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This meeting took place in 2015


Here are the related meetings in 2016:
Noncoding RNAs in Health and Disease (Q5)

For a complete list of the meetings for the upcoming/current season, see our meeting list, or search for a meeting.

Long Noncoding RNAs: From Evolution to Function (C7)


Organizer(s) Leonard Lipovich, Jeannie T. Lee, John L. Rinn and James (Ben) Brown
March 15—20, 2015
Keystone Resort • Keystone, Colorado USA
Discounted Abstract Deadline: Nov 18, 2014
Abstract Deadline: Dec 16, 2014
Scholarship Deadline: Nov 18, 2014
Discounted Registration Deadline: Jan 15, 2015

Sponsored by Cell Research, Isis Pharmaceuticals, Inc., Regeneron Pharmaceuticals, Inc. and Sarepta Therapeutics

Summary of Meeting:
It has become clear that metazoan genomes are replete with transcription from non-protein-coding regions, generating many long noncoding RNA (lncRNA) transcripts. Recent progress has enabled genome-wide mapping of lncRNAs and has unraveled unifying themes; lncRNAs function as epigenetic regulators, scaffolds, decoys, and enhancers. While these and other themes have been pursued in several meetings, the field has matured in numerous novel directions; the meeting leverages these to characterize lncRNAs comprehensively across metazoan genomes. The aim is to broaden our horizons with emerging data from humans and model systems, empowered by novel genomic technologies, including RNA-protein interaction mapping (CLIP- and RIP-seq), reverse genetics for lncRNAs not conserved in evolution (RNA sequencing in control and lncRNA-perturbed backgrounds), and proteogenomics to empirically bound the translational output of putative lncRNAomes. These topics have recently amassed diverse insights into RNA biology. The meeting should integrate novel findings, enhance previously proposed models of lncRNA function and generate new testable hypotheses. Synthesis of RNA structure, function, evolution and informatics will foster progress in this rapidly growing field.

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No registration fees are used to fund entertainment or alcohol at this conference

Conference Program    Print  |   View meeting in 12 hr (am/pm) time


SUNDAY, MARCH 15

16:00—20:00
Arrival and Registration

Keystone Lodge Lobby
18:00—20:00
Welcome Mixer
No registration fees are used to fund alcohol served at this function.

Keystone Lodge-Bighorn Bar

MONDAY, MARCH 16

07:00—08:00
Breakfast

Shavano/Torreys
08:00—08:15
Welcome Remarks
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting

Grays Peak
Leonard Lipovich, Wayne State University, USA

Jeannie T. Lee, Massachusetts General Hospital, USA

James (Ben) Brown, Lawrence Berkeley National Laboratory, USA

John L. Rinn, Harvard University, USA

08:15—09:45
Keynote Session
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting

Grays Peak
* James (Ben) Brown, Lawrence Berkeley National Laboratory, USA

Thomas R. Cech, HHMI/University of Colorado, USA
A Short History of Noncoding RNA Research

Lynne E. Maquat, University of Rochester Medical Center, USA
Control of Gene Expression via lncRNAs and mRNAs that Contain SINEs

10:05—11:45
The Multidimensional lncRNA Landscape
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
This session interrogates the genomic and subcellular cartography of long noncoding transcripts in metazoans. The speakers will leverage ENCODE and other community results and next-generation sequencing to emerge with a functional catalog of mammalian lncRNA genes and transcripts, as well as a unifying nomenclature for the lncRNA community.

Grays Peak
* John L. Rinn, Harvard University, USA

John S. Mattick, Garvan Institute of Medical Research, Australia
The Human Genome as the Zip File Extraordinaire

Nenad Bartonicek, Garvan Institute of Medical Research, Australia
Short Talk: Uncovering Hidden Genes in Intergenic GWAS Regions

Sanjida H. Rangwala, National Institutes of Health, USA
Short Talk: Curation and Evidence Reporting of Eukaryotic RefSeq Long Noncoding RNA Genes and Transcripts

09:45—10:05
Coffee Break

Longs Peak Foyer
11:45—13:00
Poster Setup

Shavano/Torreys
13:00—22:00
Poster Viewing

Shavano/Torreys
11:45—14:30
On Own for Lunch

14:30—16:30
Workshop 1

Grays Peak
* Anna Roth, German Cancer Research Center, DKFZ, Germany

Mitchell R. O'Connell, University of California, Berkeley, USA
Programmable RNA Targeting and Cleavage by CRISPR/Cas9

Guruharsha Kuthethur Gururaj, Biogen Idec, USA
Mapping RNA-Protein Interaction Modules Important in Neurodegeneration

