Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development

English version

Autoři: Katherine I. Farley-Barnes ^aff001; Engin Deniz ^aff002; Maya M. Overton ^aff001; Mustafa K. Khokha ^aff002; Susan J. Baserga ^aff001
Působiště autorů: Department of Molecular Biophysics & Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America ^aff001; Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, United States of America ^aff002; Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, United States of America ^aff003; Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, United States of America ^aff004
Vyšlo v časopise: Paired Box 9 (PAX9), the RNA polymerase II transcription factor, regulates human ribosome biogenesis and craniofacial development. PLoS Genet 16(8): e32767. doi:10.1371/journal.pgen.1008967
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008967

Souhrn

Dysregulation of ribosome production can lead to a number of developmental disorders called ribosomopathies. Despite the ubiquitous requirement for these cellular machines used in protein synthesis, ribosomopathies manifest in a tissue-specific manner, with many affecting the development of the face. Here we reveal yet another connection between craniofacial development and making ribosomes through the protein Paired Box 9 (PAX9). PAX9 functions as an RNA Polymerase II transcription factor to regulate the expression of proteins required for craniofacial and tooth development in humans. We now expand this function of PAX9 by demonstrating that PAX9 acts outside of the cell nucleolus to regulate the levels of proteins critical for building the small subunit of the ribosome. This function of PAX9 is conserved to the organism Xenopus tropicalis, an established model for human ribosomopathies. Depletion of pax9 leads to craniofacial defects due to abnormalities in neural crest development, a result consistent with that found for depletion of other ribosome biogenesis factors. This work highlights an unexpected layer of how the making of ribosomes is regulated in human cells and during embryonic development.

Klíčová slova:

Biosynthesis – Messenger RNA – Northern blot – Ribosomes – Small interfering RNA – Transcription factors – Paired box – Neural crest

Zdroje

1. Altug Teber O, Gillessen-Kaesbach G, Fischer S, Bohringer S, Albrecht B, Albert A, et al. Genotyping in 46 patients with tentative diagnosis of Treacher Collins syndrome revealed unexpected phenotypic variation. Eur J Hum Genet. 2004;12(11):879–90. doi: 10.1038/sj.ejhg.5201260 15340364

2. Dauwerse JG, Dixon J, Seland S, Ruivenkamp CA, van Haeringen A, Hoefsloot LH, et al. Mutations in genes encoding subunits of RNA polymerases I and III cause Treacher Collins syndrome. Nat Genet. 2011;43(1):20–2. doi: 10.1038/ng.724 21131976

3. Bowman M, Oldridge M, Archer C, O'Rourke A, McParland J, Brekelmans R, et al. Gross deletions in TCOF1 are a cause of Treacher-Collins-Franceschetti syndrome. Eur J Hum Genet. 2012;20(7):769–77. doi: 10.1038/ejhg.2012.2 22317976

4. Splendore A, Silva EO, Alonso LG, Richieri-Costa A, Alonso N, Rosa A, et al. High mutation detection rate in TCOF1 among Treacher Collins syndrome patients reveals clustering of mutations and 16 novel pathogenic changes. Hum Mutat. 2000;16(4):315–22. doi: 10.1002/1098-1004(200010)16:4<315::AID-HUMU4>3.0.CO;2-H 11013442

5. Rovin S, Dachi SF, Borenstein DB, Cotter WB. MANDIBULOFACIAL DYSOSTOSIS, A FAMILIAL STUDY OF FIVE GENERATIONS. J Pediatr. 1964;65:215–21. doi: 10.1016/s0022-3476(64)80522-9 14198411

6. Phelps PD, Poswillo D, Lloyd GA. The ear deformities in mandibulofacial dysostosis (Treacher Collins syndrome). Clin Otolaryngol Allied Sci. 1981;6(1):15–28. doi: 10.1111/j.1365-2273.1981.tb01782.x 7273449

