Publications

2017

Ferrai C.*, Torlai Triglia E.*, Risner-Janiczek J.R., Rito T., Rackham O.J.L., de Santiago I., Kukalev A., Nicodemi M., Akalin A., Li M., Ungless M.A. & Pombo A. RNA polymerase II primes Polycomb-repressed developmental genes throughout terminal neuronal differentiationMolecular Systems Biology. 13: 946  (2017-10)
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Cover art

Noguchi S., Arakawa T., Fukuda S., Furuno M., Hasegawa A., Hori F., Ishikawa-Kato S., Kaida K., et al. FANTOM5 CAGE profiles of human and mouse samples. Scientific Data. 4:170112. (2017-08-29)

Beagrie R.A. & Pombo A. Cell cycle: continuous chromatin changes.  Nature 547, 61–67 (06 July 2017) doi:10.1038/547034a

Kar G., Kim J.K., Kolodziejczyk A.A., Natarajan K.N., Torlai Triglia E., Mifsud B., Elderkin S., Marioni J.C., Pombo A. & Teichmann S.A. Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.  Nature Communications. 8: 36  (2017-06-26)

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 T.L.; Eggen B.J.L.; Boddeke E.W.G.M.; Kaminska B.; Beule D.; Pombo A.; Kettenmann H.; Wolf S.A. Maternal immune activation results in complex microglial transcriptome signature in the adult offspring that is reversed by minocycline treatmentTranslational Psychiatry. 7:e1120.

Caglio G.; Torlai Triglia E.; Pombo A. Keep Them Close: PRC2 Poises Enhancer-Promoter Interactions at Anterior Neuronal GenesCell Stem Cell. 20:573-5 (2017-05-04) 

June 2017 Volume 24 No 6_NSMB cover

Barbieri M.*; Xie S.Q.*; Torlai Triglia E.; Chiariello A.M.; Bianco S.; de Santiago I.; Branco M.R.; Rueda D.; Nicodemi M.§; Pombo A.§ Active and poised promoter states drive folding of the extended HoxB locus in mouse embryonic stem cells.   Nature Structural & Molecular Biology 24, 515–524 (2017) doi:10.1038/nsmb.3402  Cover art 

 


Beagrie R.A.*; Scialdone A.*; Schueler M.; Kraemer D.C.A.#; Chotalia M.#; Xie S.Q.; Barbieri M.; de Santiago I.; Lavitas L.M.; Branco M.R.; Fraser J.; Dostie J.; Game L.; Dillon N.; Edwards P.A.W.; Nicodemi M.§; Pombo A.§ Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543(7646): 519-524 (23 March 2017) doi:10.1038/nature21411

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Torlai Triglia E.; Rito T.; Pombo A. A Finer Print Than TADs: PRC1-Mediated Domains Molecular Cell. 65:374-5 (2 February 2017)

2016

Beagrie R.A.; Pombo A. Examining topological domain influence on enhancer function.
Developmental Cell. 39:523-4

Franke M.; Ibrahim D.M.; Andrey G.; Schwarzer W.; Heinrich V.; Schoepflin R.; Kraft K.; Kempfer R.; Jerkovic I.; Chan W.L.; 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. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature. 538(7624):265-269. doi: 10.1038/nature19800.

Beagrie R.A.; Pombo A. Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription.
Bioessays. 38(9):881-93

 Le H.Q.; Ghatak S.; Yeung C.C.; Tellkamp F.; Guenschmann C.; Dieterich C.; Yeroslaviz A.; Habermann B.; Pombo A.; Niessen C.M.; Wickstroem S.A. Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.
Nature Cell Biology. 18 (8): 864-75 (Epub 2016 Jul 11)

2015

Fraser J.*; Ferrai C.*; Chiariello A.M.*; Schueler M.*; Rito T.*; Laudanno G.; Barbieri M.; Moore B.L.; Kraemer D.C.A.; Aitken S.; Xie S.Q.; Morris K.J.; Itoh M.; Kawaji H.; Jaeger I.; Hayashizaki Y.; Carninci P.; Forrest A.R.R.; Semple C.A.§; Dostie J.§; Pombo A.§; Nicodemi M.§
Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
Molecular Systems Biology 11 (12): 852 (2015-12-23)

