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The Complexity of the Mammalian Transcriptome

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Long Noncoding RNA

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1363))

Abstract

Draft genome assemblies for multiple mammalian species combined with new technologies to map transcripts from diverse RNA samples to these genomes developed in the early 2000s revealed that the mammalian transcriptome was vastly larger and more complex than previously anticipated. Efforts to comprehensively catalog the identity and features of transcripts present in a variety of species, tissues and cell lines revealed that a large fraction of the mammalian genome is transcribed in at least some settings. A large number of these transcripts encode long non-coding RNAs (lncRNAs). Many lncRNAs overlap or are anti-sense to protein coding genes and others overlap small RNAs. However, a large number are independent of any previously known mRNA or small RNA. While the functions of a majority of these lncRNAs are unknown, many appear to play roles in gene regulation. Many lncRNAs have species-specific and cell type specific expression patterns and their evolutionary origins are varied. While technological challenges have hindered getting a full picture of the diversity and transcript structure of all of the transcripts arising from lncRNA loci, new technologies including single molecule nanopore sequencing and single cell RNA sequencing promise to generate a comprehensive picture of the mammalian transcriptome.

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Acknowledgements

The author wishes to thank Andrew Field for helpful discussions to define the scope of this article, and Mark Diekhans for discussions about GENCODE and for assistance generating Fig. 2.1. This work was supported by R01HG010329 and R01MH120295 to SRS.

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  1. UC Santa Cruz Genomics Institute, Department of Biomolecular Engineering and Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, USA

    Sofie R. Salama

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  1. Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA

    Susan Carpenter

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Salama, S.R. (2022). The Complexity of the Mammalian Transcriptome. In: Carpenter, S. (eds) Long Noncoding RNA. Advances in Experimental Medicine and Biology, vol 1363. Springer, Cham. https://doi.org/10.1007/978-3-030-92034-0_2

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