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Items: 28

1.

The Polycomb-Dependent Epigenome Controls β Cell Dysfunction, Dedifferentiation, and Diabetes.

Lu TT, Heyne S, Dror E, Casas E, Leonhardt L, Boenke T, Yang CH, Sagar, Arrigoni L, Dalgaard K, Teperino R, Enders L, Selvaraj M, Ruf M, Raja SJ, Xie H, Boenisch U, Orkin SH, Lynn FC, Hoffman BG, Grün D, Vavouri T, Lempradl AM, Pospisilik JA.

Cell Metab. 2018 Jun 5;27(6):1294-1308.e7. doi: 10.1016/j.cmet.2018.04.013. Epub 2018 May 10.

2.

Double deficiency of Trex2 and DNase1L2 nucleases leads to accumulation of DNA in lingual cornifying keratinocytes without activating inflammatory responses.

Manils J, Fischer H, Climent J, Casas E, García-Martínez C, Bas J, Sukseree S, Vavouri T, Ciruela F, de Anta JM, Tschachler E, Eckhart L, Soler C.

Sci Rep. 2017 Sep 19;7(1):11902. doi: 10.1038/s41598-017-12308-4.

3.

Impaired DNA replication derepresses chromatin and generates a transgenerationally inherited epigenetic memory.

Klosin A, Reis K, Hidalgo-Carcedo C, Casas E, Vavouri T, Lehner B.

Sci Adv. 2017 Aug 16;3(8):e1701143. doi: 10.1126/sciadv.1701143. eCollection 2017 Aug.

4.

Transgenerational transmission of environmental information in C. elegans.

Klosin A, Casas E, Hidalgo-Carcedo C, Vavouri T, Lehner B.

Science. 2017 Apr 21;356(6335):320-323. doi: 10.1126/science.aah6412.

PMID:
28428426
5.

The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells.

Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA.

Genome Res. 2017 Jan;27(1):118-132. doi: 10.1101/gr.207522.116. Epub 2016 Dec 20.

6.

The Exonuclease Trex2 Shapes Psoriatic Phenotype.

Manils J, Casas E, Viña-Vilaseca A, López-Cano M, Díez-Villanueva A, Gómez D, Marruecos L, Ferran M, Benito C, Perrino FW, Vavouri T, de Anta JM, Ciruela F, Soler C.

J Invest Dermatol. 2016 Dec;136(12):2345-2355. doi: 10.1016/j.jid.2016.05.122. Epub 2016 Jun 27.

7.

Trim28 Haploinsufficiency Triggers Bi-stable Epigenetic Obesity.

Dalgaard K, Landgraf K, Heyne S, Lempradl A, Longinotto J, Gossens K, Ruf M, Orthofer M, Strogantsev R, Selvaraj M, Lu TT, Casas E, Teperino R, Surani MA, Zvetkova I, Rimmington D, Tung YC, Lam B, Larder R, Yeo GS, O'Rahilly S, Vavouri T, Whitelaw E, Penninger JM, Jenuwein T, Cheung CL, Ferguson-Smith AC, Coll AP, Körner A, Pospisilik JA.

Cell. 2016 Jan 28;164(3):353-64. doi: 10.1016/j.cell.2015.12.025.

8.

The small RNA content of human sperm reveals pseudogene-derived piRNAs complementary to protein-coding genes.

Pantano L, Jodar M, Bak M, Ballescà JL, Tommerup N, Oliva R, Vavouri T.

RNA. 2015 Jun;21(6):1085-95. doi: 10.1261/rna.046482.114. Epub 2015 Apr 22.

9.

Paternal diet defines offspring chromatin state and intergenerational obesity.

Öst A, Lempradl A, Casas E, Weigert M, Tiko T, Deniz M, Pantano L, Boenisch U, Itskov PM, Stoeckius M, Ruf M, Rajewsky N, Reuter G, Iovino N, Ribeiro C, Alenius M, Heyne S, Vavouri T, Pospisilik JA.

Cell. 2014 Dec 4;159(6):1352-64. doi: 10.1016/j.cell.2014.11.005.

10.

Sperm epigenomics: challenges and opportunities.

Casas E, Vavouri T.

Front Genet. 2014 Sep 18;5:330. doi: 10.3389/fgene.2014.00330. eCollection 2014. Review.

11.

Genomic and proteomic dissection and characterization of the human sperm chromatin.

Castillo J, Amaral A, Azpiazu R, Vavouri T, Estanyol JM, Ballescà JL, Oliva R.

Mol Hum Reprod. 2014 Nov;20(11):1041-53. doi: 10.1093/molehr/gau079. Epub 2014 Sep 5.

