Ala U (2020) Competing endogenous RNAs, non-coding RNAs and diseases: an intertwined story. Cells 9:1574. https://doi.org/10.3390/cells9071574
Article CAS PubMed PubMed Central Google Scholar
Almeida M, Pintacuda G, Masui O, Koseki Y, Gdula M, Cerase A, Brown D, Mould A, Innocent C, Nakayama M, Schermelleh L, Nesterova TB, Koseki H, Brockdorff N (2017) PCGF3/5-PRC1 initiates Polycomb recruitment in X chromosome inactivation. Science 356:1081–1084. https://doi.org/10.1126/science.aal2512
Article CAS PubMed PubMed Central Google Scholar
Altemose N (2022) A classical revival: human satellite DNAs enter the genomics era. Semin Cell Dev Biol 128:2–14. https://doi.org/10.1016/j.semcdb.2022.04.012
Article CAS PubMed Google Scholar
Aly MK, Ninomiya K, Adachi S, Natsume T, Hirose T (2019) Two distinct nuclear stress bodies containing different sets of RNA-binding proteins are formed with HSATIII architectural noncoding RNAs upon thermal stress exposure. Biochem Biophys Res Commun 516:419–423. https://doi.org/10.1016/j.bbrc.2019.06.061
Article CAS PubMed Google Scholar
Arnoult N, Van Beneden A, Decottignies A (2012) Telomere length regulates TERRA levels through increased trimethylation of telomeric H3K9 and HP1alpha. Nat Struct Mol Biol 199:48–56. https://doi.org/10.1038/nsmb.2364
Bailey JA, Gu Z, Clark RA, Reinert K, Samonte RV, Schwartz S, Adams MD, Myers EW, Li PW, Eichler EE (2002) Recent segmental duplications in the human genome. Science 297:1003–1007. https://doi.org/10.1126/science.1072047
Article CAS PubMed Google Scholar
Bailey TL, Johnson J, Grant CE, Noble WS (2015) The MEME suite. Nucleic Acids Res 43:W39–W49. https://doi.org/10.1093/nar/gkv416
Article CAS PubMed PubMed Central Google Scholar
Balendra R, Isaacs AM (2018) C9orf72-mediated ALS and FTD: multiple pathways to disease. Nat Rev Neurol 14:544–558. https://doi.org/10.1038/s41582-018-0047-2
Article CAS PubMed PubMed Central Google Scholar
Barral A, Dejardin J (2020) Telomeric chromatin and TERRA. J Mol Biol 432:4244–4256. https://doi.org/10.1016/j.jmb.2020.03.003
Article CAS PubMed Google Scholar
Barrett SP, Parker KR, Horn C, Mata M, Salzman J (2017) ciRS-7 exonic sequence is embedded in a long non-coding RNA locus. PLoS Genet 13:e1007114. https://doi.org/10.1371/journal.pgen.1007114
Article CAS PubMed PubMed Central Google Scholar
Baud A, Derbis M, Tutak K, Sobczak K (2022) Partners in crime: proteins implicated in RNA repeat expansion diseases. Wiley Interdiscip Rev RNA 13:e1709. https://doi.org/10.1002/wrna.1709
Article CAS PubMed PubMed Central Google Scholar
Biamonti G, Caceres JF (2009) Cellular stress and RNA splicing. Trends Biochem Sci 34:146–153. https://doi.org/10.1016/j.tibs.2008.11.004
Article CAS PubMed Google Scholar
Blair JD, Hockemeyer D, Doudna JA, Bateup HS, Floor SN (2017) Widespread translational remodeling during human neuronal differentiation. Cell Rep 21:2005–2016. https://doi.org/10.1016/j.celrep.2017.10.095
Article CAS PubMed PubMed Central Google Scholar
Blower MD (2016) Centromeric transcription regulates Aurora-B localization and activation. Cell Rep 15:1624–1633. https://doi.org/10.1016/j.celrep.2016.04.054
Article CAS PubMed PubMed Central Google Scholar
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2220. https://doi.org/10.1093/bioinformatics/btu170
Article CAS PubMed PubMed Central Google Scholar
Bray NL, Pimentel H, Melsted P, Pachter L (2016) Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol 34:525–527. https://doi.org/10.1038/nbt.3519
Article CAS PubMed Google Scholar
Cerbini T, Funahashi R, Luo Y, Liu C, Park K, Rao M, Malik N, Zou J (2015) Transcription activator-like effector nuclease (TALEN)-mediated CLYBL targeting enables enhanced transgene expression and one-step generation of dual reporter human induced pluripotent stem cell (iPSC) and neural stem cell (NSC) lines. PLoS ONE 10:e0116032. https://doi.org/10.1371/journal.pone.0116032
Article CAS PubMed PubMed Central Google Scholar
Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY (2015) Systematic discovery of Xist RNA binding proteins. Cell 161:404–416. https://doi.org/10.1016/j.cell.2015.03.025
Article CAS PubMed PubMed Central Google Scholar
Cid-Samper F, Gelabert-Baldrich M, Lang B, Lorenzo-Gotor N, Ponti RD, Severijnen L, Bolognesi B, Gelpi E, Hukema RK, Botta-Orfila T, Tartaglia GG (2018) An integrative study of protein-RNA condensates identifies scaffolding rnas and reveals players in fragile X-associated tremor/ataxia syndrome. Cell Rep 25:3422-3434.e7. https://doi.org/10.1016/j.celrep.2018.11.076
Article CAS PubMed PubMed Central Google Scholar
Ciesiolka A, Jazurek M, Drazkowska K, Krzyzosiak WJ (2017) Structural characteristics of simple RNA repeats associated with disease and their deleterious protein interactions. Front Cell Neurosci 11:97. https://doi.org/10.3389/fncel.2017.00097
Article CAS PubMed PubMed Central Google Scholar
Crosier M, Viggiano L, Guy J, Misceo D, Stones R, Wei W, Hearn T, Ventura M, Archidiacono N, Rocchi M, Jackson MS (2002) Human paralogs of KIAA0187 were created through independent pericentromeric-directed and chromosome-specific duplication mechanisms. Genome Res 12:67–80. https://doi.org/10.1101/gr.213702
Article CAS PubMed PubMed Central Google Scholar
Denegri M, Chiodi I, Corioni M, Cobianchi F, Riva S, Biamonti G (2001) Stress-induced nuclear bodies are sites of accumulation of pre-mRNA processing factors. Mol Biol Cell 12:3502–3514. https://doi.org/10.1091/mbc.12.11.3502
Article CAS PubMed PubMed Central Google Scholar
Deng Z, Norseen J, Wiedmer A, Riethman H, Lieberman PM (2009) TERRA RNA binding to TRF2 facilitates heterochromatin formation and ORC recruitment at telomeres. Mol Cell 35:403–413. https://doi.org/10.1016/j.molcel.2009.06.025
Article CAS PubMed PubMed Central Google Scholar
DeRosa BA, El Hokayem J, Artimovich E, Garcia-Serje C, Phillips AW, Van Booven D, Nestor JE, Wang L, Cuccaro ML, Vance JM, Pericak-Vance MA, Cukier HN, Nestor MW, Dykxhoorn DM (2018) Convergent pathways in idiopathic autism revealed by time course transcriptomic analysis of patient-derived neurons. Sci Rep 8:8423. https://doi.org/10.1038/s41598-018-26495-1
Article CAS PubMed PubMed Central Google Scholar
Elguindy MM, Mendell JT (2021) NORAD-induced Pumilio phase separation is required for genome stability. Nature 595:303–308. https://doi.org/10.1038/s41586-021-03633-w
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