Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing

By Hitoshi Suzuki, Y. Zuo, Jinhua Wang, Michael Q. Zhang, A. Malhotra, A. Mayeda. Nucleic Acids Research, 2006

629 citations recorded by the source corpus.

Besides linear RNAs, pre-mRNA splicing generates three forms of RNAs: lariat introns, Y-structure introns from trans-splicing, and circular exons through exon skipping. To study the persistence of excised introns in total cellular RNA, we used three Escherichia coli 3′ to 5′ exoribonucleases. Ribonuclease R (RNase R) thoroughly degrades the abundant linear RNAs and the Y-structure RNA, while preserving the loop portion of a lariat RNA. Ribonuclease II (RNase II) and polynucleotide phosphorylase (PNPase) also preserve the lariat loop, but are less efficient in degrading linear RNAs. RNase R digestion of the total RNA from human skeletal muscle generates an RNA pool consisting of lariat and circular RNAs. RT–PCR across the branch sites confirmed lariat RNAs and circular RNAs in the pool generated by constitutive and alternative splicing of the dystrophin pre-mRNA. Our results indicate that RNase R treatment can be used to construct an intronic cDNA library, in which majority of the intron lariats are represented. The highly specific activity of RNase R implies its ability to screen for rare intragenic trans-splicing in any target gene with a large background of cis-splicing. Further analysis of the intronic RNA pool from a specific tissue or cell will provide insights into the global profile of alternative splicing.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd61038212af74eb2782997360b5aebf916e28d7

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Citations in the corpus

CircNet: a database of circular RNAs derived from transcriptome sequencing data (2015, background): “(13), which includes examining RNA-seq samples treated with RNase R (14).”
Circular RNAs: analysis, expression and potential functions (2016, methodology): “…R, an exoribonuclease capable of processively degrading RNA from its 3′ to 5′ end, is a useful tool, often used in combination with those described above, to assess whether RNA is indeed circular and to enrich for circRNA in sequencing libraries (Suzuki et al., 2006; Vincent and Deutscher, 2006).”
Circular intronic long noncoding RNAs. (2013, background): “It is known that RNase R can degrade linear RNAs and Y-structure RNAs, while preserving the loop portion of a lariat RNA (Suzuki et al., 2006).”
Diverse alternative back-splicing and alternative splicing landscape of circular RNAs (2016, positive): “Since most circRNAs are expressed at low levels, RNase R, an enzyme that digests linear RNAs but preserves circRNAs (Suzuki et al. 2006), has been used to enrich circRNAs and to further verify the existence of circRNA-specific alternative splicing from both PA1 and H9 samples that were prepared in…”
Complementary sequence-mediated exon circularization. (2014, background): “These RNAs remained stable after RNase R treatment (Suzuki et al., 2006) in both NB (Figures 1D and 1E) and divergent PCR (Figure S1C), further confirming them to be circular.”
Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types (2012, background): “RNaseR is a 39 to 59 exoribonuclease that degrades essentially all linear RNA molecules, regardless of structure, provided the RNA contains a 7 bp 39 overhang [23].”
Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis (2017, methodology): “Resistance to the RNase R exonuclease was used to test whether the selected molecules were circular (Suzuki et al., 2006).”
Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk (2010, background): “RNAse R specifically digests both structured and non-structured linear RNAs, but spares RNA circles and lariats [50].”
Non-coding RNAs in Development and Disease: Background, Mechanisms, and Therapeutic Approaches. (2016, background): “Treatment of the sample with RNase R will further decrease the amount of linear RNAs (255).”
CIRI: an efficient and unbiased algorithm for de novo circular RNA identification (2015, background): “'fake' junction reads called branch point reads [12,23].”
The RNA binding protein quaking regulates formation of circRNAs. (2015, positive): “, 1991) and continued to be reported for a number of transcripts over the following two decades (Capel et al., 1993; Cocquerelle et al., 1993; Gualandi et al., 2003; Suzuki et al., 2006; Zaphiropoulos, 1997).”
Circular RNA-protein interactions: functions, mechanisms, and identification (2020, background): “Although most circRNAs exist in the cytoplasm, they are remarkably stable and resistant to RNase R and other exonucleases because they lack free ends [27].”
Circular RNAs: diversity of form and function (2014, methodology): “For example, resistance to RNase R, which degrades most linear RNAs without destroying circular molecules, is used as a criterion for circularity (Suzuki et al. 2006; Vincent and Deutscher 2006; Suzuki and Tsukahara 2014).”
Circular RNAs are abundant, conserved, and associated with ALU repeats. (2013, methodology): “This was expected, as RNase R has been described to leave lariats intact, while degrading only the 3′ “tail” before the branch point (Suzuki et al. 2006).”