7. Kadakia S, Helman SN, Badhey AK, Saman M, Ducic Y. Treacher Collins Syndrome: The genetics of a craniofacial disease. International Journal of Pediatric Otorhinolaryngology. 2014;78(6):893–8. doi: 10.1016/j.ijporl.2014.03.006 24690222

8. Jones NC, Lynn ML, Gaudenz K, Sakai D, Aoto K, Rey JP, et al. Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function. Nature medicine. 2008;14(2):125–33. doi: 10.1038/nm1725 18246078

9. Sloan Katherine E, Bohnsack Markus T, Watkins Nicholas J. The 5S RNP Couples p53 Homeostasis to Ribosome Biogenesis and Nucleolar Stress. Cell Reports. 2013;5(1):237–47. doi: 10.1016/j.celrep.2013.08.049 24120868

10. Donati G, Peddigari S, Mercer CA, Thomas G. 5S ribosomal RNA is an essential component of a nascent ribosomal precursor complex that regulates the Hdm2-p53 checkpoint. Cell Rep. 2013;4(1):87–98. doi: 10.1016/j.celrep.2013.05.045 23831031

11. Glader BE, Backer K, Diamond LK. Elevated erythrocyte adenosine deaminase activity in congenital hypoplastic anemia. N Engl J Med. 1983;309(24):1486–90. doi: 10.1056/NEJM198312153092404 6646173

12. Halperin DS, Freedman MH. Diamond-blackfan anemia: etiology, pathophysiology, and treatment. Am J Pediatr Hematol Oncol. 1989;11(4):380–94. 2694854

13. Lipton JM, Ellis SR. Diamond-Blackfan anemia: diagnosis, treatment, and molecular pathogenesis. Hematol Oncol Clin North Am. 2009;23(2):261–82. doi: 10.1016/j.hoc.2009.01.004 19327583

14. Weaver KN, Watt KE, Hufnagel RB, Navajas Acedo J, Linscott LL, Sund KL, et al. Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction. Am J Hum Genet. 2015;96(5):765–74. doi: 10.1016/j.ajhg.2015.03.011 25913037

15. Blake JA, Ziman MR. Pax genes: regulators of lineage specification and progenitor cell maintenance. Development. 2014;141(4):737–51. doi: 10.1242/dev.091785 24496612

16. Chi N, Epstein JA. Getting your Pax straight: Pax proteins in development and disease. Trends in Genetics. 2002;18(1):41–7. doi: 10.1016/s0168-9525(01)02594-x 11750700

17. Stockton DW, Das P, Goldenberg M, D'Souza RN, Patel PI. Mutation of PAX9 is associated with oligodontia. Nat Genet. 2000;24(1):18–9. doi: 10.1038/71634 10615120

18. Nieminen P, Arte S, Tanner D, Paulin L, Alaluusua S, Thesleff I, et al. Identification of a nonsense mutation in the PAX9 gene in molar oligodontia. Eur J Hum Genet. 2001;9(10):743–6. doi: 10.1038/sj.ejhg.5200715 11781684

19. Frazier-Bowers SA, Guo DC, Cavender A, Xue L, Evans B, King T, et al. A novel mutation in human PAX9 causes molar oligodontia. J Dent Res. 2002;81(2):129–33. 11827258

20. Šerý O, Bonczek O, Hloušková A, Černochová P, Vaněk J, Míšek I, et al. A screen of a large Czech cohort of oligodontia patients implicates a novel mutation in the PAX9 gene. European journal of oral sciences. 2015;123(2):65–71. doi: 10.1111/eos.12170 25683653

21. Mostowska A, Zadurska M, Rakowska A, Lianeri M, Jagodzinski PP. Novel PAX9 mutation associated with syndromic tooth agenesis. European journal of oral sciences. 2013;121(5):403–11. doi: 10.1111/eos.12071 24028587

22. Wong SW, Han D, Zhang H, Liu Y, Zhang X, Miao MZ, et al. Nine Novel PAX9 Mutations and a Distinct Tooth Agenesis Genotype-Phenotype. J Dent Res. 2018;97(2):155–62. doi: 10.1177/0022034517729322 28910570

