Noncoding RNAs: Regulators of the Mammalian Transcription Machinery

• Published in: Journal of molecular biology Vol. 428; no. 12; pp. 2652 - 2659
• Main Authors: Eidem, Tess M., Kugel, Jennifer F., Goodrich, James A.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 19-06-2016
• Subjects: Animals; circular RNAs; divergent RNAs; DNA - genetics; enhancer RNAs; Humans; Mammals - genetics; Promoter Regions, Genetic - genetics; Promoter Regions, Genetic - physiology; RNA polymerase II; RNA Polymerase II - metabolism; RNA, Untranslated - genetics; tethered RNAs; Transcription Factors - metabolism; Transcription, Genetic - genetics; Transcription, Genetic - physiology; Pol II; EBER2; circRNA; tethered RNAs; GR; enhancer RNAs; ncRNA; snRNA; eRNA; P-TEFb; YY1; TF; Arc; circular RNAs; divergent RNAs; CLIP-seq; NELF; RdRP; EIciRNA; FISH; ciRNA; RNA polymerase II; snRNP; eB2 RNA
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2016.02.019

Transcription by RNA polymerase II (Pol II) is required to produce mRNAs and some noncoding RNAs (ncRNAs) within mammalian cells. This coordinated process is precisely regulated by multiple factors, including many recently discovered ncRNAs. In this perspective, we will discuss newly identified ncRNAs that facilitate DNA looping, regulate transcription factor binding, mediate promoter-proximal pausing of Pol II, and/or interact with Pol II to modulate transcription. Moreover, we will discuss new roles for ncRNAs, as well as a novel Pol II RNA-dependent RNA polymerase activity that regulates an ncRNA inhibitor of transcription. As the multifaceted nature of ncRNAs continues to be revealed, we believe that many more ncRNA species and functions will be discovered.
Graphical Abstract [Display omitted]
•Pol II transcription is regulated by ncRNAs.•ncRNAs facilitate DNA looping and transcription factor recruitment.•Promoter-proximal pausing by Pol II is influenced by ncRNAs.•ncRNAs interact with Pol II to activate or inhibit transcription.•Pol II uses its RNA-dependent RNA polymerase activity to regulate an ncRNA.