From Discovery to Function: The Expanding Roles of Long NonCoding RNAs in Physiology and Disease

R E V I E W From Discovery to Function: The Expanding Roles of Long NonCoding RNAs in Physiology and Disease Miao Sun and W. Lee Kraus Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390 Long noncoding RNAs (lncRNAs) are a relatively poorly understood class of RNAs with little or no coding capacity transcribed from a set of incompletely annotated genes. They have received considerable attention in the past few years and are emerging as potentially important players in biological regulation. Here we discuss the evolving understanding of this new class of molecular regulators that has emerged from ongoing research, which continues to expand our databases of annotated lncRNAs and provide new insights into their physical properties, molecular mechanisms of action, and biological functions. We outline the current strategies and approaches that have been employed to identify and characterize lncRNAs, which have been instrumental in revealing their multifaceted roles ranging from cis- to trans-regulation of gene expression and from epigenetic modulation in the nucleus to posttranscriptional control in the cytoplasm. In addition, we highlight the molecular and biological functions of some of the best characterized lncRNAs in physiology and disease, especially those relevant to endocrinology, reproduction, metabolism, immunology, neurobiology, muscle biology, and cancer. Finally, we discuss the tremendous diagnostic and therapeutic potential of lncRNAs in cancer and other diseases. (Endocrine Reviews 36: 25– 64, 2015) I. Introduction II. Defining LncRNAs A. An evolving definition of lncRNAs B. A working definition of lncRNAs III. Identifying and Cataloging LncRNAs A. Identification of lncRNA transcripts: omics approaches B. Evaluation of coding potential C. Gene-specific validations D. Cataloging lncRNAs in public databases IV. Functional Characterization of LncRNAs A. Expression profiling across spatial and temporal gradients B. Coding-noncoding coexpression relationships: guilt-by-association C. A role for lncRNAs in the cis-regulation of gene expression D. A role for lncRNAs in the trans-regulation of gene expression E. LncRNA-protein interactions drive molecular outcomes in cis and trans gene regulation F. Methods for the detection of lncRNA interaction sites across the genome G. Beyond the nucleus: a broader view of lncRNA functions ISSN Print 0163-769X ISSN Online 1945-7189 Printed in U.S.A. Copyright © 2015 by the Endocrine Society Received April 29, 2014. Accepted November 21, 2014. First Published Online November 26, 2014 doi: 10.1210/er.2014-1034 V. Lessons Learned From the Best-Characterized LncRNAs A. XIST B. MALAT1 C. HOTAIR VI. The Biology of LncRNAs in Endocrine-Related Systems A. LncRNAs and hormonal signaling: regulators, coregulators, and modulators of steroid receptors B. LncRNAs and reproduction: regulators of mammary gland development Abbreviations: AD, Alzheimer’s disease; agRNA, antigene RNA; ALC-1, atrial myosin light chain 1; AR, androgen receptor; ceRNA, competing endogenous RNA; CHART, capture hybridization analysis of RNA targets; ChIP-seq, chromatin immunoprecipitation sequencing; ChIRP, chromatin isolation by RNA purification; ciRNA, circular intronic long ncRNA; circRNA, circular RNA; CoREST, RE1-silencing transcription factor corepressor 1; CPC, coding potential calculator; CSF, codon substitution frequency; CTCF, CCCTC-binding factor; Dlx, distal-less homeobox; DMD, Duchenne muscular dystrophy; DNMT1, DNA (cytosine-5)-methyltransferase 1; eRNA, enhancer RNA; ESC, embryonic stem cell; FSHD, facioscapulohumeral muscular dystrophy; GABA, ␥-aminobutyric acid; GR, glucocorticoid receptor; GRO-seq, global nuclear run-on sequencing; HD, Huntington’s disease; hnRNP, heterogeneous nuclear ribonucleoprotein; HuR, human antigen R; lincRNA, long intergenic ncRNA; lncRNA, long ncRNA; LSD1, lysine-specific demethylase 1; ␤-MHC, myosin heavy chain ␤; MLL, mixed-lineage leukemia protein; MYH, myosin heavy chain; NAT, natural antisense transcript; ncRNA, noncoding RNA; NF, nuclear factor; nt, nucleotide; ORF, open reading frame; Pol II, polymerase II; 3P-seq, polyadenosine position profiling by sequencing; PPAR␥, peroxisome proliferator-activated receptor ␥; PR, progesterone receptor; PRC2, Polycomb repressive complex 2; PWS, Prader-Willi syndrome; RAP, RNA antisense purification; RIP, RNA immunoprecipitation; rRNA, ribosomal RNA; SCA, spinocerebellar ataxia; snoRNA, small nucleolar RNA; SRA, steroid receptor RNA activator; STAU1, Staufen double-stranded RNA binding protein 1; TSS, transcription start site; WDR5, WD repeat-containing protein 5; XCI, X-chromosome inactivation. Endocrine Reviews, February 2015, 36(1):25– 64 edrv.endojournals.org 25 26 Sun and Kraus LncRNAs in Physiology and Disease C. LncRNAs and metabolism: adipogenesis and metabolic disorders D. LncRNAs in the immune system: innate and adaptive immune responses VII. LncRNAs in Other Biological Systems A. LncRNAs in the nervous system: neural development and disorders B. LncRNAs in cardiac and skeletal muscle: muscle development and pathologies VIII. LncRNAs in Cancer: Oncogenes and Tumor Suppressors A. LncRNAs and oncogenesis B. LncRNAs and tumor suppression C. LncRNAs and metastasis IX. The Therapeutic Potential of LncRNAs X. Summary, Conclusions, and Future Directions A. Summary and Conclusions B. Future directions I. Introduction enome-wide transcriptome analyses conducted over the past decade, including recent studies by the ENCODE (Encyclopedia of DNA Elements) Consortium, have revealed that mammalian genomes are pervasively, but not indiscriminately, transcribed, giving rise to a wide variety of coding and noncoding RNA (ncRNA) transcripts (1–3). The cellular repertoire of ncRNAs consists of small housekeeping RNAs such as ribosomal RNAs (rRNAs) and transfer RNAs, microRNAs, and long ncRNAs (lncRNAs) including antisense RNAs and enhancer RNAs (eRNAs). The functions of many of these ncRNAs are poorly understood, but interests in uncovering their biological functions and molecular mechanisms of action are intense. In this review, we focus on lncRNAs, presenting the most current information on their discovery, annotation, molecular actions, and biological functions, especially as they relate to hormonal signaling systems. G Figure 1. Endocrine Reviews, February 2015, 36(1):25– 64 II. Defining LncRNAs LncRNAs, defined as non-protein-coding RNA transcripts longer than 200 nucleotides (nt), are emerging as key regulators of diverse cellular processes (4 –12). To date, a limited, but fast-growing number of lncRNAs have been functionally characterized through gene-specific studies. To further expand our understanding of lncRNAs, rapid advancements in genomic m (...truncated)