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Items: 1 to 50 of 86

1.

Polymer physics predicts the effects of structural variants on chromatin architecture.

Bianco S, Lupiáñez DG, Chiariello AM, Annunziatella C, Kraft K, Schöpflin R, Wittler L, Andrey G, Vingron M, Pombo A, Mundlos S, Nicodemi M.

Nat Genet. 2018 May;50(5):662-667. doi: 10.1038/s41588-018-0098-8. Epub 2018 Apr 16.

PMID:
29662163
2.

RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiation.

Ferrai C, Torlai Triglia E, Risner-Janiczek JR, Rito T, Rackham OJ, de Santiago I, Kukalev A, Nicodemi M, Akalin A, Li M, Ungless MA, Pombo A.

Mol Syst Biol. 2017 Oct 16;13(10):946. doi: 10.15252/msb.20177754.

3.

FANTOM5 CAGE profiles of human and mouse samples.

Noguchi S, Arakawa T, Fukuda S, Furuno M, Hasegawa A, Hori F, Ishikawa-Kato S, Kaida K, Kaiho A, Kanamori-Katayama M, Kawashima T, Kojima M, Kubosaki A, Manabe RI, Murata M, Nagao-Sato S, Nakazato K, Ninomiya N, Nishiyori-Sueki H, Noma S, Saijyo E, Saka A, Sakai M, Simon C, Suzuki N, Tagami M, Watanabe S, Yoshida S, Arner P, Axton RA, Babina M, Baillie JK, Barnett TC, Beckhouse AG, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Carlisle AJ, Clevers HC, Davis CA, Detmar M, Dohi T, Edge ASB, Edinger M, Ehrlund A, Ekwall K, Endoh M, Enomoto H, Eslami A, Fagiolini M, Fairbairn L, Farach-Carson MC, Faulkner GJ, Ferrai C, Fisher ME, Forrester LM, Fujita R, Furusawa JI, Geijtenbeek TB, Gingeras T, Goldowitz D, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Hasegawa Y, Herlyn M, Heutink P, Hitchens KJ, Hume DA, Ikawa T, Ishizu Y, Kai C, Kawamoto H, Kawamura YI, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klein S, Klinken SP, Knox AJ, Kojima S, Koseki H, Koyasu S, Lee W, Lennartsson A, Mackay-Sim A, Mejhert N, Mizuno Y, Morikawa H, Morimoto M, Moro K, Morris KJ, Motohashi H, Mummery CL, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nozaki T, Ogishima S, Ohkura N, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Passier R, Patrikakis M, Pombo A, Pradhan-Bhatt S, Qin XY, Rehli M, Rizzu P, Roy S, Sajantila A, Sakaguchi S, Sato H, Satoh H, Savvi S, Saxena A, Schmidl C, Schneider C, Schulze-Tanzil GG, Schwegmann A, Sheng G, Shin JW, Sugiyama D, Sugiyama T, Summers KM, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tomoiu A, Toyoda H, van de Wetering M, van den Berg LM, Verardo R, Vijayan D, Wells CA, Winteringham LN, Wolvetang E, Yamaguchi Y, Yamamoto M, Yanagi-Mizuochi C, Yoneda M, Yonekura Y, Zhang PG, Zucchelli S, Abugessaisa I, Arner E, Harshbarger J, Kondo A, Lassmann T, Lizio M, Sahin S, Sengstag T, Severin J, Shimoji H, Suzuki M, Suzuki H, Kawai J, Kondo N, Itoh M, Daub CO, Kasukawa T, Kawaji H, Carninci P, Forrest ARR, Hayashizaki Y.

Sci Data. 2017 Aug 29;4:170112. doi: 10.1038/sdata.2017.112.

4.

Cell cycle: Continuous chromatin changes.

Beagrie RA, Pombo A.

Nature. 2017 Jul 5;547(7661):34-35. doi: 10.1038/547034a. No abstract available.

PMID:
28682328
5.

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA.

Nat Commun. 2017 Jun 26;8(1):36. doi: 10.1038/s41467-017-00052-2.

6.

Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatment.

Mattei D, Ivanov A, Ferrai C, Jordan P, Guneykaya D, Buonfiglioli A, Schaafsma W, Przanowski P, Deuther-Conrad W, Brust P, Hesse S, Patt M, Sabri O, Ross TL, Eggen BJL, Boddeke EWGM, Kaminska B, Beule D, Pombo A, Kettenmann H, Wolf SA.