23. Daw EM, Saliba C, Grech G, Camilleri S. A novel PAX9 mutation causing oligodontia. Arch Oral Biol. 2017;84:100–5. doi: 10.1016/j.archoralbio.2017.09.018 28965043

24. Sarkar T, Bansal R, Das P. A novel G to A transition at initiation codon and exon-intron boundary of PAX9 identified in association with familial isolated oligodontia. Gene. 2017;635:69–76. doi: 10.1016/j.gene.2017.08.020 28847717

25. Fauzi NH, Ardini YD, Zainuddin Z, Lestari W. A review on non-syndromic tooth agenesis associated with PAX9 mutations. Jpn Dent Sci Rev. 2018;54(1):30–6. doi: 10.1016/j.jdsr.2017.08.001 29628999

26. Yu M, Wong S-W, Han D, Cai T. Genetic analysis: Wnt and other pathways in nonsyndromic tooth agenesis. Oral Diseases. 2018:1–6.

27. Peters H, Neubuser A, Kratochwil K, Balling R. Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities. Genes Dev. 1998;12(17):2735–47. doi: 10.1101/gad.12.17.2735 9732271

28. Phillips HM, Stothard CA, Shaikh Qureshi WM, Kousa AI, Briones-Leon JA, Khasawneh RR, et al. Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis. Development. 2019;146(18).

29. Farley-Barnes KI, Ogawa LM, Baserga SJ. Ribosomopathies: Old Concepts, New Controversies. Trends Genet. 2019;35(10):754–67. doi: 10.1016/j.tig.2019.07.004 31376929

30. Jia S, Zhou J, Fanelli C, Wee Y, Bonds J, Schneider P, et al. Small-molecule Wnt agonists correct cleft palates in Pax9 mutant mice in utero. Development. 2017;144(20):3819–28. doi: 10.1242/dev.157750 28893947

31. Li C, Lan Y, Krumlauf R, Jiang R. Modulating Wnt Signaling Rescues Palate Morphogenesis in Pax9 Mutant Mice. Journal of Dental Research. 2017;96(11):1273–81. doi: 10.1177/0022034517719865 28692808

32. Jia S, Zhou J, Wee Y, Mikkola ML, Schneider P, D’Souza RN. Anti-EDAR Agonist Antibody Therapy Resolves Palate Defects in Pax9-/- Mice. Journal of Dental Research. 2017;96(11):1282–9. doi: 10.1177/0022034517726073 28813171

33. Jia S, Zhou J, D'Souza RN. Pax9's dual roles in modulating Wnt signaling during murine palatogenesis. Dev Dyn. 2020.

34. Farley-Barnes KI, McCann KL, Ogawa LM, Merkel J, Surovtseva YV, Baserga SJ. Diverse Regulators of Human Ribosome Biogenesis Discovered by Changes in Nucleolar Number. Cell Rep. 2018;22(7):1923–34. doi: 10.1016/j.celrep.2018.01.056 29444442

35. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 2006;7(10):R100. doi: 10.1186/gb-2006-7-10-r100 17076895

36. Weiss WA, Taylor SS, Shokat KM. Recognizing and exploiting differences between RNAi and small-molecule inhibitors. Nat Chem Biol. 2007;3(12):739–44. doi: 10.1038/nchembio1207-739 18007642

37. Mohr SE, Smith JA, Shamu CE, Neumuller RA, Perrimon N. RNAi screening comes of age: improved techniques and complementary approaches. Nat Rev Mol Cell Biol. 2014;15(9):591–600. doi: 10.1038/nrm3860 25145850

38. Freed EF, Prieto JL, McCann KL, McStay B, Baserga SJ. NOL11, implicated in the pathogenesis of North American Indian childhood cirrhosis, is required for pre-rRNA transcription and processing. PLoS genetics. 2012;8(8):e1002892. doi: 10.1371/journal.pgen.1002892 22916032

