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Verification and characterization of circRNAs in two holophilic archaea

  • Department of Life Science and Medicine, University of Science and Technology of China,Hefei 230027, China

Cite this:
https://doi.org/10.3969/j.issn.0253-2778.2020.04.010
  • Received Date: 16 January 2020
  • Accepted Date: 22 April 2020
  • Rev Recd Date: 22 April 2020
  • Publish Date: 30 April 2020
    Abstract

  • Abstract

    Circular RNA (circRNA) is a special type of RNA, which forms covalent-closed continuous loop in most cases through 5’ to 3’ ends via back-splicing. CircRNAs demonstrate a certain degree of conservation and show some tissue specificity in multicellular animals. Archaea is one of the three domains of life, and archaeal organisms often live in high temperature, high salt, low oxygen, or other extreme environments.

    Abstract

    Circular RNA (circRNA) is a special type of RNA, which forms covalent-closed continuous loop in most cases through 5’ to 3’ ends via back-splicing. CircRNAs demonstrate a certain degree of conservation and show some tissue specificity in multicellular animals. Archaea is one of the three domains of life, and archaeal organisms often live in high temperature, high salt, low oxygen, or other extreme environments.
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    • References(38)
  • [1]
    SANGER H L, KLOTZ G, RIESNER D, et al. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rodlike structures[J]. Proc Natl Acad Sci USA, 1976, 73: 3852-3856.
    [2]
    GUO J U, AGARWAL V, GUO H,et al. Expanded identification and characterization of mammalian circular RNAs[J]. Genome Biology, 2014, 15(7): Article number 409.
    [3]
    LASDA E, PARKER R. Circular RNAs: Diversity of form and function[J]. RNA, 2014, 20(12):1829-1842.
    [4]
    DU W W, ZHANG C, YANG W,et al. Identifying and characterizing circRNA-protein interaction[J]. Theranostics, 2017, 7(17): 4183-4191.
    [5]
    HOLDT L M, KOHLMAIER A, TEUPSER D. Molecular roles and function of circular RNAs in eukaryotic cells[J]. Cellular and Molecular Life Sciences, 2018, 75(6): 1071-1098.
    [6]
    LI F, ZHANG L, LI W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway[J]. Oncotarget, 2015, 6: 6001-13.
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    ASHWAL-FLUSS R, MEYER M, PAMUDURTI N R, et al. circRNA biogenesis competes with pre-mRNA splicing[J]. Mol Cell, 2014, 56: 55-66.
    [8]
    CHEN Y, LI C, TAN C,et al. Circular RNAs: A new frontier in the study of human diseases[J]. Journal of Medical Genetics, 2016, 53(6): 359-365.
    [9]
    TAKEMATA N, SAMSON R Y, BELL S D. Physical and functional compartmentalization of archaeal chromosomes[J]. Cell, 2019, 179(1):165-179.
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    DANAN M, SCHWARTZ S, EDELHEIT S, et al. Transcriptome-wide discovery of circular RNAs in Archaea[J]. Nucleic Acids Res, 2011, 40: 3131-3142.
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    SINGH S K, GURHA P, TRAN E J, et al. Sequential 2’-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA[J]. J Biol Chem, 2004, 279: 47661-47671.
    [13]
    CLOUET D’ORVAL B, BORTOLIN M L, GASPIN C, et al. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp[J].Nucleic Acids Res, 2001, 29: 4518-4529.
    [14]
    SALGIA S R, SINGH S K, GURHA P, et al. Two reactions of Haloferax volcanii RNA splicing enzymes: Joining of exons and circularization of introns[J]. RNA, 2003, 9: 319-330.
    [15]
    TANG T H, ROZHDESTVENSKY T S, D’ORVAL B C, et al. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing[J]. Nucleic Acids Res, 2002, 30: 921-930.
    [16]
    MIAO Di. Construction of a novel shuttle expression vector based on haloarchaeal plasmid pSCM201 and studies on replicon of minichromosome pHM300[D]. Beijing: Institute of Microbiology, Chinese Academy of Sciences, 2009.
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    MEMCZAK S, JENS M, ELEFSINIOTI A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature, 2013, 495(7441): 333-338
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    LI Z, HUANG C, BAO C,et al. Exon-intron circular RNAs regulate transcription in the nucleus[J]. Nat Struct Mol Biol, 2015, 22: 256-264.
    [19]
    SUZUKI H, ZUO Y, WANG J, et al. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing[J]. Nucleic Acids Res, 2006, 34: e63.
    [20]
