EPIGENOMICS 2016

 

January 31 – February 5, 2016

Rio Grande, Puerto Rico


 

Sunday, January 31                    


 

17:30   Dinner

 

19:00   OPENING SESSION

 

Chairperson:   Dirk Schubeler, Friedrich Miescher Institute

 

Genetic effects on molecular phenotypes and disease biology

Emmanouil Dermitzakis

 

Shaping the blood: Lessons from Chromatin and single cell RNA dynamics

Ido Amit

 

Nucleotide characteristics, chromatin composition, and transcriptional relationships of RNA:DNA hybrids in the human genome

John Greally

 

Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), a novel ligation-free approach

Ana Pombo, Robert A. Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C.A. Kraemer, Mita Chotalia, Sheila Xie, Mariano Barbieri, Ines de Santiago, Liron-Mark Lavitas, Miguel R. Branco, James Fraser, Josee Dostie, Laurence Game, Niall Dillon, Paul Edwards and Mario Nicodemi

 

Regulatory roles of RNA repeats

Ezgi Hacisuleyman, Chinmay Shukula and John Rinn

 

Reading and writing DNA methylation

Dirk Schubeler

 

21:30   Social

 

Monday, February 1                    


 

7:30     Breakfast

 

9:00     SESSION 2 – CANCER EPIGENOMICS

 

Chairperson:   Kim McAllister, NIEHS

 

The 3D architecture of the breast cancer genome reveals oncogenic noncoding mutations regulating ESR1 expression

Swneke D. Bailey, Kinjal Desai, Parisa Mazrooei, Nicholas A. Sinnott-Armstrong, Mark Dowar, Xue Wu, Rossanna C. Pezo, Benjamin Haibe-Kains, Philippe L. Bedard, Trevor J. Pugh, Richard  C. Sallari and Mathieu Lupien

 

Mammalian SWI/SNF (BAF) complex structure and function in human cancer

Cigall Kadoch

 

Characterization of the Anti-Tumour Effects of EZH2 Inhibition in Atypical Teratoid Rhabdoid Tumours

Shengrui Feng, King Ching Ho, Rajat Singhania, Jonathon Torchia, Annie Huang and Daniel De Carvalho      

 

Cancer Mutations of mSWI/SNF Enhance Polycomb Activity at CpG- Island Promoters

Courtney Hodges, Benjamin Z. Stanton, Wai Lim Ku, Keji Zhao and Gerald R. Crabtree          

 

Integrated regulator genomics of renal cell carcinoma

Shreeram Akilesh, Kyle Siebenthall, Richard Sandstrom, Alex Reynolds,  Audra Johnson, Jemma Nelson and John Stamatoyannopoulos

 

Balancing Genomic Accessibility by BAF-Polycomb Opposition

Gerald Crabtree

 

TMPRSS2-ERG drives global mistargeting of mammalian SWI/SNF (BAF) complexes in prostate cancer

Gabriel Sandoval, John Pulice, Monica Schenone, David Takeda, Marius Pop, Gaylor Boulay, Miguel Rivera, Lucienne Ronco, William Hahn and Cigall Kadoch       

 

Genome-wide chromatin accessibility changes regulated by Nfib defines SCLC metastatic state and drives SCLC metastatic ability

Sarah Denny, Dian Yang, Monte Winslow, Julian Sage and William Greenleaf 

 

Profound TET loss-of-function results in genome instability and oncogenesis

Isaac López-Moyado, Ageliki Tsagaratou, Sini Rautio, Edah’ Gonz‡lez- Avalos, James Scott-Browne, David Adams, Harri LŠhdesmŠki and Anjana Rao     

 

A genome-epigenome perspective of clonal evolution in human tumors

Joseph Costello, Tali Mazor, Alex Pankov and Jun Song         

 

 

12:00   Lunch

 

13:30   WORKSHOP I – Accessing and Visualizing Epigenomic Data

 

Engaging epigenomics resources

Ting Wang, Washington University

 

