activity of the murine methylation modifier locus Ssm1

Silencing of chromosomal domains has been described in diverse systems such as position effect variegation in insects, silencing near yeast telomeres, and mammalian X chromosome inactivation. In mammals, silencing is associated with methylation at CpG dinucleotides, but little is known about how methylation patterns are established or altered during development. We previously described a strain-specific modifier locus, Ssm1, that controls the methylation of a complex transgene. In this study we address the questions of the nature of Ssm1's targets and whether its effect extends into adjacent sequences. By examining the inheritance of methylation patterns in a series of mice harboring deletion derivatives of the original transgene, we have identified a discrete segment, derived from the gpt gene of Escherichia coli, that is a major determinant for Ssm1-mediated methylation. Methylation analysis of sequences adjacent to a transgenic target indicates that the influence of this modifier extends into the surrounding chromosome in a strain-dependent fashion. Implications for the mechanism of Ssm1 action are discussed.     

Genetic mapping of lung cancer modifier loci specifically affecting tumor initiation and progression

Mouse inbred strains with inherited predisposition and resistance to lung cancer provide a tool for the dissection of the complex genetics of this disease. In the present report, we have crossed the BALB/c with the SWR/J strain and performed whole-genome scanning for loci affecting lung tumor development in their F2 progeny. Both parental strains carry the pulmonary adenoma susceptibility 1 (Pas1) locus, a major locus affecting predisposition to lung cancer in mice. On distal chromosome 18 and on centromere of chromosome 6, we have mapped two pulmonary adenoma resistance loci (Par2 and Par4, respectively), which reduce lung tumor multiplicity strongly, up to 15-fold. Par2 and Par4, however, do not affect lung tumor size, which is instead controlled by an additional locus that we have mapped on the central region of chromosome 4. We designated this locus as "pulmonary adenoma progression 1" (Papg1), because it specifically modifies lung tumor size but not multiplicity. The present results, therefore, provide evidence for the existence of cancer modifier loci acting on specific stages of lung tumorigenesis.     

LCR-dependent gene expression in beta-globin YAC transgenics: detailed structural studies validate functional analysis even in the presence of fragmented YACs

Yeast artificial chromosome (YAC) transgenesis is associated with a high frequency of deletions in the integrated transgenes. To determine the impact of these rearrangements on the ability to derive structure-function relationships using YACs, transgenic mice were generated with 248 or 155 kb beta-globin locus YACs. The transgenics were examined for structural integrity of the YAC using an approach of structural analysis that unambiguously demonstrates intactness of YAC transgene copies. Globin gene expression per copy of each integrated transgene and the profiles of globin gene expression during development were determined. Diverse deletion patterns were observed in one or more integrated YACs in all the 248 and most of the 155 kb transgenic lines we analyzed. However, when the structure of the major regulatory element of the beta-globin locus, the locus control region, was preserved, the genes of the beta-globin locus functioned normally and globin transgenes of both the 248 and 155 kb beta-YACs were expressed in a position-independent, copy number-dependent manner. Furthermore, the globin genes of both beta-YACs displayed normal developmental regulation. We conclude that YACs can be used for analysis of structure-function relationships of large genes or multigene loci in spite of the tendency for rearrangements and deletions of the integrated transgenes. However, detailed structural evidence for integrity and continuity of locus sequences is required for correct interpretation of functional data.     

Influence of CpG methylation and target spacing on V(D)J recombination in a transgenic substrate

We have previously described a line of transgenic mice with multiple head-to-tail copies of an artificial V-J recombination substrate and have shown that the methylation of this transgene is under the control of a dominant strain-specific modifier gene, Ssm-1. When the transgene array is highly methylated, no recombination is detectable, but when it is unmethylated, V-J joining is seen in the spleen, bone marrow, lymph nodes, and Peyer's patches but not in the thymus or nonlymphoid tissues, including brain tissue. Strikingly, in mice with partially methylated transgene arrays, rearrangement preferentially occurs in hypomethylated copies. Therefore, V-J recombination is negatively correlated with methylated DNA sequences. In addition, it appears that recombination occurs randomly between any two recombination signal sequences within the transgene array. This lack of target preference in an unselectable array of identical targets rules out simple mechanisms of one-dimensional tracking of a V(D)J recombinase complex.     

Direct detection and isolation of restriction landmark genomic scanning (RLGS) spot DNA markers tightly linked to a specific trait by using the RLGS spot-bombing method

We have developed a technique for isolating DNA markers tightly linked to a target region that is based on RLGS, named RLGS spot-bombing (RLGS-SB). RLGS-SB allows us to scan the genome of higher organisms quickly and efficiently to identify loci that are linked to either a target region or gene of interest. The method was initially tested by analyzing a C57BL/6-GusS mouse congenic strain. We identified 33 variant markers out of 10,565 total loci in a 4.2-centimorgan (cM) interval surrounding the Gus locus in 4 days of laboratory work. The validity of RLGS-SB to find DNA markers linked to a target locus was also tested on pooled DNA from segregating backcross progeny by analyzing the spot intensity of already mapped RLGS loci. Finally, we used RLGS-SB to identify DNA markers closely linked to the mouse reeler (rl) locus on chromosome 5 by phenotypic pooling. A total of 31 RLGS loci were identified and mapped to the target region after screening 8856 loci. These 31 loci were mapped within 11.7 cM surrounding rl. The average density of RLGS loci located in the rl region was 0.38 cM. Three loci were closely linked to rl showing a recombination frequency of 0/340, which is < 1 cM from rl. Thus, RLGS-SB provides an efficient and rapid method for the detection and isolation of polymorphic DNA markers linked to a trait or gene of interest.     

