About

Professor Emma Farley established the Farley Lab at the University of California San Diego (UCSD) in September 2016. She holds a joint appointment in the School of Medicine and Biological Sciences. Her research focuses on pinpointing enhancer variants that alter gene expression and phenotypes. The lab employs high-throughput functional genomics approaches to understand how the instructions for development are encoded in genomes. Professor Farley's work has been published in prominent journals such as Nature, reflecting her contributions to the field of functional genomics and enhancer biology.

Research topics

• Genetics
• Biology
• Computer Science
• Artificial Intelligence
• Evolutionary biology
• Computational biology
• Chemistry
• Linguistics

Selected publications

• A Germline Variant at the TERT Locus Predicts Intra-Tumor T Cell Exhaustion and Response to Immune Checkpoint Blockade

  SSRN Electronic Journal · 2026-01-01

  preprintOpen access
  PublisherDOI

• A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening

  Nature Methods · 2024-11-19 · 30 citations

  articleOpen access

  Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Here we assembled a prime editing platform capable of high-efficiency substitution editing suitable for functional interrogation of small genetic variants. We benchmarked this platform for pooled, loss-of-function screening using a library of ~240,000 engineered prime editing guide RNAs (epegRNAs) targeting ~17,000 codons with 1-3 bp substitutions. Comparing the abundance of these epegRNAs across screen samples identified negative selection phenotypes for 7,996 nonsense mutations targeted to 1,149 essential genes and for synonymous mutations that disrupted splice site motifs at 3' exon boundaries. Rigorous evaluation of codon-matched controls demonstrated that these phenotypes were highly specific to the intended edit. Altogether, we established a prime editing approach for multiplexed, functional characterization of genetic variants with simple readouts.

  PublisherDOI

• Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage

  STAR Protocols · 2024-07-03

  articleOpen accessSenior authorCorresponding

  Electroporation is a technique to introduce DNA constructs into cells using electric current. Here, we present a protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. We describe steps for setting up and conducting electroporation. We then detail procedures for collecting, fixing, and mounting embryos and counting expression. This protocol can be used to study the expression of enhancers via reporter assays, manipulating cells using genes or modified genes such as dominant negatives, and genome editing. For complete details on the use and execution of this protocol, please refer to Song, et al.1

  PublisherDOI

• Affinity-optimizing enhancer variants disrupt development

  Nature · 2024 · 95 citations

  Senior authorCorresponding
  • Computational biology
  • Biology
  • Chemistry

  . However, how this enhancer encodes tissue-specific activity, and the mechanisms by which SNVs alter the number of digits, are poorly understood. Here we show that the ETS sites within the ZRS are low affinity, and identify a functional ETS site, ETS-A, with extremely low affinity. Two human SNVs and a synthetic variant optimize the binding affinity of ETS-A subtly from 15% to around 25% relative to the strongest ETS binding sequence, and cause polydactyly with the same penetrance and severity. A greater increase in affinity results in phenotypes that are more penetrant and more severe. Affinity-optimizing SNVs in other ETS sites in the ZRS, as well as in ETS, interferon regulatory factor (IRF), HOX and activator protein 1 (AP-1) sites within a wide variety of enhancers, cause gain-of-function gene expression. The prevalence of binding sites with suboptimal affinity in enhancers creates a vulnerability in genomes whereby SNVs that optimize affinity, even slightly, can be pathogenic. Searching for affinity-optimizing SNVs in genomes could provide a mechanistic approach to identify causal variants that underlie enhanceropathies.

  PublisherOA PDFDOI

• Conserved enhancers control notochord expression of vertebrate Brachyury

  Nature Communications · 2023-10-18 · 15 citations

  articleOpen access

  The cell type-specific expression of key transcription factors is central to development and disease. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three conserved Brachyury-controlling notochord enhancers, T3, C, and I, in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, in cis deletion of all three enhancers in mouse abolishes Brachyury/T/Tbxt expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. The three Brachyury-driving notochord enhancers are conserved beyond mammals in the brachyury/tbxtb loci of fishes, dating their origin to the last common ancestor of jawed vertebrates. Our data define the vertebrate enhancers for Brachyury/T/TBXTB notochord expression through an auto-regulatory mechanism that conveys robustness and adaptability as ancient basis for axis development.