39. Ghoshal K, Majumder S, Datta J, Motiwala T, Bai S, Sharma SM, et al. Role of human ribosomal RNA (rRNA) promoter methylation and of methyl-CpG-binding protein MBD2 in the suppression of rRNA gene expression. J Biol Chem. 2004;279(8):6783–93. doi: 10.1074/jbc.M309393200 14610093

40. Wang M, Anikin L, Pestov DG. Two orthogonal cleavages separate subunit RNAs in mouse ribosome biogenesis. Nucleic Acids Research. 2014;42(17):11180–91. doi: 10.1093/nar/gku787 25190460

41. Schmidt EK, Clavarino G, Ceppi M, Pierre P. SUnSET, a nonradioactive method to monitor protein synthesis. Nat Meth. 2009;6(4):275–7.

42. Dieudonné F-X, O’Connor PBF, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, et al. The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics. 2015;16(1):986.

43. Bernstein KA, Bleichert F, Bean JM, Cross FR, Baserga SJ. Ribosome biogenesis is sensed at the Start cell cycle checkpoint. Mol Biol Cell. 2007;18(3):953–64. doi: 10.1091/mbc.e06-06-0512 17192414

44. Fumagalli S, Ivanenkov VV, Teng T, Thomas G. Suprainduction of p53 by disruption of 40S and 60S ribosome biogenesis leads to the activation of a novel G2/M checkpoint. Genes Dev. 2012;26(10):1028–40. doi: 10.1101/gad.189951.112 22588717

45. Lessard F, Igelmann S, Trahan C, Huot G, Saint-Germain E, Mignacca L, et al. Senescence-associated ribosome biogenesis defects contributes to cell cycle arrest through the Rb pathway. Nature Cell Biology. 2018;20(7):789–99. doi: 10.1038/s41556-018-0127-y 29941930

46. Shamsuzzaman M, Bommakanti A, Zapinsky A, Rahman N, Pascual C, Lindahl L. Analysis of cell cycle parameters during the transition from unhindered growth to ribosomal and translational stress conditions. PLoS One. 2017;12(10):e0186494. doi: 10.1371/journal.pone.0186494 29028845

47. Turi Z, Lacey M, Mistrik M, Moudry P. Impaired ribosome biogenesis: mechanisms and relevance to cancer and aging. Aging (Albany NY). 2019;11(8):2512–40.

48. James A, Wang Y, Raje H, Rosby R, DiMario P. Nucleolar stress with and without p53. Nucleus. 2014;5(5):402–26. doi: 10.4161/nucl.32235 25482194

49. Hayashi Y, Fujimura A, Kato K, Udagawa R, Hirota T, Kimura K. Nucleolar integrity during interphase supports faithful Cdk1 activation and mitotic entry. Science Advances. 2018;4(6):eaap7777. doi: 10.1126/sciadv.aap7777 29881774

50. Jarboui MA, Wynne K, Elia G, Hall WW, Gautier VW. Proteomic profiling of the human T-cell nucleolus. Molecular immunology. 2011;49(3):441–52. doi: 10.1016/j.molimm.2011.09.005 22014684

51. Ahmad Y, Boisvert FM, Gregor P, Cobley A, Lamond AI. NOPdb: Nucleolar Proteome Database—2008 update. Nucleic Acids Res. 2009;37(Database issue):D181–4. doi: 10.1093/nar/gkn804 18984612

52. Thul PJ, Akesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, et al. A subcellular map of the human proteome. Science. 2017;356(6340):eaal3321. doi: 10.1126/science.aal3321 28495876

53. Kramer A, Green J, Pollard J Jr., Tugendreich S. Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics. 2014;30(4):523–30. doi: 10.1093/bioinformatics/btt703 24336805

54. Sivakamasundari V, Kraus P, Sun W, Hu X, Lim SL, Prabhakar S, et al. A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development. Biology open.s 2017;6(2):187–99.

