Evolution and Core Processes in Gene Expression

May 9–12, 2019
Michigan State University, East Lansing, Mich.


David Arnosti, Michigan State University
Ingo Braasch, Michigan State University
Justin Fay, Washington University in St. Louis
Shin-han Shiu, Michigan State University
Julia Zeitlinger, Stowers Institute

Focus: Connections between gene expression and evolution, bringing in new aspects of plant genomics and computational evolution

We have recruited an exciting lineup of internationally prominent speakers for this year’s meeting, and look forward to highlighting trends in evolution and gene expression, including applications in computational and experimental evolution and plant sciences.

Evolutionary processes operate at all levels of gene expression, and increasingly detailed mechanistic understanding has provided rich hunting grounds for pathways and processes that underlie evolutionary variation. Attendees of previous meetings have been especially pleased with the wide disciplinary scope of our talks, as well as the high quality of invited speakers. We see much new ground to break in this area, including further exploration of how systems biology data points to the combined effects of evolutionary variation in central and peripheral processes (not simply changes that affect enhancers of specific target genes).

Michigan State University scientists will bring special expertise to the 2019 meeting in plant genetics and genomics, an area anchored by outstanding researchers of the DOE-supported Plant Research Laboratory and over 100 faculty in related sciences. The essential outlines of the Central Dogma that is key to gene expression (in particular the biochemical aspects) has been built on microbial and metazoan, not plant, systems. At the same time plants offer a degree of sophistication in metabolic pathways that put animals to shame, and the evolutionary diversification and selection of these paths offer important lessons in molecular evolutionary “engineering”.

Michigan State University also has strengths in computational evolution, a hybrid study area that has led to the creation of the NSF-supported BEACON (“evolution in action”) center. BEACON brings together scientists studying in the laboratory as well as scientists pioneering computational evolutionary approaches that impact biomedicine, engineering and behavioral studies. Our conference will benefit from presentations from top researchers in this field, stimulating discussion how in silico modeling and analysis can test specific features of gene expression control and evolution, and identify novel regulation that may be important for gene regulation in the context of synthetic biology.

Program schedule

Thursday May 9
Friday May 10
Saturday May 11
Sunday May 12

Thursday agenda

2:00 PM - 3:20 PM

Diversity of systems for evolutionary gene expression

Chair: David Arnosti

Cell-type specific regulatory evolution of human brains
Soojin Yi, Georgia Tech
The genomic basis of communication signal variation in electric fish
Jason Gallant, Michigan State University
Replaying the evolutionary tape in synthetic Brassica napus polyploids: How deterministic is subgenome dominance?
Kevin Bird, Michigan State University
Empirical measures of mutational effects define neutral models of regulatory evolution in budding yeast
Andrea Hodgins-Davis, University of Michigan
4:00 PM - 5:30 PM

Systems and computational approaches to regulation

Chair: Julia Zeitlinger

Underground regulatory networks
Phil Benfey, Duke University
Transcriptomes as phenotypes
David Angeles-Albores, Massachusetts Institute of Technology
Identification and characterization of regulatory sequences in Zea mays
Maike Stam, University of Amsterdam
Combinatorial control of specialized plant metabolism pathways
Erich Grotewold, Michigan State University
Evolution of potato: The world’s most important vegetable crop
Robin Buell, Michigan State University

Friday agenda

9:00 AM - 10:20 AM

Endless forms most wonderful

Chair: Shinhan Shiu

Dynamics of genome evolution during a 30-year experiment with E. coli
Rich Lenski, Michigan State University
RNA polymerase mutation and bacterial growth rate
Sean Crosson, University of Chicago
Identification of a novel Gcn5 histone acetyltransferase complex in Drosophila that is essential for development and contains the Dbf4 ortholog Chiffon
Vikki Weake, Purdue University
Acoel genome reveals the regulatory landscape of whole-body regeneration
Andrew Gehrke, Harvard University
11:00 AM - 12:20 PM

Fish and chips

Chair: Justin Fay

Extensive changes in transcriptional regulation underlie life history evolution in sea urchins
Greg Wray, Duke University
Odyssey of strange fish: 'Ancient fishes' illuminate vertebrate genome evolution
Ingo Braasch, Michigan State University
Regulatory evolution in metabolic adaptation of Astyanax mexicanus
Jaya Krishnan, Stowers Institute for Medical Research
Evolution of regulatory landscapes
Jose-Luis Gomez-Skarmeta, Pablo de Olavide University
12:20 PM - 12:30 PM

Flash talks

Christina Akirtava, Pinar Onal, Baldur Kristiansson, Isabella Schember, Eliza Argyridou, Elizabeth Alger, Kyle Fowler.

