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Long non-coding RNAs: evolution of new epigenetic and post-transcriptional functions
Theo Murphy scientific meeting organised by Professor Leonard Lipovich, Professor John Rinn, Professor Douglas Higgs FRS, Professor Nicholas Proudfoot FRS and Professor Lynne Maquat
Event details
The discovery that long non-protein-coding RNAs (lncRNAs) are prevalent in metazoan transcriptomes has been a highlight of the second post-genomic decade. Unexpectedly, lncRNAs mediate remarkably diverse cellular mechanisms. This meeting will synthesise insights that derive from next-generation sequencing, functional genomics, and lncRNA structure and function to augment our understanding of how lncRNAs contribute to species uniqueness and to human disease.
Biographies of the speakers are available below. Recorded audio of the presentations will be available on this page after the event.
Attending this event
This is a residential conference, which allows for increased discussion and networking. It is free to attend, however participants need to cover their accommodation and catering costs if required.
Enquiries: Contact the events team
Organisers
Schedule
Chair
Professor Lynne Maquat, University of Rochester, USA
Professor Lynne Maquat, University of Rochester, USA
Lynne Elizabeth Maquat is the J Lowell Orbison Endowed Chair and Professor of Biochemistry & Biophysics in the School of Medicine and Dentistry, Director of the Center for RNA Biology, and Chair of Graduate Women in Science at the University of Rochester, Rochester, NY, USA. After obtaining her PhD in Biochemistry from the University of Wisconsin-Madison and undertaking post-doctoral work at the McArdle Laboratory for Cancer Research, she joined Roswell Park Cancer Institute before moving to the University of Rochester. In 1981, Professor Maquat discovered nonsense-mediated mRNA decay (NMD) in mammalian cells and subsequently, while elucidating the mechanism of NMD, the splicing-dependent “mark”, i.e. the exon-junction complex (EJC), and how the EJC marks mRNAs for a quality-control “pioneer” round of protein synthesis. She also discovered Staufen-mediated mRNA decay, which mechanistically competes with NMD and, by so doing, new roles for short interspersed elements and long non-coding RNAs. Additional current interests include microRNA decay and functional links between transcription factors and RNA-binding proteins.
She is an elected Fellow of the American Association for the Advancement of Science (2006), and an elected Member of the American Academy of Arts & Sciences (2006), the National Academy of Sciences (2011), and the National Academy of Medicine (2017). Lynne was a Batsheva de Rothschild Fellow of the Israel Academy of Sciences & Humanities (2012-2013) and has received the William C. Rose Award from the American Society for Biochemistry & Molecular Biology (2014), a Canada Gairdner International Award (2015), the international RNA Society Lifetime Achievement Award in Service (2010) and in Science (2017), the Vanderbilt Prize in Biomedical Science (2017), the Federation of American Societies for Experimental Biology (FASEB) Excellence in Science Award (2018), and the Wiley Prize in Biomedical Sciences (2018).
| 09:05 - 09:30 |
Conserved functions of lncRNAs during vertebrate development
Thousands of long intervening noncoding RNAs (lincRNAs) have been identified in mammals. To better understand functions and evolution of these enigmatic RNAs, we identified more than 550 lincRNAs in zebrafish, an established vertebrate model for development. Although zebrafish lincRNAs share many characteristics with mammalian lincRNAs, only 5% have detectable sequence similarity with putative mammalian counterparts, typically restricted to short regions of high conservation. To understand if evolutionarily pressure on conserved lincRNA sequences is associated with their important biological functions, Dr Shkumatava is generating multiple genetic zebrafish mutants of the ultra-conserved lincRNA motifs using Crispr/Cas9 genome editing. They are subsequently analyzing the impact of lincRNA loss-of-function on normal embryonic development and adult animals. For one of the ultra-conserved lincRNAs that they called cyrano, they recognized that the conserved region of cyrano contains an unusually complementary, near-perfect microRNA miR-7 site that is bound by Argonaute proteins and is highly conserved in all examined vertebrates. The analyses of zebrafish cyrano mutant show that the interaction between miR-7 and cyrano differs from the canonical miRNA—target regulation suggesting that lincRNA—miRNA complex has an additional, novel function important for normal development. To identify the exact molecular function of the cyrano–miR-7 pairing, they aim to identify proteins binding at the extended conserved region of Cyrano using a novel high-throughput method. 
Dr Alena Shkumatava, Institut Curie, France
Dr Alena Shkumatava, Institut Curie, FranceAlena Shkumatava obtained her PhD at the European Molecular Biology Laboratory (EMBL) Heidelberg, Germany. Following this she conducted postdoctoral research at the Whitehead Institute and MIT in USA. In 2013 Alena was appointed group leader at the Developmental Biology and Genetics Unit, Institut Curie, France and is now an ERC Investigator. Alena's research aims to understand developmental functions of lincRNAs and she has identified over 550 lincRNAs in zebrafish. Her research group previously demonstrated that two novel lincRNAs, megamind and cyrano, are required for proper embryonic development, in particular for brain morphogenesis and neurogenesis. |
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| 09:30 - 09:55 |
The nature and scaling of the regulatory superstructure of human development and cognition
It is now evident that the majority of the mammalian genome is dynamically transcribed during differentiation and development to produce tens if not hundreds of thousands of short and long non-protein-coding RNAs that show highly specific expression patterns and subcellular locations. Increasing numbers of these RNAs are being shown to have functions at many different levels of gene expression, including translational control and the guidance of epigenetic processes that underpin development, physiological adaptation, cognition and transgenerational communication, augmented by the superimposition of plasticity by RNA editing, RNA modification and retrotransposon mobilization. This suggests that there is there is a massive hidden layer of RNA-based communication and that the simple protein-centric operator-repressor model of ‘gene regulation’ derived from studies of bacteria is incorrect in highly organized and spatially specialized multicellular entities. This in turn requires reassessment of the nature, scaling and hierarchies of the regulatory systems and processes that control the 4-dimensional assembly and cognitive capacities of complex organisms. It is not simply a matter of adding RNA to the picture but rather of constructing a new landscape. 
Professor John Mattick, The Garvan Institute of Medical Research, Australia
Professor John Mattick, The Garvan Institute of Medical Research, AustraliaJohn Mattick undertook his undergraduate and graduate studies at the University of Sydney and Monash University in Melbourne, respectively. He did his postdoctoral training with Dr Salih Wakil at Baylor College of Medicine, and subsequently worked at the CSIRO Division of Molecular Biology in Sydney, the Universities of Cambridge, Oxford and Cologne, and the University of Queensland in Brisbane, where he was the Foundation Director of the Institute for Molecular Bioscience and the Australian Genome Research Facility. He is currently the Director of the Garvan Institute of Medical Research in Sydney. John Mattick has published over 270 papers, which have been cited over 31,000 times. His honours and awards include the inaugural Gutenberg Professorship of the University of Strasbourg, Honorary Fellowship of the Royal College of Pathologists of Australasia, the Order of Australia and Australian Government Centenary Medal, Associate Membership of the European Molecular Biology Organization, Fellowship of the Australian Academy of Science, the International Union of Biochemistry and Molecular Biology Medal, and the Human Genome Organisation Chen Award for Distinguished Achievement in Human Genetic and Genomic Research. |
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| 10:45 - 11:10 |
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, they study a collection of 75 CLIP-Seq experiments mapping the RNA binding sites for a diverse set of 51 human proteins to explore the role of TEs in post-transcriptional regulation of human mRNAs and lncRNAs via RNA-protein interactions. 
Professor John Rinn, Harvard University, USA
Professor John Rinn, Harvard University, USAJohn Rinn received a B.S. in chemistry from the University of Minnesota and a Ph.D. from Yale University in molecular biophysics and biochemistry where, as a member of Mike Snyder’s lab, he studied genome-wide transcription and uncovered a plethora of large non-coding RNAs. As a Damon Runyon Cancer Research Foundation fellow at Stanford University, in Howard Chang’s lab, he identified and functionally characterized large non-coding RNAs. Specifically, he studied the role of HOX genes and non-coding RNAs during skin fate specification and maintenance. Professor Rinn’s lab at Harvard continues to identify new RNA genes and to unravel their roles in establishing cellular identity and their misregulation in diseases such as cancer. |
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| 11:10 - 11:35 |
Long non-coding RNAs that regulate hematopoiesis and adipogenesis
To obtain a comprehensive view of how lncRNAs contribute to erythropoiesis, the Lodish lab performed and analyzed data from high depth RNA-sequencing on RNAs from erythroid progenitor cells and terminally differentiating erythroblasts. They focused on differentiation-induced lncRNAs, including novel erythroid-specific lncRNAs conserved in humans that are nuclear-localized and identified 13 erythroid-specific lncRNAs that are greatly induced during erythroid terminal differentiation. Importantly, shRNA-mediated loss-of-function assays reveal that all 13 are important for red cell formation. One intergenic lncRNA, LincRNA-EPS, prevents the apoptosis of progenitors that is normally induced by erythropoietin deprivation and represses expression of several proapoptotic genes including Pycard, a caspase activator. A second lncRNA is transcribed by the erythroid- specific enhancer of Band 3, encoding a major erythrocyte membrane protein. To uncover brown adipose tissue (BAT)-specific long non-coding RNAs (lncRNAs), they used high depth RNA-sequencing on RNAs from mouse brown, inguinal white, and epididymal white fat. They identified ~1500 lncRNAs, including 127 BAT-restricted loci induced during differentiation and often targeted by key regulators PPARγ, C/EBPα and C/EBPβ. One of them, lnc-BATE1, is required for establishment and maintenance of BAT identity and thermogenic capacity. lnc-BATE1 inhibition impairs concurrent activation of brown fat and repression of white fat genes, and is partially rescued by exogenous lnc-BATE1 with mutated siRNA-targeting sites, demonstrating a trans function of lnc-BATE1. Thus diverse types of intergenic, enhancer, and antisense lncRNAs are expressed only in specific types of hematopoietic and adipose cells and are essential for their proper development; they participate in the regulatory circuitry underlying lineage-specific development. 
Professor Harvey Lodish, Massachusetts Institute of Technology, USA
Professor Harvey Lodish, Massachusetts Institute of Technology, USADr Lodish received his A.B. degree Summa Cum Laude in Chemistry and Mathematics from Kenyon College and his Ph.D. degree in genetics from the Rockefeller University. Following two years of postdoctoral research at the M.R.C. Laboratory of Molecular Biology he joined the MIT Department of Biology. He was promoted to Professor in 1976, and in 1983 was appointed Founding Member of the new Whitehead Institute for Biomedical Research. In 1999 he also became Professor of Biological Engineering in the new MIT Biological Engineering department. He is a member of the National Academy of Sciences, a fellow of the American Association for the Advancement of Science, and a fellow of the American Academy of Arts and Sciences. He is a member of the Board of Trustees of Boston Children's Hospital and the lead author of 7 editions of the textbook Molecular Cell Biology. During 2004 he served as President of the American Society for Cell Biology. |
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| 11:35 - 12:00 |
The theory of RNA-mediated gene evolution
Observations over the last decade suggest that some non-coding RNAs function in regulating the transcriptional and epigenetic state of gene expression. DNA methylation appears operative in non-coding RNA regulation of gene expression. Interestingly, methylated cytosines undergo deamination to remove the methylation, which if not properly repaired results in the methylated cytosine being recognized by the cell as a thymine. Professor Morris finds that several of the key deamination based repair enzymes, APOBEC3a, Methyl-CpG (mCpG) binding domain protein 4 (MBD4), SMUG, and Uracil N-Glycosylase (UNG) localize to small and long non-coding RNA target loci. These observations suggest that the process of RNA directed epigenetic targeting also has the potential to alter the genomic landscape of the cell by changing cytosines to thymines and ultimately influence the evolution of the cell. This proposed theory of “RNA-mediated gene evolution” might be one possible mechanism of action whereby RNA participates in the natural selective process to drive cellular and possibly organismal evolution. 
Professor Kevin Morris, University of New South Wales, Australia
Professor Kevin Morris, University of New South Wales, AustraliaKevin Morris received his BS degree from Humboldt State University in 1996 and his PhD in 2001 from the University of California Davis. During his post-doctoral training at the University of California San Diego (2001-2004) he determined that non-coding RNAs were capable of modulating epigenetic directed transcriptional silencing in human cells. The Morris lab has since determined the mechanistic underpinnings of non-coding RNA mediated regulation of gene transcription in human cells, with evidence suggesting a role for longer forms of non-coding RNAs as endogenous effectors involved in epigenetically remodeling target loci in human cells. The lab is specifically interested in utilizing endogenous non-coding RNA pathways in human cells to epigenetically modulate gene expression of those genes involved in HIV, cystic fibrosis, and cancer. Notably, evidence suggests that these endogenous RNA pathways can be utilized to either epigenetically silence or activate a genes expression. The Morris lab is also active in developing cell targeted non-coding RNA delivery vehicles, such as lentiviral derived conditionally replicating vector systems and cell-targeted aptamers. |
Chair
Professor John Rinn, Harvard University, USA
Professor John Rinn, Harvard University, USA
John Rinn received a B.S. in chemistry from the University of Minnesota and a Ph.D. from Yale University in molecular biophysics and biochemistry where, as a member of Mike Snyder’s lab, he studied genome-wide transcription and uncovered a plethora of large non-coding RNAs. As a Damon Runyon Cancer Research Foundation fellow at Stanford University, in Howard Chang’s lab, he identified and functionally characterized large non-coding RNAs. Specifically, he studied the role of HOX genes and non-coding RNAs during skin fate specification and maintenance. Professor Rinn’s lab at Harvard continues to identify new RNA genes and to unravel their roles in establishing cellular identity and their misregulation in diseases such as cancer.
| 13:30 - 13:55 |
The origins and potential roles of non-coding RNAs in a well-defined mammalian chromosomal landscape
Gene expression in mammalian cells is a complex process which is often influenced by distal regulatory elements. The alpha globin gene locus, amongst others, has been thoroughly characterized as a model of such long-range gene regulation. Mutations which affect some or all of the distal regulatory elements in the human alpha globin gene locus result in alpha thalassemia, illustrating the relevance of long-range gene regulation in vivo. Recent studies have shown that distal regulatory elements (e.g. enhancers) physically interact with their target gene promoters and are themselves actively transcribed by RNA Pol II. Production of RNA transcripts from enhancer elements has been shown on a genome-wide scale in a number of different cell types, including terminally differentiated erythroid cells, but whether these transcripts have a biological function or merely represent transcriptional noise is not fully understood. Dr Graham has optimized a method to recapitulate mouse erythropoiesis in vitro, and use this system to characterize the transcriptional activity of enhancer elements through the differentiation of haematopoietic progenitors to terminally differentiated erythroid cells. Using genetic knockout models of individual regulatory elements within the well-defined alpha globin locus, she asks whether transcriptional activity at an enhancer reflects its ability to regulate activity at a downstream promoter in vivo. 
Dr Bryony Graham, University of Oxford, UK
Dr Bryony Graham, University of Oxford, UKBryony graduated from the University of Nottingham in 2008 with First Class Honours in Human Genetics. During her undergraduate studies, she worked at the Wellcome Trust Sanger Institute in Cambridge in Professor Allan Bradley’s lab, where she generated a cell line for assaying drugs for the treatment of leukaemia. Bryony undertook her PhD at Imperial College London, under the supervision of Matthias Merkenschlager and Mandy Fisher at the MRC Clinical Sciences Centre. During her PhD, she worked on the role of microRNAs in regulation of lineage-specific gene expression. She continues her work on non-protein coding RNAs in Professor Doug Higgs’ lab in Oxford, where she is interested in the biological function of transcription at regulatory elements in the alpha globin locus. |
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| 13:55 - 14:20 |
Policing the mammalian transcriptome: restricting non-coding RNAs by transcriptional termination, gene loops and R-loops
The highly unstable nature of lncRNA requires their analysis by truly nascent transcription procedures. Professor Proudfoot has developed mammalian native elongation transcript sequencing (mNET-seq) analysis as a way to determine nascent transcription profiles and their association with specific phosphorylation states of RNA polymerase II CTD (Nojima et al Cell 161: 526, 2015). Their analysis to date has concentrated on the HeLa cell transcriptome. mNET-seq involves the isolation and sequencing of RNA from the Pol II active site and gives single nucleotide transcript resolution. Their results so far indicate that lncRNA and pre-mRNA are transcribed in significantly different ways. While pre-mRNA are associated with specific CTD phosphorylation states indicative of co-transcriptional splicing and 3’ end processing/polyadenylation, lncRNA are largely transcribed by different Pol II CTD isoforms. Furthermore most lncRNA are retained on chromatin where they are co-transcriptionally degraded. He further shows that some lncRNA initiate from single stranded DNA formed as a result of RNA:DNA hybrid formation; R-loop regions. Overall he shows that the transcriptional and RNA processing mechanisms that generate lncRNA appear radically different to pre-mRNA. Our results imply that lncRNA are in most cases transcriptional bi-products that need to be degraded in situ to prevent their deleterious effects on cell physiology. 