Evidence that a gene for essential tremor maps to chromosome 2p in four families

In this Journal, we previously reported genetic linkage between loci on chromosome (chr)2p(ETM) and dominantly inherited essential tremor (ET) in a large American kindred of Czech ancestry. Other investigators reported another ET susceptibility locus on chr 3q (FET1) which accounted for over half of the Icelandic families that were studied. We now report evidence for linkage to the ETM locus in three additional, unrelated American families with ET and exclude the FET1 locus in these families. Fine mapping results, using an "affecteds-only" model in all four American families, demonstrate positive combined pairwise lod scores (Z) at the ETM locus with aZ(max) = 5.94 at a recombination fraction (theta) = 0.00 for locus D2S220. Haplotype reconstruction places the ETM gene in a 9.10 cM interval between the D2S224 and D2S405 loci. Multipoint linkage analysis suggests that the ETM gene is in the 2.18 cM interval between loci D2S2150 and D2S220 with a Z(max) = 8.12. These findings may facilitate the search for a gene that causes ET and may further our understanding of other disorders that are associated with tremor [corrected].     

Frequent occurrence of transgene deletion in transgenic plants

The status of the transgene in tobacco plants transformed by Agrobacterium was analyzed with PCR. Twelve percent of the transgenic plants with the nptII gene showed different levels of transgene deletion, which was also found in transgenic watermelon (10-30%) and carrot (40-60%). It appeared that the percentage of transgenic plants carrying deleted transgenes depended on both the transgene and the plant. It is suggested that the transgene should be inserted between a right border and a selection marker to reduce the number of transgenic plants containing deleted transgenes after selection.     

Fine genetic mapping defines the genetic order of Pax9, Tcf3a, and Acrodysplasia (Adp)

We present here the fine genetic mapping of the proximal part of mouse Chromosome (Chr) 12 between D12Mit54 and D12Mit4. This chromosomal region contains three loci, Pax9, Tcf3a, and Acrodysplasia (Adp), which seem to play an important role in pattern formation during mouse embryogenesis. The Adp mutation, which was created by transgene integration, causes skull, paw, and tail deformities. Pax9, which is expressed in the face, paws, and tail, once qualified as a possible candidate for the Adp locus. We analyzed 997 interspecific backcross progeny for recombination between the markers D12Mit54 and D12Mit4; we recovered 117 recombinants, which were further typed for Pax9, Tcf3a, Adp, D12Mit88, D12Nds1, D12Mit36, and D12Mit34. This study represents the first instance in which all the above loci have been included in a single analysis, thereby allowing unambiguous determination of the genetic order and distance between D12Mit54 and D12Mit4. From our results, we conclude that the Adp locus is distinct from either Pax9 or Tcf3a.     

Microsatellites in the sand lizard (Lacerta agilis): description, variation, inheritance, and applicability

We developed microsatellite markers for the sand lizard (Lacerta agilis) to enable investigations of the genetic variability within and among populations with a heterogeneous spatial distribution in Sweden. The populations, which could not be characterized by variation in allozymes or mitochondrial DNA, had a substantial level of variability in microsatellite loci. However, the variability in Swedish populations was limited compared to a large, outbred Hungarian population. In the sand lizard, the number of (GT/CA)n repeats was approximately three times higher than that for (CT/GA)n. The number of repeats and the frequency of microsatellites were within the range reported for other species. Three of nine microsatellite loci showed alleles that could not be amplified, which is in agreement with recent reports describing microsatellite "null alleles" as a common occurrence. We discuss the caution which this calls for when calculating paternity probabilities and when estimating between-population allelic differentiation. A potential problem with different mutation rates for alleles within the same locus is discussed.     

Loci of signal probability effects and of the attentional blink bottleneck.

To investigate the locus of signal probability effects and the influence of stimulus quality on this locus, the authors manipulated probability in Task 2 of a psychological refractory period (PRP) paradigm. The effect was additive with stimulus onset asynchrony (SOA) when the target was not masked but underadditive with decreasing SOA when the target was masked. Even with masking, however, a range of probabilities had effects additive with SOA. The results suggest loci of stimulus probability before the PRP bottleneck as well as at or after the bottleneck. A second issue addressed was the locus of interference in the attentional blink (AB). The AB was larger when the probability of the first of 2 targets was lower. The results lead to the conclusion that one cause of the AB effect is a locus at least as late as the PRP bottleneck. (PsycINFO Database Record (c) 2010 APA, all rights reserved)