Online resources of the Roadmap Epigenomics project

Wouter Meuleman, MIT

 

The WashU Epigenome Browser (Hands-on demo)

Renee Sears, Washington University

 

The Roadmap Epigenome Browser (Hands-on demo)

Nicole Rockweiler, Washington University

 

 

15:30   SESSION 3 – CHROMATIN ARCHITECTURE AND FUNCTION

 

Chairperson:   Job Dekker, University of Massachusetts

 

Sex chromosomes: models for structure-function studies of Chromosomes

Job Dekker

           

Analyzing the dynamic landscape of 3D genome structures

Frank Alber

 

Gene expression changes in neuronal dierentiation captured by Hi-C Trees

Tiago Rito, Markus Schueler, Stuart Aitken, Andrea Maria Chiariello, James Fraser, Carmelo Ferrai, Mariano Barbieri, Kelly J. Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, The FANTOM Consortium, Colin A. Semple, Josee Dostie, Mario Nicodemi and Ana Pombo           

 

Genomic characterization of the developing bat wing

Walter Eckalbar, Stephen Schlebusch, Mandy Mason, Zoe Gill, Betty Booker, Nadja Makki, Tara Friedrich, Katherine Pollard, Lucia Carbone, Jeff Wall, Nicola Illing and Nadav Ahituv

 

Chromatin interactions in single cells

Peter Fraser     

 

Genome-wide characterization of mammalian retrotransposon exaptation due to tissue-specific regulatory function

Aaron Hardin, Navneet Matharu and Nadav Ahituv

 

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

Jay Shendure, Matthew Snyder, Martin Kircher and Andrew Hill

 

Massively multiplexed single-cell Hi-C by combinatorial barcoding

Vijay Ramani, Xinxian Deng, Christine Disteche, Zhijun Duan and Jay Shendure

 

Enhancer States during Drosophila Development

Julia Zeitlinger  

 

18:05   Dinner –'Bievenidos a Puerto Rico'

 

19:30   KEYNOTE LECTURE

 

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

Joseph R. Ecker Salk Institute for Biological Studies and HHMI

 

20:30   Welcome Reception

 

Tuesday, February 2                   


 

 

7:30     Breakfast

 

9:00     SESSION 4 – EPIGENOME REGULATION AND DYNAMICS

 

Chairperson: Henk Stunnenberg, Radboud University, Netherlands

 

Genome-wide analysis of protein-DNA interactions

Arttu Jolma, Yimeng Yin, Bei Wei, Jian Yan, Teemu Kivioja, Syed Khund-Sayeed, Ekaterina Morgunova, Charles Vinson and Jussi Taipale

 

Blocks of tightly coupled DNA methylation in human stem cells and cancers.

Kun Zhang, Shicheng Guo, Dinh Diep and Nongluk Plongthongkum

 

Insights from methylome analysis

Stephan Beck

 

Nucleosome density ChIP-seq identifies distinct promoter associated chromatin modification signatures

Martin Hirst and Alireza Lorzadeh

 

Epigenomic establishment of macrophage tolerance and training

Henk Stunnenberg

 

Massively parallel reporter assays reveal glucocorticoid receptor interaction modules that direct gene expression responses to corticosteroids

Christopher Vockley, Anthony D'lppolito, Ian McDowell, William Majoros, Alexias Safi, Lingyun Song, Gregory Crawford and Timothy Reddy

 

Large-scale Inference of Activating and Repressive Nucleotides at High Resolution in Human Cell Types Using Tiling Reporter Assays

Jason Ernst, Tarjei Mikkelsen and Manolis Kellis

 

Synchronized mitochondrial and cytosolic translation programs

Stirling Churchman

 

Exploring the role of Tet1 in genomic imprinting

Jennifer Myers, Lara Abramowitz and Marisa Bartolomei

 

Towards Quantitative Epigenetics: Building the Foundation of Epigenomcis Roadmaps

Zhaoyu Li        

 

