Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer

References

• Miller KD, Nogueira L, Mariotto AB, et al. Cancer treatment and survivorship statistics, 2019. CA Cancer J Clin. 2019;69(5):363–385.
   PubMed Web of Science ®Google Scholar
• Burstein HJ, Temin S, Anderson H, et al. Adjuvant endocrine therapy for women with hormone receptor-positive breast cancer: american society of clinical oncology clinical practice guideline focused update. J Clin Oncol. 2014;32:2255–2269.
   PubMed Web of Science ®Google Scholar
• Moggs JG, Orphanides G. Estrogen receptors: orchestrators of pleiotropic cellular responses. EMBO Rep. 2001;2:775–781.
   PubMed Web of Science ®Google Scholar
• Pink JJ, Jordan VC. Models of estrogen receptor regulation by estrogens and antiestrogens in breast cancer cell lines. Cancer Res. 1996;56:2321–2330.
   PubMed Web of Science ®Google Scholar
• Murata T, Jinno H, Takahashi M, et al. Clinicopathologic features of hormone-receptor-positive breast cancer patients with late recurrence. Breast J. 2019;25(1):9–15.
   PubMed Web of Science ®Google Scholar
• Ring A, Dowsett M. Mechanisms of tamoxifen resistance. Endocr Relat Cancer. 2004;11:643–658.
   PubMed Web of Science ®Google Scholar
• Carroll JS, Meyer CA, Song J, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006;38(11):1289–1297.
   PubMed Web of Science ®Google Scholar
• Zhu C, Li L, Zhang Z, et al. A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer. Mol Cell. 2019;75(4):791–806 e8.
   PubMed Web of Science ®Google Scholar
• Visel A, Rubin EM, Pennacchio LA. Genomic views of distant-acting enhancers. Nature. 2009;461(7261):199–205.
   PubMed Web of Science ®Google Scholar
• Heinz S, Romanoski CE, Benner C, et al. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol. 2015;16(3):144–154.
   PubMed Web of Science ®Google Scholar
• De Santa F, Barozzi I, Mietton F, et al. A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol. 2010;8(5):e1000384.
   PubMed Web of Science ®Google Scholar
• Kim TK, Hemberg M, Gray JM, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465:182–187.
   PubMed Web of Science ®Google Scholar
• Hah N, Danko CG, Core L, et al. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 2011;145(4):622–634.
   PubMed Web of Science ®Google Scholar
• Wang D, Garcia-Bassets I, Benner C, et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature. 2011;474(7351):390–394.
   PubMed Web of Science ®Google Scholar
• Hah N, Murakami S, Nagari A, et al. Enhancer transcripts mark active estrogen receptor binding sites. Genome Res. 2013;23(8):1210–1223.
   PubMed Web of Science ®Google Scholar
• Kim T-K, Shiekhattar R. Architectural and Functional Commonalities between Enhancers and Promoters. Cell. 2015;162(5):948–959.
   PubMed Web of Science ®Google Scholar
• Carroll JS, Liu XS, Brodsky AS, et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005;122(1):33–43.
   PubMed Web of Science ®Google Scholar
• Hurtado A, Holmes KA, Ross-Innes CS, et al. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat Genet. 2011;43(1):27–33.
   PubMed Web of Science ®Google Scholar
• Jozwik KM, Carroll JS. Pioneer factors in hormone-dependent cancers. Nat Rev Cancer. 2012;12(6):381–385.
   PubMed Web of Science ®Google Scholar
• Kraus WL, Kadonaga JT. p300 and estrogen receptor cooperatively activate transcription via differential enhancement of initiation and reinitiation. Genes Dev. 1998;12(3):331–342.
   PubMed Web of Science ®Google Scholar
• Zhang X, Krutchinsky A, Fukuda A, et al. MED1/TRAP220 exists predominantly in a TRAP/Mediator subpopulation enriched in RNA polymerase II and is required for ER-mediated transcription. Mol Cell. 2005;19:89–100.