Hans E. Johansson, Biosearch Technologies, Inc., USA
Duplex Imaging of Pre-lncRNAs and Mature lncRNAs by Stellaris® RNA Fluorescence in situ Hybridization (RNA FISH)

* Mathew Thayer, Oregon Health & Science University, USA
Large Noncoding RNA Genes Control Chromosome-Wide Replication Timing and Stability

Karyn Schmidt, Dana-Farber Cancer Institute, Harvard Medical School, USA
Characterization of a lncRNA Contributing to Melanoma Invasion

Martin A. Smith, Garvan Institute of Medical Research, Australia
The Modular Transcriptome: Unraveling a Network of Functional, Structured Noncoding RNA Domains

Per A. Johnsson, Karolinska Institutet, Sweden
A Novel Role of PTENpg1 as RNA in Drug Response and Outcome in Melanoma

16:30—17:00
Coffee Available

Longs Peak Foyer
17:00—19:15
LncRNA Form and Function
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
This session introduces current challenges in, and methods for studying, lncRNA secondary structure and lncRNA-containing ribonucleoprotein complexes. Presentations will inspire and motivate whole-genome approaches to lncRNA structure, lncRNPs and lncRNA post-transcriptional modifications.

Grays Peak
* Karissa Y. Sanbonmatsu, Los Alamos National Laboratory, USA

Phillip A. Sharp, Massachusetts Institute of Technology, USA
Origins of Long Noncoding RNAs and New Families of Argonaute-Associated Nuclear RNAs

Ingrid Grummt, German Cancer Research Center, Germany
DNA:RNA Triplexes Guide Chromatin Modifiers to Regulatory Gene Sequences

Boris Guennewig, Garvan Institute of Medical Research, Australia
Short Talk: Functional Characterization of the Human Brain Transcriptome in Parkinson’s Disease

Howard Y. Chang, Stanford University, USA
Genome Regulation by Long Noncoding RNAs

Anindya Dutta, University of Virginia, USA
Short Talk: Long Noncoding RNAs, H19 and MUNC, Promote Skeletal Muscle Differentiation by Two Different Mechanisms

19:15—20:15
Social Hour with Lite Bites
No registration fees are used to fund alcohol served at this function.

Shavano/Torreys
19:30—22:00
Poster Session 1

Shavano/Torreys

TUESDAY, MARCH 17

07:00—08:00
Breakfast

Shavano/Torreys
08:00—11:15
LncRNA Evolution: Non-Conserved Functions and Species Uniqueness
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
Here, we will focus on one of the grandest challenges in contemporary biology: Why are the sequences of biologically essential lncRNAs - in contrast to protein-coding genes - often not conserved, even between closely related species? The speakers will discuss functions of non-conserved lncRNAs, focusing on lncRNA roles in species phenotypic uniqueness, species-specific disease, and networks that highlight the need to leverage clinical studies and samples in the pursuit of basic science.

Grays Peak
* Kevin V. Morris, University of New South Wales, Australia

Leonard Lipovich, Wayne State University, USA
The Primate-Specific LncRNAome: Roles in Species Uniqueness, Human Brain and Cancer

Jennifer Harrow, Wellcome Trust Sanger Institute, UK
Identifying and Cataloguing Functional LncRNAs in Reference Genomes

Nikolaus Rajewsky, Max Delbruck Center for Molecular Medicine, Germany
Circular RNAs in the Mammalian Brain

Piero Carninci, RIKEN Center for Life Science Technologies/TransSINE Technologies Inc.
Discovery and Potential Therapeutic Applications of SINEUPs, lncRNA that Stimulate Protein Translation

Jonathan S. Weissman, University of California, San Francisco, USA
Exploring Translation Outside of Canonical Protein Coding Region with Ribosome Profiling

09:20—09:40
Coffee Break

Longs Peak Foyer
11:15—13:00
Poster Setup

Shavano/Torreys
13:00—22:00
Poster Viewing

Shavano/Torreys
11:15—14:30
On Own for Lunch

14:30—16:30
Workshop 2

Grays Peak
* Howard Y. Chang, Stanford University, USA

* Marina Barriocanal, University of Navarra - FIMA, Spain

Brian S. Clark, Johns Hopkins University, USA
Dynamic Expression of lncRNAs and Examination of their Role in Retinal Progenitor Competence

Rohit Malik, University of Michigan, USA
Integrative Analysis of Androgen Receptor Regulated Long Noncoding RNA in Prostate Cancer

Maninjay K. Atianand, University of Massachusetts Medical School, USA
LincRNA-Eps Controls Immune Responses in Macrophage and Mice