Single molecule characterization of histone marks co-occurrence reveals extensive dynamics of bivalent domains in mammalian development

Assaf Weiner, David Lara-Aristo, Vladik Krupalnik, Eyal David, Jacob Hanna and Ido Amit

 

Comprehensive mapping of chromatin dynamics during blood formation

David Lara Astiaso and Assaf Weiner

 

 

12:00   Lunch

 

13:30 WORKSHOP II – Analyzing DNA Methylation Data: A hands-on workshop

Fabian Müller, Max-Planck-Institut für Informa

 

16:00 SESSION 5 – EPIGENOME VARIATION

 

Chairperson: Aleksander Milosavljevic, Baylor College of Medicine

 

From genomics to precision medicine: Uncovering and manipulating the genetic circuits underlying common disease

Manolis Kellis

 

Systematic identification of predictive casual GWAS SNPs within transcription factor binding sites that control chromatin landscape

Yunxian Liu and Michael Guertin

 

Sequence variation affecting transcription factor occupancy in highly diverged mouse strains

Matthew T Maurano, Jessica M Halow, Rachel Byron, Mark Groudine, M A Bender and John A

Stamatoyannopoulos

 

Systematic identification and characterization of regulatory variants in GWAS regions

Cong Guo, Christopher M. Vockley, Ian C. McDowell, William H. Majoros and Timothy E. Reddy

 

Allelic epigenomes shed light on the function of noncoding variants in the human genome

Vitor Onuchic, Ivenise Carrero, Eugene Lurie, Piotr Pawliczek, Ronak Patel, Timur Galeev, Joel Rozowsky, Robert Altshuler, Zhuoyi Huang, Zhizhuo Zhang, Alan Harris, Fuli Yu, Mark Gerstein, Manolis Kellis and Aleksandar Milosavljevic

 

Epigenomic deconvolution of tumor tissue biology

Aleksandar Milosavljevic

 

Impact of transposable elements on transcription regulation in human

Guillaume Bourque

 

 

18:15               Dinner - Seafood by the Sea

 

 

20:00 SESSION 6 – TRANSCRIPTION AND NON-CODING RNA

 

Chairperson: Lisa Chadwick, NIEHS and 4D Nucleome Program

 

Many promoters of lncRNAs and mRNAs act as enhancers in local gene regulatory networks

Jesse Engreitz, Jenna Haines, Glen Munson, Patrick McDonel, Mitchell Guttman and Eric Lander

 

Differential enhancer transcription defines a gene regulatory network

Rangarajan Nadadur, Jenna Bekeny and Ivan Moskowitz

 

How a lncRNA shapes chromatin structure to control gene expression

Mitchell Guttman

 

Genome-wide views into the mechanisms of transcription regulation triggered by the stress response

John Lis, Charles Danko, Fabiana Duarte, Michael Guertin and Dig Bijay Mahat

 

Comprehensive RNA Polymerase II Interactomes Reveal the Distinct and Varied Roles for Each Phospho-CTD Residue

Kevin Harlen, Kristine Trotta, Erin Smith, Mohammad Mosaheb, Stephen Fuchs and Stirling Churchman

 

Integration of regulatory information at promoters through combinatorial control of the transcriptional cycle

Clarissa Scholes, Angela H. Depace and Alvaro Sanchez

 

 

21:30   Social / Poster Session I

 

Wednesday, February 3


 

7:30 Breakfast

 

8:45 SESSION 7 – ENVIRONMENT AND AGING

 

Chairperson: Frederick Tyson, NIEHS

 

Cumulative impact of large chromosomal duplications and polychlorinated biphenyl exposure on DNA methylation, chromatin, and expression of synaptic genes

Keith Dunaway, Saharul Islam, Roy Chu, Rochelle Coulson, Dag Yasui, Diane Schroeder, Isaac Pessah, Paul Lott, Makiko Meguro-Horike, Shin-Ichi Horike, Ian Korf, Jesse Lopez and Janine Lasalle

 