Transl Psychiatry. 2017 May 9;7(5):e1120. doi: 10.1038/tp.2017.80.

7.

Keep Them Close: PRC2 Poises Enhancer-Promoter Interactions at Anterior Neuronal Genes.

Caglio G, Torlai Triglia E, Pombo A.

Cell Stem Cell. 2017 May 4;20(5):573-575. doi: 10.1016/j.stem.2017.04.006.

8.

Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.

Barbieri M, Xie SQ, Torlai Triglia E, Chiariello AM, Bianco S, de Santiago I, Branco MR, Rueda D, Nicodemi M, Pombo A.

Nat Struct Mol Biol. 2017 Jun;24(6):515-524. doi: 10.1038/nsmb.3402. Epub 2017 Apr 24.

PMID:
28436944
9.

Complex multi-enhancer contacts captured by genome architecture mapping.

Beagrie RA, Scialdone A, Schueler M, Kraemer DC, Chotalia M, Xie SQ, Barbieri M, de Santiago I, Lavitas LM, Branco MR, Fraser J, Dostie J, Game L, Dillon N, Edwards PA, Nicodemi M, Pombo A.

Nature. 2017 Mar 23;543(7646):519-524. doi: 10.1038/nature21411. Epub 2017 Mar 8.

10.

A Finer Print Than TADs: PRC1-Mediated Domains.

Torlai Triglia E, Rito T, Pombo A.

Mol Cell. 2017 Feb 2;65(3):373-375. doi: 10.1016/j.molcel.2017.01.028.

11.

Examining Topological Domain Influence on Enhancer Function.

Beagrie RA, Pombo A.

Dev Cell. 2016 Dec 5;39(5):523-524. doi: 10.1016/j.devcel.2016.11.011.

12.

Formation of new chromatin domains determines pathogenicity of genomic duplications.

Franke M, Ibrahim DM, Andrey G, Schwarzer W, Heinrich V, Schöpflin R, Kraft K, Kempfer R, Jerković I, Chan WL, Spielmann M, Timmermann B, Wittler L, Kurth I, Cambiaso P, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S.

Nature. 2016 Oct 13;538(7624):265-269. doi: 10.1038/nature19800. Epub 2016 Oct 5.

PMID:
27706140
13.

Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription.

Beagrie RA, Pombo A.

Bioessays. 2016 Sep;38(9):881-93. doi: 10.1002/bies.201600032. Epub 2016 Jul 25. Review.

PMID:
27452946
14.

Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.

Le HQ, Ghatak S, Yeung CY, Tellkamp F, Günschmann C, Dieterich C, Yeroslaviz A, Habermann B, Pombo A, Niessen CM, Wickström SA.

Nat Cell Biol. 2016 Aug;18(8):864-75. doi: 10.1038/ncb3387. Epub 2016 Jul 11.

PMID:
27398909
15.

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation.

Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DC, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, Hayashizaki Y, Carninci P, Forrest AR; FANTOM Consortium, Semple CA, Dostie J, Pombo A, Nicodemi M.

Mol Syst Biol. 2015 Dec 23;11(12):852. doi: 10.15252/msb.20156492.

16.

Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.

Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A.

Elife. 2015 Dec 19;4. pii: e11215. doi: 10.7554/eLife.11215.

17.

Physical mechanisms behind the large scale features of chromatin organization.

Pombo A, Nicodemi M.

Transcription. 2014;5(2):e28447. doi: 10.4161/trns.28447. Review.

18.

Three-dimensional genome architecture: players and mechanisms.

Pombo A, Dillon N.

Nat Rev Mol Cell Biol. 2015 Apr;16(4):245-57. doi: 10.1038/nrm3965. Epub 2015 Mar 11. Review. Erratum in: Nat Rev Mol Cell Biol. 2015 Sep;16(9):576.

PMID:
25757416
19.

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.

Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.

20.

Stem cell epigenetics: looking forward.

Benitah SA, Bracken A, Dou Y, Huangfu D, Ivanova N, Koseki H, Laurent L, Lim DA, Meshorer E, Pombo A, Sander M, Xu GL.

Cell Stem Cell. 2014 Jun 5;14(6):706-9. No abstract available.

21.

Models of chromosome structure.

Nicodemi M, Pombo A.

Curr Opin Cell Biol. 2014 Jun;28:90-5. doi: 10.1016/j.ceb.2014.04.004. Epub 2014 May 4. Review.

PMID:
24804566
22.

