Published OnlineFirst October 19, 2016; DOI: 10.1158/2159-8290.CD-16-0745 REVIEW Emergence of the Noncoding Cancer Genome: A Target of Genetic and Epigenetic Alterations Stanley Zhou 1 , 2 , Aislinn E. Treloar 1 , 2 , and Mathieu Lupien 1 , 2 , 3 ABSTRACT The emergence of whole-genome annotation approaches is paving the way for the comprehensive annotation of the human genome across diverse cell and tissue types exposed to various environmental conditions. This has already unmasked the positions of thou- sands of functional cis-regulatory elements integral to transcriptional regulation, such as enhancers, promoters, and anchors of chromatin interactions that populate the noncoding genome. Recent studies have shown that cis-regulatory elements are commonly the targets of genetic and epigenetic altera- tions associated with aberrant gene expression in cancer. Here, we review these fi ndings to showcase the contribution of the noncoding genome and its alteration in the development and progression of can- cer. We also highlight the opportunities to translate the biological characterization of genetic and epi- genetic alterations in the noncoding cancer genome into novel approaches to treat or monitor disease. Signifi cance: The majority of genetic and epigenetic alterations accumulate in the noncoding genome throughout oncogenesis. Discriminating driver from passenger events is a challenge that holds great promise to improve our understanding of the etiology of different cancer types. Advancing our under- standing of the noncoding cancer genome may thus identify new therapeutic opportunities and acceler- ate our capacity to fi nd improved biomarkers to monitor various stages of cancer development. Cancer Discov; 6(11); 1215–29. ©2016 AACR. THE IDENTIFICATION AND ANNOTATION is a source of investigation and debate ( 1, 3 ). Nearly half of the OF CIS-REGULATORY ELEMENTS IN THE noncoding genome consists of repetitive elements, including HUMAN GENOME interspersed satellites, short interspersed nuclear elements, long interspersed nuclear elements, ribosomal DNA, DNA The Human Genome Is More Than a transposons, and retrotransposons, that affect various bio- Collection of Genes logical functions ( 4 ). Additionally, the noncoding genome The diploid human genome consists of over 6 billion bases harbors nonrepetitive elements, including cis-regulatory ele- of DNA that provide the genetic basis for our phenotypic indi- ments such as promoters, enhancers, and anchors of chro- viduality ( 1, 2 ). Approximately 20,000 genes are encoded in the matin interactions ( 5, 6 ). These cis-regulatory elements are human genome and are transcribed into ∼80,000 transcripts directly involved in modulating gene expression and noncod- that are subsequently translated into various proteins. Despite ing RNA transcription through long-range chromatin inter- the importance of proteins in diverse cellular processes, pro- actions ( Fig. 1A–D ; refs. 7, 8 ). Identifying and characterizing tein coding sequences account for under 2% of the human functional noncoding elements within the genome hold great genome (less than 120 million bases of DNA in the diploid promise to improve our understanding of the human genome genome). The role for the remaining noncoding bases (∼98%) in health and disease. In this review, we focus on the pro- gress in noncoding functional element annotation and recent advances demonstrating the central role of genetic and epige- 1 Princess Margaret Cancer Centre, University Health Network, Toronto, netic alterations affecting noncoding cis-regulatory elements Ontario, Canada . 2 Department of Medical Biophysics, University of of relevance to cancer initiation and progression. Toronto, Toronto, Ontario, Canada. 3Ontario Institute for Cancer Research, Toronto, Ontario, Canada. Identifi cation and Annotation of Noncoding S. Zhou and A.E. Treloar contributed equally to this article. Functional Elements across the Genome Corresponding Author: Mathieu Lupien , University of Toronto, Princess The noncoding genome has historically been overlooked Margaret Cancer Centre-University Health Network, Ontario Institute for Cancer Research , TMDT 11-706, 101 College Street, Toronto, Ontario, because of technical limitations hindering the characteriza- Canada M5G 1L7. Phone: 416-581-7434; Fax: 416-581-7435 ; E-mail: tion of its genetic and epigenetic nature. Recent advances [email protected] in whole-genome annotation, inclusive of next-generation doi: 10.1158/2159-8290.CD-16-0745 sequencing technologies, now offer the means to effec- ©2016 American Association for Cancer Research. tively delineate functional noncoding regions of the human NOVEMBER 2016CANCER DISCOVERY | 1215 Downloaded from cancerdiscovery.aacrjournals.org on October 2, 2021. © 