Epigenomics and prenatal exposure to environmental pollutants: New Data from CHAMACOS Birth Cohort Study

Nina Holland, Paul Yousefi, Karen Huen, Daneida Lizarraga, Gwen Tindula, Kim Harley and Brenda Eskenazi

 

Regulatory landscape remodeling by endocrine disruptors

Kyle Siebenthall, Richard Sandstrom, Jessica Halow, Kristen Lee, R. Scott Hansen, Peter Sabo, Rajinder Kaul and John Stamatoyannopoulos

 

Epigenetic variation in the brain: neurodevelopment and neuropsychiatric disease

Jonathan Mill

 

Non-Genomic Signaling to MLL Developmentally Reprograms Histone Methylation and Susceptibility to Prostate Carcinogenesis

Quan Wang, Lindsey Treviño, Mario Medvedovic, Shuk-Mei Ho, Charles Foulds, Bert O'Malley and Cheryl Walker

 

Schizophrenia-associated epigenetic variation in the brain

Joana Viana, Eilis Hannon, Ruth Pidsley, Emma Dempster, Helen Spiers,Ruby Macdonald, Claire Troakes, Safa Al-Saraj, Naguib Mechawar, Gustavo Turecki, Leonard Schalkwyk, Nicholas Bray and Jonhattan Mill

 

Increased DNA Methylation Variability in Type 1 Diabetes Across Three Immune Effector Cell Types

Dirk Paul and Stephan Beck

 

Lactose intolerance is directed by DNA haplotype-dependent epigenetic aging

Viviane Labrie, Orion J Buske,Edward Oh, Richie Jeremian, Carolyn Ptak, Giedrius Gasiunas, Almantas Maleckas, Ruta Petereit, Aida Zvirbliene, Kestutis Adamonis, Edita Kriukienė, Karolis Koncevicius, Juozas Gordevičius, Akhil Nair, Aiping Zhang, Sasha Ebrahimi, Gabriel Oh, Virginijus Siksnys, Limas Kupcinskas, Michael Brudno, Art Petronis

 

Importance of single cell resolution in tissue based epigenomic research

Tan A. Ince, Sandro Santagata, E. Andres Houseman and J. Chuck Harrell

 

Metabolic and Gene Regulatory Networks

Marian Walhout

 

12:00   Lunch

 

13:00 WORKSHOP III – Integrative Tools and Resources

 

ChromHMM: Chromatin state discovery and characterization

Jason Ernst, UCLA

 

The ENCODE encyclopedia and variant annotation using RegulomeDB and HaploReg

Jill Moore, University of Massachusetts Medical School

 

Juicebox: Visualization software for Hi-C data

Erez Lieberman-Aiden, Baylor College of Medicine

 

 

15:00   SESSION 8 – X-INACTIVATION, IMPRINTING, AND MONOALLELIC EXPRESSION

 

Chairperson: Marisa Bartolomei, University of Pennsylvania

 

Factors involved in maintaining the organization of the human inactive chromosome

Brian Chadwick, Emily Darrow, Andrew Seberg and Zhuo Sun

 

Allele-specific FISH reveals epigenetic mosaicism in an imprinting mutant

Paul Ginard, Jennifer Kalish, Connie Jiang, Arjun Raj and Marisa Bartolomei

 

The Xist lncRNA recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing

Chun-Kan Chen, Mario Blanco, Constanza Jackson, Erik Aznauryan, Christine Surka, Amy Chow and Mitchell Guttman

 

Unusual maintenance of X-chromosome Inactivation predisposes female lymphocytes for increased expression from the inactive X

Montserrat Anguera

 

The mammalian sperm epigenome

Oliver Rando

 

Relationship between Xi compaction and gene silencing

Zhuo Sun and Brian Chadwick

 

Diploid maps of chromatin interactions reveal allele-specific looping and the unique structural conformation of the inactive X chromosome

