The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of cohesin onto chromatin, but how and where cohesin is loaded in vertebrate cells is unclear. Heterozygous mutations of NIPBL were found in 50% of the cases of Cornelia de Lange Syndrome (CdLS), a human developmental syndrome with a complex phenotype. However, no defects in the mitotic function of cohesin have been observed so far and the links between NIPBL mutations and the observed developmental defects are unclear. We show that NIPBL binds to chromatin in somatic cells with a different timing than cohesin. Further, we observe that high-affinity NIPBL binding sites localize to different regions than cohesin and almost exclusively to the promoters of active genes. NIPBL or cohesin knockdown reduce transcription of these genes differently, suggesting a cohesin-independent role of NIPBL for transcription. Motif analysis and comparison to published data show that NIPBL co-localizes with a specific set of other transcription factors. In cells derived from CdLS patients NIPBL binding levels are reduced and several of the NIPBL-bound genes have previously been observed to be mis-expressed in CdLS. In summary, our observations indicate that NIPBL mutations might cause developmental defects in different ways. First, defects of NIPBL might lead to cohesin-loading defects and thereby alter gene expression and second, NIPBL deficiency might affect genes directly via its role at the respective promoters.
Vyšlo v časopise: A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS. PLoS Genet 10(2): e32767. doi:10.1371/journal.pgen.1004153 Kategorie: Research Article prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004153
1. PetersJM, TedeschiA, SchmitzJ (2008) The cohesin complex and its roles in chromosome biology. Genes Dev 22 : 3089–3114.
2. SjogrenC, StromL (2010) S-phase and DNA damage activated establishment of sister chromatid cohesion–importance for DNA repair. Exp Cell Res 316 : 1445–1453.
3. WendtKS, YoshidaK, ItohT, BandoM, KochB, et al. (2008) Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451 : 796–801.
4. ParelhoV, HadjurS, SpivakovM, LeleuM, SauerS, et al. (2008) Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132 : 422–433.
5. StedmanW, KangH, LinS, KissilJL, BartolomeiMS, et al. (2008) Cohesins localize with CTCF at the KSHV latency control region and at cellular c-myc and H19/Igf2 insulators. Embo J 27 : 654–666.
6. HadjurS, WilliamsLM, RyanNK, CobbBS, SextonT, et al. (2009) Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus. Nature 460 : 410–413.
7. MishiroT, IshiharaK, HinoS, TsutsumiS, AburataniH, et al. (2009) Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. Embo J 28 : 1234–1245.
8. NativioR, WendtKS, ItoY, HuddlestonJE, Uribe-LewisS, et al. (2009) Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus. PLoS Genet 5: e1000739.
9. HorsfieldJA, AnagnostouSH, HuJK, ChoKH, GeislerR, et al. (2007) Cohesin-dependent regulation of Runx genes. Development 134 : 2639–2649.
10. PauliA, van BemmelJG, OliveiraRA, ItohT, ShirahigeK, et al. (2010) A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol 20 : 1787–1798.
11. PauliA, AlthoffF, OliveiraRA, HeidmannS, SchuldinerO, et al. (2008) Cell-Type-Specific TEV Protease Cleavage Reveals Cohesin Functions in Drosophila Neurons. Dev Cell 14 : 239–251.
12. SchuldinerO, BerdnikD, LevyJM, WuJS, LuginbuhlD, et al. (2008) piggyBac-Based Mosaic Screen Identifies a Postmitotic Function for Cohesin in Regulating Developmental Axon Pruning. Dev Cell 14 : 227–238.
13. KageyMH, NewmanJJ, BilodeauS, ZhanY, OrlandoDA, et al. (2010) Mediator and cohesin connect gene expression and chromatin architecture. Nature 467 : 430–435.
14. HaeringCH, FarcasAM, ArumugamP, MetsonJ, NasmythK (2008) The cohesin ring concatenates sister DNA molecules. Nature 454 : 297–301.
15. HaeringCH, LoweJ, HochwagenA, NasmythK (2002) Molecular architecture of SMC proteins and the yeast cohesin complex. Mol Cell 9 : 773–788.