2016 American Association for Cancer Research. Published OnlineFirst October 19, 2016; DOI: 10.1158/2159-8290.CD-16-0745 REVIEW Zhou et al. A C Enhancer–promoter B Interaction frequency interaction anchors High Low TAD boundary TAD Inactive Active TAD boundary D TAD boundaries POL2 Enhancer Mediator ZNF143 /Coactivator Promoter CTCF Anchor of chromatin TF Cohesin interaction Figure 1. The genome is organized through a hierarchy of long-range interactions. A, large chromosomal neighborhoods associate with each other in the nuclear space. Euchromatic regions that are associated with high transcriptional activity tend to cluster in the center of the nucleus. In contrast, heterochro- matic regions associated with transcriptional repression tend to cluster at the nuclear periphery. B, heat map representing virtual genome-wide chromatin interaction maps. Megabase scale chromatin interaction partitions the genome into domains of interactions known as topologically associated domains (TAD). TAD boundaries preclude interactions between neighboring TADs, therefore restricting most interactions to within their borders. C, enhancer– promoter chromatin interactions are mediated by the chromatin interaction factors ZNF143 and CTCF, in concert with several accessory/cobinding proteins. These factors act in concert with several cobinding/accessory/associated proteins to infl uence genome organization via enhancer–promoter interactions. Enhancer–promoter interactions are at the kilobase (Kb) scale and are highly cell-type specifi c. D, anchors of chromatin interactions that defi ne TAD boun- daries are enriched for CTCF and cohesin binding. TADs are up to a megabase (Mb) in scale and are highly conserved across cell types. genome. This annotation takes into account multiple def- suggested by a comparative study of cis-regulatory elements initions of functionality to incorporate the evolutionary, between the human and mouse genomes revealing conserva- genetic, and molecular biology perspectives. tion at the level of transcription factor networks between these From an evolutionary perspective, comparative analyses are two species ( 12 ). Similar multispecies comparative analyses commonly used to identify conservation of DNA sequences based on the chromatin binding profi les for multiple tran- across related species ( 9 ). Genetic elements that are retained scription factors with different DNA-binding motifs exhibit across species are generally considered biologically important conserved DNA-binding sequence preferences but with limited and are thus considered functional. In a recent study, about 8% binding event alignment across species ( 13–15 ). This supports of the human genome was reported to be under evolutionary the integration of epigenomics and comparative genomics to constraint ( 10 ). Taking into account protein-coding sequences, assist in the identifi cation of functional elements in the con- this implies that functionality can be ascribed to approximately text of the evolutionary perspective. 6% of the noncoding genome ( 10, 11 ). Identifying conserved From a genetic perspective, functional elements of the DNA sequences through sequence alignment along a linear genome are defi ned by the ability of a variation in their DNA genome, however, disregards the three-dimensionality of the sequence, either a structural alteration or a single nucleo- genome in which the sequence identity of cis-regulatory ele- tide variant (SNV), to cause quantifi able phenotypic changes, ments regulating the same gene, for instance, may be conserved inclusive of differential gene expression. This is exemplifi ed across species despite localizing to neighboring yet distinct by the mutations reported in the TERT gene promoter in positions along the linear genome of different species. This is patients with melanoma that increases TERT gene expression 1216 | CANCER DISCOVERYNOVEMBER 2016 www.aacrjournals.org Downloaded from cancerdiscovery.aacrjournals.org on October 2, 2021. © 2016 American Association for Cancer Research. Published OnlineFirst October 19, 2016; DOI: 10.1158/2159-8290.CD-16-0745 The Noncoding Cancer Genome REVIEW ( 16, 17 ). Until recently, the genetic approach was hampered by transcription involves the recruitment of coactivator proteins low-to-modest throughput methodologies. The recent devel- to assist in a series of steps, culminating in the assembly opment of high-throughput in vitro assays, however, includ- of the transcription preinitiation complex consisting of gen- ing the Massively Parallel Reporter Assay (MPRA), Massively eral transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, Parallel Functional Dissection (MPFD) assay, Self-Transcribing and TFIIH) and RNA polymerase II. The activation of the RNA Active Regulatory