Miriam Huntley, Suhas Rao, Neva Durand, Elena Stamenova, Ivan Bochkov, James Robinson, Adrian Sanborn, Ido Machol, Arina Omer, Eric Lander and Erez Lieberman Aiden

 

Nucleoporin-mediated regulation of a genomic imprinted domain

Mellissa Mann, Saqib Sachani, Liyue Zhang, Carlee White and Lauren Landschoot

 

Deciphering mechanisms of monoallelic olfactory receptor expression

Stavros Lomvardas and Kevin Monahan

 

 

17:50   Dinner - 'Taste of Caribbean Islands'

 

19:05   SESSION 9 – COMPUTATIONAL EPIGENOMICS

 

Chairperson: Steven Jones, Canada's Michael Smith Genome Sciences Centre

 

Deep learning frameworks for regulatory genomics and epigenomics

Chuan Sheng Foo, Nicholas Sinnott-Armstrong, Avanti Shrikumar, Yonatan Israeli, William Greenleaf and Anshul Kundaje

 

Not Just a Black Box: Interpretable Deep Learning for Genomics and Epigenomics

Avanti Shrikumar and Anshul Kundaje

 

epilogos: A statistical approach for mining multi-tissue chromatin state annotations

Wouter Meuleman and Manolis Kellis

 

Global models of transcriptional regulation in 127 human cell types

Brian Cleary, Aviv Regev and Eric Lander

 

Modular Combinatorial Binding among Human Trans-acting Factors Reveals Direct and Indirect Factor Binding

Yuchun Guo and David Gifford

 

Integrating regulatory information away from equilibrium

Angela DePace, Clarissa Scholes, Javier Estrada, Felix Wong, Alvaro Sanchez and Jeremy Gunawardena

 

Deciphering the Role of Various Mechanisms in Transcription Factor-DNA Binding on a Protein Family-Specific Basis

Beibei Xin, Satyanarayan Rao, Tsu-Pei Chiu, Lin Yang and Remo Rohs

 

Principles of epigenome conservation

Ting Wang

 

 

21:30   Social / Poster Session II

 

Thursday, February 4


 

7:30     Breakfast

 

8:40     SESSION 10 – SINGLE CELL EPIGENOMICS & NEW TECHNOLOGIES

 

Chairperson: John Satterlee, NIDA and 4D Nucleome Program

 

The Human Genome's 3D Code

Erez Lieberman-Aiden  

 

Analysis of RNA binding specificities of proteins using RHT-SELEX

Estefania Mondragon, Arttu Jolma, Jussi Taipale and Louis J. Maher

 

Leveraging spectral encoding for high-dimensional biological multiplexing

H. Q. Nguyen, B. C. Baxter, C. A. Diaz-Botia, K. Brower, J. L. DeRisi, K.S. Thorn and P.M. Fordyce

 

A Novel Tool to Comprehensively Map Organization of RNA and DNA in Higher-Order Nuclear Structures

Sofia Quinodoz, Noah Ollikainen, Alexander Shishkin, Pamela Russell, Mason Lai, Amy Chow and Mitchell Guttman

 

Single-cell chromatin accessibility reveals principles of regulatory variation

Jason Buenrostro, Beijing Wu, Ulrike Litzenburger, Dave Ruff, Michael Gonzales, Michael Snyder, Chang Howard, Ravi Majeti, Ryan Corces and William Greenleaf

 

Single-cell transcriptional profiling of the mouse dentate gyrus

Hannah Hochgerner, Amit Zeisel, Peter Lönnerberg and Sten Linnarsson

 

Elucidating Chromatin Architecture by Combinatorial Co-ImmunePrecipitation (co-ChIP)

Ronen Sadeh, Roee Launer-Wachs, Hava Wandel, Ayelet Rahat and Nir Friedman

 

Epigenetic priming of enhancers predicts developmental competence during endodermal lineage differentiation

Feng Yue, Allen Wang, Yan Li, Maike Sander and Bing Ren

 

Molecular anatomy of the brain by single-cell RNA-seq

Sten Linnarsson

 

 

12:00   Lunch

Excursions (El Yunque, Rain Forest and Old San Juan)

 

 

18:00   SESSION 11 – RAPID-FIRE TALKS

 

Chairperson: John Rinn, Harvard University

 

Repeat Browser: a resource to wrangle sequencing data in a TEcentric manner

Deepak Purushotham, Daofeng Li and Ting Wang

 

Targets for Developmental Reprogramming in the Liver

Lindsey Treviño, Cristian Coarfa, Quan Wang, Charles Foulds, Bert O'Malley and Cheryl Walker

 

Mapping epigenomic pathways of resilience acquired in early life

Annie Ciernia, Dag Yasui, Akanksha Singh, Jessica Cope, Tallie Baram, Keith Dunaway and Janine Lasalle

 

Aberrant DNA hypomethylation following loss or amplification of mutant IDH1 in glioma

Tali Mazor, Llewellyn E. Jalbert, Aleksandr Pankov, Josie Hayes, Sarah J. Nelson, Andrew W. Bollen, Susan Chang, Arie Perry, Adam B. Olshen, Henrik Bengtsson, Joanna J. Phillips and Joseph Costello

 

The impact of metabolic adaptations on epigenetic profiles in taxane resistance in triple-negative breast cancer

Genevieve Deblois, Yunchi Kao, Alexandra Fedor, Benjamin Haibe-Kains and Mathieu Lupien

 

A comprehensive map and comparative analysis of cis-regulatory elements in the zebrafish genome

Hongbo Yang, Tingting Liu, Yanli Wang, Glenn Gerhard and Feng Yue

 

The roles of tRNA modifications in translation in Saccharomyces cerevisiae

Hsin-Jung Chou, Elisa Donnard and Oliver Rando

 

Epigenome changes of osteoblasts during zebrafish fin regeneration

Hyung Joo Lee, Stephen Johnson and Ting Wang

 

Limited sets of transcription factors are strongly active in specific cell types

Bei Wei, Inderpreet Sur, Arttu Jolma and Jussi Taipale

 

 

19:10   Dinner – Pig Roast

 

20:30   Beach Party

 

 

Friday, February 5


 

7:30     Breakfast

 

9:00     SESSION 12 – EPIGENOME EDITING AND ENGINEERING

 

Chairperson: John Stamatoyannopulos, University of Washington

 

Epigenome Editing with CRISPR/Cas9 Technologies for Programming Cell Phenotype and Functional Epigenomics

Charles Gersbach, Pablo Perez-Pinera, Lauren Polstein, Ami Kabadi, Isaac Hilton, Pratiksha Thakore, Joshua Black, Tyler Klann, Gregory Crawford and Timothy Reddy

 

Epigenome Editing with CRISPR/Cas9 for Annotating Regulatory Element Function

Tyler Klann, Pratiksha Thakore, Isaac Hilton, Gregory Crawford, Timothy Reddy and Charles Gersbach

 

Conditional "Carpet Bombing" CRISPR/Cas9-based genome engineering in zebrafish

Hyo Sik Jang, Stephen L. Johnson and Ting Wang

 

Cas9-mediated in situ saturating mutagenesis for enhancer functional dissection

Daniel Bauer

 

Finding chromatin marks that matter using a CRISPR-based epigenetic screening method

Anna Köferle, Stefan H. Stricker, James Barrett, Catherine King and Stephan Beck

 

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Adrian Sanborn, Suhas Rao, Su-Chen Huang, Neva Durand, Miriam Huntley, Andrew Jewett, Ivan Bochkov, Dharmaraj Chinnappan, Ashok Cutkosky, Jian Li, Kristopher Geeting, Andreas Gnirke, Alexandre Melnikov, Doung McKenna, Elena Stamenova, Eric Lander and Erez Lieberman Aiden

 

CRISPR/Cas9 for complex transcription regulation and disease modeling

Stanley Qi

 

11:30   Lunch

 

Departure