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SUPPLEMENTARY DATA SUPPLEMENTARY FIGURES: Supplementary Figure S1: Correlations of the 2-week change in the breast cancer hypoxia metagene with the 2-week change in AvERG and TFF1/pS2 A. Two-week change in the breast cancer hypoxia metagene versus 2-week change in AvERG. B. Two-week change in the breast cancer hypoxia metagene versus 2-week change in TFF1/pS2. 1 SUPPLEMENTARY TABLES: Supplementary Table S1: Annotation of the proliferation metagene Gene Accession symbol Number Gene name apolipoprotein B mRNA editing enzyme, catalytic APOBEC3B NM_004900 polypeptide-like 3B asp (abnormal spindle) homolog, microcephaly associated ASPM NM_018136 (Drosophila) AURKB NM_004217 aurora kinase B BIRC5 NM_001012270 baculoviral IAP repeat-containing 5 BUB1 NM_004336 budding uninhibited by benzimidazoles 1 homolog (yeast) budding uninhibited by benzimidazoles 1 homolog beta BUB1B NM_001211 (yeast) C21orf45 NM_018944 chromosome 21 open reading frame 45 CCNA2 NM_001237 cyclin A2 CCNB1 NM_031966 cyclin B1 CCNB2 NM_004701 cyclin B2 CCNE2 NM_057749 cyclin E2 CDC2 NM_001170407 cyclin-dependent kinase 1 CDC23 NM_004661 cell division cycle 23, yeast, homolog CDC7 NM_001134419 cell division cycle 7 homolog (S. cerevisiae) CDCA3 NM_031299 cell division cycle associated 3 CDCA8 NM_018101 cell division cycle associated 8 CDKN3 NM_001130851 cyclin-dependent kinase inhibitor 3 CENPA NM_001042426 centromere protein A CENPF NM_016343 centromere protein F, 350/400kDa (mitosin) CEP55 NM_001127182 centrosomal protein 55kDa CKAP2 NM_001098525 cytoskeleton associated protein 2 CKS2 NM_001827 CDC28 protein kinase regulatory subunit 2 CLCC1 NM_001048210 chloride channel CLIC-like 1 COP9 constitutive photomorphogenic homolog subunit 6 COPS6 NM_006833 (Arabidopsis) CSE1L NM_001316 CSE1 chromosome segregation 1-like (yeast) CTPS NM_001905 CTP synthase DDX39 NM_005804 DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 DLG7 NM_014750 discs, large (Drosophila) homolog-associated protein 5 DNAJC9 NM_015190 DnaJ (Hsp40) homolog, subfamily C, member 9 DONSON NM_017613 downstream neighbor of SON DTL NM_016448 denticleless homolog (Drosophila) ECT2 NM_018098 epithelial cell transforming sequence 2 oncogene elongation of very long chain fatty acids (FEN1/Elo2, ELOVL1 NM_022821 SUR4/Elo3, yeast)-like 1 ENOSF1 NM_001126123 enolase superfamily member 1 2 EZH2 NM_004456 enhancer of zeste homolog 2 (Drosophila) FBXO5 NM_001142522 F-box protein 5 FEN1 NM_004111 flap structure-specific endonuclease 1 FOXM1 NM_021953 forkhead box M1 gamma-glutamyl hydrolase (conjugase, GGH NM_003878 folylpolygammaglutamyl hydrolase) GMNN NM_015895 geminin, DNA replication inhibitor HMGB2 NM_001130688 high-mobility group box 2 HMGB3 NM_005342 high-mobility group box 3 HMMR NM_001142556 hyaluronan-mediated motility receptor (RHAMM) HSPA14 NM_016299 heat shock 70kDa protein 14 KIAA0101 NM_001029989 KIAA0101 KIF11 NM_004523 kinesin family member 11 KIF14 NM_014875 kinesin family member 14 KIF23 NM_004856 kinesin family member 23 KIF2C NM_006845 kinesin family member 2C KIF4A NM_012310 kinesin family member 4A KNTC1 NM_014708 kinetochore associated 1 MAD2L1 NM_002358 MAD2 mitotic arrest deficient-like 1 (yeast) MCM2 NM_004526 minichromosome maintenance complex component 2 MCM6 NM_005915 minichromosome maintenance complex component 6 MCM7 NM_005916 minichromosome maintenance complex component 7 MELK NM_014791 maternal embryonic leucine