Stanley Fields
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Dosa: A method to covalently barcode proteins for high-throughput biochemistry Open
Deep mutational scanning couples a protein’s activity to DNA sequencing for high-throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like cell proliferation, as proxy for protei…
Dosa: A method to covalently barcode proteins for high throughput biochemistry Open
Deep mutational scanning couples a protein’s activity to DNA sequencing for high throughput assessment of the effects of all single amino acid substitutions, but it largely uses indirect assays, like growth, as proxy for protein activity. …
Small DNA elements can act as both insulators and silencers in plants Open
Insulators are cis-regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the …
Late Pleistocene onset of mutualistic human/canid ( <i>Canis</i> spp.) relationships in subarctic Alaska Open
Large canids (wolves, dogs, and coyote) and people form a close relationship in northern (subarctic and arctic) socioecological systems. Here, we document the antiquity of this bond and the multiple ways it manifested in interior Alaska, a…
View article: Understanding genetic variants in context
Understanding genetic variants in context Open
Over the last three decades, human genetics has gone from dissecting high-penetrance Mendelian diseases to discovering the vast and complex genetic etiology of common human diseases. In tackling this complexity, scientists have discovered …
Small DNA elements that act as both insulators and silencers in plants Open
Insulators are cis -regulatory elements that separate transcriptional units, whereas silencers are elements that repress transcription regardless of their position. In plants, these elements remain largely uncharacterized. Here, we use the…
Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability Open
The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 termin…
Plant enhancers exhibit both cooperative and additive interactions among their functional elements Open
Enhancers are cis-regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed to explain how enhancers integrate the activity of multiple transc…
Cooperativity and additivity in plant enhancers Open
Enhancers are cis -regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed to explain how enhancers integrate the activity of multiple trans…
Impact on splicing in<i>Saccharomyces cerevisiae</i>of random 50-base sequences inserted into an intron Open
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing—5′ and 3′ splice sites and a branchpoint—are especially well-characterized in Saccharomyces cerevisiae , but our under…
Impact of random 50-base sequences inserted into an intron on splicing in <i>Saccharomyces cerevisiae</i> Open
Intron splicing is a key regulatory step in gene expression in eukaryotes. Three sequence elements required for splicing – 5’ and 3’ splice sites and a branch point – are especially well- characterized in Saccharomyces cerevisiae , but our…
<i>Arabidopsis</i> and Maize Terminator Strength is Determined by GC Content, Polyadenylation Motifs and Cleavage Probability Open
The 3’ end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 termin…
Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments Open
Massively parallel measurements of dominant-negative inhibition by protein fragments have been used to map protein interaction sites and discover peptide inhibitors. However, the underlying principles governing fragment-based inhibition ha…
Proteome-wide identification of amino acid substitutions deleterious for protein function Open
DNA sequencing has led to the discovery of millions of mutations that change the encoded protein sequences, but the impact of nearly all of these mutations on protein function is unknown. We addressed this scarcity of functional data by de…
Comprehensive Mutational Analysis of the Lasso Peptide Klebsidin Open
Antibiotic resistance is a growing threat to public health, making the development of antibiotics of critical importance. One promising class of potential new antibiotics are ribosomally synthesized and post-translationally modified peptid…
Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments Open
Massively-parallel measurements of dominant negative inhibition by protein fragments have been used to map protein interaction sites and discover peptide inhibitors. However, the underlying principles governing fragment-based inhibition ha…
Source Data for Savinov et al. 2022: protein fragment mapping Open
Source Data associated with the following article: A. Savinov, A. Fernandez, S. Fields. Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments. bioRxiv 2022.01.04.474984 (2022). https://doi.org/…
Source Data for Savinov et al. 2022: protein fragment mapping Open
Source Data and higher-resolution figure files associated with the following article: A. Savinov, A. Fernandez, S. Fields. Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments. Proc. Natl. Aca…
Expanding the binding specificity for RNA recognition by a PUF domain Open
The ability to design a protein to bind specifically to a target RNA enables numerous applications, with the modular architecture of the PUF domain lending itself to new RNA-binding specificities. For each repeat of the Pumilio-1 PUF domai…
Effects of sequence motifs in the yeast 3′ untranslated region determined from massively-parallel assays of random sequences Open
The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression, through effects on activities such as mRNA stability and translation. The underlying functional elements within this region have largely bee…
MaveRegistry: a collaboration platform for multiplexed assays of variant effect Open
Summary Multiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating ‘variant effect maps’, which provide biochemical insig…
Balance between promiscuity and specificity in phage λ host range Open
As hosts acquire resistance to viruses, viruses must overcome that resistance to re-establish infectivity, or go extinct. Despite the significant hurdles associated with adapting to a resistant host, viruses are evolutionarily successful a…
Synthetic Promoter Designs Enabled by a Comprehensive Analysis of Plant Core Promoters Open
Targeted engineering of plant gene expression holds great promise for ensuring food security and for producing biopharmaceuticals in plants. However, this engineering requires thorough knowledge of cis -regulatory elements in order to prec…
Source Data for Savinov et al. 2021: 3' UTRs Open
Source Data associated with the following article:A. Savinov, B. M. Brandsen, B. E. Angell, J. T. Cuperus, S. Fields. Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequen…