Navigating Non-coding RNA

1. Non-coding RNAs: History and Definition
Ruth Seal, University of Cambridge School of Clinical Medicine, UK
Jeannie T. Lee, Harvard Medical School, US
Starting with the discovery of transfer RNA and ribosomal RNA in the 1950s, non-coding (nc) RNAs with biological roles have been known for almost 60 years. This chapter will provide a brief overview of the events that led to the discovery of various types of ncRNAs, along with their specific properties, i.e. locus position with respect to protein-coding genes, subcellular localization, tissue-specific expression.


2. Housekeeping Non-coding RNAs
Alexey Petrov, Auburn University, US
Gaby Fuchs, SUNY, University at Albany, US
This section will introduce different types of housekeeping ncRNAs, i.e., ribosomal RNA, transfer RNA, small nuclear RNA, small nucleolar RNA, telomerase RNA, tRNA-derived fragments, tRNA halves, discuss their biogenesis, abundance, and involvement in regulating cellular functions.


3. Regulatory Non-coding RNAs
Anthony M Jevnikar, University of Western Ontario, US
Barbara Uszczynska-Ratajczak, University of Warsaw, Poland
This section will introduce different types of regulatory ncRNAs, i.e., microRNAs, small interfering RNAs, piwi-interacting RNAs, enhancer RNAs, long non-coding RNAs, circular RNAs, Y RNAs and vault RNAs. Their biogenesis, functions as regulators of gene expression at epigenetic, transcriptional, and post-transcriptional levels will be discussed.


4. Non-coding RNAs: mechanisms of action
Marc Weinberg, Department of Molecular and Experimental Medicine, The Scripps Research Institute, California, US; University of the Witwatersrand Medical School, Johannesburg, South Africa
Phillip D. Zamore, University of Massachusetts Medical School, US
Molecular mechanisms of ncRNA action will be addressed, and include their function as signals, decoys, guides, and scaffolds. Also, ncRNAs intermolecular interactions including 1) RNA:DNA:DNA triplex (trans), 2) RNA:DNA hybrid, 3) RNA:RNA hybrid of ncRNA with a nascent transcript, 4) RNA-protein interaction (cis/trans), as well as the concept of global interactome network will be covered.


5. Identification of Non-coding RNAs: Methods
Julia Salzman, Stanford University School of Medicine, US
Holger Prokisch, Technical University of Munich, Munich, Germany
Pierfrancesco Tassone, Magna Graecia University, Catanzaro, Italy
Jennifer Harrow, Wellcome Trust Sanger Institute, UK
Roderic Guigó, Barcelona Institute of Science and Technology, Spain
Description of methodologies used for the identification of ncRNAs functionality will be provided, and include old-school methods, i.e., microarray, serial analysis of gene expression, RACE PCR, as well as novel methodologies, including next-generation sequencing, CAGE-seq, direct RNA sequencing, chromatin signature-based approach, computational methods (comparative genomics).


6. Functional Characterization of Non-coding RNAs
Mitchell Guttman, California Institute of Technology, US
Bin Xu, University of Michigan Medical Center, US
Katalin Fejes Tóth, California Institute of Technology, US
Denise P. Barlow, Research Center for Molecular Medicine, Universitat Wien, Austria
Susan J. Baserga, Yale University, US
Thomas Preiss, The John Curtin School of Medical Research, Australia
The overview of methodologies used for addressing ncRNAs functionality will be discussed, and include overexpression, knockout/knockdown experiments, i.e., RNAi, CRISPR/Cas, methods addressing ncRNA interactome network, i.e, PARIS (psoralen analysis of RNA interactions and structures), protein binding assays, i.e., RIP.


7. Structural Characterization of Non-coding RNAs
Jessica Brown, University of Notre Dame, France
Karissa Sanbonmatsu, Los Alamos National Laboratory, New Mexico, US
Maria Pyle, Yale University, US
Non-coding RNA structure determines their function by acting as scaffold and decoy for other effectors. The overview of methodologies used to address secondary and tertiary structure of ncRNAs will be discussed and include: conventional chemical probing, enzymatic probing, and novel next-generation sequencing-based methods, i.e., SHAPE, SHAPE-MaP, DMS-seq, computational approaches, as well as methods addressing tertiary structure, i.e, SAXS.


8. Regulation of Non-coding RNAs
Joanna Sztuba-Solinska, Auburn University, Alabama, US
Marieta Costache, University of Bucharest, Romania
Epitranscriptomic (post-transcriptional) modifications emerged as a new layer of molecular code shaping RNA biology, metabolism, and function. This chapter will discuss different types of epitranscriptomic modifications and their involvement in regulating ncRNAs’ structure, stability, and intermolecular interactions.


9. Non-coding RNAs in Human Non-infectious Diseases
Clay Pandorf, Edward Via College of Osteopathic Medicine, Auburn, Alabama, US
Giovanni Di Bernardo, University of Campania Luigi Vanvitelli, Italy
Stefanie Dimmeler, Goethe University Frankfurt, Germany
NcRNAs are involved in most human diseases, from neurological disorders, cancers, to cardiovascular problems. Specific miRNAs and lncRNAs are disrupted in intellectual disabilities and neurodegenerative syndromes and contribute to atherosclerosis, and snoRNA and lncRNA functions are impaired in imprinting syndromes.


10. Non-coding RNAs in Human Infectious Diseases
Joseph Ziegelbauer, National Cancer Institue, National Institute of Health, US
Rolf Renne, University of Florida, US
Non-coding RNAs (ncRNAs) identified in pathogen and/or their human hosts that play a specific role in the biology and etiology of an infectious disease. Specific ncRNAs which transcriptional profile changes upon pathogenic infection will be covered, and their role in regulating (positively and negatively) host immune response and pathogen proliferation will be described.


11. Therapeutic Targeting Non-coding RNAs
Amanda Hargrove, Department of Chemistry Duke University, North Carolina, US
Matthew Disney, Scripps Research Institute, US
David Spector, Cold Spring Harbor Laboratory, New York, US
Steven M Jay, University of Maryland, US
Thomas Thum, Institute of Molecular and Translational Therapeutic Strategies, Hannover, Germany