zipper kinase MKI67 NM_001145966 antigen identified by monoclonal antibody Ki-67 MPP1 NM_001166460 membrane protein, palmitoylated 1, 55kDa MRPL47 NM_020409 mitochondrial ribosomal protein L47 MRS2L NM_020662 MRS2 magnesium homeostasis factor homolog-like MSH2 NM_000251 mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli) MYBL2 NM_002466 v-myb myeloblastosis viral oncogene homolog (avian)-like 2 NEK2 NM_002497 NIMA (never in mitosis gene a)-related kinase 2 NUP155 NM_004298 nucleoporin 155kDa NUSAP1 NM_001129897 nucleolar and spindle associated protein 1 OIP5 NM_007280 Opa interacting protein 5 ORC6L NM_014321 origin recognition complex, subunit 6 PBK NM_018492 PDZ binding kinase POLE2 NM_001197330 polymerase (DNA directed), epsilon 2 (p59 subunit) PRC1 NM_003981 protein regulator of cytokinesis 1 PSME4 NM_014614 proteasome (prosome, macropain) activator subunit 4 RACGAP1 NM_001126103 Rac GTPase activating protein 1 RAD51AP1 NM_001130862 RAD51 associated protein 1 RFC3 NM_002915 replication factor C (activator 1) 3, 38kDa RFC4 NM_002916 replication factor C (activator 1) 4, 37kDa RPL39L NM_052969 ribosomal protein L39-like RPP40 NM_006638 ribonuclease P/MRP 40kDa subunit RRM2 NM_001034 ribonucleotide reductase M2 3 SEPHS1 NM_001195602 selenophosphate synthetase 1 solute carrier family 4, sodium bicarbonate cotransporter, SLC4A5 NM_021196 member 5 SRPK1 NM_003137 SRSF protein kinase 1 STIL NM_001048166 SCL/TAL1 interrupting locus STMN1 NM_001145454 stathmin 1 TACC3 NM_006342 transforming, acidic coiled-coil containing protein 3 TFRC NM_001128148 transferrin receptor (p90, CD71) TOP2A NM_001067 topoisomerase (DNA) II alpha 170kDa TPX2 NM_012112 TPX2, microtubule-associated, homolog (Xenopus laevis) TRIP13 NM_001166260 thyroid hormone receptor interactor 13 TTK NM_001166691 TTK protein kinase UBE2C NM_007019 ubiquitin-conjugating enzyme E2C UNG NM_003362 uracil-DNA glycosylase VRK1 NM_003384 vaccinia related kinase 1 WDR12 NM_018256 WD repeat domain 12 ZWINT NM_001005413 ZW10 interactor Supplementary Table S2: Proliferation-associated genes in the original breast cancer metagene Gene Accession Gene name symbol number ADM NM_001124 Adrenomedullin BTG3 NM_006806 BTG family, member 3 BUB1 NM_004336 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) CCNB1 NM_031966 Cyclin B1 CCNB2 NM_004701 Cyclin B2 CDC2 NM_033379 Cell division cycle 2, G1 to S and G2 to M CDC20 NM_001255 Cell division cycle 20 homolog (S. cerevisiae) CDKN3 NM_005192 Cyclin-dependent kinase inhibitor 3 (CDK2-associated dual specificity phosphatase) CEP55 NM_018131 Centrosomal protein 55kDa DLG7 NM_014750 Disc large (Drosophila) homolog-associated protein 5 GGH NM_003878 Gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase) HMGB3 NM_005342 High-mobility group box 3 KIF4A NM_012310 Kinesin family member 4A MAD2L1 NM_002358 MAD2 mitotic arrest deficient-like 1 (yeast) MCTS1 NM_014060 Malignant T cell amplified sequence 1 MELK NM_014791 Maternal embryonic leucine zipper kinase MIF NM_002415 Macrophage migration inhibitory factor (glycosylation- inhibiting factor) NUP155 NM_004298 Nucleoporin 155kDa 4 PTTG1 NM_004219 Pituitary tumor-transforming 1 RACGAP1 NM_013277 Rac GTPase activating protein 1 RRM2 NM_001034 Ribonucleotide reductase M2 polypeptide STK6 NM_198434 Aurora kinase A TFRC NM_003234 Transferrin receptor (p90, CD71) TPX2 NM_012112 TPX2, microtubule-associated, homolog (Xenopus laevis) Supplementary Table S3: Annotation of the breast cancer