    MEMCZAK S, JENS M, ELEFSINIOTI A,et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J]. Nature, 2013, 495: 333-338.
    [21]
    CONN S J, PILLMAN K A, TOUBIA J, et al. The RNA binding protein quaking regulates formation of circRNAs[J]. Cell, 2015, 160: 1125-1134.
    [22]
    SOTA M, TOP E M. Horizontal gene transfer mediated by plasmids[C]// Plasmids: Current Research and Future Trends. Poole, UK: Caister Academic Press, 2008.
    [23]
    HUANG C, LIANG D, TATOMER D C, et al. A length-depengdent evolutionarily conserved pathway controls nuclear export of circular RNAs[J]. Genes Dev, 2018, 32: 639-644.
    [24]
    WANY, HOPPER A K. Size matters: Conserved proteins function in length-dependent nuclear export of circular RNAs[J]. Genes Dev, 2018, 32: 600-601.
    [25]
    BARRETT S P,WANG P L, SALZMAN J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor[J]. eLife, 2015, 4: e07540.
    [26]
    METGE F, CZAJA-HASSE L F, REINHARDT R, et al. FUCHS-towards full circular RNA characterization using RNAsEq[J]. PeerJ, 2017, 5: e2934.
    [27]
    GLAZAR P, PAPAVASILEIOU P, RAJEWSKY N. circBase: A database for circular RNAs[J]. RNA, 2014, 20:1666-1670.
    [28]
    MEMCZAK S, JENS M, ELEFSINIOTI A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J]. Nature, 2013, 495: 333-338.
    [29]
    RYBAK-WOLF A, STOTTMEISTER C, GLAZAR P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed[J]. Mol Cell,2015, 58: 870-885.
    [30]
    SALZMAN J, CHEN R E, OLSEN M N, et al. Cell-type specific features of circular RNA expression[J]. PLoS Genet, 2013, 9: e1003777.
    [31]
    IVANOV A, MEMCZAK S, WYLER E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals[J]. Cell Rep, 2015, 10:170-177.
    [32]
    SHEN Y, GUO X, WANG W. Identification and characterization of circular RNAs in zebrafish[J]. FEBS Lett, 2017, 591: 213-220.
    [33]
    HOUSELEY J M, GARCIA-CASADO Z, PASCUAL M, et al. Noncanonical RNAs from transcripts of the Drosophila muscleblind gene[J]. J Hered, 2006, 97: 253-260.
    [34]
    WANG P L, BAO Y, YEE M C, et al. Circular RNA is expressed across the eukaryotic tree of life[J]. PLoS One, 2014, 9: e90859.
    [35]
    JECK W R, SORRENTINO J A, WANG K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats[J]. RNA , 2013, 19: 141-157.
    [36]
    WESTHOLM J O, MIURA P, OLSON S, et al. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation[J]. Cell Rep, 2014, 9: 1966-1980.
    [37]
    YOU X, VLATKOVIC I, BABIC A, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity[J]. Nat Neurosci, 2015, 18: 603-610.
    [38]
    CLOUET D’ORVAL B, BORTOLIN M L, GASPIN C, et al. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp[J]. Nucleic Acids Res, 2001, 29(22): 4518-4529.)
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    [1]
    SANGER H L, KLOTZ G, RIESNER D, et al. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rodlike structures[J]. Proc Natl Acad Sci USA, 1976, 73: 3852-3856.
    [2]
    GUO J U, AGARWAL V, GUO H,et al. Expanded identification and characterization of mammalian circular RNAs[J]. Genome Biology, 2014, 15(7): Article number 409.
    [3]
    LASDA E, PARKER R. Circular RNAs: Diversity of form and function[J]. RNA, 2014, 20(12):1829-1842.
    [4]
    DU W W, ZHANG C, YANG W,et al. Identifying and characterizing circRNA-protein interaction[J]. Theranostics, 2017, 7(17): 4183-4191.
    [5]
    HOLDT L M, KOHLMAIER A, TEUPSER D. Molecular roles and function of circular RNAs in eukaryotic cells[J]. Cellular and Molecular Life Sciences, 2018, 75(6): 1071-1098.
    [6]
    LI F, ZHANG L, LI W, et al. Circular RNA ITCH has inhibitory effect on ESCC by suppressing the Wnt/β-catenin pathway[J]. Oncotarget, 2015, 6: 6001-13.
    [7]
    ASHWAL-FLUSS R, MEYER M, PAMUDURTI N R, et al. circRNA biogenesis competes with pre-mRNA splicing[J]. Mol Cell, 2014, 56: 55-66.
    [8]
    CHEN Y, LI C, TAN C,et al. Circular RNAs: A new frontier in the study of human diseases[J]. Journal of Medical Genetics, 2016, 53(6): 359-365.
    [9]
    TAKEMATA N, SAMSON R Y, BELL S D. Physical and functional compartmentalization of archaeal chromosomes[J]. Cell, 2019, 179(1):165-179.
    [10]
    DANAN M, SCHWARTZ S, EDELHEIT S, et al. Transcriptome-wide discovery of circular RNAs in Archaea[J]. Nucleic Acids Res, 2011, 40: 3131-3142.
    [11]
    LYKKE-ANDERSEN J, AAGAARD C, SEMIONENKOV M, et al. Archaeal introns: Splicing, intercellular mobility and evolution[J]. Trends Biochem Sci, 1997, 22: 326-331.
