July 21–24, 2022 | Kansas City, Mo.

Evolution and Core Processes in Gene Expression

Evolution and core processes in gene expression
July 21–24, 2022 | Stowers Institute for Medical Research, Kansas City, Mo.

The focus of this meeting is to discuss the most recent insights into the cis-regulatory code, how cis-regulatory information is read out by transcription factors, signaling pathways and other proteins, how cellular diversity is created during development and how we can study this problem using cutting-edge genomics technology and computational methods.

We will simultaneously examine the problem from an evolutionary perspective: how cis-regulatory elements evolve, how regulatory variation affects gene expression and phenotypes, how these changes have shaped development and parallel evolution, and how noise affects regulatory circuits and their evolution.



Julia Zeitlinger Stowers Institute for Medical Research
David Arnosti Michigan State University
Justin Fay University of Rochester
Nicolas Rohner Stowers Institute for Medical Research

Program schedule

Thursday July 21
Friday July 22
Saturday July 23
Sunday July 24

Thursday agenda

12:00 PM - 5:00 PM
Auditorium foyer

Badge and program pickup

1:45 PM - 2:00 PM

Welcome and meeting introduction

2:00 PM - 3:10 PM

Session I: Enhancer evolution

Session chair: Julia Zeitlinger

How do enhancers evolve?
Emily Wong, Victor Chang Cardiac Research Institute
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning
Irene Kaplow, Carnegie Mellon University
The robustness and evolvability of a developmental enhancer
Timothy Fuqua, University of Zurich
Evolutionary modulation of transcriptional enhancer activity and accessibility in Drosophila
Nicolas Gompel, Ludwig-Maximilians Universität München
3:10 PM - 3:45 PM


3:50 PM - 5:00 PM

Session II: Mechanisms of regulatory divergence

Session chair: Nick Rohner

Inferring evolutionary mechanisms and transcription factor function from profiles of cis-regulatory divergence between mouse species
Rachel Brem, University of California, Berkeley
Development of stem cell approaches to characterize cell type and stage-specific cis-regulatory variation in mouse embryonic development
Thomas Vierbuchen, Memorial Sloan Kettering Cancer Center
Evolutionary dynamics of a robust transcriptional network
Pinar Onal, Northwestern University
5:00 PM - 5:10 PM

Flash talks

SLAM-seq disentangles the maternal-to-zygotic transition in early zebrafish development
Danielson Baia Amaral, Stowers Institute for Medical Research
Characterization of caffeine transcriptional response regulatory variants in vascular endothelial cells
Carly Boye, Wayne State University
Concentration-dependent transcription factor activity regulates target gene transcriptional onset
Eleanor Degen, Northwestern University
Active machine learning to improve predictions of cis-regulatory activity
Ryan Friedman, Washington University, St. Louis
Structure of Saccharomyces cerevisiae mediator-RNA polymerase II pre-initiation complex for divergent transcription
Jose Gorbea Colon, University of Pennsylvania
Multiplexed screening of developmental enhancers with high-sensitivity single-cell expression reporters
Jean-Benoit Lalanne, University of Washington at Seattle
False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5’ UTR annotations
Joel McManus, Carnegie Mellon University
Stochastic modeling of gene expression evolution uncovers tissue and sex specific properties of expression evolution in the Drosophila genus
Soumitra Pal, National Institutes of Health
Competitive DNA-binding of transcription factors
Yuning Zhang, Duke University
5:30 PM - 7:30 PM

Poster session I (odd numbers present)

Friday agenda

8:00 AM - 5:00 PM
Auditorium foyer

Badge and program pickup

9:00 AM - 10:15 AM

Session III: The cis-regulatory code of enhancers

Session chair: Dimple Notani

Decoding transcriptional regulation in Drosophila
Alex Stark, Research Institute of Molecular Pathology
Towards predicting gene expression from sequence
Jussi Taipale, University of Helsinki
Learning causal rules of immune cell differentiation within and across species
Sara Mostafavi, University of Washington
So just what is an enhancer, anyway?
Marc Halfon, State University of New York at Buffalo
10:15 AM - 10:35 AM


10:35 AM - 12:00 PM

Session IV: Cis-regulatory code and chromatin

Session chair: Michael White

Paralogous transcription factors diversify their DNA-binding targets via differential abilities to engage inaccessible chromatin
Shaun Mahony, Pennsylvania State University
Using genomics to study chromatin structure and dynamics
Srinivas Ramachandran, University of Colorado Anschutz Medical Campus
Control of enhancer activity by DNA methylation
Arnaud Krebs, European Molecular Biology Laboratory
The mutagenic cost of transcriptional regulation
Raluca Gordan, Duke University
11:50 AM - 12:00 PM

Flash talks

GADD45a gene as a reporter system to study enhancer–promoter communication
Gabrielle Baniulyte, State University of New York at Albany
Surfactant-like near-stochastic interactions are the key for the novel mechanism of eukaryotic gene activation
Brad Broyles, Butler University
Deciphering the cis-regulatory grammar of Hippo signaling transcription factors in mouse trophoblast stem cells
Khyati Dalal, Stowers Institute for Medical Research
Visualization of cis-regulatory sequence rules learned by neural networks
Charles McAnany, Stowers Institute for Medical Research
Regulation of Pol II transcriptomes through rigid pausing and premature termination
Sergei Nechaev, University of North Dakota
Evolutionary divergence of GAPDH genes through changes in gene expression levels and dynamics
Mohammad Siddiq, University of Michigan
Massively parallel reporter assays reveal differences in cis-regulatory function caused by disease causing mutations in a transcription factor
Michael White, Washington University, St. Louis
Understanding determinants of long-range enhancer-promoter interactions
Yawei Wu, Washington University, St. Louis
12:30 PM - 1:30 PM