Professor Nicholas Proudfoot FRS, University of Oxford, UK
Professor Nicholas Proudfoot FRS, University of Oxford, UKNick Proudfoot was a graduate student and postdoc at the MRC Laboratory of Molecular Biology Cambridge (1972-1979). He initially worked on mRNA sequencing and discovered the ubiquitous AAUAAA poly(A) signal. He then began a study to clone and sequence globin genes which led to 2 year postdoc position at first Caltech and then Harvard with Tom Maniatis (1979-1981). He was then appointed University lecturer at the Sir William Dunn School of Pathology and Tutor in Biochemistry at Brasenose College Oxford and subsequently Professor of Molecular Biology (2003 onwards). At Oxford he initially focused on poly(A) signals, their genetics and molecular biology. His lab discovered that mRNA processing is coupled to transcription which led into detailed analysis of the mechanism and biological significance of transcriptional termination. During this period the field of RNA 3’ end processing and termination has moved from a relatively small focus into an interconnecting series of topics central to gene expression. In particular he has organized six four yearly RNA 3’ end workshops at Oxford which have provided a forum for this expanding research area. He was elected an EMBO member in 1982 and Fellow of the Royal Society in 2005. |
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| 15:10 - 15:35 |
Epitranscriptome and transcriptome dynamics in single-cells, nanopores and space stations
The avalanche of easy-to-create genomics data has impacted almost all areas of medicine and science, and here Dr Mason reports the implementation of genomics technologies from the single-cell to an entire city. Recent methods and algorithms enable single-cell and clonal resolution of phenotypes as they evolve, both in normal and diseased tissues. He shows that tumours evolve quickly at the genetic, epigenetic, transcriptional, and epitranscripional level, enabling many means by which tumours can resist therapy. Notably, some of these changes can be resolved by single-cell analysis and enable prognostic relevance. Finally, he will discuss pilot data for creating enabling patients to become more involved in their ‘omics data, including to an integrative genomics view of an entire city (based on our Pathomap project) that leverages longitudinal genomics and microbiome profiles of the NYC subway system and in situ sequencing with the oxford nanopore system of sequencing. All of these pieces work together to guide the most comprehensive, longitudinal, mutli-omic view of human physiology with the NASA Twins Study. 
Dr Christopher Mason, Weill Cornell Medical College, USA
Dr Christopher Mason, Weill Cornell Medical College, USAChristopher E. Mason completed his dual B.S. in Genetics and Biochemistry from University of Wisconsin-Madison in 2001, his Ph.D. in Genetics from Yale University in 2006, and his post-doctoral training at Yale Medical School, while also holding a fellowship at Yale Law School. In 2009, Dr. Mason founded his laboratory as an assistant professor at Weill Cornell Medical College in the Department of Physiology and Biophysics and at the Institute for Computational Biomedicine. Professor Mason also holds an appointment in the Tri-Institutional Program on Computational Biology and Medicine between Cornell, Memorial Sloan-Kettering Cancer Center and Rockefeller University and he also has an appointment at the Weill Cornell Cancer Center and the Brain and Mind Research Institute. In 2013, he won the Hirschl-Weill-Caulier Career Scientist Award. In 2014, he won the Vallee Foundation Young Investigator Award, the CDC Honor Award for Standardization of Clinical Testing, and he was just named as one of the “Brilliant Ten” Scientists in the world by Popular Science magazine. |
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| 15:45 - 17:00 | Poster session |
Chair
Professor Douglas Higgs FRS, University of Oxford, UK
Professor Douglas Higgs FRS, University of Oxford, UK
Douglas Higgs FRS qualified in Medicine at King’s College Hospital Medical School in 1974 and trained as a haematologist. He joined the MRC Molecular Haematology Unit (Oxford) in 1977 and is currently Professor of Molecular Haematology at the University of Oxford and Director of the MRC Molecular Haematology Unit. The current interests of the Unit are (i) to understand the processes by which stem cells undergo lineage commitment in haematopoiesis; (ii) to understand how genes are activated and repressed during normal haematopoiesis; (iii) to study the human genetic diseases affecting these processes. The main interest of Professor Higgs’s laboratory have been to understand how the globin genes are regulated during haematopoiesis from their natural chromosomal environment in the telomeric region of 16p13.3. His group has characterised the terminal 2 Mb of chromosome 16 and concentrated on understanding how globin gene expression is influenced by the transcriptional programme and epigenetic modifications of this region (e.g. chromatin structure, histone acetylation, methylation, timing of replication, nuclear positioning). This work contributes to our understanding of the normal process of blood formation and provides an unusually well characterised model for understanding the mechanisms underlying mammalian gene regulation. He has previously supervised 30 graduate students, 8 Biochemistry Part 2 projects, and numerous laboratory visitors. In addition Professor Higgs has trained over 30 post doctoral Fellows and Clinical Training Fellows. He regularly examines PhD and DPhil theses (approximately 2-3 per year for the past 25 years).
