Alan Rose

Alan Rose
University of California, Davis | UCD · Department of Molecular and Cellular Biology

PhD

About

31
Publications
4,497
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2,136
Citations
Citations since 2017
4 Research Items
911 Citations
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2017201820192020202120222023050100150200
2017201820192020202120222023050100150200

Publications

Publications (31)
Article
Full-text available
Certain introns significantly increase mRNA accumulation by a poorly understood mechanism. These introns have no effect when located upstream, or more than ~1 Kb downstream, of the start of transcription. We tested the ability of a formerly non-stimulating intron containing 11 copies of the sequence TTNGATYTG, which is over-represented in promoter-...
Article
Full-text available
A picture is beginning to emerge from a variety of organisms that for a subset of genes, the most important sequences that regulate expression are situated not in the promoter but rather are located within introns in the first kilobase of transcribed sequences. The actual sequences involved are difficult to identify either by sequence comparisons o...
Preprint
Full-text available
Certain introns strongly increase mRNA accumulation by a poorly understood mechanism known as Intron-Mediated Enhancement (IME). Introns that boost expression by IME have no effect when located upstream of or more than ~1 Kb downstream from the start of transcription. The sequence TTNGATYTG, which is over-represented in promoter-proximal introns in...
Article
To more precisely define the positions from which certain intronic regulatory sequences increase mRNA accumulation, the effect of a UBIQUITIN intron on gene expression was tested from 6 different positions surrounding the transcription start site (TSS) of a reporter gene fusion in Arabidopsis thaliana. The intron increased expression from all trans...
Preprint
Full-text available
In diverse eukaryotes, certain introns increase mRNA accumulation through the poorly understood mechanism of intron-mediated enhancement (IME). A distinguishing feature of IME is that these introns have no effect from upstream or more than 1 Kb downstream of the transcription start site (TSS). To more precisely define the intron position requiremen...
Article
Full-text available
Key message: Related motifs strongly increase gene expression when added to an intron located in coding sequences. Many introns greatly increase gene expression through a mechanism that remains elusive. An obstacle to understanding intron-mediated enhancement (IME) has been the difficulty of locating the specific intron sequences responsible for b...
Article
Within two years of their discovery in 1977, introns were found to have a positive effect on gene expression. Numerous examples of stimulatory introns have been described since then in very diverse organisms, including plants. In some cases, the mechanism through which the intron affects expression is readily understood. However, many introns that...
Article
Introns are often added to transgenes to increase expression, although the mechanism through which introns stimulate gene expression in plants and other eukaryotes remains mysterious. While introns vary in their effect on expression, it is unknown whether different genes respond similarly to the same stimulatory intron. Furthermore, the degree to w...
Article
Full-text available
Nodulation in legumes requires recognition of rhizobially made Nod factors. Genetic studies have revealed that perception of Nod factors involves LysM domain receptor-like kinases, while biochemical approaches have identified lectin nucleotide phosphohydrolase (LNP) as a Nod factor binding protein. Here we show that antisense inhibition of LNP bloc...
Article
Full-text available
Many introns significantly increase gene expression through a process termed intron-mediated enhancement (IME). Introns exist in the transcribed DNA and the nascent RNA, and could affect expression from either location. To determine which is more relevant to IME, hybrid introns were constructed that contain sequences from stimulating Arabidopsis th...
Article
Full-text available
Introns in a wide range of organisms including plants, animals and fungi are able to increase the expression of the gene that they are contained in. This process of intron-mediated enhancement (IME) is most thoroughly studied in Arabidopsis thaliana, where it has been shown that enhancing introns are typically located near the promoter and are comp...
Article
Full-text available
Important patterns can be found in strings of characters such as nucleotides in a DNA sequence by examining the frequency of occurrence of specific character combinations or words. The abundance of words can reveal the presence of underlying trends governing the order of characters, even if the biological reasons for those trends remain mysterious....
Article
Full-text available
Introns that elevate mRNA accumulation have been found in a wide range of eukaryotes. However, not all introns affect gene expression, and direct testing is currently the only way to identify stimulatory introns. Our genome-wide analysis in Arabidopsis thaliana revealed that promoter-proximal introns as a group are compositionally distinct from dis...
Article
Full-text available