Dias J.D.; Rito T.; Torlai Triglia E.; Kukalev A.; Ferrai C.; Chotalia M.; Brookes E.; Kimura H.§; Pombo A.§
Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.
eLIFE 10.7554/eLife.11215 (2015-12)

Pombo A.; Dillon N.
Three-dimensional genome architecture: players and mechanisms
Nature Reviews Molecular Cell Biology : 16, 245-257 (2015-04)

Chiariello AM, Bianco S, Piccolo A, Annunziatella C, Barbieri M, Pombo A, Nicodemi M
Polymer models of the organization of chromosomes in the nucleus of cells. 
Modern Physics Letters B 29, 1530003. (2015-04-10)

Arner E.; Daub C.O.; Vitting-Seerup K.; Andersson R.; Lilje B.; Drablos F.; Lennartsson A.; Roennerblad M.; Hrydziuszko O.; Vitezic M.; Freeman T.C.; Alhendi A.; Arner P.; Axton R.; Baillie J.K.; Beckhouse A.; Bodega B.; Briggs J.; Brombacher F.; Davis M.; Detmar M.; Ehrlund A.; Endoh M.; Eslami A.; Fagiolini M.; Fairbairn L.; Faulkner G.J.; Ferrai C.; Fisher M.E.; Forrester L.; Goldowitz D.; Guler R.; Ha T.; Hara M.; Herlyn M.; Ikawa T.; Kai C.; Kawamoto H.; Khachigian L.; Klinken P.S.; Kojima S.; Koseki H.; Klein S.; Mejhert N.; Miyaguchi K.; Mizuno Y.; Morimoto M.; Morris K.J.; Mummery C.; Nakachi Y.; Ogishima S.; Okada-Hatakeyama M.; Okazaki Y.; Orlando V.; Ovchinnikov D.; Passier R.; Patrikakis M.; Pombo A.; Qin X.Y.; Roy S.; Sato H.; Savvi S.; Saxena A.; Schwegmann A.; Sugiyama D.; Swoboda R.; Tanaka H.; Tomoiu A.; Winteringham L.N.; Wolvetang E.; Yanagi-Mizuochi C.; Yoneda M.; Zabierowski S.; Zhang P.; Abugessaisa I.; Bertin N.; Diehl A.D.; 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 T.F.; Mungall C.J.; Murata M.; Nishiyori-Sueki H.; Sahin S.; Sato-Nagao S.; Severin J.; de Hoon M.J.; Kawai J.; Kasukawa T.; Lassmann T.; Suzuki H.; Kawaji H.; Summers K.M.; Wells C.; Hume D.A.; Forrest A.R.R.; Sandelin A.; Carninci P.; Hayashizaki Y.
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
Science 347 (6225): 1010-1014 (2015-02-27)

2014

Benitah S.A.; Bracken A.; Dou Y.; Huangfu D.; Ivanova N.; Koseki H.; Laurent L.; Lim D.A.; Meshorer E.; Pombo A.; Sander M.; Xu G.L.
Stem cell epigenetics: looking forward
Cell Stem Cell 14 (6): 706-709 (2014-06-05)

Nicodemi M.; Pombo A.
Models of chromosome structure
Current Opinion in Cell Biology 28: 90-95 (2014-06-01)

Pombo A.; Nicodemi M.
Physical mechanisms behind the large scale features of chromatin organization
Transcription 5: (2014-03-21)

Sabbattini P.; Sjoberg M.; Nikic S.; Frangini A.; Holmqvist P.H.; Kunowska N.; Carroll T.; Brookes E.; Arthur S.J.; Pombo A.; Dillon N.
A H3K9/S10 methyl-phospho switch modulates Polycomb and Pol II binding at repressed genes during differentiation
Molecular Biology of the Cell 25 (6): 904-915 (2014-03)