16. LiuJ, KrantzID (2009) Cornelia de Lange syndrome, cohesin, and beyond. Clin Genet 76 : 303–314.
17. LiuJ, BaynamG (2010) Cornelia de Lange syndrome. Adv Exp Med Biol 685 : 111–123.
18. LiuJ, ZhangZ, BandoM, ItohT, DeardorffMA, et al. (2009) Transcriptional dysregulation in NIPBL and cohesin mutant human cells. PLoS Biol 7: e1000119.
19. KawauchiS, CalofAL, SantosR, Lopez-BurksME, YoungCM, et al. (2009) Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/−) mouse, a model of Cornelia de Lange Syndrome. PLoS Genet 5: e1000650.
20. BorckG, ZarhrateM, CluzeauC, BalE, BonnefontJP, et al. (2006) Father-to-daughter transmission of Cornelia de Lange syndrome caused by a mutation in the 5′ untranslated region of the NIPBL Gene. Hum Mutat 27 : 731–735.
21. CastronovoP, GervasiniC, CeredaA, MasciadriM, MilaniD, et al. (2009) Premature chromatid separation is not a useful diagnostic marker for Cornelia de Lange syndrome. Chromosome Res 17 : 763–771.
22. RollinsRA, KoromM, AulnerN, MartensA, DorsettD (2004) Drosophila nipped-B protein supports sister chromatid cohesion and opposes the stromalin/Scc3 cohesion factor to facilitate long-range activation of the cut gene. Mol Cell Biol 24 : 3100–3111.
23. JahnkeP, XuW, WullingM, AlbrechtM, GabrielH, et al. (2008) The Cohesin loading factor NIPBL recruits histone deacetylases to mediate local chromatin modifications. Nucleic Acids Res 36 : 6450–6458.
24. LechnerMS, SchultzDC, NegorevD, MaulGG, RauscherFJ3rd (2005) The mammalian heterochromatin protein 1 binds diverse nuclear proteins through a common motif that targets the chromoshadow domain. Biochem Biophys Res Commun 331 : 929–937.
25. BartekJ, BartkovaJ, KyprianouN, LalaniEN, StaskovaZ, et al. (1991) Efficient immortalization of luminal epithelial cells from human mammary gland by introduction of simian virus 40 large tumor antigen with a recombinant retrovirus. Proc Natl Acad Sci U S A 88 : 3520–3524.
26. SchmidtD, WilsonMD, SpyrouC, BrownGD, HadfieldJ, et al. (2009) ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods 48 : 240–248.
27. HakimiMA, BocharDA, SchmiesingJA, DongY, BarakOG, et al. (2002) A chromatin remodelling complex that loads cohesin onto human chromosomes. Nature 418 : 994–998.
28. TanakaT, CosmaMP, WirthK, NasmythK (1999) Identification of cohesin association sites at centromeres and along chromosome arms. Cell 98 : 847–858.
29. WaizeneggerIC, HaufS, MeinkeA, PetersJM (2000) Two distinct pathways remove mammalian cohesin from chromosome arms in prophase and from centromeres in anaphase. Cell 103 : 399–410.
30. JurkaJ, KapitonovVV, PavlicekA, KlonowskiP, KohanyO, et al. (2005) Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110 : 462–467.
31. ErnstJ, KheradpourP, MikkelsenTS, ShoreshN, WardLD, et al. (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473 : 43–49.
32. ConsortiumEP (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
33. BaileyTL, ElkanC (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2 : 28–36.
34. VaquerizasJM, KummerfeldSK, TeichmannSA, LuscombeNM (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet 10 : 252–263.
35. RhodesJM, BentleyFK, PrintCG, DorsettD, MisulovinZ, et al. (2010) Positive regulation of c-Myc by cohesin is direct, and evolutionarily conserved. Dev Biol 344 : 637–649.
36. RubioED, ReissDJ, WelcshPL, DistecheCM, FilippovaGN, et al. (2008) CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A 105 : 8309–8314.
