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W T Garrard

Publications and source records attributed to W T Garrard.

At least 37 records · Page 2Linked to original sources
PubMed1992

Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure.

Previous studies have located transcriptional enhancer elements within both the intron and 3'-region of the mouse kappa immunoglobulin gene. Here we address the role of these two enhancers in specifying gene activity and specific chromatin structures. MOPC41 kappa gene constructs, either intact or containing deletions of one or both enhancers, were introduced into S194 mouse plasmacytoma cells for transient and stable expression studies. Transient expression assays revealed that the basal level expression exhibited by enhancerless constructs was activated 100-200-fold by the two enhancers together in a synergistic fashion. A similar trend was observed when both enhancers were present in stably integrated constructs, although the synergy was less pronounced. Analysis of DNase I hypersensitive sites in the chromatin revealed that stably integrated constructs established hypersensitive sites about the enhancer sequences. These sites demonstrated the same nuclease susceptibility as those associated with the endogenous gene(s), and their establishment was independent of the presence of the other enhancer. Thus, although both enhancers are required for maximal gene expression, the elements act independently in determining specific chromatin structures.

Animals↗
PubMed1992

Uncoupling gene activity from chromatin structure: promoter mutations can inactivate transcription of the yeast HSP82 gene without eliminating nucleosome-free regions.

DNase I-hypersensitive sites represent "nucleosome-free" regions in chromatin where the underlying DNA sequence is highly accessible to trans-acting proteins. Here we demonstrate that it is possible to uncouple gene activity from hypersensitive site formation. Point or substitution mutations were introduced into the promoter of the yeast chromosomal HSP82 gene, encoding the 83-kDa heat shock protein (HSP), via site-directed integration. Mutating either the TATA box or heat shock element 1 (HSE1) significantly reduced basal and heat-induced transcription while mutating both essentially inactivated expression. Dormant transcription units exhibited arrays of sequence-positioned nucleosomes; nevertheless, the inactivated genes still retained a hypersensitive site within their mutated promoters. In addition, all yeast strains maintained a heat-inducible hypersensitive site at -600 base pairs (bp), while several mutant strains converted a constitutive hypersensitive site at -300 bp into a heat-inducible one. Thus, mutations in cis-acting elements within a promoter can inactivate transcription without eliminating nucleosome-free regions.

Alleles↗
PubMed1991

Positive DNA supercoiling generates a chromatin conformation characteristic of highly active genes.

During transcription, positive DNA supercoils generated ahead of RNA polymerase could theoretically uncoil the negative DNA supercoils associated with nucleosomes and thereby decondense the chromatin fiber in preparation for RNA polymerase passage. Here we examine the effect of positive DNA supercoiling on the structure of yeast 2-microns minichromosomes. We utilized a conditional topoisomerase mutant expressing Escherichia coli topoisomerase I to convert the DNA supercoiling state from negative to positive in vivo. Minichromosomes containing positively supercoiled DNA exhibited a striking increase in DNase I sensitivity. They also displayed additional micrococcal nuclease cleavage sites but yielded nearly typical nucleosomal ladders after extensive digestion. Upon in vitro relaxation with eukaryotic topoisomerase I, the minichromosomes remained DNase I sensitive but were converted to negative DNA supercoiling with a slightly increased linking number compared to typical minichromosomes, thus indicating the presence of bound histones. Therefore, positive DNA supercoiling provides a mechanism for generating, but is not required for maintaining, a conformation in chromatin characteristic of highly transcribed genes.

Base Sequence↗
PubMed1991

Transcription-induced nucleosome 'splitting': an underlying structure for DNase I sensitive chromatin.

Utilizing yeast strains containing promoter mutations, we demonstrate that transcription of the HSP82 gene causes nucleosomes toward the 3'-end to become DNase I sensitive and 'split' into structures that exhibit a 'half-nucleosomal' cleavage periodicity. Splitting occurs even when only a few RNA polymerase II molecules are engaged in basal level transcription or during the first round of induced transcription. The split nucleosomal structure survives nuclear isolation suggesting that it may be stabilized by post-translational modifications or non-histone proteins, and may require DNA replication for reversal to a whole nucleosomal structure. Split nucleosomes represent a structure for DNase I sensitive chromatin and are probably of common occurrence but difficult to detect experimentally. We suggest that transient positive supercoils downstream of traversing RNA polymerase lead to nucleosome splitting.

Chromatin↗
PubMed1990

Identification within the simian virus 40 genome of a chromosomal loop attachment site that contains topoisomerase II cleavage sites.

We demonstrate that the simian virus 40 genome contains a single MAR (matrix association region) that maps within a large T-antigen coding region (nucleotides 4071 to 4377). This region contains topoisomerase II cleavage sites, exhibits sequence similarity with cellular MARs, and recognizes the same evolutionarily conserved, abundant nuclear binding sites seen by cellular MARs.

Animals↗
PubMed1989

Immunoglobulin kappa gene expression after stable integration. I. Role of the intronic MAR and enhancer in plasmacytoma cells.

Rearranged MOPC41 immunoglobulin kappa gene constructs have been stably introduced into cultured S194 mouse plasmacytoma cells to investigate the effects of deleting the intronic enhancer and/or matrix association region (MAR) on gene expression. Intact single-copy kappa genes containing 1.5 kilobase pairs of upstream and 8.5 kilobase pairs of downstream flanking sequences exhibited sensitivity to chromosome position effects and were expressed at a mean level of 27% relative to the endogenous kappa gene expression or only 6% with respect to the MOPC41 kappa mRNA levels in the tumor. Deletion of the intronic MAR led to a 4-fold decrease in expression, while deletion of both the MAR and enhancer led to an 11-fold decline. These effects were dampened by preselecting for integration into a transcriptionally poised chromatin location as demonstrated by linkage to a selectable marker which lacked both a MAR and an enhancer. Significantly, we found that sequences downstream of the poly(A) addition site compensated 150-fold for deletion of the intronic enhancer.