   PubMed Web of Science ®Google Scholar
• Liu Z, Merkurjev D, Yang F, et al. Enhancer activation requires trans-recruitment of a mega transcription factor complex. Cell. 2014;159(2):358–373.
   PubMed Web of Science ®Google Scholar
• Niknafs YS, Han S, Ma T, et al. The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression. Nat Commun. 2016;7(1):12791.
   PubMedGoogle Scholar
• Jonsson P, Coarfa C, Mesmar F, et al. Single-Molecule Sequencing Reveals Estrogen-Regulated Clinically Relevant lncRNAs in Breast Cancer. Mol Endocrinol. 2015;29(11):1634–1645.
   PubMedGoogle Scholar
• Mattick JS, Makunin IV, Non-coding RNA Human molecular genetics 2006; 15 Spec No 1:R17–29.
   Google Scholar
• Palazzo AF, Lee ES. Non-coding RNA: what is functional and what is junk? Front Genet. 2015;6:2.
   PubMed Web of Science ®Google Scholar
• Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775–1789.
   PubMed Web of Science ®Google Scholar
• GENCODE. Statistics about the current GENCODE Release (version 33). 2019, Aug.
   Google Scholar
• Agliano F, Rathinam VA, Medvedev AE, et al. Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol. 2019;40:492–510.
   PubMed Web of Science ®Google Scholar
• Deng SJ, Chen HY, Ye Z, et al. Hypoxia-induced LncRNA-BX111 promotes metastasis and progression of pancreatic cancer through regulating ZEB1 transcription. Oncogene. 2018;37:5811–5828.
   PubMed Web of Science ®Google Scholar
• Li W, Li H, Zhang L, et al. Long non-coding RNA LINC00672 contributes to p53 protein-mediated gene suppression and promotes endometrial cancer chemosensitivity. J Biol Chem. 2017;292(14):5801–5813.
   PubMed Web of Science ®Google Scholar
• Chen X, Xie R, Gu P, et al. Long Noncoding RNA LBCS Inhibits Self-Renewal and Chemoresistance of Bladder Cancer Stem Cells through Epigenetic Silencing of SOX2. Clin Cancer Res. 2019;25(4):1389–1403.
   PubMed Web of Science ®Google Scholar
• Wang H, Guan Z, He K, et al. LncRNA UCA1 in anti-cancer drug resistance. Oncotarget. 2017;8(38):64638–64650.
   PubMedGoogle Scholar
• Xue X, Yang YA, Zhang A, et al. LncRNA HOTAIR enhances ER signaling and confers tamoxifen resistance in breast cancer. Oncogene. 2016;35:2746–2755.
   PubMed Web of Science ®Google Scholar
• Sun M, Gadad SS, Kim DS, et al. Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells. Mol Cell. 2015;59:698–711.
   PubMed Web of Science ®Google Scholar
• Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.
   PubMed Web of Science ®Google Scholar
• Tseng YY, Moriarity BS, Gong W, et al. PVT1 dependence in cancer with MYC copy-number increase. Nature. 2014;512:82–86.
   PubMed Web of Science ®Google Scholar
• Cho SW, Xu J, Sun R, et al. Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. Cell. 2018;173(6):1398–412 e22.
   PubMed Web of Science ®Google Scholar
• Misawa A, Takayama K, Urano T, et al. Androgen-induced Long Noncoding RNA (lncRNA) SOCS2-AS1 Promotes Cell Growth and Inhibits Apoptosis in Prostate Cancer Cells. J Biol Chem. 2016;291(34):17861–17880.
   PubMed Web of Science ®Google Scholar
• Xu J, Meng Q, Li X, et al. Long Noncoding RNA MIR17HG Promotes Colorectal Cancer Progression via miR-17-5p. Cancer Res. 2019;79(19):4882–4895.
   PubMed Web of Science ®Google Scholar
• Thomas C, Gustafsson JA. The different roles of ER subtypes in cancer biology and therapy. Nat Rev Cancer. 2011;11:597–608.
