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Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

Nature Reviews Molecular Cell Biology volume 23, pages 389–406 (2022)Cite this article

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An Author Correction to this article was published on 13 October 2022

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Abstract

Mammalian genomes express two principal gene categories through RNA polymerase II-mediated transcription: protein-coding transcription units and non-coding RNA transcription units. Non-coding RNAs are further divided into relatively abundant structural RNAs, such as small nuclear RNAs, and into a myriad of long non-coding RNAs (lncRNAs) of often low abundance and low stability. Although at least some lncRNA synthesis may reflect transcriptional ‘noise’, recent studies define unique functions for either specific lncRNAs or for the process of lncRNA synthesis. Notably, the transcription, processing and metabolism of lncRNAs are regulated differently from protein-coding genes. In this Review, we provide insight into the regulation of lncRNA transcription and processing gleaned from the application of recently devised nascent transcriptomics technology. We first compare and contrast different methodologies for studying nascent transcription. We then discuss the molecular mechanisms regulating lncRNA transcription, especially transcription initiation and termination, which emphasize fundamental differences in their expression as compared with protein-coding genes. When perturbed, lncRNA misregulation leads to genomic stress such as transcription–replication conflict and R-loop-mediated DNA damage. We discuss many unresolved but important questions about the synthesis and potential functions of lncRNAs.

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Fig. 1: Unstable lncRNAs and other mammalian transcription units.
Fig. 2: Nascent RNA analysis in mammalian cells.
Fig. 3: Regulation of transcription initiation of lncRNAs.
Fig. 4: Different mechanisms of transcription termination of lncRNAs in mammals.
Fig. 5: Factors affecting pc-gene transcription readthrough.
Fig. 6: Mechanisms leading to premature transcription termination.
Fig. 7: ncRNA transcription associated with DNA damage.

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Acknowledgements

The authors are indebted to L. Vasilieva, S. West, K. Kamieniarz-Gdula and H. Mischo for advice on this Review. The N.J.P. laboratory was supported by grants from the European Research Council (Advanced Grant no. 339170), the Wellcome Trust (Investigator Award no. 107928/Z/15/Z) and currently by the Wellcome Trust (Investigator Award no. 219443/Z/19/Z). The T.N. laboratory is supported by MEXT/JSPS Kakenhi (no. 19K24692) and JST FOREST program (no. JPMJFR2050). The authors apologize for not citing all the literature in this ever-expanding research area due to space limitations.

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  1. Medical institute of Bioregulation, Kyushu University, Fukuoka, Japan

    Takayuki Nojima

  2. Sir William Dunn School of Pathology, University of Oxford, Oxford, UK

    Nick J. Proudfoot

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Glossary

Small nuclear RNA

(snRNA). Non-coding nuclear RNAs of about 150 nt. Uridine (U)-rich snRNAs are core components of the spliceosome; other snRNAs function in RNA processing and transcription regulation.

Steady-state RNA levels

Levels of fully processed RNA, determined by a balance between synthesis and degradation.

Functional PAS

Functional polyadenylation sites (PAS) recruit cleavage and polyadenylation complex to transcript 3′ end sites.

Cryptic PAS

Polyadenylation sites (PAS) that are generally inactive and located within protein-coding gene introns. Splicing disruption can activate cryptic PAS.

Nascent RNA

The initial transcript made by RNA polymerase, which has not yet undergone processing.

Torpedo mechanism

Following 3′-end RNA cleavage, the 5′ product is released as polyadenylated mRNA, leaving the 3′ product still attached to elongating polymerase II (Pol II). This product is degraded 5′-3′ by 5′-3′ exoribonuclease 2 (XRN2); if XRN2 reaches Pol II, it somehow triggers Pol II release from DNA.

Template switching

During cDNA synthesis, reverse transcriptase adds untemplated nucleotides (usually CCC) to the cDNA 3′ end, to which an adaptor with 3′ GGG can hybridize to prime the synthesis of the complementary DNA strand.

Transcription foci

Nuclear particles (often condensates) in which RNA synthesis has just occurred that then recruit further multiple chromatin-associated RNA and RNA-binding proteins together with the polymerase II elongation complex forming a membrane-less particle.

Pioneer transcription factors

Factors that are capable of directly binding DNA sequences buried within compact chromatin. Upon binding, they recruit chromatin remodelling and modification factors to allow chromatin opening and gene expression.

General transcription factors

(GTFs). Factors that bind DNA cooperatively to form a multisubunit complex at gene promoters, resulting in polymerase II recruitment and the formation of a pre-initiation complex.

Enhancer RNAs

(eRNAs). RNAs synthesized by Pol II at nucleosome depleted regions of enhancers. Enhancers display bidirectional promoter activity in synthesising eRNA.

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Nojima, T., Proudfoot, N.J. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 23, 389–406 (2022). https://doi.org/10.1038/s41580-021-00447-6

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