| 09:00 - 09:25 |
"Alu"strious effects on human RNA metabolism: a complicated network
Staufen1-mediated mRNA decay (SMD), which occurs when translation terminates sufficiently upstream of a STAU-binding site (SBS), is important to developmental and homeostatic pathways. An SBS can be created by intramolecular base-pairing within an mRNA 3'UTR or by intermolecular base-pairing between a 3'UTR and one or more lncRNAs. Intermolecular base-pairing in humans involves Alu elements, which are a type of short interspersed repetitive element (SINE), whereas intermolecular base-pairing in rodents involves B and identifier SINEs. The STAU1 paralog STAU2, and STAU1 and STAU2 homodimerization and heterodimerization also promote SMD. In addition to mRNA−lncRNA interactions, they have found that mRNAs crosstalk in a way that involves direct mRNA−mRNA interactions between 3'UTR Alu elements in each mRNA, uncovering a new role for mammalian-cell mRNAs. This unexpected function, together with them discovering how STAU1 binding to inverted repeated 3'UTR Alu elements (IRAlus) (i) competes with nuclear (i.e., paraspeckle) retention mediated by p54nrb binding to 3'UTR IRAlus and also (ii) the repression of cytoplasmic translation mediated by PKR binding to 3'UTR IRAlus add new layers of complexity to the network of post-transcriptional interactions that regulate gene expression and involve ncRNA. They are in the process of purifying individual Alu element-containing lncRNAs together with the associated transcripts (both mRNAs and other lncRNAs) and proteins to gain insight into lncRNA structure and function.
Professor Lynne Maquat, University of Rochester, USA
Professor Lynne Maquat, University of Rochester, USALynne Elizabeth Maquat is the J Lowell Orbison Endowed Chair and Professor of Biochemistry & Biophysics in the School of Medicine and Dentistry, Director of the Center for RNA Biology, and Chair of Graduate Women in Science at the University of Rochester, Rochester, NY, USA. After obtaining her PhD in Biochemistry from the University of Wisconsin-Madison and undertaking post-doctoral work at the McArdle Laboratory for Cancer Research, she joined Roswell Park Cancer Institute before moving to the University of Rochester. In 1981, Professor Maquat discovered nonsense-mediated mRNA decay (NMD) in mammalian cells and subsequently, while elucidating the mechanism of NMD, the splicing-dependent “mark”, i.e. the exon-junction complex (EJC), and how the EJC marks mRNAs for a quality-control “pioneer” round of protein synthesis. She also discovered Staufen-mediated mRNA decay, which mechanistically competes with NMD and, by so doing, new roles for short interspersed elements and long non-coding RNAs. Additional current interests include microRNA decay and functional links between transcription factors and RNA-binding proteins. She is an elected Fellow of the American Association for the Advancement of Science (2006), and an elected Member of the American Academy of Arts & Sciences (2006), the National Academy of Sciences (2011), and the National Academy of Medicine (2017). Lynne was a Batsheva de Rothschild Fellow of the Israel Academy of Sciences & Humanities (2012-2013) and has received the William C. Rose Award from the American Society for Biochemistry & Molecular Biology (2014), a Canada Gairdner International Award (2015), the international RNA Society Lifetime Achievement Award in Service (2010) and in Science (2017), the Vanderbilt Prize in Biomedical Science (2017), the Federation of American Societies for Experimental Biology (FASEB) Excellence in Science Award (2018), and the Wiley Prize in Biomedical Sciences (2018). |
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| 09:25 - 09:50 |
A bi-functional long non-coding RNA links neuronal differentiation to survival after stress
To gain insight into the complex cellular roles performed by long non-coding RNAs, Dr Valadkhan analyzed the function of an intergenic lncRNA, BORG, which is almost exclusively expressed in neuronal cells in both mouse and human. Study of the function of BORG indicated that it is required for neuronal differentiation in mouse cell culture-based systems. In addition, they show that BORG plays a critical role in the stress response that was distinct from its neuronal differentiation function. Knock down and overexpression studies indicated a strong, positive correlation between the expression level of BORG and post-stress survival in cultured mammalian cells. In order to determine if BORG plays a role similar to what we have observed in cultured cells in vivo, they developed a transgenic mouse model that overexpresses BORG from a tet-regulated promoter. Induction of expression of BORG from the transgene in postnatal mice resulted in potentiation of the stress response, similar to what we had observed in cell culture-based systems. Despite inducing an increase in pro-survival factors, overexpression of BORG in vivo does not seem to be tumorigenic. Their observations indicate that both in vivo and in cultured cells, BORG RNA is a strong regulator of the stress response and suggest that the pro-survival function of BORG can have a protective effect against neurodegeneration and other conditions characterized by stress-mediated cell death. 