55. Bailey TL, Machanick P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Research. 2012;40(17):e128–e. doi: 10.1093/nar/gks433 22610855

56. Epstein J, Cai J, Glaser T, Jepeal L, Maas R. Identification of a Pax paired domain recognition sequence and evidence for DNA-dependent conformational changes. Journal of Biological Chemistry. 1994;269(11):8355–61. 8132558

57. Badertscher L, Wild T, Montellese C, Alexander LT, Bammert L, Sarazova M, et al. Genome-wide RNAi Screening Identifies Protein Modules Required for 40S Subunit Synthesis in Human Cells. Cell Rep. 2015;13(12):2879–91. doi: 10.1016/j.celrep.2015.11.061 26711351

58. Neumuller RA, Gross T, Samsonova AA, Vinayagam A, Buckner M, Founk K, et al. Conserved regulators of nucleolar size revealed by global phenotypic analyses. Sci Signal. 2013;6(289):ra70. doi: 10.1126/scisignal.2004145 23962978

59. O'Donohue MF, Choesmel V, Faubladier M, Fichant G, Gleizes PE. Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. J Cell Biol. 2010;190(5):853–66. doi: 10.1083/jcb.201005117 20819938

60. Tafforeau L, Zorbas C, Langhendries JL, Mullineux ST, Stamatopoulou V, Mullier R, et al. The Complexity of Human Ribosome Biogenesis Revealed by Systematic Nucleolar Screening of Pre-rRNA Processing Factors. Mol Cell. 2013;51(4):539–51. doi: 10.1016/j.molcel.2013.08.011 23973377

61. McLeay RC, Bailey TL. Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data. BMC bioinformatics. 2010;11(1):165.

62. Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 2017;45(D1):D331–D8. doi: 10.1093/nar/gkw1108 27899567

63. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–9. doi: 10.1038/75556 10802651

64. Mi H, Huang X, Muruganujan A, Tang H, Mills C, Kang D, et al. PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. Nucleic Acids Res. 2017;45(D1):D183–D9. doi: 10.1093/nar/gkw1138 27899595

65. Carneiro M, Hu D, Archer J, Feng C, Afonso S, Chen C, et al. Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus. Genetics. 2017;205(2):955–65. doi: 10.1534/genetics.116.196667 27986804

66. Sondalle SB, Longerich S, Ogawa LM, Sung P, Baserga SJ. Fanconi anemia protein FANCI functions in ribosome biogenesis. Proceedings of the National Academy of Sciences. 2019;116(7):2561–70.

67. Ross AP, Zarbalis KS. The emerging roles of ribosome biogenesis in craniofacial development. Front Physiol. 2014;5:26–. doi: 10.3389/fphys.2014.00026 24550838

68. Trainor PA, Merrill AE. Ribosome biogenesis in skeletal development and the pathogenesis of skeletal disorders. Biochimica et biophysica acta. 2014;1842(6):769–78. doi: 10.1016/j.bbadis.2013.11.010 24252615

69. Dixon J, Jones NC, Sandell LL, Jayasinghe SM, Crane J, Rey J-P, et al. Tcof1/Treacle is required for neural crest cell formation and proliferation deficiencies that cause craniofacial abnormalities. Proceedings of the National Academy of Sciences. 2006;103(36):13403–8.

70. Griffin JN, Sondalle SB, del Viso F, Baserga SJ, Khokha MK. The Ribosome Biogenesis Factor Nol11 Is Required for Optimal rDNA Transcription and Craniofacial Development in Xenopus. PLoS genetics. 2015;11(3):e1005018. doi: 10.1371/journal.pgen.1005018 25756904

71. Calo E, Gu B, Bowen ME, Aryan F, Zalc A, Liang J, et al. Tissue-selective effects of nucleolar stress and rDNA damage in developmental disorders. Nature. 2018;554(7690):112–7. doi: 10.1038/nature25449 29364875

72. Chen JY, Tan X, Wang ZH, Liu YZ, Zhou JF, Rong XZ, et al. The ribosome biogenesis protein Esf1 is essential for pharyngeal cartilage formation in zebrafish. FEBS J. 2018;285(18):3464–83. doi: 10.1111/febs.14622 30073783

