• Evolution and Core Processes in Gene Expression

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


The lectures will take place in Room 1415 of the Biomedical and Physical Sciences Building (BPS), 567 Wilson Road, East Lansing, MI 48824.

Thursday, May 9

Diversity of Systems for Evolutionary Gene Expression

Chair: David Arnosti

2:00–2:20 p.m.
Cell-type specific regulatory evolution of human brains
Soojin Yi, Georgia Tech
2:20–2:40 p.m.
The genomic basis of communication signal variation in electric fish
Jason Gallant, Michigan State University
2:40–3:00 p.m.
Replaying the evolutionary tape in synthetic Brassica napus polyploids: How deterministic is subgenome dominance?
Kevin Bird, Michigan State University
3:00–3:20 p.m.
Empirical measures of mutational effects define neutral models of regulatory evolution in budding yeast
Andrea Hodgins-Davis, University of Michigan

Systems and Computational Approaches to Regulation

Chair: Julia Zeitlinger

4:00–4:20 p.m.
Underground regulatory networks
Phil Benfey, Duke University
4:20–4:40 p.m.
Transcriptomes as phenotypes
David Angeles-Albores, Massachusetts Institute of Technology
4:40–5:00 p.m.
Identification and characterization of regulatory sequences in Zea mays
Maike Stam, University of Amsterdam
5:00–5:20 p.m.
Combinatorial control of specialized plant metabolism pathways
Erich Grotewold, Michigan State University
5:20–5:40 p.m.
Evolution of potato: The world’s most important vegetable crop
Robin Buell, Michigan State University

Friday, May 10

Endless Forms Most Wonderful

Chair: Shinhan Shiu

9:00–9:20 a.m.
Dynamics of genome evolution during a 30-year experiment with E. coli
Rich Lenski, Michigan State University
9:20–9:40 a.m.
RNA polymerase mutation and bacterial growth rate
Sean Crosson, University of Chicago
9:40–10:00 a.m.
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
10:00–10:20 a.m.
Acoel genome reveals the regulatory landscape of whole-body regeneration
Andrew Gehrke, Harvard University

Fish and Chips

Chair: Justin Fay

11:00–11:20 a.m.
Extensive changes in transcriptional regulation underlie life history evolution in sea urchins
Greg Wray, Duke University
11:20–11:40 a.m.
Odyssey of strange fish: 'Ancient fishes' illuminate vertebrate genome evolution
Ingo Braasch, Michigan State University
11:40 a.m. – 12:20 p.m.
Regulatory evolution in metabolic adaptation of Astyanax mexicanus
Jaya Krishnan, Stowers Institute for Medical Research
12:00–12:20 p.m.
Evolution of regulatory landscapes
Jose-Luis Gomez-Skarmeta, Pablo de Olavide University

Flash Talks

12:20–12:30 p.m.
Christina Akirtava, Pinar Onal, Baldur Kristiansson, Isabella Schember, Eliza Argyridou, Elizabeth Alger, Kyle Fowler.
1:30–3:30 p.m.
Poster Session in the Atrium

Engineering and Re-engineering of Regulatory Systems

Chair: Ingo Braasch

3:30–3:50 p.m.
Decoding development: from gene regulatory structure to function
Justin Crocker, European Molecular Biology Laboratory
3:50–4:10 p.m.
(Evolution of gene regulation)
Hunter Fraser, Stanford University
4:10–4:30 p.m.
(Evolution of stress responses)
Audrey Gasch, University of Wisconsin–Madison
4:30–4:45 p.m.
Harmonizing a million transcriptomes by imputing missing values and predicting sample sources
Arjun Krishnan, Michigan State University
4:45–4:50 p.m.
Poster prize announcements

Developmental Constraints and Evolution

Chair: Yongliang Yang

5:20–5:40 p.m.
Conservation and variation in embryonic developmental mechanisms
Mike Eisen, University of California, Berkeley
5:40–6:00 p.m.
Transcriptome changes after compensatory selection suppressed the phenotypic effects of two antagonizing developmental genes
Arnar Pálsson, University of Iceland
6:00–6:20 p.m.
Regulation of the maternal-zygotic transition in the haplo-diploid wasp Nasonia
Jeremy Lynch, University of Illinois at Chicago
6:20–6:40 p.m.
Both Drosophila- and mammalian-style dosage compensation on the neo Z chromosome in the monarch butterfly
Liuqi Gu, University of Kansas

Saturday, May 11

Nuts and Bolts of Evolutionary Processes - Transcription

Chair: Audrey Gasch

9:00–9:20 a.m.
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
9:20–9:40 a.m.
How pioneer factors potentiate transcription factor activity
Chris Rushlow, New York University
9:40–10:00 a.m.
Dissecting transcriptional regulation from nascent transcription
Robin Dowell, University of Colorado Boulder
10:00–10:20 a.m.
Lola-PI is a promoter pioneer factor that primes promoters for tissue-specific activation
Vivekanandan Ramalingam, Stowers Institute for Medical Research
10:20–10:40 a.m.
The RSC complex coordinates with histone acetyltransferases to regulate chromatin structure and transcription, genome-wide, in Saccharomyces cerevisiae
Chhabi Govind, Oakland University

The Life of RNA in Gene Expression

Chair: Mark Hill

11:00–11:20 a.m.
Ribosomes in gene regulation: Controlling the diversity of proteins that can be produced in specific cells, tissues & organisms
Maria Barna, Stanford University
11:20–11:40 a.m.
Analysis of uORF functions using a massively parallel reporter assay
Joel McManus, Carnegie Mellon University
11:40 a.m. – 12:00 p.m.
Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling
Polly Hsu, Michigan State University
12:00–12:20 p.m.
Post-transcriptional regulation by microRNAs mediates pigmentation development in Drosophila melanogaster: expanding a classic model of gene regulatory evolution
Abigail Lamb, University of Michigan
12:20–12:40 p.m.
Alpha-Proteobacterial mRNA decay is organized by a membraneless organelle
Jared Schrader, Wayne State University

Free time

2:00–6:00 p.m.

Sunday, May 12

Cellular States and Modifications

Chair: Arjun Krishnan

9:00–9:15 a.m.
A non-enzymatic function associated with a histone demethylase licenses epigenetic inheritance
Kaushik Ragunathan, University of Michigan
9:15–9:30 a.m.
The NAD+-dependent deacetylase Sir2 enables evolutionary adaptations by regulating distinct gene sets in two yeast species
Laura Rusche, SUNY Buffalo
9:30–9:45 a.m.
Long-range enhancer regulatory network construction and evolutionary analysis
Jianrong Wang, Michigan State University
9:45–10:00 a.m.
Determinants of cell type-specificity and cis-regulatory activity within the p53 family of transcription factors
Morgan Sammons, SUNY Albany

Patterns of Regulatory Variation

Chair: TBD

10:30–10:45 p.m.
Evolution of transcriptional dynamics in yeast
Justin Fay, University of Rochester
10:45–11:00 p.m.
Inter- and intra-population gene expression variation in the fat body during Drosophila melanogaster development
Amanda Glaser-Schmitt, Ludwig-Maximilians University
11:00–11:15 p.m.
Leaf vein patterning: Growth regulator dynamics of normal and transport-disrupted development
David Holloway, British Columbia Institute of Technology
11:15–11:30 p.m.
Convergent evolution of phosphatase gene families allows for specialization in phosphate and thiamine starvation in multiple yeast species
Bin He, Carnegie Mellon University
11:30–11:45 p.m.
Evolutionary dynamics of transcription initiation landscapes in budding and fission yeasts
Zhenguo Lin, Saint Louis University