Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells

• Published in: Molecular cell 2015-08, Vol.59 (4), p.698-711
• Main Authors: Sun, Miao, Gadad, Shrikanth S., Kim, Dae-Seok, Kraus, W. Lee
• Format: Article
• Language: English
• Subjects: Base Sequence; breast neoplasms; Breast Neoplasms - genetics; Breast Neoplasms - metabolism; Breast Neoplasms - pathology; cell cycle; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Cell Proliferation; Female; gene expression; Gene Expression Regulation, Neoplastic; genes; histones; Humans; MCF-7 Cells; Molecular Sequence Annotation; neoplasm cells; non-coding RNA; patients; RNA, Long Noncoding - physiology; sequence analysis; Transcriptome
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2015.06.023

We describe a computational approach that integrates GRO-seq and RNA-seq data to annotate long noncoding RNAs (lncRNAs), with increased sensitivity for low-abundance lncRNAs. We used this approach to characterize the lncRNA transcriptome in MCF-7 human breast cancer cells, including >700 previously unannotated lncRNAs. We then used information about the (1) transcription of lncRNA genes from GRO-seq, (2) steady-state levels of lncRNA transcripts in cell lines and patient samples from RNA-seq, and (3) histone modifications and factor binding at lncRNA gene promoters from ChIP-seq to explore lncRNA gene structure and regulation, as well as lncRNA transcript stability, regulation, and function. Functional analysis of selected lncRNAs with altered expression in breast cancers revealed roles in cell proliferation, regulation of an E2F-dependent cell-cycle gene expression program, and estrogen-dependent mitogenic growth. Collectively, our studies demonstrate the use of an integrated genomic and molecular approach to identify and characterize growth-regulating lncRNAs in cancers. •A sensitive approach for annotating lncRNAs that integrates GRO-seq and RNA-seq data•Identification of lncRNAs in breast cancer cells, including >700 not yet annotated•Differences between lncRNA and mRNA gene promoters; similarities with enhancers•LncRNAs 152 and 67 control the cell cycle and gene expression in breast cancer cells Sun et al. use a computational genomics pipeline with GRO-seq and RNA-seq data to identify ∼1,900 lncRNAs in breast cancer cells, including >700 lncRNAs not previously annotated. Functional analyses of lncRNA152 and lncRNA67 indicate roles in cell proliferation and the regulation of an E2F-dependent cell-cycle gene expression program.