  PublisherDOI

• Predictive analyses of regulatory sequences with EUGENe

  Nature Computational Science · 2023-11-16 · 21 citations

  articleOpen access

  Deep learning has become a popular tool to study cis-regulatory function. Yet efforts to design software for deep-learning analyses in regulatory genomics that are findable, accessible, interoperable and reusable (FAIR) have fallen short of fully meeting these criteria. Here we present elucidating the utility of genomic elements with neural nets (EUGENe), a FAIR toolkit for the analysis of genomic sequences with deep learning. EUGENe consists of a set of modules and subpackages for executing the key functionality of a genomics deep learning workflow: (1) extracting, transforming and loading sequence data from many common file formats; (2) instantiating, initializing and training diverse model architectures; and (3) evaluating and interpreting model behavior. We designed EUGENe as a simple, flexible and extensible interface for streamlining and customizing end-to-end deep-learning sequence analyses, and illustrate these principles through application of the toolkit to three predictive modeling tasks. We hope that EUGENe represents a springboard towards a collaborative ecosystem for deep-learning applications in genomics research.

  PublisherOA PDFDOI

• Diverse logics and grammar encode notochord enhancers

  Cell Reports · 2023-01-31 · 18 citations

  articleOpen accessSenior authorCorresponding

  The notochord is a defining feature of all chordates. The transcription factors Zic and ETS regulate enhancer activity within the notochord. We conduct high-throughput screens of genomic elements within developing Ciona embryos to understand how Zic and ETS sites encode notochord activity. Our screen discovers an enhancer located near Lama, a gene critical for notochord development. Reversing the orientation of an ETS site within this enhancer abolishes expression, indicating that enhancer grammar is critical for notochord activity. Similarly organized clusters of Zic and ETS sites occur within mouse and human Lama1 introns. Within a Brachyury (Bra) enhancer, FoxA and Bra, in combination with Zic and ETS binding sites, are necessary and sufficient for notochord expression. This binding site logic also occurs within other Ciona and vertebrate Bra enhancers. Collectively, this study uncovers the importance of grammar within notochord enhancers and discovers signatures of enhancer logic and grammar conserved across chordates.