Physical mechanisms behind the large scale features of chromatin organization.

Pombo A, Nicodemi M.

Transcription. 2014 Mar 21;5. [Epub ahead of print] Review.

PMID:
24802900
23.

An H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation.

Sabbattini P, Sjoberg M, Nikic S, Frangini A, Holmqvist PH, Kunowska N, Carroll T, Brookes E, Arthur SJ, Pombo A, Dillon N.

Mol Biol Cell. 2014 Mar;25(6):904-15. doi: 10.1091/mbc.E13-10-0628. Epub 2014 Jan 15.

24.

A polymer model explains the complexity of large-scale chromatin folding.

Barbieri M, Fraser J, Lavitas LM, Chotalia M, Dostie J, Pombo A, Nicodemi M.

Nucleus. 2013 Jul-Aug;4(4):267-73. doi: 10.4161/nucl.25432. Epub 2013 Jun 19.

25.

Polymer models of chromatin organization.

Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M.

Front Genet. 2013 Jun 20;4:113. doi: 10.3389/fgene.2013.00113. eCollection 2013. No abstract available.

26.

A model of the large-scale organization of chromatin.

Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, Nicodemi M.

Biochem Soc Trans. 2013 Apr;41(2):508-12. doi: 10.1042/BST20120238. Review.

PMID:
23514144
27.

Mean Expression of the X-Chromosome is Associated with Neuronal Density.

Swingland JT, Durrenberger PF, Reynolds R, Dexter DT, Pombo A, Deprez M, Roncaroli F, Turkheimer FE.

Front Neurosci. 2012 Nov 12;6:161. doi: 10.3389/fnins.2012.00161. eCollection 2012.

28.

Complexity of chromatin folding is captured by the strings and binders switch model.

Barbieri M, Chotalia M, Fraser J, Lavitas LM, Dostie J, Pombo A, Nicodemi M.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16173-8. doi: 10.1073/pnas.1204799109. Epub 2012 Sep 17.

29.

Code breaking: the RNAPII modification code in pluripotency.

Brookes E, Pombo A.

Cell Cycle. 2012 Apr 1;11(7):1267-8. doi: 10.4161/cc.19990. Epub 2012 Apr 1. No abstract available.

PMID:
22421158
30.

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.

Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A.

Cell Stem Cell. 2012 Feb 3;10(2):157-70. doi: 10.1016/j.stem.2011.12.017.

31.

Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease.

Möller A, Xie SQ, Hosp F, Lang B, Phatnani HP, James S, Ramirez F, Collin GB, Naggert JK, Babu MM, Greenleaf AL, Selbach M, Pombo A.

Mol Cell Proteomics. 2012 Jun;11(6):M111.011767. doi: 10.1074/mcp.M111.011767. Epub 2011 Dec 22.

32.

Polycomb targets seek closest neighbours.

Chotalia M, Pombo A.

PLoS Genet. 2011 Mar;7(3):e1002031. doi: 10.1371/journal.pgen.1002031. Epub 2011 Mar 24. No abstract available.

33.

Nuclear cell biology.

Pombo A, Starr DA.

Mol Biol Cell. 2011 Mar 15;22(6):722. doi: 10.1091/mbc.E10-12-0966. No abstract available.

34.

Nuclear architecture in stem cells.

Morris KJ, Chotalia M, Pombo A.

Adv Exp Med Biol. 2010;695:14-25. doi: 10.1007/978-1-4419-7037-4_2.

PMID:
21222196
35.

CryoFISH: fluorescence in situ hybridization on ultrathin cryosections.

Xie SQ, Lavitas LM, Pombo A.

Methods Mol Biol. 2010;659:219-30. doi: 10.1007/978-1-60761-789-1_15.

PMID:
20809314
36.

Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment.

Alder O, Lavial F, Helness A, Brookes E, Pinho S, Chandrashekran A, Arnaud P, Pombo A, O'Neill L, Azuara V.

Development. 2010 Aug 1;137(15):2483-92. doi: 10.1242/dev.048363. Epub 2010 Jun 23.

37.

Nucleus and gene expression: the structure and function conundrum.

Pombo A, Gilbert DM.

Curr Opin Cell Biol. 2010 Jun;22(3):269-70. doi: 10.1016/j.ceb.2010.04.010. Epub 2010 May 22. No abstract available.

PMID:
20547046
38.

Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2.