1:30 PM - 3:30 PM

Poster session

3:30 PM - 4:50 PM

Engineering and re-engineering of regulatory systems

Chair: Ingo Braasch

Decoding development: from gene regulatory structure to function
Justin Crocker, European Molecular Biology Laboratory
Evolution of gene regulation
Hunter Fraser, Stanford University
Evolution of stress responses
Audrey Gasch, University of Wisconsin–Madison
Harmonizing a million transcriptomes by imputing missing values and predicting sample sources
Arjun Krishnan, Michigan State University
5:20 PM - 6:40 PM

Developmental constraints and evolution

Chair: Yongliang Yang

Conservation and variation in embryonic developmental mechanisms
Mike Eisen, University of California, Berkeley
Transcriptome changes after compensatory selection suppressed the phenotypic effects of two antagonizing developmental genes
Arnar Pálsson, University of Iceland
Regulation of the maternal-zygotic transition in the haplo-diploid wasp Nasonia
Jeremy Lynch, University of Illinois at Chicago
Both Drosophila- and mammalian-style dosage compensation on the neo Z chromosome in the monarch butterfly
Liuqi Gu, University of Kansas

Saturday agenda

9:00 AM - 10:40 AM

Nuts and bolts of evolutionary processes — transcription

Chair: Audrey Gasch

Sibling cooperation and interparental conflict in a seed: How plant mothers, fathers and siblings behave during the act of reproduction in flowering plants
Ned Friedman, Harvard University
How pioneer factors potentiate transcription factor activity
Chris Rushlow, New York University
Dissecting transcriptional regulation from nascent transcription
Robin Dowell, University of Colorado, Boulder
Lola-PI is a promoter pioneer factor that primes promoters for tissue-specific activation
Vivekanandan Ramalingam, Stowers Institute for Medical Research
The RSC complex coordinates with histone acetyltransferases to regulate chromatin structure and transcription, genome-wide, in Saccharomyces cerevisiae
Chhabi Govind, Oakland University
11:00 AM - 12:40 PM

The life of RNA in gene expression

Chair: Mark Hill

Ribosomes in gene regulation: Controlling the diversity of proteins that can be produced in specific cells, tissues and organisms
Maria Barna, Stanford University
Analysis of uORF functions using a massively parallel reporter assay
Joel McManus, Carnegie Mellon University
Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling
Polly Hsu, Michigan State University
Post-transcriptional regulation by microRNAs mediates pigmentation development in Drosophila melanogaster: Expanding a classic model of gene regulatory evolution
Abigail Lamb, University of Michigan
Alpha-Proteobacterial mRNA decay is organized by a membraneless organelle
Jared Schrader, Wayne State University

Sunday agenda

9:00 AM - 10:00 AM

Cellular states and modifications

Chair: Arjun Krishnan

A non-enzymatic function associated with a histone demethylase licenses epigenetic inheritance
Kaushik Ragunathan, University of Michigan
The NAD+-dependent deacetylase Sir2 enables evolutionary adaptations by regulating distinct gene sets in two yeast species
Laura Rusche, SUNY Buffalo
Long-range enhancer regulatory network construction and evolutionary analysis
Jianrong Wang, Michigan State University
Determinants of cell type-specificity and cis-regulatory activity within the p53 family of transcription factors
Morgan Sammons, SUNY Albany
10:30 AM - 11:45 AM

Patterns of regulatory variation

Evolution of transcriptional dynamics in yeast
Justin Fay, University of Rochester
Inter- and intra-population gene expression variation in the fat body during Drosophila melanogaster development
Amanda Glaser-Schmitt, Ludwig-Maximilians University
Leaf vein patterning: Growth regulator dynamics of normal and transport-disrupted development
David Holloway, British Columbia Institute of Technology
Convergent evolution of phosphatase gene families allows for specialization in phosphate and thiamine starvation in multiple yeast species
Bin He, Carnegie Mellon University
Evolutionary dynamics of transcription initiation landscapes in budding and fission yeasts
Zhenguo Lin, Saint Louis University