2013

Barbieri M.; Scialdone A.; Gamba A.; Pombo A.; Nicodemi M.
Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus
Soft Matter 9 (36): 8631-8635 (2013-09-28)

Barbieri M.; Fraser J.; Lavitas L.M.; Chotalia M.; Dostie J.; Pombo A.; Nicodemi M.
A polymer model explains the complexity of large-scale chromatin folding
Nucleus 4 (4): 267-273 (2013-06-19)

Barbieri M.; Scialdone A.; Piccolo A.; Chiariello A.M.; di Lanno C.; Prisco A.; Pombo A.; Nicodemi M.
Polymer models of chromatin organization
Frontiers in Genetics 4: 113 (2013-06)

Barbieri M.; Chotalia M.; Fraser J.; Lavitas L.M.; Dostie J.; Pombo A.; Nicodemi M.
A model of the large-scale organization of chromatin
Biochemical Society Transactions 41 (2): 508-512 (2013-04)

2012

Swingland J.T.; Durrenberger P.F.; Reynolds R.; Dexter D.T.; Pombo A.; Deprez M.; Roncaroli F.; Turkheimer F.E.
Mean expression of the X-chromosome is associated with neuronal density
Frontiers in Neuroscience 6: 161 (2012-11-12)

Barbieri M.; Chotalia M.; Fraser J.; Lavitas L.M.; Dostie J.; Pombo A.; Nicodemi M.
Complexity of chromatin folding is captured by the strings and binders switch model
Proceedings of the National Academy of Sciences of the United States of America 109 (40): 16173-16178 (2012-10-02)

Moeller A.; Xie S.Q.; Hosp F.; Lang B.; Phatnani H.P.; James S.; Ramirez F.; Collin G.B.; Naggert J.K.; Babu M.M.; Greenleaf A.L.; Selbach M.; Pombo A.
Proteomic analysis of mitotic RNA polymerase II reveals novel interactors and association with proteins dysfunctional in disease
Molecular & Cellular Proteomics 11 (6): M111.011767 (2012-06)

Brookes E.; Pombo A.
Code breaking: the RNAPII modification code in pluripotency
Cell Cycle 11 (7): 1267-1268 (2012-04-01)

Brookes E.; de Santiago I.; Hebenstreit D.; Morris K.J.; Carroll T.; Xie S.Q.; Stock J.K.; Heidemann M.; Eick D.; Nozaki N.; Kimura H.; Ragoussis J.; Teichmann S.A.; Pombo A.
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs
Cell Stem Cell 10 (2): 157-170 (2012-02-03)

2011

Pombo A.; Starr D.A.
Nuclear cell biology
Molecular Biology of the Cell 22 (6): 722 (2011-03-15)

Chotalia M.; Pombo A.
Polycomb targets seek closest neighbours
PLoS Genetics 7 (3): e1002031 (2011-03)

2010

Alder O.; Lavial F.; Helness A.; Brookes E.; Pinho S.; Chandrashekran A.; Arnaud P.; Pombo A.; O’Neill L.; Azuara V.
Ring1B and Suv39h1 delineate distinct chromatin states at bivalent genes during early mouse lineage commitment
Development 137 (15): 2483-2492 (2010-08-01)

Kanhere A.; Viiri K.; Araujo C.C.; Rasaiyaah J.; Bouwman R.D.; Whyte W.A.; Pereira C.F.; Brookes E.; Walker K.; Bell G.W.; Pombo A.; Fisher A.G.; Young R.A.; Jenner R.G.
Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2
Molecular Cell 38 (5): 675-688 (2010-06-11)

Ferrai C.; de Castro I.J.; Lavitas L.; Chotalia M.; Pombo A.
Gene positioning
Cold Spring Harbor Perspectives in Biology 2 (6): a000588 (2010-06)

Pombo A.; Gilbert D.M.
Nucleus and gene expression: the structure and function conundrum
Current Opinion in Cell Biology 22 (3): 269-270 (2010-06)