73. Zhao C, Andreeva V, Gibert Y, LaBonty M, Lattanzi V, Prabhudesai S, et al. Tissue specific roles for the ribosome biogenesis factor Wdr43 in zebrafish development. PLoS genetics. 2014;10(1):e1004074–e. doi: 10.1371/journal.pgen.1004074 24497835

74. Noack Watt KE, Achilleos A, Neben CL, Merrill AE, Trainor PA. The Roles of RNA Polymerase I and III Subunits Polr1c and Polr1d in Craniofacial Development and in Zebrafish Models of Treacher Collins Syndrome. PLoS genetics. 2016;12(7):e1006187. doi: 10.1371/journal.pgen.1006187 27448281

75. Watt KEN, Neben CL, Hall S, Merrill AE, Trainor PA. tp53-dependent and independent signaling underlies the pathogenesis and possible prevention of Acrofacial Dysostosis–Cincinnati type. Human Molecular Genetics. 2018;27(15):2628–43. doi: 10.1093/hmg/ddy172 29750247

76. Monsoro-Burq AH. PAX transcription factors in neural crest development. Semin Cell Dev Biol. 2015;44:87–96. doi: 10.1016/j.semcdb.2015.09.015 26410165

77. Sanchez RS, Sanchez SS. Characterization of pax1, pax9, and uncx sclerotomal genes during Xenopus laevis embryogenesis. Dev Dyn. 2013;242(5):572–9. doi: 10.1002/dvdy.23945 23401059

78. Peters H, Neubuser A, Balling R. Pax genes and organogenesis: Pax9 meets tooth development. European journal of oral sciences. 1998;106 Suppl 1:38–43.

79. Griffin JN, Sondalle SB, Robson A, Mis EK, Griffin G, Kulkarni SS, et al. RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus. Development. 2018;145(20).

80. Robson A, Owens NDL, Baserga SJ, Khokha MK, Griffin JN. Expression of ribosomopathy genes during Xenopus tropicalis embryogenesis. BMC Dev Biol. 2016;16(1):38–. doi: 10.1186/s12861-016-0138-5 27784267

81. Deniz E, Jonas S, Hooper M, J NG, Choma MA, Khokha MK. Analysis of Craniocardiac Malformations in Xenopus using Optical Coherence Tomography. Sci Rep. 2017;7:42506. doi: 10.1038/srep42506 28195132

82. Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat Rev Genet. 2014;15(12):829–45. doi: 10.1038/nrg3813 25365966

83. Brannan KW, Jin W, Huelga SC, Banks CA, Gilmore JM, Florens L, et al. SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. Mol Cell. 2016;64(2):282–93. doi: 10.1016/j.molcel.2016.09.003 27720645

84. Cook KB, Kazan H, Zuberi K, Morris Q, Hughes TR. RBPDB: a database of RNA-binding specificities. Nucleic Acids Research. 2011;39(suppl_1):D301–D8.

85. Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, et al. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013;499(7457):172–7. doi: 10.1038/nature12311 23846655

86. Sobecki M, Mrouj K, Camasses A, Parisis N, Nicolas E, Lleres D, et al. The cell proliferation antigen Ki-67 organises heterochromatin. Elife. 2016;5:e13722. doi: 10.7554/eLife.13722 26949251

87. Owens NDL, Blitz IL, Lane MA, Patrushev I, Overton JD, Gilchrist MJ, et al. Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development. Cell Rep. 2016;14(3):632–47. doi: 10.1016/j.celrep.2015.12.050 26774488

88. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth. 2012;9(4):357–9.

89. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech. 2010;28(5):511–5.