Kanhere A, Viiri K, Araújo CC, Rasaiyaah J, Bouwman RD, Whyte WA, Pereira CF, Brookes E, Walker K, Bell GW, Pombo A, Fisher AG, Young RA, Jenner RG.

Mol Cell. 2010 Jun 11;38(5):675-88. doi: 10.1016/j.molcel.2010.03.019.

39.

Gene positioning.

Ferrai C, de Castro IJ, Lavitas L, Chotalia M, Pombo A.

Cold Spring Harb Perspect Biol. 2010 Jun;2(6):a000588. doi: 10.1101/cshperspect.a000588. Epub 2010 May 19. Review.

40.

Jarid2 is a PRC2 component in embryonic stem cells required for multi-lineage differentiation and recruitment of PRC1 and RNA Polymerase II to developmental regulators.

Landeira D, Sauer S, Poot R, Dvorkina M, Mazzarella L, Jørgensen HF, Pereira CF, Leleu M, Piccolo FM, Spivakov M, Brookes E, Pombo A, Fisher C, Skarnes WC, Snoek T, Bezstarosti K, Demmers J, Klose RJ, Casanova M, Tavares L, Brockdorff N, Merkenschlager M, Fisher AG.

Nat Cell Biol. 2010 Jun;12(6):618-24. doi: 10.1038/ncb2065. Epub 2010 May 16.

41.

Poised transcription factories prime silent uPA gene prior to activation.

Ferrai C, Xie SQ, Luraghi P, Munari D, Ramirez F, Branco MR, Pombo A, Crippa MP.

PLoS Biol. 2010 Jan;8(1):e1000270. doi: 10.1371/journal.pbio.1000270. Epub 2010 Jan 5.

42.

The molecular basis for stability of heterochromatin-mediated silencing in mammals.

Hiragami-Hamada K, Xie SQ, Saveliev A, Uribe-Lewis S, Pombo A, Festenstein R.

Epigenetics Chromatin. 2009 Nov 4;2(1):14. doi: 10.1186/1756-8935-2-14.

43.

Measurement of replication structures at the nanometer scale using super-resolution light microscopy.

Baddeley D, Chagin VO, Schermelleh L, Martin S, Pombo A, Carlton PM, Gahl A, Domaing P, Birk U, Leonhardt H, Cremer C, Cardoso MC.

Nucleic Acids Res. 2010 Jan;38(2):e8. doi: 10.1093/nar/gkp901. Epub 2009 Oct 28.

44.

Modifications of RNA polymerase II are pivotal in regulating gene expression states.

Brookes E, Pombo A.

EMBO Rep. 2009 Nov;10(11):1213-9. doi: 10.1038/embor.2009.221. Epub 2009 Oct 16. Review.

45.

Mechanisms regulating S phase progression in mammalian cells.

Maya-Mendoza A, Tang CW, Pombo A, Jackson DA.

Front Biosci (Landmark Ed). 2009 Jan 1;14:4199-213. Review.

PMID:
19273345
46.

3D chromatin regulation of Sonic hedgehog in the limb buds.

Ferrai C, Pombo A.

Dev Cell. 2009 Jan;16(1):9-11. doi: 10.1016/j.devcel.2008.12.010.

47.

Eukaryotic gene regulation in three dimensions and its impact on genome evolution.

Babu MM, Janga SC, de Santiago I, Pombo A.

Curr Opin Genet Dev. 2008 Dec;18(6):571-82. doi: 10.1016/j.gde.2008.10.002. Epub 2008 Nov 27.

PMID:
19007886
48.

Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH.

Branco MR, Branco T, Ramirez F, Pombo A.

Chromosome Res. 2008;16(3):413-26. doi: 10.1007/s10577-008-1230-x.

PMID:
18461481
49.

Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region.

Noordermeer D, Branco MR, Splinter E, Klous P, van Ijcken W, Swagemakers S, Koutsourakis M, van der Spek P, Pombo A, de Laat W.

PLoS Genet. 2008 Mar 7;4(3):e1000016. doi: 10.1371/journal.pgen.1000016. Erratum in: PLoS Genet. 2008 Mar;4(3). doi: 10.1371/annotation/b4241c5d-5403-4797-8579-913ef9be560b. Pombo, Ana [added].

50.

Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells.

Stock JK, Giadrossi S, Casanova M, Brookes E, Vidal M, Koseki H, Brockdorff N, Fisher AG, Pombo A.

Nat Cell Biol. 2007 Dec;9(12):1428-35. Epub 2007 Nov 25.

PMID:
18037880

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