Landeira D.; Sauer S.; Poot R.; Dvorkina M.; Mazzarella L.; Jorgensen H.F.; Pereira C.F.; Leleu M.; Piccolo F.M.; Spivakov M.; Brookes E.; Pombo A.; Fisher C.; Skarnes W.C.; Snoek T.; Bezstarosti K.; Demmers J.; Klose R.J.; Casanova M.; Tavares L.; Brockdorff N.; Merkenschlager M.; Fisher A.G.
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
Nature Cell Biology 12 (6): 618-624 (2010-06)

Baddeley D.; Chagin V.O.; Schermelleh L.; Martin S.; Pombo A.; Carlton P.M.; Gahl A.; Domaing P.; Birk U.; Leonhardt H.; Cremers C.W.; Cardoso M.C.
Measurement of replication structures at the nanometer scale using super-resolution light microscopy
Nucleic Acids Research 38 (2): e8 (2010-03)

Ferrai C.; Xie S.Q.; Luraghi P.; Munari D.; Ramirez F.; Branco M.R.; Pombo A.; Crippa M.P.
Poised transcription factories prime silent uPA gene prior to activation
PLoS Biology 8 (1): e1000270 (2010-01)

Xie S.Q.; Lavitas L.M.; Pombo A.
CryoFISH: fluorescence in situ hybridization on ultrathin cryosections
Methods in Molecular Biology 659: 219-230 (2010)

Morris K.J.; Chotalia M.; Pombo A.
Nuclear architecture in stem cells
Advances in Experimental Medicine and Biology 695: 14-25 (2010)

2009

Hiragami-Hamada K.; Xie S.Q.; Saveliev A.; Uribe-Lewis S.; Pombo A.; Festenstein R.
The molecular basis for stability of heterochromatin-mediated silencing in mammals
Epigenetics & Chromatin 2 (1): 14 (2009-11-04)

Brookes E.; Pombo A.
Modifications of RNA polymerase II are pivotal in regulating gene expression states
EMBO Reports 10 (11): 1213-1219 (2009-11)

Ferrai C.; Pombo A.
3D chromatin regulation of Sonic hedgehog in the limb buds
Developmental Cell 16 (1): 9-11 (2009-01)

Maya-Mendoza A.; Tang C.W.; Pombo A.; Jackson D.A.
Mechanisms regulating S phase progression in mammalian cells
Frontiers in Bioscience 14: 4199-4213 (2009-01-01)

2008

Babu M.M.; Janga S.C.; de Santiago I.; Pombo A.
Eukaryotic gene regulation in three dimensions and its impact on genome evolution
Current Opinion in Genetics & Development 18 (6): 571-582 (2008-12)

Branco M.R.; Branco T.; Ramirez F.; Pombo A.
Changes in chromosome organization during PHA-activation of resting human lymphocytes measured by cryo-FISH
Chromosome Research 16 (3): 413-426 (2008-05-01)

Noordermeer D.; Branco M.R.; Splinter E.; Klous P.; van Ijcken W.; Swagemakers S.; Koutsourakis M.; van der Spek P.; Pombo A.; de Laat W.
Transcription and chromatin organization of a housekeeping gene cluster containing an integrated beta-globin locus control region
PLoS Genetics 4 (3): e1000016 (2008-03-07)

2007

Stock J.K.; Giadrossi S.; Casanova M.; Brookes E.; Vidal M.; Koseki H.; Brockdorff N.; Fisher A.G.; Pombo A.
Ring1-mediated ubiquitination of H2A restrains poised RNA polymerase II at bivalent genes in mouse ES cells
Nature Cell Biology 9 (12): 1428-1435 (2007-12)

Pombo A.; Branco M.R.
Functional organisation of the genome during interphase
Current Opinion in Genetics & Development 17 (5): 451-455 (2007-10)

Pombo A.
Advances in imaging the interphase nucleus using thin cryosections
Histochemistry and Cell Biology 128 (2): 97-104 (2007-08)