  PublisherOA PDFDOI

• <i>Ciona</i>, an ideal research organism to study the role of enhancers

  genesis · 2023-11-01

  articleOpen access1st authorCorresponding

  Watching documentaries as a child, I became fascinated by how genomes encode the instructions to make all the cells of an organism. I studied Biochemistry at Oxford University as the subject seemed to provide a mechanistic understanding of living systems. During my time at Oxford, I completed my part II thesis (similar to a master's project) in Prof. Doug Higgs' lab. I learned about the regulation of gene expression during development of blood cells and the disease ATRX which causes alpha thalassemia and neurological defects in patients via misregulation of gene expression. While we were studying the effects of this disease on gene expression within the blood system, I wondered if studying both the blood and the brain may help find generalizable principles and mechanisms driving the disease. For this reason, I wanted to do my Ph.D. in a system where I could study many different types of cells. I decided to work with stem cells and transcription factors involved in the specification of cell fate. I did my Ph.D. at Imperial College London at the MRC London Medical Sciences Center with Dr. Meng Li. I studied how midbrain dopaminergic neurons are made in developing mouse and chick brains and applied this knowledge to stem cells to create dopaminergic neurons in a dish. The hope was that these stem cell-derived dopaminergic neurons would serve as a platform for drug screening and therapeutic approaches for patients with Parkinson's disease. While I value the stem cell system, at the time, it was not the ideal system to explore how genomes encode gene expression in time and space. My stem cell cultures were often heterogenous; a mixture of neural-like cells and other cells, most commonly cardiac cells beating in the dish. And one could never truly know if the cells in the dish recapitulated the endogenous dopaminergic neurons. Through my research experiences, I thought that experimental approaches in whole developing embryos would be better suited for understanding how our genomes encode the instructions for making an organism. I set about looking for a system in which I could study enhancers in high-throughput within whole developing organisms. Prof. Mike Levine spoke about Ciona at a British Society of Developmental Biology meeting, and I was hooked. I realized that Ciona, with its close relation to vertebrates and the power of electroporation to incorporate plasmids into millions of embryos, would be an ideal organism for whole embryo high-throughput reporter assays to study enhancers. Thus, Ciona is an ideal system to decipher how the instructions for development are encoded in our genomes. I started my postdoc with Prof. Mike Levine in 2012. I developed a synthetic enhancer library screen (SEL-seq) to test many millions of enhancers for activity in developing Ciona (Figure 1a). I used SEL-Seq to test 2.5 million variants of a neural Otx-a enhancer to examine how this enhancer activated by two pleiotropic factors (ETS and GATA) encodes neural-specific expression within the anterior sensory vesicle and dorsal nerve cord (Farley et al., 2015) (Figure 1b). From these screens, we discovered that enhancers need low or suboptimal affinity transcription factor binding sites to correctly encode tissue-specific expression. If these low-affinity sites are replaced with high-affinity sites, then the enhancer is no longer restricted to the neural lineages but is also active in many other tissues where FGF signaling or GATA are present. These studies illustrate that the use of suboptimal affinity sites is critical to ensure that the enhancer remains under combinatorial control of ETS and GATA and is only active where the concentration of these two factors is just right. Similar results showing that low-affinity Hox sites were important for specificity in flies were also reported (Crocker et al., 2015). We also found that the organization of sites (order, spacing, and orientation) in the endogenous Otx-a sequence is not optimal for the highest level of transcription (Farley et al., 2015). Changing the spacing between the sites within the enhancer could increase the levels of transcription, giving stronger neural expression. Indeed, optimizing the affinity and spacing within a version of the Otx-a enhancer results in a complete loss of tissue specificity; expression is no longer restricted to the neural tissue (a6.5 and b6.5 lineages) but is also seen in the notochord, endoderm, and posterior sensory vesicle (Figure 1b,c). The use of low-affinity sites that are non-optimally organized prevents aberrant activation of the enhancers by a single factor and means that combinatorial control is required to activate transcription (Farley et al., 2015). The realization that enhancers contain incredibly degenerate binding sites was alarming as it meant enhancers were even more complex than we originally thought. Luckily, we noticed a relationship between the affinity and organization of the binding sites. Low-affinity sites within native enhancers had an organization that led to higher levels of transcriptional output, while higher-affinity sites had less optimal spacing for transcriptional output. Thus, there appeared to be an interplay between affinity and organization of binding sites (enhancer grammar) (Farley et al., 2015; Farley et al., 2016; Jindal & Farley, 2021). As a postdoc and in my own lab, we have used these grammatical rules to find tissue-specific enhancers within the genome (Farley et al., 2016; Song et al., 2023). In my own lab at UC San Diego, I continue to harness Ciona for high-throughput enhancer screens to find rules governing enhancers. We have found signatures of enhancer grammar conserved across chordates—in Ciona, mice, and humans (Song et al., 2023). We've also expanded to look at how violations in regulatory principles governing enhancers can drive organismal-level phenotypes in Ciona and other species, such as mice and humans (Jindal et al., 2023; Lim et al., 2022). We've found that single nucleotide variants (SNVs) can increase binding site affinity driving ectopic expression and organismal phenotypes as severe as a second heart in Ciona and extra fingers in mice and humans (Jindal et al., 2023; Lim et al., 2022). Thus, the principle of suboptimization of developmental enhancers to encode tissue-specific expression, which we initially discovered in Ciona, applies to other organisms too. Furthermore, violating this principle leads to major phenotypes in tunicates and vertebrates. I am incredibly grateful to Prof. Mike Levine for supporting me while I pursued the high-throughput enhancer screens in Ciona. If it were not for him, I would not have been able to realize these experiments, which formed the foundation of the research conducted within my own lab. While occasionally challenging, the Levine lab was also fun. I'd never been around so many people who loved enhancers as much as I did. My time in the Levine lab was full of exciting conversations and brainstorming, which helped me develop into the scientist I am today. Now in my own lab, I enjoy being surrounded by enhancerophiles all the time. So far, two graduate students and one postdoc have graduated from my lab and joined industry. My lab now consists of two postdocs, three graduate students, and three undergraduates (Figure 2). I hope many of them remain in the Ciona community. To support my research, I've been fortunate to receive the NIH New Innovator Award, NSF CAREER Award, and NHGRI R01. I'd like to thank everyone who has worked with me during the course of my research. Special thanks to all members of the Farley lab, past and present, for contributing to our discoveries. I'd also like to thank all Levine lab alumni, but especially members of the Levine lab from 2012-2016, for helpful discussions and support. Thanks to Doug Higgs for introducing me to gene regulation and his continued support and advice. Thank you Meng Li and Emily Gale for mentoring me through my PhD. Finally, thank you, Mike Levine, for introducing me to the amazing model organism and proto-vertebrate – Ciona, and for supporting me as I developed high-throughput enhancers screens in Ciona.

