Detection of Single-Base Changes Using a Bioluminometric Primer Extension Assay

Nyrén, Pål; Karamohamed, Samer; Ronaghi, Mostafa

doi:10.1006/abio.1996.9913

Cited by 58 publications

(38 citation statements)

References 6 publications

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“…The B73 inbred line contained a 346-bp Tourist element within the Y1 gene, whereas the Mo17 did not, enabling the indel to be typed using agarose gel electrophoresis. SNPs within sbe1 and PCO131338 were typed by using pyrosequencing (19) and direct DNA sequencing, respectively. Because individual plants were pooled for each recombinant inbred line in the tissue collection stage, heterozygosity of a portion of the recombinant inbred lines in this region was expected.…”

Section: Shotgun Sequencing Of Y1-containing Bacterial Artificial Chrmentioning

confidence: 99%

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Palaisa

Morgante

Tingey

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

205

153

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Both yellow and white corn occurs among ancestral open pollinated varieties. More recently, breeders have selected yellow endosperm variants of maize over ancestral white phenotypes for their increased nutritional value resulting from the up-regulation of the Y1 phytoene synthase gene product in endosperm tissue. As a result, diversity within yellow maize lines at the Y1 gene is dramatically decreased as compared to white corn. We analyzed patterns of sequence diversity and linkage disequilibrium in nine low copy regions located at varying distances from the Y1 gene, including a homolog of the barley Mlo gene. Patterns consistent with a selective sweep, such as significant associations of informative single-nucleotide polymorphisms with endosperm color phenotype, linkage disequilibrium, and significantly reduced diversity within the yellow endosperm haplotypes, were observed up to 600 kb downstream of Y1, whereas the upstream region showed a more rapid recovery. The starch branching enzyme 1 (sbe1) gene is the first region downstream of Y1 that does not have a highly conserved haplotype in the yellow endosperm germplasm.S elective forces acting on allelic variants of genes have a profound effect on local levels of genetic diversity and linkage disequilibria (LD). Positive directional selection leads to reduced variability and increased LD in the respective region (1-6), and the so-called selective sweep regions provide clues to genes that have been subjects of evolutionary forces as well as selection by humans. Recently, Clark et al. (7) characterized a selective sweep in the promoter region of teosinte branched1 (tb1). The sweep extends 60-90 kb upstream of the gene and is indicative of the gene's role in the domestication of maize from teosinte between 6,000 and 10,000 years ago.The maize Y1 gene on chromosome 6 has undergone recent selection for endosperm color phenotype. A recent study (8) uncovered a dramatic reduction in diversity at this gene for the yellow endosperm maize inbred lines only, over the entire 6-kb gene region. This footprint of selection was characterized by a conserved yellow endosperm haplotype at the 5Ј end of the gene with evidence of recombination toward the 3Ј end. Strong haplotype conservation at the 5Ј end is suggestive of the location of the causal variant associated with the gain-of-function mutation to yellow endosperm and may be indicative of further extension of the selective sweep in the 5Ј direction. The presence of recombinants in the 3Ј UTR region, however, suggested that the extent of the selective sweep may be limited downstream of the coding region.The white endosperm lines did not show characteristics of a selective sweep (8), despite the fact that the white endosperm phenotype is also a target of selection due to human taste preference (9). This is because white is the predicted ancestral state of the gene (John Doebley, personal communication), and thus multiple haplotypes are associated with the white endosperm phenotype.Understanding the boundaries of the selective ...

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Section: Shotgun Sequencing Of Y1-containing Bacterial Artificial Chrmentioning

confidence: 99%

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Palaisa

Morgante

Tingey

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

205

153

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“…We have earlier shown that dATP, but not dATP α S, interferes with the luciferase (18,23). In addition, dATP α S was found to be a good substrate for the AMV-RT (Figure 4).…”

Section: Discussionmentioning

confidence: 84%

Bioluminometric Method for Real-Time Detection of Reverse Transcriptase Activity

1998

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“…The intensity of the bioluminescent signal is directly proportional to the concentration of PPi and is also predicted to correlate with the number of transcripts ( Figure 3B). Such an approach has been developed for sequencing purposes (33)(34)(35) as well as for assaying the activity of RNA-dependent RNAP (36). We modified this assay to detect abortive transcription activity of DNA-dependent RNAPs and obtained reliable results both for E. coli RNAP and T7 RNAP and reached a degree of sensitivity which was comparable to gel-based assays (Figure 3 C,D).…”

Section: A Bioluminescent Read-out Methods Suitable For Automationmentioning

confidence: 91%

Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase

Wiesler

Werner

Weinzierl

2013

Methods in Molecular Biology

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Several co-crystals of the TFIIB-RNAP II interface exist suggesting the TFIIB linker region to penetrate the active centre, yet the understanding of the resulting protein-protein interactions and their impact on the transcription cycle has remained elusive. Promoter-independent abortive initiation assays exploit the intrinsic ability of RNAP enzymes to initiate transcription from nicked DNA templates and measuring the phosphodiester bond formation they catalyse. These assays can be used to measure the effect of transcription factors and mutations on the rate of the catalytic reaction. Notably, they have served to reveal and characterise a significant stimulation activity of TFIIB on RNAP that was previously unknown.

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Detection of Single-Base Changes Using a Bioluminometric Primer Extension Assay

Cited by 58 publications

References 6 publications

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep

Bioluminometric Method for Real-Time Detection of Reverse Transcriptase Activity

Promoter Independent Abortive Transcription Assays Unravel Functional Interactions Between TFIIB and RNA Polymerase

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