Animals↗
PubMed1989

Immunoglobulin kappa gene expression after stable integration. II. Role of the intronic MAR and enhancer in transgenic mice.

MOPC41 immunoglobulin kappa gene constructs have been stably introduced into the mouse germ line to investigate the effects of deleting the conserved intronic sequences on gene expression. Intact kappa genes containing 1.5 kilobase pairs of upstream and 8.5 kilobase pairs of downstream flanking sequences were highly expressed tissue-specifically, raising the total level of kappa mRNA in spleens severalfold in most transgenic animals. This high expression was often accompanied by marked suppression of endogenous kappa gene activity. Transgenes containing a deletion of the matrix association region (MAR) or both the MAR and enhancer were expressed tissue-specifically at mean levels only 2- and 3-fold lower, respectively, than that of intact transgenes. Therefore, while the intronic enhancer and MAR appear to play a quantitative role in gene expression, these sequences are not absolutely essential for transcriptional activation of rearranged kappa genes in a normal developmental environment.

Animals↗
PubMed1989

Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II.

A family of A + T-rich sequences termed MARs ("matrix association regions") mediate chromosomal loop attachment. Here we demonstrate that several MARs both specifically bind and contain multiple sites of cleavage by topoisomerase II, a major protein of the mitotic chromosomal scaffold. Interestingly, "hotspots" of enzyme cutting occur within the MAR of the mouse immunoglobulin kappa-chain gene at the breakpoint of a previously described chromosomal translocation. Since topoisomerase II can mediate illegitimate recombination in prokaryotes, we explored further the possibility that MARs might be targets for this process in eukaryotes. We found that a MAR had been deleted from one of the two rabbit immunoglobulin kappa-chain genes and that MARs reside next to a long interspersed repetitive element within the recombination junction of a human ring chromosome 21. These results, taken together with other accounts of nonhomologous recombination, lead to the proposal that a dysfunction of MARs is illegitimate recombination.

Animals↗
PubMed1989

Basal-level expression of the yeast HSP82 gene requires a heat shock regulatory element.

Previous studies have shown that heat shock factor is constitutively bound to heat shock elements in Saccharomyces cerevisiae. We demonstrate that mutation of the heat shock element closest to the TATA box of the yeast HSP82 promoter abolishes basal-level transcription without markedly affecting inducibility. The mutated heat shock element no longer bound putative heat shock factor, either in vitro or in vivo, but still resided within a nuclease-hypersensitive site in the chromatin. Thus, constitutive binding of heat shock factor to heat shock elements in S. cerevisiae appears to functionally direct basal-level transcription.

Base Sequence↗
PubMed1989

Protein:DNA interactions at chromosomal loop attachment sites.

We have recently identified an evolutionarily conserved class of sequences that organize chromosomal loops in the interphase nucleus, which we have termed "matrix association regions" (MARs). MARs are about 200 bp long, AT-rich, contain topoisomerase II consensus sequences and other AT-rich sequence motifs, often reside near cis-acting regulatory sequences, and their binding sites are abundant (greater than 10,000 per mammalian nucleus). Here we demonstrate that the interactions between the mouse kappa immunoglobulin gene MAR and topoisomerase II or the "nuclear matrix" occur between multiple and sometimes overlapping binding sites. Interestingly, the sites most susceptible to topoisomerase II cleavage are localized near the breakpoints of a previously described illegitimate recombination event. The presence of multiple binding sites within single MARs may allow DNA and RNA polymerase passage without disrupting primary loop organization.

Animals↗
PubMed1988

Vacuum blotting: a simple method for transferring DNA from sequencing gels to nylon membranes.

We describe a vacuum blotting procedure for transferring DNA fragments from conventional polyacrylamide sequencing gels to nylon membranes. The method employs a combination of vacuum-assisted diffusion (effected by a standard gel drier) and an osmotic gradient (effected by over- and underlying filters presoaked in ammonium acetate). Fragments up to 310 nucleotides in length transfer at 40-60% efficiency within 90 min. When combined with indirect end-labelling, the method allows genomic sequencing of a single-copy gene of Saccharomyces cerevisiae employing as little as 5 micrograms DNA per lane.

Autoradiography↗
PubMed1987

The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements.

We have located presumptive chromosomal loop anchorage elements within the mouse heavy chain immunoglobulin locus. Analysis of 31 kilobases spanning diversity, joining, enhancer, switch, and the mu and delta constant regions reveals that only a single 1-kilobase segment exhibits specific binding to nuclear matrices. It is of particular significance that the transcriptional enhancer element resides within this matrix association region (MAR). Fine structure mapping indicates that binding is mediated by A+T-rich approximately 350-base pair segments that reside on either side of the enhancer. The MAR sequences residing 5' of the enhancer contain topoisomerase II consensus sequences like the MAR located upstream of the kappa light chain gene enhancer. The heavy chain gene MARs, however, exhibit a lower affinity for matrix association compared to the kappa gene MAR. Significantly, the juxtaposition of enhancer elements with MARs appears to be evolutionarily conserved within the immunoglobulin genes, suggesting that MARs may act as positive and/or negative regulators of enhancer function.

Animals↗