  PublisherOA PDFDOI

• Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development

  Developmental Cell · 2023-10-16 · 43 citations

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• Conserved enhancer logic controls the notochord expression of vertebrate <i>Brachyury</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-04-20 · 2 citations

  preprintOpen access

  ABSTRACT The cell type-specific expression of key transcription factors is central to development. Brachyury/T/TBXT is a major transcription factor for gastrulation, tailbud patterning, and notochord formation; however, how its expression is controlled in the mammalian notochord has remained elusive. Here, we identify the complement of notochord-specific enhancers in the mammalian Brachyury/T/TBXT gene. Using transgenic assays in zebrafish, axolotl, and mouse, we discover three Brachyury -controlling notochord enhancers T3, C , and I in human, mouse, and marsupial genomes. Acting as Brachyury-responsive, auto-regulatory shadow enhancers, deletion of all three enhancers in mouse abolishes Brachyury/T expression selectively in the notochord, causing specific trunk and neural tube defects without gastrulation or tailbud defects. Sequence and functional conservation of Brachyury -driving notochord enhancers with the brachyury/tbxtb loci from diverse lineages of fishes dates their origin to the last common ancestor of jawed vertebrates. Our data define the enhancers for Brachyury/T/TBXTB notochord expression as ancient mechanism in axis development.

  PublisherOA PDFDOI

Recent grants

• CAREER Deciphering how enhancers encode tissue-specificity and phenotypes

  NSF · $1.2M · 2022–2027

• Deciphering the regulatory principles governing enhancer specificity

  NIH · $2.5M · 2021–2022

Frequent coauthors

• Fabian Lim

  University of California, San Diego

  14 shared

• K.M. Olson

  University of California, San Diego

  13 shared

• Michael Levine

  University of California, Los Angeles

  10 shared

• Emily Gale

  Emory University

  9 shared

• E Aiden

  Broad Institute

  8 shared

• Meng Li

  Changhai Hospital

  8 shared

• Granton A. Jindal

  University of California, San Diego

  7 shared

• Michele Di Pierro

  Northeastern University

  7 shared

Labs

• Farley LabPI

Education

• MBioChem, Molecular and Cellular Biochemistry

  University of Oxford

• PhD, MRC Clinical Sciences Center

  Imperial College London

  2011