Dr Saba Valadkhan, Case Western Reserve University, USA
Dr Saba Valadkhan, Case Western Reserve University, USASaba Valadkhan received her M.D. from Iran University of Medical Sciences and her Ph.D. from Columbia University in the laboratory of Dr James Manley in 2003. She has been a faculty member at Case Western Reserve University School of Medicine since 2004, where she has been studying the role of small nuclear RNAs in spliceosomal catalysis and the impact of long non-coding RNAs on regulation of cellular processes, including neurogenesis, stress response and innate immunity. She has been the recipient of a Searle Scholar award, Harold Weintraub award, and the Young Scientist Award from the American Association for Advancement of Science (AAAS). |
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| 10:40 - 11:05 |
Structural architecture of lncRNAs in plants and mammals
Many genome-wide studies of long non-coding RNAs (lncRNAs) have been performed; however, few structural studies of individual lncRNAs exist. A clear consensus has not been achieved on the level of structure occurring in lncRNA systems. Structures are necessary not only to establish a mechanistic framework for lncRNAs, but also to establish the level of conservation of each lncRNA, since this cannot be achieved from sequence alone. Historically, secondary structures of the 16S and 23S rRNA provided an important framework for biochemical investigations and for structural studies of the ribosome, which is a 5-10 kB non-coding RNA, depending on species. Dr Sanbonmatsu establishes similar structural frameworks by determining secondary structures of individual lncRNA systems. In the case of smaller RNA systems, chemical probing has proved an instrumental methodology for directly determining secondary structures. In the case of larger systems, chemical probing alone has significant limitations due to the exponentially large number of possible secondary folds. To address this challenge, they developed Shotgun Secondary Structure (3S), a divide-and-conquer experimental strategy to derive secondary structures of lncRNAs. The 3S experimental strategy allows us to produce the secondary fold with minimal need for computational predictions. Here, they chemically probe the entire lncRNA transcript. Next, they repeat the probing on several overlapping fragments on the transcript. If the SHAPE profile for the fragment matches the profile for the same region of RNA in the context of the full transcript, this strongly suggests the fragment folds into a modular sub-domain or modular secondary motif, eliminating a large number of other possible folds. They applied this method to the Coolair lncRNA in A. thaliana and Braveheart in mouse, both of which possess clear phenotypes. They also applied the method to the human steroid receptor RNA activator (SRA-1). Coolair, Braveheart and SRA-1 each show highly structured sub-domains and share a unique expansive internal loop (‘right hand turn’ motif). They then use the secondary structure to find examples of the same lncRNA in other species, demonstrating conservation of structure.
Dr Karissa Sanbonmatsu, Los Alamos National Laboratory, USA
Dr Karissa Sanbonmatsu, Los Alamos National Laboratory, USAKarissa Sanbonmatsu is a principal investigator at Los Alamos National Laboratory. Karissa received her BA in Physics from Columbia University and PhD in Astrophysical, Planetary and Atmospheric Sciences from the University of Colorado at Boulder, studying wave-particle interactions in the Earth’s auroral ionosphere. She did her post-doctoral fellowship on plasma turbulence in laser fusion at Los Alamos. She changed to biophysics after becoming a principal investigator, where she performed biophysical studies of the ribosome and also started an RNA biochemistry lab. Sanbonmatsu's current research is focused on the molecular mechanism of non-coding RNAs, including long non-coding RNAs in epigenetics, riboswitches in bacterial metabolism, and ribosomes in bacterial and human protein synthesis. She received the Presidential Early Career Award for Scientists and Engineers and was elected fellow of the American Physical Society. |
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| 11:05 - 11:30 |
Long non-coding RNAs in cancer
The majority of the human genome is transcribed into non-protein-coding RNA. Hence, RNA is also the primary product of the cancer genome. Dr Diederichs lab have defined the ncRNA expression landscape of lung, breast and liver cancer providing a comprehensive expression map of over 17000 long ncRNAs and discovering new lncRNAs associated with cancer whose molecular and cellular functions they are currently elucidating. The nuclear lncRNA MALAT1 was one of the first lncRNAs associated with cancer: it is associated with metastasis development in lung cancer. However, its high abundance and nuclear localization have hampered its functional analysis. To uncover its functional importance, they developed a MALAT1 knockout model in human lung tumor cells by genomically integrating RNA destabilizing elements site-specifically into the MALAT1 locus. This approach yielded a 1000-fold silencing of MALAT1 providing a unique loss-of-function model. Proposed mechanisms of MALAT1 action include regulation of splicing or gene expression. In lung cancer, MALAT1 does not alter alternative splicing but regulates gene expression inducing a signature of metastasis-associated genes. Consequently, MALAT1-deficient cells are impaired in migration and form fewer tumor nodules in a mouse xenograft model. Encouraged by this discovery of the essential function of MALAT1 in lung cancer metastasis, they analyzed whether MALAT1 could serve as therapeutic target for an Antisense oligonucleotide (ASO). Notably, MALAT1-ASO treatment prevented metastasis formation after tumor implantation. Thus, targeting MALAT1 with ASOs provided a therapeutic approach to prevent lung cancer metastasis with MALAT1 serving as both, predictive marker and therapeutic target. In summary, ten years after the discovery of the lncRNA MALAT1 as a biomarker for lung cancer metastasis, their loss-of-function model unraveled the active function of MALAT1 as a regulator of gene expression governing hallmarks of lung cancer metastasis. 