Evan S. Forsythe, University of Arizona, USA
Phylogenetic Analysis of lincRNA Origins and Evolution in the Plant Family Brassicaceae

Jhumku D. Kohtz, Feinberg School of Medicine, Northwestern University, USA
The Ultraconserved Evf2 lncRNA Reduces Seizure Susceptibility in Mice

Hazuki Takahashi, RIKEN, Japan
Mapping of Functional Domains of SINEUPs, Antisense lncRNAs that Enhance Protein Translation

Susan A. Boackle, University of Colorado School of Medicine, USA
Altered Expression of Long Noncoding RNA Is Associated with a Lupus-Associated Variant in Complement Receptor 2

16:30—17:00
Coffee Available

Longs Peak Foyer
17:00—19:15
In vivo Roles of lncRNAs: The Promises and Limitations of Animal Models
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
Animal models for conserved lncRNAs with crucial human disease functions, such as MALAT-1, have surprisingly failed to recapitulate the human phenotypes. The goal of this session is to develop a mechanistic understanding of these limitations - and to highlight other animal models in which human lncRNAs, including non-conserved ones, can be more tractable.

Grays Peak
* Leonard Lipovich, Wayne State University, USA

Alexandra Henrion-Caude, Necker Hospital – Imagine Foundation, France
Learning about Human lncRNA by Repetition and Reduction

Kevin G. Nyberg, University of Maryland, College Park, USA
Short Talk: Comparative Transcriptomics of Long Intergenic Noncoding RNAs in Drosophila

Ciro Bonetti, Memorial Sloan Kettering Cancer Center, USA
Short Talk: Mouse Models to Dissect Oncogenic and Tumor-Suppressive Functions of lincRNAs

Sven Diederichs, German Cancer Research Center DKFZ, Germany
Long Noncoding RNA Function in Cancer

Caio F. Damski, University of New South Wales, Australia
Short Talk: Saving the Devil; lncRNA Directed Epigenetic Changes in a Contagious Cancer

Matthew G. Schwartz, Harvard Medical School, USA
Short Talk: The Role of Long Noncoding RNAs in Regulating Chicken Limb Development

19:15—20:15
Social Hour with Lite Bites
No registration fees are used to fund alcohol served at this function.

Shavano/Torreys
19:30—22:00
Poster Session 2

Shavano/Torreys

WEDNESDAY, MARCH 18

07:00—08:00
Breakfast

Shavano/Torreys
08:00—11:00
LncRNA Mechanisms: Diversity and Heterogeneity
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
Epigenetic or post-transcriptional? Nuclear or cytoplasmic? Single-gene antisense regulators or network cascade amplifiers? This session will present the frontiers of current knowledge about metazoan lncRNA functional mechanisms, and motivate the development of specific approaches to survey and target these mechanisms on a whole-transcriptome scale.

Grays Peak
* Jhumku D. Kohtz, Feinberg School of Medicine, Northwestern University, USA

Ramin Shiekhattar, University of Miami, USA
Biogenesis and Mechanism of Action of Enhancer RNA

Kevin V. Morris, University of New South Wales, Australia
RNA-Directed Modulation of Phenotypic Plasticity in Human Cells

Nicholas Lister, University of New South Wales, Australia
Short Talk: Promoter-Associated Transcripts Are Required for PTENpg1 Antisense RNA-Directed Epigenetic Regulation of PTEN

Jeannie T. Lee, Massachusetts General Hospital, USA
RNA-Protein Interactions in Epigenetic Regulation

Richard G. Jenner, University College London, UK
Short Talk: Polycomb Repressive Complex 2 Directly Interacts with RNA through Suz12 and Is Independent of Chromatin Association

Reini F. Luco, Centre National de la Recherche Scientifique, France
Short Talk: A Long Noncoding RNA Regulates Chromatin-Mediated Modulation of Alternative Splicing

09:20—09:40
Coffee Break

Longs Peak Foyer
11:00—13:00
Poster Setup

Shavano/Torreys
13:00—22:00
Poster Viewing

Shavano/Torreys
11:00—17:00
On Own for Lunch

14:30—16:30
Workshop 3

Grays Peak
* Ranjan J. Perera, Sanford-Burnham Medical Research Institute, USA

* Emily R. Feldman, University of Florida, USA

Zhuo Zhou, NIDDK, National Institutes of Health, USA
RNA-Dependent Triplex Formation Regulates Expression of Erythroid Genes

Valerie Brid O'Leary, Helmholtz Zentrum Muenchen, Germany
PARTICLE – A Long Noncoding RNA Modulator of Cellular Methylation in Response to Low Dose Irradiation