Piercy R.J.; Zhou H.; Feng L.; Pombo A.; Muntoni F.; Brown S.C.
Desmin immunolocalisation in autosomal dominant Emery-Dreifuss muscular dystrophy
Neuromuscular Disorders 17 (4): 297-305 (2007-04)

Branco M.R.; Pombo A.
Chromosome organization: new facts, new models
Trends in Cell Biology 17 (3): 127-34 (2007-03)

2006

Branco M.R.; Pombo A.
Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations
PLoS Biology 4 (5): e138 (2006-05)

Xie S.Q.; Martin S.; Guillot P.V.; Bentley D.L.; Pombo A.
Splicing speckles are not reservoirs of RNA polymerase II, but contain an inactive form, phosphorylated on serine2 residues of the C-terminal domain
Molecular Biology of the Cell 17 (4): 1723-1733 (2006-04)

Xie S.Q.; Pombo A.
Distribution of different phosphorylated forms of RNA polymerase II in relation to Cajal and PML bodies in human cells: an ultrastructural study
Histochemistry and Cell Biology 125 (1-2): 21-31 (2006-01)

Branco M.R.; Xie S.Q.; Martin S.; Pombo A.
Correlative microscopy using Tokuyasu cryosections: applications for immunogold labelling and in situ hybridisation
Cell Imaging (Methods Express Series) : 201-217 (2006)

2005

Chow C.M.; Georgiou A.; Szutorisz H.; Maia e Silva A.; Pombo A.; Barahona I.; Dargelos E.; Canzonetta C.; Dillon N.
Variant histone H3.3 marks promoters of transcriptionally active genes during mammalian cell division
EMBO Reports 6 (4): 354-360 (2005-04)

Guillot P.V.; Martin S.; Pombo A.
The organization of transcription in the nucleus of mammalian cells
Visions of the Cell Nucleus : 95-105 (2005)

Ribeiro A.C.; Maia e Silva A.; Santa-Marta M.; Pombo A.; Moniz-Pereira J.; Goncalves J.; Barahona I.
Functional analysis of Vif protein shows less restriction of human immunodeficiency virus type 2 by APOBEC3G
Journal of Virology 79 (2): 823-833 (2005-01)

2004

Martin S.; Failla A.V.; Spoeri U.; Cremer C.; Pombo A.
Measuring the size of biological nanostructures with spatially modulated illumination microscopy
Molecular Biology of the Cell 15 (5): 2449-2455 (2004-05)

Guillot P.V.; Xie S.Q.; Hollinshead M.; Pombo A.
Fixation-induced redistribution of hyperphosphorylated RNA polymerase II in the nucleus of human cells
Experimental Cell Research 295 (2): 460-468 (2004-05-01)

Kenny E.; Mason D.; Saoudi A.; Pombo A.; Ramirez F.
CD8 alpha is an activation marker for a subset of peripheral CD4 T cells
European Journal of Immunology 34 (5): 1262-1271 (2004-05)

2003

Boyd D.C.; Pombo A.; Murphy S.
Interaction of proteins with promoter elements of the human U2 snRNA genes in vivo
Gene 315 (1-2): 103-112 (2003-10-02)

Martin S.; Pombo A.
Transcription factories: quantitative studies of nanostructures in the mammalian nucleus
Chromosome Research 11 (5): 461-470 (2003-07-01)

O’Brien T.P.; Bult C.J.; Cremer C.; Grunze M.; Knowles B.B.; Langowski J.; McNally J.; Pederson T.; Politz J.C.; Pombo A.; Schmahl G.; Spatz J.P.; van Driel R.
Genome function and nuclear architecture: from gene expression to nanoscience
Genome Research 13 (6A): 1029-1041 (2003-06)

Politz J.; van Driel R.; Sauer M.; Pombo A.
From linear genome sequence to three-dimensional organization of the cell nucleus
Genome Biology 4 (3): 310 (2003-02-28)

Pombo A.
Cellular genomics: which genes are transcribed, when and where?
Trends in Biochemical Sciences 28 (1): 6-9 (2003-01)
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