Grad student and postdoc round tables

1:30 PM - 3:30 PM

Poster session II (even numbers present)

3:30 PM - 4:40 PM

Session V: Enhancer interactions and development decisions

Session chair: Nicolas Gompel

Dissecting enhancers hierarchy: one enhancer cluster at a time
Dimple Notani, National Centre for Biological Sciences
Distal and proximal cis-regulatory elements sense X chromosome dosage and developmental state at the Xist locus
Till Schwämmle, Max Planck Institute for Molecular Genetics
Spatial specificity of mammalian enhancer loops in vivo
Evgeny Kvon, University of California, Irvine
Reverse engineering gene regulatory circuitries underlying neural crest development
Tatjana Sauka–Spengler, Stowers Institute for Medical Research/University of Oxford
4:35 PM - 5:00 PM


5:00 PM - 6:35 PM

Session VI: Predictive modeling and biophysics

Session chair: Raluca Gordon

Using physics as a microscope to dissect transcriptional dynamics in development
Hernan Garcia, University of California, Berkeley
Massively parallel reporter assays, machine learning, and the biophysics of gene regulation
Justin Kinney, Cold Spring Harbor Laboratory
The cis-regulatory code of chromatin accessibility in the early Drosophila embryo
Julia Zeitlinger, Stowers Institute for Medical Research
The dynamic cis-regulatory sequence syntax on transcriptional regulatory elements in the human genome
Vivek Ramalingam, Stanford University

Saturday agenda

8:00 AM - 5:00 PM
Auditorium foyer

Badge and program pickup

9:00 AM - 10:10 AM

Session VII: Predictive models and divergence

Session chair: Sara Mostafavi

Understanding cis-regulatory evolution using machine learning and random DNA
Carl de Boer, University of British Columbia
Multi-factor ChIP-exo reveals TF binding dynamics within conserved orthologous cis regulatory modules in the mammalian liver
Michael Wilson, Hospital for Sick Children, Toronto
Turn it off or keep it on: the role of silencers and maintenance elements in phenotypic evolution
Mark Rebeiz, University of Pittsburgh
Identifying the enhancers and evolutionary processes shaping the Drosophila innate immune response
Zeba Wunderlich, Boston University
10:05 AM - 10:30 AM


10:30 AM - 11:20 AM

Session VIII: Causes and consequences of regulatory variation

Session chair: Zeba Wunderlich

Pleiotropic effects of cis- and trans-regulatory mutations on fitness and gene expression
Patricia Wittkopp, University of Michigan
Loss of heterochromatin at endogenous retroviruses creates competition for transcription factor binding
Ryan O’Hara, University of Texas Southwestern Medical Center
Evolutionary innovations in eukaryotic histone repertoires drive biological novelties
Pravrutha Raman, Fred Hutchinson Cancer Center
1:00 PM - 3:00 PM
Library, Conf. 114, Conf. B1

Breakout sessions

3:00 PM - 4:10 PM

Session IX: Cell gene regulation

Session chair: Patricia Wittkopp

Quantifying the impact of genomic and cellular environments on gene expression noise
Clarice Hong, Washington University in St. Louis
Multiplex functional dissection of cis-regulatory landscapes in early mammalian development
Samuel Regalado, University of Washington
Regulatory networks underlying metabolic adaptation and physiological resilience in animals
Nicolas Rohner, Stowers Institute for Medical Research
An ultra high-throughput, massively multiplexible, single-cell RNA-seq platform in yeasts that facilitates the extensive study of core processes in gene expression
Leandra Brettner, Arizona State University
4:10 PM - 4:30 PM


4:30 PM - 5:40 PM

Session X: Evolutionary divergence and stress

Session chair: Bin He

Genetic variation in the ubiquitin system creates complex, pathway-specific effects on proteasomal protein degradation
Frank Albert, University of Minnesota
Characterizing the grammar of stress-dependent gene regulatory elements
Morgan Sammons, State University of New York at Albany
Why do transcription factors depend on coactivators?
Lindsey Snyder, University of Iowa
Dual roles for valosin-containing protein in stress granule assembly and disassembly
Stephanie Moon, University of Michigan
5:45 PM - 6:15 PM

Breakout session summary presentations

Sunday agenda

9:00 AM - 10:25 AM

Session XI: Evolution of novelty/diversity

Session chair: David Arnosti

Cis-regulatory basis of developmental plasticity and sex-biased growth in the development and evolution of beetle horns
Phillip Davidson, Indiana University Bloomington
A regulatory network of Sox and Six transcription factors initiate a cell fate transformation during hearing regeneration in adult zebrafish
Erin Jimenez, National Institutes of Health
Evolution and binding specificity SIX homeodomain transcription factors
Jose Rodriguez–Martinez, University of Puerto Rico, Río Piedras Campus
Evolution of thermal tolerance in the Saccharomyces species
Justin Fay, University of Rochester
10:25 AM - 10:35 AM


10:45 AM - 11:35 AM

Session XII: Rapid evolution

Session chair: Marc Halfon

Fish(ing) in the Hi(gh)-C(sea)
Tathagata Biswas, Stowers Institute for Medical Research
Transcription factor binding sites are frequently under accelerated evolution in primates
Xinru Zhang, Pennsylvania State University
The landscape of molecular changes underlying 22 years of bacterial adaptation
Premal Shah, Rutgers University
11:35 AM - 12:00 PM

Poster prizes and conference conclusion