Professional Education

  • Bachelor of Science, University of Texas Austin (2006)
  • Doctor of Philosophy, University of California San Francisco (2011)

Stanford Advisors


All Publications

  • Shockingly Early: Chromatin-Mediated Loss of the Heat Shock Response. Molecular cell Booth, L. N., Brunet, A. 2015; 59 (4): 515-516


    In this issue of Molecular Cell, Labbadia and Morimoto (2015) show that there is a precipitous decline in stress resistance at the onset of reproduction in C. elegans and that this transition is regulated by changes in repressive chromatin marks.

    View details for DOI 10.1016/j.molcel.2015.08.004

    View details for PubMedID 26295957

  • Intersecting transcription networks constrain gene regulatory evolution NATURE Sorrells, T. R., Booth, L. N., Tuch, B. B., Johnson, A. D. 2015; 523 (7560): 361-?


    Epistasis-the non-additive interactions between different genetic loci-constrains evolutionary pathways, blocking some and permitting others. For biological networks such as transcription circuits, the nature of these constraints and their consequences are largely unknown. Here we describe the evolutionary pathways of a transcription network that controls the response to mating pheromone in yeast. A component of this network, the transcription regulator Ste12, has evolved two different modes of binding to a set of its target genes. In one group of species, Ste12 binds to specific DNA binding sites, while in another lineage it occupies DNA indirectly, relying on a second transcription regulator to recognize DNA. We show, through the construction of various possible evolutionary intermediates, that evolution of the direct mode of DNA binding was not directly accessible to the ancestor. Instead, it was contingent on a lineage-specific change to an overlapping transcription network with a different function, the specification of cell type. These results show that analysing and predicting the evolution of cis-regulatory regions requires an understanding of their positions in overlapping networks, as this placement constrains the available evolutionary pathways.

    View details for DOI 10.1038/nature14613

    View details for Web of Science ID 000357950900045

    View details for PubMedID 26153861

  • Males Shorten the Life Span of C. elegans Hermaphrodites via Secreted Compounds SCIENCE Maures, T. J., Booth, L. N., Benayoun, B. A., Izrayelit, Y., Schroeder, F. C., Brunet, A. 2014; 343 (6170): 541-544


    How an individual's longevity is affected by the opposite sex is still largely unclear. In the nematode Caenorhabditis elegans, the presence of males accelerated aging and shortened the life span of individuals of the opposite sex (hermaphrodites), including long-lived or sterile hermaphrodites. The male-induced demise could occur without mating and required only exposure of hermaphrodites to medium in which males were once present. Such communication through pheromones or other diffusible substances points to a nonindividual autonomous mode of aging regulation. The male-induced demise also occurred in other species of nematodes, suggesting an evolutionary conserved process whereby males may induce the disposal of the opposite sex to save resources for the next generation or to prevent competition from other males.

    View details for DOI 10.1126/science.1244160

    View details for Web of Science ID 000330343700047

    View details for PubMedID 24292626

  • Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification CELL Baker, C. R., Booth, L. N., Sorrells, T. R., Johnson, A. D. 2012; 151 (1): 80-95


    We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

    View details for DOI 10.1016/j.cell.2012.08.018

    View details for Web of Science ID 000309544200012

    View details for PubMedID 23021217

  • Intercalation of a new tier of transcription regulation into an ancient circuit NATURE Booth, L. N., Tuch, B. B., Johnson, A. D. 2010; 468 (7326): 959-U358


    Changes in gene regulatory networks are a major source of evolutionary novelty. Here we describe a specific type of network rewiring event, one that intercalates a new level of transcriptional control into an ancient circuit. We deduce that, over evolutionary time, the direct ancestral connections between a regulator and its target genes were broken and replaced by indirect connections, preserving the overall logic of the ancestral circuit but producing a new behaviour. The example was uncovered through a series of experiments in three ascomycete yeasts: the bakers' yeast Saccharomyces cerevisiae, the dairy yeast Kluyveromyces lactis and the human pathogen Candida albicans. All three species have three cell types: two mating-competent cell forms (a and α) and the product of their mating (a/α), which is mating-incompetent. In the ancestral mating circuit, two homeodomain proteins, Mata1 and Matα2, form a heterodimer that directly represses four genes that are expressed only in a and α cells and are required for mating. In a relatively recent ancestor of K. lactis, a reorganization occurred. The Mata1-Matα2 heterodimer represses the same four genes (known as the core haploid-specific genes) but now does so indirectly through an intermediate regulatory protein, Rme1. The overall logic of the ancestral circuit is preserved (haploid-specific genes ON in a and α cells and OFF in a/α cells), but a new phenotype was produced by the rewiring: unlike S. cerevisiae and C. albicans, K. lactis integrates nutritional signals, by means of Rme1, into the decision of whether or not to mate.

    View details for DOI 10.1038/nature09560

    View details for Web of Science ID 000285344600046

    View details for PubMedID 21164485

  • Arginine-rich motifs present multiple interfaces for specific binding by RNA RNA-A PUBLICATION OF THE RNA SOCIETY Bayer, T. S., Booth, L. N., Knudsen, S. M., Ellington, A. D. 2005; 11 (12): 1848-1857


    A number of proteins containing arginine-rich motifs (ARMs) are known to bind RNA and are involved in regulating RNA processing in viruses and cells. Using automated selection methods we have generated a number of aptamers against ARM peptides from various natural proteins. Aptamers bind tightly to their cognate ARMs, with K(d) values in the nanomolar range, and frequently show no propensity to bind to other ARMs or even to single amino acid variants of the cognate ARM. However, at least some anti-ARM aptamers can cross-recognize a limited set of other ARMs, just as natural RNA-binding sites have been shown to exhibit so-called "chameleonism." We expand upon the number of examples of cross-recognition and, using mutational and circular dichroism (CD) analyses, demonstrate that there are multiple mechanisms by which RNA ligands can cross-recognize ARMs. These studies support a model in which individual arginine residues govern binding to an RNA ligand, and the inherent flexibility of the peptide backbone may make it possible for "semi-specific" recognition of a discrete set of RNAs by a discrete set of ARM peptides and proteins.

    View details for DOI 10.1261/rna.2167605

    View details for Web of Science ID 000233758900012

    View details for PubMedID 16314457

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