Fabien Dachet, University of Illinois at Chicago School of Medicine, USA
Epigenetic Organization of Protein Coding and Large Noncoding Transcripts in Electrically Active Human Brain

Yuya Ogawa, Cincinnati Children's Hospital Medical Center, USA
Xist Exon 7 Contributes to the Stable Localization of Xist RNA on the Inactive X-Chromosome

Karissa Y. Sanbonmatsu, Los Alamos National Laboratory, USA
Structural Studies of Long Noncoding RNAs

Luis Arnes, Columbia University, USA
Examining the Role of Novel Long Noncoding RNAs in beta Cell Biology

16:30—17:00
Coffee Available

Longs Peak Foyer
17:00—19:00
Conserved lncRNA Functions
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
This session serves as a forum for whole-transcriptome lncRNA functional studies in model organisms, with an emphasis on observations that point to transgenerational transmission. This emerging frontier of lncRNA research holds intriguing implications for development and behavior.

Grays Peak
* Alexandra Henrion-Caude, Necker Hospital – Imagine Foundation, France

James (Ben) Brown, Lawrence Berkeley National Laboratory, USA
Long Noncoding RNAs and Adaptive Responses to Environmental Stressors

Mridula (Millie) K. Ray, Harvard University, Massachusetts General Hospital, USA
Short Talk: lncRNAs Interact with PRC1 to Impact Development in Human and Zebrafish

John L. Rinn, Harvard University, USA
Linking RNA from Mouse to Mechanism

David J. Waxman, Boston University, USA
Short Talk: Mouse Liver lincRNAs: Gene Structures, Chromatin States, Conservation and Regulation of Sex-Specific Transcription by Pituitary Growth Hormone (GH)

Colleen A. McHugh, California Institute of Technology, USA
Short Talk: Uncovering Mechanisms of lncRNA Function through Comprehensive Identification of Direct lncRNA-Interacting Proteins in vivo

19:00—20:00
Social Hour with Lite Bites
No registration fees are used to fund alcohol served at this function.

Shavano/Torreys
19:30—22:00
Poster Session 3

Shavano/Torreys

THURSDAY, MARCH 19

07:00—08:00
Breakfast

Shavano/Torreys
08:00—11:30
Transcription Factors and lncRNAs: Direct Endogenous Riboregulation
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
A highlight of 21st-century lncRNAomics has been the discovery that transcription factors including homeobox proteins and multiple nuclear hormone receptors, as well as epigenetic modifiers, directly interact with lncRNAs. This session discusses the impact of these interactions on gene regulation.

Grays Peak
* Jeannie T. Lee, Massachusetts General Hospital, USA

David R. Corey, University of Texas Southwestern Medical Center, USA
Nuclear RNAi: Connecting lncRNAs with Sequence-Specific Regulation of Transcription and Splicing

Vladimir Bajic, King Abdullah University of Science and Technology, Saudi Arabia
Protein-Coding and lncRNA Genes Are Regulated Differently: Feedback Loops with lncRNA-Interacting Transcription Factors

Michael G. Rosenfeld, HHMI/University of California, San Diego, USA
Enhancer Signatures eRNAs and Nuclear Architecture in Regulated Gene Transcription

Veronica Peschansky, University of Miami, USA
Short Talk: Fragile X-Associated lncRNA FMR4 Is Trans-Active, Involved in Neural Development and Localized to Chromatin

Katelin R. Haynes, University of Queensland Diamantina Institute, Australia
Short Talk: Identification of Monocyte-Specific eRNAs at an Intergenic GWAS Locus Associated with Ankylosing Spondylitis Reveals Potential Mechanism in Disease

Jennifer F. Kugel, University of Colorado Boulder, USA
Regulation of RNA Polymerase II by SINE-Encoded ncRNAs

Jesse M. Engreitz, Broad Institute of Harvard and MIT, USA
Short Talk: Many Nuclear-Localized lincRNAs Regulate Gene Expression in cis

09:20—09:40
Coffee Break

Longs Peak Foyer
11:30—14:30
On Own for Lunch

14:30—16:30
Workshop 4

Grays Peak
* Saba Valadkhan, Case Western Reserve University, USA

* Ashley R. Hoover, University of Texas Southwestern Medical Center, USA

Fan Lai, University of Miami, USA
Integrator Mediates the Biogenesis of Enhancer RNAs

Shrikanth S. Gadad, University of Texas Southwestern Medical Center, USA
Functional Characterization of an Estrogen-Regulated Long Noncoding RNA that Controls the Growth of Breast Cancer Cells