   PubMed Web of Science ®Google Scholar
• Li W, Notani D, Ma Q, et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013;498(7455):516–520.
   PubMed Web of Science ®Google Scholar
• Tan Y, Jin C, Ma W, et al. Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program. Mol Cell. 2018;71(4):526–39 e8.
   PubMed Web of Science ®Google Scholar
• Schmidt D, Schwalie PC, Ross-Innes CS, et al. A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res. 2010;20(5):578–588.
   PubMed Web of Science ®Google Scholar
• Thomas-Claudepierre AS, Robert I, Rocha PP, et al. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med. 2016;213(3):303–312.
   PubMed Web of Science ®Google Scholar
• Raab JR, Resnick S, Magnuson T. Genome-Wide Transcriptional Regulation Mediated by Biochemically Distinct SWI/SNF Complexes. PLoS Genet. 2015;11(12):e1005748.
   PubMed Web of Science ®Google Scholar
• Bao X, Rubin AJ, Qu K, et al. A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63. Genome Biol. 2015;16(1):284.
   PubMedGoogle Scholar
• Chimge NO, Little GH, Baniwal SK, et al. RUNX1 prevents oestrogen-mediated AXIN1 suppression and beta-catenin activation in ER-positive breast cancer. Nat Commun. 2016;7(1):10751.
   PubMedGoogle Scholar
• Mercado-Matos J, Matthew-Onabanjo AN, Shaw LM. RUNX1 and breast cancer. Oncotarget. 2017;8(23):36934–36935.
   PubMedGoogle Scholar
• Li G, Ruan X, Auerbach RK, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148(1–2):84–98.
   PubMed Web of Science ®Google Scholar
• Tang Z, Li C, Kang B, et al. GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017;45(W1):W98–W102.
   PubMed Web of Science ®Google Scholar
• Dixon JR, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376–380.
   PubMed Web of Science ®Google Scholar
• Yu NY, Iftimi A, Yau C, et al. Assessment of Long-term Distant Recurrence-Free Survival Associated With Tamoxifen Therapy in Postmenopausal Patients With Luminal A or Luminal B Breast Cancer. JAMA Oncol. 2019;5(9):1304.
   Web of Science ®Google Scholar
• Wu Y, Zhang Z, Cenciarini ME, et al. Tamoxifen Resistance in Breast Cancer Is Regulated by the EZH2-ERalpha-GREB1 Transcriptional Axis. Cancer Res. 2018;78(3):671–684.
   PubMed Web of Science ®Google Scholar
• Hong D, Fritz AJ, Finstad KH, et al. Suppression of Breast Cancer Stem Cells and Tumor Growth by the RUNX1 Transcription Factor. Mol Cancer Res. 2018;16(12):1952–1964.
   PubMed Web of Science ®Google Scholar
• Buenrostro JD, Wu B, Chang HY, et al. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol. 2015;109(1)::21 9 1–9.
   PubMedGoogle Scholar
• Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
   PubMed Web of Science ®Google Scholar
• Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–930.
   PubMed Web of Science ®Google Scholar
• Langmead B, Trapnell C, Pop M, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
   PubMed Web of Science ®Google Scholar
• Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17:10–12.
   Google Scholar
• Zhou X, Maricque B, Xie M, et al. The Human Epigenome Browser at Washington University. Nat Methods. 2011;8(12):989–990.
   PubMed Web of Science ®Google Scholar
• Zhou Y, Gerrard DL, Wang J, et al. Temporal dynamic reorganization of 3D chromatin architecture in hormone-induced breast cancer and endocrine resistance. Nat Commun. 2019;10(1):1522.
   PubMedGoogle Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–359.
   PubMed Web of Science ®Google Scholar
• Servant N, Varoquaux N, Lajoie BR, et al. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Genome Biol. 2015;16(1):259.
   PubMedGoogle Scholar
• Ay F, Bailey TL, Noble WS. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 2014;24(6):999–1011.
   PubMed Web of Science ®Google Scholar