90. del Viso F, Khokha M. Generating diploid embryos from Xenopus tropicalis. Methods Mol Biol. 2012;917:33–41. doi: 10.1007/978-1-61779-992-1_3 22956081

91. Khokha MK, Chung C, Bustamante EL, Gaw LW, Trott KA, Yeh J, et al. Techniques and probes for the study of Xenopus tropicalis development. Dev Dyn. 2002;225(4):499–510. doi: 10.1002/dvdy.10184 12454926

92. Bhattacharya D, Marfo CA, Li D, Lane M, Khokha MK. CRISPR/Cas9: An inexpensive, efficient loss of function tool to screen human disease genes in Xenopus. Dev Biol. 2015;408(2):196–204. doi: 10.1016/j.ydbio.2015.11.003 26546975

93. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat Protoc. 2013;8(11):2281–308. doi: 10.1038/nprot.2013.143 24157548

94. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9(7):676–82. doi: 10.1038/nmeth.2019 22743772

95. Hensey C, Gautier J. Programmed cell death during Xenopus development: a spatio-temporal analysis. Developmental biology. 1998;203(1):36–48. doi: 10.1006/dbio.1998.9028 9806771

96. Spandidos A, Wang X, Wang H, Seed B. PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification. Nucleic Acids Research. 2010;38(suppl_1):D792–D9.

97. Galiveti CR, Rozhdestvensky TS, Brosius J, Lehrach H, Konthur Z. Application of housekeeping npcRNAs for quantitative expression analysis of human transcriptome by real-time PCR. RNA. 2010;16(2):450–61. doi: 10.1261/rna.1755810 20040593

98. Rice SJ, Lai S-C, Wood LW, Helsley KR, Runkle EA, Winslow MM, et al. MicroRNA-33a Mediates the Regulation of High Mobility Group AT-Hook 2 Gene (HMGA2) by Thyroid Transcription Factor 1 (TTF-1/NKX2–1). Journal of Biological Chemistry. 2013;288(23):16348–60. doi: 10.1074/jbc.M113.474643 23625920

99. Gordon CA, Gong X, Ganesh D, Brooks JD. NUSAP1 promotes invasion and metastasis of prostate cancer. Oncotarget. 2017;8(18):29935–50. doi: 10.18632/oncotarget.15604 28404898

100. Wiza C, Chadt A, Blumensatt M, Kanzleiter T, Herzfeld De Wiza D, Horrighs A, et al. Over-expression of PRAS40 enhances insulin sensitivity in skeletal muscle. Archives of Physiology and Biochemistry. 2014;120(2):64–72. doi: 10.3109/13813455.2014.894076 24576065

101. Guo L, Zhong D, Lau S, Liu X, Dong X-Y, Sun X, et al. Sox7 is an independent checkpoint for β-catenin function in prostate and colon epithelial cells. Molecular cancer research: MCR. 2008;6(9):1421–30. doi: 10.1158/1541-7786.MCR-07-2175 18819930

102. Luo C, Yao Y, Yu Z, Zhou H, Guo L, Zhang J, et al. UBE2T knockdown inhibits gastric cancer progression. Oncotarget. 2017;8(20):32639–54. doi: 10.18632/oncotarget.15947 28427240

Článek Immediate activation of chemosensory neuron gene expression by bacterial metabolites is selectively induced by distinct cyclic GMP-dependent pathways in Caenorhabditis elegans

Článek Phospho-regulation of the Shugoshin - Condensin interaction at the centromere in budding yeast

Článek Gα/GSA-1 works upstream of PKA/KIN-1 to regulate calcium signaling and contractility in the Caenorhabditis elegans spermatheca

Článek Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia

Článek Transcriptional regulators of the Golli/myelin basic protein locus integrate additive and stealth activities

Článek Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics

Článek DAnkrd49 and Bdbt act via Casein kinase Iε to regulate planar polarity in Drosophila

Článek Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

Článek Endogenization and excision of human herpesvirus 6 in human genomes

Článek A subset of broadly responsive Type III taste cells contribute to the detection of bitter, sweet and umami stimuli

Článek On the cross-population generalizability of gene expression prediction models

Článek How many familial relationship testing results could be wrong?