Maren M. Gross, Dharmacon, Part of GE Healthcare, USA
Knockdown of Long Noncoding RNAs in Breast Cancer

Musa M. Mhlanga, Council for Scientific and Industrial Research, South Africa
HIV-1 Targets MAP2K1/ERK2 to Evade lincRNA-p21-Mediated Apoptosis

Margaret D. Ballantyne, University of Glasgow, UK
Cytokine and Growth Factor Induction of lncRNA in Vascular Smooth Muscle Cells

Damien Hermand, University of Namur, Belgium
Timely Entry into Gametogenesis Regulated by a Modified cis-Acting LINC-RNA in Fission Yeast

Felipe Beckedorff, Universidade de Sao Paulo, Brazil
LincRNAs Enriched for Enhancer Histone Signatures Are Involved in the Activation of Genes Regulated by Androgen

16:30—17:00
Coffee Available

Longs Peak Foyer
17:00—19:30
LncRNAs in Human Disease: Toward Rational Ribo-Therapeutics
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
This session will survey direct functional evidence implicating lncRNAs as causes of human disease, and also identify settings where lncRNAs without obvious endogenous function may serve as therapeutic targets. Harnessing the power of lncRNAomics to impute and perturb lncRNA-dependent regulatory networks, the session will canvass cutting-edge developments in industry, where rational therapeutics targeting lncRNA disease mechanisms are being developed.

Grays Peak
* Luis Arnes, Columbia University, USA

Frank W. Rigo, Isis Pharmaceuticals, USA
Towards a Therapy for Angelman Syndrome by Targeting a Long Noncoding RNA to Active UBE3A

James Barsoum, RaNA Therapeutics Inc., USA
Selective Activation of Gene Expression by Targeting Long Noncoding RNA

Saba Valadkhan, Case Western Reserve University, USA
A Bi-Functional Long Noncoding RNA Links Neuronal Differentiation to Survival after Stress

Eleonora Leucci, KU Leuven, Belgium
Short Talk: Targeting the Melanoma-Specific Long Noncoding RNA LINC01212 as an Effective Antimelanoma Strategy

Claes Wahlestedt, University of Miami/CURNA-OPKO
Long Noncoding RNAs: Therapeutic Opportunities

19:30—19:45
Concluding Remarks
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting

Leonard Lipovich, Wayne State University, USA

Jeannie T. Lee, Massachusetts General Hospital, USA

James (Ben) Brown, Lawrence Berkeley National Laboratory, USA

John L. Rinn, Harvard University, USA

19:45—20:45
Social Hour with Lite Bites
No registration fees are used to fund alcohol served at this function.

Shavano/Torreys
20:30—23:00
Entertainment
Entertainment is not subsidized by conference registration fees nor any U.S. federal government grants. Funding for this expense is provided by other revenue sources.

Shavano/Torreys

FRIDAY, MARCH 20

 
Departure


*Session Chair †Invited, not yet responded.



Keystone Symposia thanks our Sponsors for generously supporting this meeting:

Cell Research Isis Pharmaceuticals, Inc.
Regeneron Pharmaceuticals, Inc. Sarepta Therapeutics

We gratefully acknowledge additional support for this conference from:

Biosearch Technologies Dharmacon, part of GE Healthcare
Exiqon A/S RaNA Therapeutics Inc.

We gratefully acknowledge support for this conference from:


Directors' Fund


These generous unrestricted gifts allow our Directors to schedule meetings in a wide variety of important areas, many of which are in the early stages of research.

Click here to view all of the donors who support the Directors' Fund.



We gratefully acknowledge the generous grant for this conference provided by:


National Institutes of Health

Grant No. 1R13HG008329-01

Funding for this conference was made possible (in part) by 1 R13 HG 008329 - 01 from the National Human Genome Research Institute (NHGRI) and the National Institute for Environmental Health Sciences (NIEHS). The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.


We gratefully acknowledge additional in-kind support for this conference from those foregoing speaker expense reimbursements:



Isis Pharmaceuticals, Inc.


RaNA Therapeutics Inc.


We appreciate the organizations that provide Keystone Symposia with additional support, such as marketing and advertising:


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Special thanks to the following for their support of Keystone Symposia initiatives to increase participation at this meeting by scientists from underrepresented backgrounds:


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If your organization is interested in joining these entities in support of Keystone Symposia, please contact: Sarah Lavicka, Assistant Director of Development, Email: sarahl@keystonesymposia.org,
Phone:+1 970-262-2690

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If you are interested in becoming an advertising/marketing in-kind partner, please contact:
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Phone:+1 970-262-2676