Dr Sven Diederichs, University of Heidelberg, Germany
Dr Sven Diederichs, University of Heidelberg, GermanySven Diederichs leads the junior research group “Molecular RNA Biology & Cancer” at the German Cancer Research Center DKFZ and the Institute of Pathology at the University of Heidelberg since 2008. His research is focused on the one hand side on microRNA biogenesis and the improvement of RNA interference - on the other hand, he investigates the expression and function of long non-coding RNAs in human cancer. He studied Biochemistry at the University of Tübingen and the University of Witten/Herdecke and continued his education towards his PhD at the University of Münster. In 2005, he moved to Boston as a postdoctoral fellow with Daniel Haber at Harvard Medical School / MGH Cancer Center. His scientific work has been recognized by several awards and honors. |
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| 11:50 - 12:30 | Poster session |
Chair
Professor Nicholas Proudfoot FRS, University of Oxford, UK
Professor Nicholas Proudfoot FRS, University of Oxford, UK
Nick Proudfoot was a graduate student and postdoc at the MRC Laboratory of Molecular Biology Cambridge (1972-1979). He initially worked on mRNA sequencing and discovered the ubiquitous AAUAAA poly(A) signal. He then began a study to clone and sequence globin genes which led to 2 year postdoc position at first Caltech and then Harvard with Tom Maniatis (1979-1981). He was then appointed University lecturer at the Sir William Dunn School of Pathology and Tutor in Biochemistry at Brasenose College Oxford and subsequently Professor of Molecular Biology (2003 onwards). At Oxford he initially focused on poly(A) signals, their genetics and molecular biology. His lab discovered that mRNA processing is coupled to transcription which led into detailed analysis of the mechanism and biological significance of transcriptional termination. During this period the field of RNA 3’ end processing and termination has moved from a relatively small focus into an interconnecting series of topics central to gene expression. In particular he has organized six four yearly RNA 3’ end workshops at Oxford which have provided a forum for this expanding research area. He was elected an EMBO member in 1982 and Fellow of the Royal Society in 2005.
| 13:30 - 13:55 |
What hallmarks for long non-coding RNA? The mitochondrial connection
A crucial role of mitochondria is to provide the universal currency for energy. This task forces them to be in tight communication with the rest of the cell machinery, and more specifically with the nucleus, which represents the control center. Connections take place not only through the cytoskeleton but also through intense genomic cross-talk with the nucleus, which provides mitochondria with nuclear-encoded proteins as well as non-coding RNAs that are required for mitochondrial homeostasis and function. Conversely, both strands of the mitochondrial DNA are entirely transcribed that generate also some non-coding sequences. Although information about mitochondrial long non-coding RNAs (lncRNAs) per se is still limited, candidates non-coding RNAs of various sizes recovered in mitochondrial fraction open up a rich field of information and investigation. Some insights as to mitochondrial lncRNAs as regulators of gene expression and as biomarkers will be presented. Some of these biological insights will hopefully find application in the steadily increasing number of pathologies that are related to dysfunctions of mitochondria, in conditions where pathogenicity and phenotypic expression are not readily understandable. 
Dr Alexandra Henrion-Caude, Inserm, France
Dr Alexandra Henrion-Caude, Inserm, FranceAlexandra Henrion Caude is a geneticist at Necker Hospital in Paris. Her research has focused for over 20 years on how environmental cues are translated into genetic information. Recently, her interest has expanded to consider the huge contribution of non-coding RNA to the regulatory circuitry, and in particular to identify the variations that could influence genetic diseases. Her curiosity goes to formulate hypotheses on the functioning of non-coding RNA from other systems of communication than the ones in biology spanning from mathematics to music. Dr. Henrion-Caude owes her motivation in Genetics to Pr Sir Alec Jeffreys. After earning her PhD in Paris, she spent her postdoctorate in Harvard Medical School, and was tenured in 1998 from Inserm, France, where she was recently appointed as Director of Research. |
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| 13:55 - 14:20 |
LncRNAs and adaptation to environmental stress via post-transcriptional gene regulation
In phyla ranging from arthropods to mammals, lncRNAs are expressed in spatially restricted patterns – in one or a few tissues on average. Temporal expression patterns are similarly restricted; in Drosophila, expression during more than two hours of development is predominantly limited to neural tissues and the germ line. Environmental challenges reveal a host of largely non-coding genes that are not otherwise at detectable levels in any tissue or time point. In a diverse set of environmental challenges surveyed in Drosophila and Daphnia, lncRNAs are among the strongest and earliest responsive genes. Daphnia is an ecologically critical clade and forms the basis of the metazoan food web in over 90% of fresh water bodies on earth. Daphnia magna responds to microcystin (toxic algae; blooms cost the US >$2B per year) with the over-expression of a single gene, in which the longest ORF is 57aa and is not conserved. The modENCODE Consortium and the Consortium for Environmental Omics and Toxicology have generated large datasets interrogating the patterns of expression and interaction of lncRNAs. Dr Brown will discuss the developing picture of lncRNAs as rapidly evolving, adaptive molecules that help to shape the emergence of new ecological niches, as well as cell types and tissues, and hence, species. 