37. SchmidtD, SchwaliePC, Ross-InnesCS, HurtadoA, BrownGD, et al. (2010) A CTCF-independent role for cohesin in tissue-specific transcription. Genome Res 20 : 578–588.
38. WatrinE, SchleifferA, TanakaK, EisenhaberF, NasmythK, et al. (2006) Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biol 16 : 863–874.
39. GerlichD, KochB, DupeuxF, PetersJM, EllenbergJ (2006) Live-cell imaging reveals a stable cohesin-chromatin interaction after but not before DNA replication. Curr Biol 16 : 1571–1578.
40. CioskR, ShirayamaM, ShevchenkoA, TanakaT, TothA, et al. (2000) Cohesin's binding to chromosomes depends on a separate complex consisting of Scc2 and Scc4 proteins. Mol Cell 5 : 243–254.
41. LengronneA, KatouY, MoriS, YokobayashiS, KellyGP, et al. (2004) Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature 430 : 573–578.
42. HuB, ItohT, MishraA, KatohY, ChanKL, et al. (2011) ATP hydrolysis is required for relocating cohesin from sites occupied by its Scc2/4 loading complex. Curr Biol 21 : 12–24.
43. KogutI, WangJ, GuacciV, MistryRK, MegeePC (2009) The Scc2/Scc4 cohesin loader determines the distribution of cohesin on budding yeast chromosomes. Genes Dev 23 : 2345–2357.
44. MisulovinZ, SchwartzYB, LiXY, KahnTG, GauseM, et al. (2008) Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma 117 : 89–102.
45. MalikS, RoederRG (2010) The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet 11 : 761–772.
46. MutoA, CalofAL, LanderAD, SchillingTF (2011) Multifactorial origins of heart and gut defects in nipbl-deficient zebrafish, a model of Cornelia de Lange Syndrome. PLoS Biol 9: e1001181.
47. LuZH, BooksJT, LeyTJ (2005) YB-1 is important for late-stage embryonic development, optimal cellular stress responses, and the prevention of premature senescence. Mol Cell Biol 25 : 4625–4637.
48. LuZH, BooksJT, LeyTJ (2006) Cold shock domain family members YB-1 and MSY4 share essential functions during murine embryogenesis. Mol Cell Biol 26 : 8410–8417.
49. TakedaK, NoguchiK, ShiW, TanakaT, MatsumotoM, et al. (1997) Targeted disruption of the mouse Stat3 gene leads to early embryonic lethality. Proc Natl Acad Sci U S A 94 : 3801–3804.
50. RheeJW, ArataA, SelleriL, JacobsY, ArataS, et al. (2004) Pbx3 deficiency results in central hypoventilation. Am J Pathol 165 : 1343–1350.
51. Di GiacomoG, KossM, CapelliniTD, BrendolanA, PopperlH, et al. (2006) Spatio-temporal expression of Pbx3 during mouse organogenesis. Gene Expr Patterns 6 : 747–757.
52. ArringtonCB, DowseBR, BleylSB, BowlesNE (2012) Non-synonymous variants in pre-B cell leukemia homeobox (PBX) genes are associated with congenital heart defects. Eur J Med Genet 55 : 235–237.
53. YoneyamaM, SuharaW, FujitaT (2002) Control of IRF-3 activation by phosphorylation. J Interferon Cytokine Res 22 : 73–76.
54. EferlR, WagnerEF (2003) AP-1: a double-edged sword in tumorigenesis. Nat Rev Cancer 3 : 859–868.
55. SumaraI, VorlauferE, GieffersC, PetersBH, PetersJM (2000) Characterization of vertebrate cohesin complexes and their regulation in prophase. J Cell Biol 151 : 749–762.
56. ZhangY, LiuT, MeyerCA, EeckhouteJ, JohnsonDS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
57. BrouwerRW, van den HoutMC, GrosveldFG, van IjckenWF (2011) NARWHAL, a primary analysis pipeline for NGS data. Bioinformatics 28 : 284–285.
58. MortazaviA, WilliamsBA, McCueK, SchaefferL, WoldB (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5 : 621–628.
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