Introns can significantly affect gene expression in plants and many other eukaryotes in a variety of ways. Several types of gene regulation, both positive and negative, that involve plant introns are reviewed in this chapter. Some introns contain enhancer elements or alternative promoters, while many others elevate mRNA accumulation by a different...
Article
Whereas many important biological discoveries have been made using plants, subsequent progress in some areas of plant research has fallen behind that in other organisms for which funding and in vitro assays are more readily available. Gene expression is one such field in which importance continues to grow because many potential plant biotechnology–...
Article
The extensive mechanistic and regulatory interconnections between the various events of mRNA biogenesis are now recognized as a fundamental principle of eukaryotic gene expression, yet the specific details of the coupling between the various steps of mRNA biogenesis do differ, and sometimes dramatically, between the different kingdoms. In this revi...
Article
Introns are often required for full expression of genes in organisms as diverse as plants, insects, nematodes, yeast, and mammals. To explore the potential mechanisms of intron-mediated enhancement in Arabidopsis thaliana, the effect of varying the position of an intron was determined using a series of reporter gene fusions between TRYPTOPHAN BIOSY...
Article
Full-text available
To explore possible mechanisms of intron-mediated enhancement of gene expression, the features of PAT1 intron 1 required to elevate mRNA accumulation were systematically tested in transgenic Arabidopsis. This intron is remarkably resilient, retaining some ability to increase mRNA accumulation when splicing was prevented by mutation of 5' and 3' spl...
Article
To investigate how plants acquire and assimilate sulfur from their environment, we isolated and characterized two mutants of Arabidopsis thaliana deficient in sulfate transport. The mutants are resistant to selenate, a toxic analogue of sulfate. They are allelic to each other and to the previously isolated sel1 (selenate-resistant) mutants, and hav...
Article
Full-text available
Either of the first two introns of the Arabidopsis tryptophan pathway gene PAT1 elevates mRNA accumulation from a PAT1:beta-glucuronidase (GUS) fusion roughly 5-fold without affecting the rate of PAT1:GUS transcription. To further explore the mechanism of this intron-mediated enhancement of gene expression, we wanted to determine whether splicing o...
Article
Full-text available
The properties of Penicillium chrysogenum adenosine 5′-phosphosulfate (APS) kinase mutated at Ser-107 were examined. Ser-107 is analogous to a serine of the E. coli enzyme that has been shown to serve as an intermediate acceptor in the transfer of a phosphoryl group from ATP to APS. Replacement of Ser-107 with alanine yielded an active enzyme with...
Article
The expression of the Arabidopsis thaliana PAT1 gene, which encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase, was investigated using translational fusions of the PAT1 promoter to the GUS reporter gene. Independent stably transformed A. thaliana lines containing a single copy of a fusion that includes the entire plas...
Article
Full-text available
Nine blue fluorescent mutants of the flowering plant Arabidopsis thaliana were isolated by genetic selections and fluorescence screens. Each was shown to contain a recessive allele of trp1, a previously described locus that encodes the tryptophan biosynthetic enzyme phosphoribosylanthranilate transferase (PAT, called trpD in bacteria). The trp1 mut...
Article
Full-text available
Phosphoribosylanthranilate isomerase (PAI) catalyzes the third step of the tryptophan biosynthetic pathway. Arabidopsis PAI cDNAs were cloned from a cDNA expression library by complementation of an Escherichia coli trpC- PAI deficiency mutation. Genomic DNA blot hybridization analysis detected three nonallelic genes encoding PAI in the Arabidopsis...
Chapter
A long term goal for this laboratory is to obtain a detailed understanding of the biochemical and genetic mechanisms that plants use to regulate the synthesis of the amino acid tryptophan (Last et al., 1992; Last, 1993). In addition to its role in the production of tryptophan for protein synthesis, this pathway gives rise to many indolic secondary...
Article
Full-text available
An Arabidopsis thaliana gene encoding phosphoribosylanthranilate transferase is shown to be the gene that is defective in blue fluorescent trp1 mutant plants. This gene, named PAT1, was isolated using an A. thaliana cDNA clone that suppressed an Escherichia coli trpD(-) mutation. The PAT1 coding region is homologous to those for the phosphoribosyla...
Conference Paper
It has been known for several decades that introns can increase gene expression in diverse eukaryotes, although the mechanism remains unclear. Many efficiently spliced introns have no effect on expression, demonstrating that splicing is insufficient and suggesting that the introns that boost expression must contain stimulating sequences. However, d...

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Project
Some introns strongly increase gene expression. We recently found that deleting the core promoter, including all known transcription start sites, did not diminish the expression of a gene containing a stimulating intron in Arabidopsis. We are investigating the mechanism through which introns affect the amount and site of transcript initiation.