Dr James B. "Ben" Brown, Lawrence Berkeley National Laboratory, USA
Dr James B. "Ben" Brown, Lawrence Berkeley National Laboratory, USADr Brown completed a BA in Mathematics at UC Santa Cruz, followed by a PhD in Applied Science and Technology at UC Berkeley in 2009. During his postdoctoral work with Susan Celniker (LBNL) and Peter Bickel (UCB), he received a highly competitive K99 award from the National Human Genome Research Institute. In 2013, he joined the faculty of the LBNL Life Sciences Division and is currently building a program focused on the development and application of tools for the integrative analysis of large, diverse and multi-scale biological datasets. In 2015, Dr. Brown joined the UC Berkeley Statistics faculty as an Adjunct Assistant Professor to further his work on ensemble models and network analysis. He has been a member of the ENCODE Project since 2004, and in the modENCODE Consortium (2009-2014), led the analysis of the data generated by the fly transcription consortium (2011-2014). He currently leads integrative analysis for the Consortium for Environmental Omics and Toxicology (CEOT). He is also actively involved in the Microbes to Biomes Initiative (M2B) at Berkeley Lab, within which he leads the computational analysis for a DOE sponsored Laboratory Directed Research and Development Project aimed at understanding host-microbiome interactions that may aid adaption to environmental challenges. |
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| 15:10 - 15:35 |
LncRNA regulators of metabolism
Efficient enzymatic activity of the mitochondrial electron transport chain depends on replenishment of its subunits whose availability is determined by their rates of transcription, translation, import, and protein and mRNA turnover. We have shown that Cerox1, an unusually abundant and conserved long noncoding RNA (lncRNA), substantially alters complex I enzymatic activity, reactive oxygen species production, and levels of transcripts encoding 12 complex I subunits. These enzymatic changes are similar to those observed in disorders with mitochondrial dysfunction, such as Parkinson’s and Alzheimer’s diseases. Increased Cerox1 levels reduce cell division, protect cells against the cytotoxic effects of the complex I inhibitor rotenone and decoy microRNAs which otherwise reduce the abundance of complex I proteins. MicroRNA-488 overexpression reduces Cerox1 levels 13-fold, and mutation of its single response element in Cerox1 alters complex I transcripts’ levels. Cerox1 is the first lncRNA known to regulate mitochondrial energy metabolism. 
Professor Chris Ponting, University of Oxford
Professor Chris Ponting, University of OxfordProfessor Ponting provided seminal contributions to the rapid change of biomedical science into data-rich disciplines, publishing widely across protein science, evolutionary biology, genetics and genomics. He is among the Top 200 most cited researchers in Molecular Biology & Genetics 2014. His studies forced a reconsideration of the extent and importance of transcribed noncoding DNA in the human genome. Prior to his 2007 paper, most researchers wrote off the possibility that long noncoding RNAs (lncRNAs) were functional, arguing instead that they represent ‘transcriptional noise’. Since then, he has demonstrated scientific rigour in research on lncRNA evolution, splicing, nuclear function and microRNA-mediated cytoplasmic function in health and disease. |
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| 15:35 - 16:00 |
Primate-specific lncRNAs: from species phenotypic uniqueness to human disease
Long non-coding RNA (lncRNA) genes are at least as abundant as protein-coding genes in humans. LncRNA genes have low interspecies conservation: over 60% are not conserved beyond primates. Diverse regulatory roles – positive and negative, epigenetic and post-transcriptional, nuclear and cytoplasmic – have been identified for over a hundred human lncRNA genes to date, still a small number in contrast to the approximately 20,000 lncRNA genes discovered in the first one and a half decades of post-genomic biology. Our integration of the Gencode lncRNA resource with the NHGRI catalog of significant disease-associated SNPs from Genome-Wide Association Studies (GWAS) revealed specific diseases where a highly statistically significant portion of GWAS hits occurs in lncRNA exons, including obesity and several cancers. Notably, one obesity-associated lncRNA, LOC1572723, lacking conservation beyond primates, was independently pinpointed by 19 published GWAS datasets. Professor Lipovich pursued functional lncRNAomics in another lncRNA-associated disease – breast cancer – using the human estrogen receptor α positive cell line MCF7. Overexpression and knockdown of 26 estrogen-responsive lncRNAs shifted breast cancer cells along the apoptosis-proliferation axis. Reduced cell growth and increased cell death were consistently observed upon knockdown of estrogen-induced, and overexpression of estrogen-repressed, lncRNAs. 12 of these 26 lncRNAs originated after the prosimian split. Overexpression of BC041455, a primate-specific estrogen-repressed lncRNA, reduced ERK phosphorylation uniquely in ERα-positive cells, indicating modulation of the conserved MAP kinase pathway. Professor Lipovich shows by ribosome profiling that BC041455's polysome occupancy is distinct from that of highly translated mRNAs, with implications for hormone dependence of ectopic lncRNA translation in disease. 
Professor Leonard Lipovich, Wayne State University, USA
Professor Leonard Lipovich, Wayne State University, USALeonard Lipovich, a proud graduate of Stuyvesant High School, New York City, earned his B.A. (cum laude) in Genetics and Development from Cornell University (Ithaca, N.Y.) in 1998, and his Ph.D. in Genome Sciences from the University of Washington, Seattle, where Mary-Claire King was his dissertation advisor, in 2003. After postdoctoral training at the Genome Institute of Singapore, where he discovered the first ever mammalian long non-coding RNA directly functional in stem cell pluripotency and pioneered the concept of sense-antisense gene pair evolutionary non-conservation, Dr. Lipovich joined Wayne State University in Detroit, Michigan in 2007 as an assistant professor, and was promoted to associate professor with tenure in 2013. In 2014, Dr. Lipovich received a $1,500,000 National Institutes of Health (NIH) Director's New Innovator Award for his work on how primate-specific long non-coding RNAs cause cell growth and cell death in human cancer. Current research in the Lipovich laboratory interrogates the contribution of long non-coding RNA genes to human cancer and metabolic disorders, using integrated computational and experimental approaches: high-throughput reverse genetics, non-coding RNA proteogenomics, Genome-Wide Association Studies and whole-genome sequencing. Dr. Lipovich is the author of 50 peer-reviewed publications, and was the chair of the 2015 Keystone Symposium on Long Non-Coding RNA. He is a funded co-investigator of both the ENCODE (Encyclopedia of DNA Elements) Consortium and the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) Consortium. His long-term goal is to improve human health, and the human condition, through personalized, lncRNA-targeted rational therapeutics. |
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| 16:20 - 17:00 | Panel discussion |