The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA

  • Philipp Kapranov1Email author,

    Affiliated with

    • Georges St Laurent2, 8,

      Affiliated with

      • Tal Raz1,

        Affiliated with

        • Fatih Ozsolak1,

          Affiliated with

          • C Patrick Reynolds3,

            Affiliated with

            • Poul HB Sorensen4,

              Affiliated with

              • Gregory Reaman5,

                Affiliated with

                • Patrice Milos1,

                  Affiliated with

                  • Robert J Arceci6,

                    Affiliated with

                    • John F Thompson1Email author and

                      Affiliated with

                      • Timothy J Triche7Email author

                        Affiliated with

                        BMC Biology20119:86

                        DOI: 10.1186/1741-7007-9-86

                        Received: 16 December 2011

                        Accepted: 20 December 2011

                        Published: 20 December 2011

                        The publisher notes typographical errors which were introduced to the first paragraph of page 10 (beginning "Previously, human large intergenic non-coding (linc) RNAs were identified in normal human embryonic and stem cell lines...") during the production process. The publisher apologises for the errors caused. The online article HTML was corrected on 19 October 2011, and the article PDF on 31 October 2011; readers with previous versions of the article are advised to update to the corrected version [1].

                        Corrected paragraph:

                        "Previously, human large intergenic non-coding (linc) RNAs were identified in normal human embryonic and stem cell lines [twenty seven] and we sought to determine whether the vlinc regions were overlapping those. In fact, the majority of the vlinc transcribed regions we have identified did not overlap the known human lincRNA regions and, thus, represent novel RNAs that are also large, intergenic and non-coding, as exemplified in the four examples shown (Figure four c and four d, Figure five a and five b). These latter regions have known lincRNA regions located nearby, without overlap, while the former do not have lincRNA regions in their vicinity. Furthermore, the intergenic regions identified here achieve much greater lengths than known lincRNAs, with a median size of ~84 kb versus 21 kb for the lincRNAs (significant at P = 1.72 × 10-53, t-test). Overall, 37% (215/580) of the vlinc regions overlapped the K4-K36 domains harbouring lincRNAs as reported by Khalil et al. [twenty seven]. However, even when overlapping, the lincRNA regions corresponded to only a fraction of our intergenic regions: the overlap of base pairs in the intergenic regions found here with the lincRNA regions was only approximately 19% (13.51/68.51 Mbp). However, the overlap between the two categories of the intergenic transcribed regions is highly significant (P-value < 10-16, chi-square test)."

                        Authors’ Affiliations

                        (1)
                        Helicos BioSciences Corporation, One Kendall Square
                        (2)
                        Department of Molecular Biology, Cell Biology and Biochemistry, Brown University
                        (3)
                        Cancer Center, Departments of Cell Biology & Biochemistry, Pediatrics, and Internal Medicine, School of Medicine, Texas Tech University Health Sciences Center
                        (4)
                        British Columbia Cancer Research Centre
                        (5)
                        Department of Pediatrics, The George Washington University School of Medicine and Health Sciences, Division of Oncology, Children’s National Medical Center
                        (6)
                        Department of Oncology/Pediatric Oncology, Kimmel Comprehensive Cancer Center at John Hopkins
                        (7)
                        Department of Pathology, University of Southern California
                        (8)
                        Grupo de Inmunovirologia, SIU, Universidad de Antioquia

                        References

                        1. Kapranov P, St Laurent G, Raz T, Ozsolak F, Reynolds CP, Sorenson PHB, Reaman G, Milos P, Arceci RJ, Thompson JF, Triche TJ: The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' unannotated RNA. BMC Biol 2010, 8:149.PubMedView Article

                        Copyright

                        © Kapranov et al; licensee BioMed Central Ltd. 2011

                        This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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