PMID:
25193639
12.

Parallel evolution of chordate cis-regulatory code for development.

Doglio L, Goode DK, Pelleri MC, Pauls S, Frabetti F, Shimeld SM, Vavouri T, Elgar G.

PLoS Genet. 2013 Nov;9(11):e1003904. doi: 10.1371/journal.pgen.1003904. Epub 2013 Nov 21. Erratum in: PLoS Genet. 2013 Nov;9(11). doi:10.1371/annotation/1fc82a4b-f9ea-461a-8987-1152078688e4.

13.

Human genes with CpG island promoters have a distinct transcription-associated chromatin organization.

Vavouri T, Lehner B.

Genome Biol. 2012 Nov 27;13(11):R110. doi: 10.1186/gb-2012-13-11-r110.

14.

Chromatin organization in sperm may be the major functional consequence of base composition variation in the human genome.

Vavouri T, Lehner B.

PLoS Genet. 2011 Apr;7(4):e1002036. doi: 10.1371/journal.pgen.1002036. Epub 2011 Apr 7.

15.

Predicting genetic modifier loci using functional gene networks.

Lee I, Lehner B, Vavouri T, Shin J, Fraser AG, Marcotte EM.

Genome Res. 2010 Aug;20(8):1143-53. doi: 10.1101/gr.102749.109. Epub 2010 Jun 9.

16.

Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity.

Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B.

Cell. 2009 Jul 10;138(1):198-208. doi: 10.1016/j.cell.2009.04.029.

17.

Conserved noncoding elements and the evolution of animal body plans.

Vavouri T, Lehner B.

Bioessays. 2009 Jul;31(7):727-35. doi: 10.1002/bies.200900014. Review.

PMID:
19492354
18.

Widespread conservation of genetic redundancy during a billion years of eukaryotic evolution.

Vavouri T, Semple JI, Lehner B.

Trends Genet. 2008 Oct;24(10):485-8. doi: 10.1016/j.tig.2008.08.005. Epub 2008 Sep 9.

PMID:
18786741
19.

Tuning in to the signals: noncoding sequence conservation in vertebrate genomes.

Elgar G, Vavouri T.

Trends Genet. 2008 Jul;24(7):344-52. doi: 10.1016/j.tig.2008.04.005. Epub 2008 May 29. Review.

PMID:
18514361
20.

A simple principle concerning the robustness of protein complex activity to changes in gene expression.

Semple JI, Vavouri T, Lehner B.

BMC Syst Biol. 2008 Jan 2;2:1. doi: 10.1186/1752-0509-2-1.

21.
22.

Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis.

McEwen GK, Woolfe A, Goode D, Vavouri T, Callaway H, Elgar G.

Genome Res. 2006 Apr;16(4):451-65. Epub 2006 Mar 13.

23.

Characterisation of conserved non-coding sequences in vertebrate genomes using bioinformatics, statistics and functional studies.

Edwards YJ, Walter K, McEwen G, Vavouri T, Kelly KA, Abnizova I, Woolfe A, Goode DK, Goodson M, North P, Snell P, Callaway H, Smith SF, Gilks WR, Cooke JE, Elgar G.

Comp Biochem Physiol Part D Genomics Proteomics. 2006 Mar;1(1):46-58. doi: 10.1016/j.cbd.2005.03.001. Epub 2005 Sep 15.

PMID:
20483234
24.

Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key.

Vavouri T, McEwen GK, Woolfe A, Gilks WR, Elgar G.

Trends Genet. 2006 Jan;22(1):5-10. Epub 2005 Nov 10.

PMID:
16290136
25.
26.

Molecular characterisation of the SAND protein family: a study based on comparative genomics, structural bioinformatics and phylogeny.

Cottage A, Mullan L, Portela MB, Hellen E, Carver T, Patel S, Vavouri T, Elgar G, Edwards YJ.

Cell Mol Biol Lett. 2004;9(4A):739-53.

27.

Highly conserved non-coding sequences are associated with vertebrate development.

Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, Vavouri T, Smith SF, North P, Callaway H, Kelly K, Walter K, Abnizova I, Gilks W, Edwards YJ, Cooke JE, Elgar G.

PLoS Biol. 2005 Jan;3(1):e7. Epub 2004 Nov 11.

28.

Theatre: A software tool for detailed comparative analysis and visualization of genomic sequence.

Edwards YJ, Carver TJ, Vavouri T, Frith M, Bishop MJ, Elgar G.

Nucleic Acids Res. 2003 Jul 1;31(13):3510-7.

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