    [12]
    SINGH S K, GURHA P, TRAN E J, et al. Sequential 2’-O-methylation of archaeal pre-tRNATrp nucleotides is guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA[J]. J Biol Chem, 2004, 279: 47661-47671.
    [13]
    CLOUET D’ORVAL B, BORTOLIN M L, GASPIN C, et al. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp[J].Nucleic Acids Res, 2001, 29: 4518-4529.
    [14]
    SALGIA S R, SINGH S K, GURHA P, et al. Two reactions of Haloferax volcanii RNA splicing enzymes: Joining of exons and circularization of introns[J]. RNA, 2003, 9: 319-330.
    [15]
    TANG T H, ROZHDESTVENSKY T S, D’ORVAL B C, et al. RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing[J]. Nucleic Acids Res, 2002, 30: 921-930.
    [16]
    MIAO Di. Construction of a novel shuttle expression vector based on haloarchaeal plasmid pSCM201 and studies on replicon of minichromosome pHM300[D]. Beijing: Institute of Microbiology, Chinese Academy of Sciences, 2009.
    [17]
    MEMCZAK S, JENS M, ELEFSINIOTI A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature, 2013, 495(7441): 333-338
    [18]
    LI Z, HUANG C, BAO C,et al. Exon-intron circular RNAs regulate transcription in the nucleus[J]. Nat Struct Mol Biol, 2015, 22: 256-264.
    [19]
    SUZUKI H, ZUO Y, WANG J, et al. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing[J]. Nucleic Acids Res, 2006, 34: e63.
    [20]
    MEMCZAK S, JENS M, ELEFSINIOTI A,et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J]. Nature, 2013, 495: 333-338.
    [21]
    CONN S J, PILLMAN K A, TOUBIA J, et al. The RNA binding protein quaking regulates formation of circRNAs[J]. Cell, 2015, 160: 1125-1134.
    [22]
    SOTA M, TOP E M. Horizontal gene transfer mediated by plasmids[C]// Plasmids: Current Research and Future Trends. Poole, UK: Caister Academic Press, 2008.
    [23]
    HUANG C, LIANG D, TATOMER D C, et al. A length-depengdent evolutionarily conserved pathway controls nuclear export of circular RNAs[J]. Genes Dev, 2018, 32: 639-644.
    [24]
    WANY, HOPPER A K. Size matters: Conserved proteins function in length-dependent nuclear export of circular RNAs[J]. Genes Dev, 2018, 32: 600-601.
    [25]
    BARRETT S P,WANG P L, SALZMAN J. Circular RNA biogenesis can proceed through an exon-containing lariat precursor[J]. eLife, 2015, 4: e07540.
    [26]
    METGE F, CZAJA-HASSE L F, REINHARDT R, et al. FUCHS-towards full circular RNA characterization using RNAsEq[J]. PeerJ, 2017, 5: e2934.
    [27]
    GLAZAR P, PAPAVASILEIOU P, RAJEWSKY N. circBase: A database for circular RNAs[J]. RNA, 2014, 20:1666-1670.
    [28]
    MEMCZAK S, JENS M, ELEFSINIOTI A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency[J]. Nature, 2013, 495: 333-338.
    [29]
    RYBAK-WOLF A, STOTTMEISTER C, GLAZAR P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed[J]. Mol Cell,2015, 58: 870-885.
    [30]
    SALZMAN J, CHEN R E, OLSEN M N, et al. Cell-type specific features of circular RNA expression[J]. PLoS Genet, 2013, 9: e1003777.
    [31]
    IVANOV A, MEMCZAK S, WYLER E, et al. Analysis of intron sequences reveals hallmarks of circular RNA biogenesis in animals[J]. Cell Rep, 2015, 10:170-177.
    [32]
    SHEN Y, GUO X, WANG W. Identification and characterization of circular RNAs in zebrafish[J]. FEBS Lett, 2017, 591: 213-220.
    [33]
    HOUSELEY J M, GARCIA-CASADO Z, PASCUAL M, et al. Noncanonical RNAs from transcripts of the Drosophila muscleblind gene[J]. J Hered, 2006, 97: 253-260.
    [34]
    WANG P L, BAO Y, YEE M C, et al. Circular RNA is expressed across the eukaryotic tree of life[J]. PLoS One, 2014, 9: e90859.
    [35]
    JECK W R, SORRENTINO J A, WANG K, et al. Circular RNAs are abundant, conserved, and associated with ALU repeats[J]. RNA , 2013, 19: 141-157.
    [36]
    WESTHOLM J O, MIURA P, OLSON S, et al. Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation[J]. Cell Rep, 2014, 9: 1966-1980.
    [37]
    YOU X, VLATKOVIC I, BABIC A, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity[J]. Nat Neurosci, 2015, 18: 603-610.
    [38]
    CLOUET D’ORVAL B, BORTOLIN M L, GASPIN C, et al. Box C/D RNA guides for the ribose methylation of archaeal tRNAs. The tRNATrp intron guides the formation of two ribose-methylated nucleosides in the mature tRNATrp[J]. Nucleic Acids Res, 2001, 29(22): 4518-4529.)
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