Thousands of RNA-cached copies of whole chromosomes are present in the ciliate Oxytricha during development

RNA

Volumn 23, Issue 8, 2017, Pages 1200-1208

  Lindblad, Kelsi A ^a   Bracht, John R ^b   Williams, April E ^a,c   Landweber, Laura F ^d  

^a PRINCETON UNIVERSITY   (United States)

^b AMERICAN UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Ciliate; Epigenetics; LncRNA; Long noncoding RNA; Oxytricha

Indexed keywords

LONG UNTRANSLATED RNA; PROTOZOAL RNA;

ARTICLE; CHROMOSOME; CONTROLLED STUDY; DEVELOPMENT; GENE EXPRESSION; GENOME ANALYSIS; MICROBIAL GENOME; NONHUMAN; OXYTRICHA; OXYTRICHA TRIFALLAX; PRIORITY JOURNAL; RNA SEQUENCE; RNA TRANSCRIPTION; TELOMERE; ANIMAL; COPY NUMBER VARIATION; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

ANIMALS; CHROMOSOMES; DNA COPY NUMBER VARIATIONS; GENOME, PROTOZOAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; OXYTRICHA; RNA, LONG NONCODING; RNA, PROTOZOAN; TELOMERE;

EID: 85021316395     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.058511.116     Document Type: Article

References (31)

1. Ammermann D, Steinbrück G, von Berger DL, Hennig W. 1974. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Chromosoma 45: 401-429.
2. Angeleska A, Jonoska N, Saito M, Landweber LF. 2007. RNA-guided DNA assembly. J Theor Biol 248: 706-720.
3. Bracht JR, Perlman DH, Landweber LF. 2012. Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax. Genome Biol 13: R99.
4. Chang WJ, Stover NA, Addis VM, Landweber LF. 2004. A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha. Protist 155: 245-255.
5. Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, et al. 2014. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell 158: 1187-1198.
6. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. 2012. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22: 1775-1789.
7. Elemento O, Slonim N, Tavazoie S. 2007. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
8. FangW,Wang X, Bracht JR, Nowacki M, Landweber LF. 2012. Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. Cell 151: 1243-1255.
9. Fuhrmann G, Jönsson F, Weil PP, Postberg J, Lipps HJ. 2016. RNA-template dependent de novo telomere addition. RNA Biol 13: 733-739.
10. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. 2010. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464: 1071-1076.
11. Khurana JS, Wang X, Chen X, Perlman DH, Landweber LF. 2014. Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax. Genetics 197: 839-849.
12. Koren A, Handsaker RE, Kamitaki N, Karlić R, Ghosh S, Polak P, Eggan K, McCarroll SA. 2014. Genetic variation in human DNA replication timing. Cell 159: 1015-1026.
13. Latos PA, Pauler FM, Koerner MV, Şenergin HB, Hudson QJ, Stocsits RR, Allhoff W, Stricker SH, Klement RM, Warczok KE, et al. 2012. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338: 1469-1472.
14. Lepère G, Bétermier M, Meyer E, Duharcourt S. 2008. Maternal noncoding transcripts antagonize the targeting of DNA elimination by scanRNAs in Paramecium tetraurelia. Genes Dev 22: 1501-1512.
15. Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: p1303.3997.
16. Lolle SJ, Victor JL, Young JM, Pruitt RE. 2005. Genome-wide non-Mendelian inheritance of extra-genomic information in Arabidopsis. Nature 434: 505-509.
17. Mochizuki K, Fine NA, Fujisawa T, Gorovsky MA. 2002. Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in Tetrahymena. Cell 110: 689-699.
18. Möllenbeck M, Zhou Y, Cavalcanti ARO, Jönsson F, Higgins BP, Chang W-J, Juranek S, Doak TG, Rozenberg G, Lipps HJ, et al. 2008. The pathway to detangle a scrambled gene. PLoS One 3: e2330.
19. Noto T, Kataoka K, Suhren JH, Hayashi A, Woolcock KJ, Gorovsky MA, Mochizuki K. 2015. Small-RNA-mediated genome-wide transrecognition network in Tetrahymena DNA elimination. Mol Cell 59: 229-242.
20. Nowacki M, Vijayan V, Zhou Y, Schotanus K, Doak TG, Landweber LF. 2008. RNA-mediated epigenetic programming of a genome-rearrangement pathway. Nature 451: 153-158.
21. Nowacki M, Haye JE, Fang W, Vijayan V, Landweber LF. 2010. RNAmediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci 107: 22140-22144.
22. Prescott DM. 1994. The DNA of ciliated protozoa. Microbiol Rev 58: 233-267.
23. Prescott DM, Ehrenfeucht A, Rozenberg G. 2003. Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates. J Theor Biol 222: 323-330.
24. R Development Core Team. 2013. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org/.
25. Robinson DG, Storey JD. 2014. subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics 30: 3424-3426.
26. Sandoval PY, Swart EC, Arambasic M, Nowacki M. 2014. Functional diversification of dicer-like proteins and small RNAs required for genome sculpting. Dev Cell 28: 174-188.
27. Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, et al. 2013. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol 11: e1001473.
28. Wickham H. 2009. ggplot2: elegant graphics for data analysis. Springer Science & Business Media, NY.
29. Yerlici VT, Landweber LF. 2014. Programmed genome rearrangements in the ciliate Oxytricha. Microbiol Spectr 2. doi: 10.1128/microbiolspec. MDNA3-0025-2014.
30. Yoon J-H, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S, Huarte M, Zhan M, Becker KG, Gorospe M. 2012. LincRNA-p21 suppresses target mRNA translation. Mol Cell 47: 648-655.
31. Zahler AM, Neeb ZT, Lin A, Katzman S. 2012. Mating of the stichotrichous ciliate Oxytricha trifallax induces production of a class of 27 nt small RNAs derived from the parental macronucleus. PLoS One 7: e42371.