hypoxia metagene excluding proliferation-associated genes Gene symbol Accession Gene name Meta- number connectivity score PGAM1 NM_002629 Phosphoglycerate mutase 1 (brain) 1.00 GARS NM_002047 Glycyl-tRNA synthetase 1.00 BNIP3 NM_004052 BCL2/adenovirus E1B 19kDa interacting 1.00 protein 3 LDHA NM_005566 Lactate dehydrogenase A 1.00 P4HA1 NM_000917 Procollagen-proline, 2-oxoglutarate 4- 1.00 dioxygenase (proline 4-hydroxylase), alpha polypeptide I GPI NM_000175 Glucose phosphate isomerase 0.99 NDRG1 NM_006096 N-myc downstream regulated 1 0.99 GAPDH NM_002046 glyceraldehyde-3-phosphate 0.99 dehydrogenase DDIT4 NM_019058 DNA-damage-inducible transcript 4 0.99 VEGF NM_001025366 vascular endothelial growth factor A 0.99 PFKP NM_002627 Phosphofructokinase, platelet 0.99 LOC388642 XM_934933 TPI1 pseudogene 0.99 PGK1 NM_000291 Phosphoglycerate kinase 1 0.99 ENO1 NM_001428 Enolase 1, (alpha) 0.98 DSCR2 NM_203433 proteosome assembly chaperone 1 0.98 SLC16A3 NM_004207 Solute carrier family 16, member 3 0.98 (monocarboxylic acid transporter 4) PRDX4 NM_006406 Peroxiredoxin 4 0.98 SLC2A1 NM_006516 Solute carrier family 2 (facilitated glucose 0.98 transporter), member 1 AK3L1 NM_016282 Adenylate kinase 3 like 1 0.97 GOLT1B NM_016072 Golgi transport 1 homolog B (S. 0.97 cerevisiae) RANBP1 NM_002882 RAN binding protein 1 0.97 RALA NM_005402 V-ral simian leukemia viral oncogene 0.97 homolog A (ras related) RIS1 NM_015444 transmembrane protein 158 0.97 SEC61G NM_001012456 Sec61 gamma subunit 0.97 ENY2 NM_020189 Enhancer of yellow 2 homolog 0.97 5 (Drosophila) MRPS17 NM_015969 Mitochondrial ribosomal protein S17 0.97 MTFR1 NM_014637 Mitochondrial fission regulator 1 0.97 MRPL15 NM_014175 Mitochondrial ribosomal protein L15 0.97 ANKRD37 NM_181726 Ankyrin repeat domain 37 0.97 CTSL2 NM_001333 Cathepsin L2 0.97 SLC7A5 NM_003486 Solute carrier family 7 (cationic amino 0.97 acid transporter, y+ system), member 5 MMP1 NM_002421 Matrix metallopeptidase 1 (interstitial 0.96 collagenase) PSMB5 NM_002797 Proteasome (prosome, macropain) 0.96 subunit, beta type, 5 TMEM70 NM_017866 Transmembrane protein 70 0.96 IMPAD1 NM_017813 Inositol monophosphatase domain 0.96 containing 1 PDIA6 NM_005742 Protein disulfide isomerase family A, 0.96 member 6 MRPL13 NM_014078 Mitochondrial ribosomal protein L13 0.96 IL8 NM_000584 interleukin 8 0.96 MTCH2 NM_014342 Mitochondrial carrier homolog 2 (C. 0.96 elegans) PSMA5 NM_002790 Proteasome (prosome, macropain) 0.95 subunit, alpha type, 5 KIF20A NM_005733 Kinesin family member 20A 0.95 ATP1B3 NM_001679 ATPase, Na+/K+ transporting, beta 3 0.95 polypeptide ATP5G3 NM_001002256 ATP synthase, H+ transporting, 0.95 mitochondrial F0 complex, subunit
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    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
  • Trypanosoma Brucei Ribonuclease H2A Is an Essential Enzyme That Resolves R-Loops Associated with Transcription Initiation and Antigenic Variation

    Trypanosoma Brucei Ribonuclease H2A Is an Essential Enzyme That Resolves R-Loops Associated with Transcription Initiation and Antigenic Variation

    bioRxiv preprint doi: https://doi.org/10.1101/541300; this version posted February 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Trypanosoma brucei ribonuclease H2A is an essential enzyme that resolves R-loops associated with transcription initiation and antigenic variation Emma Briggs1, Kathryn Crouch1, Leandro Lemgruber1, Graham Hamilton2, Craig Lapsley1 and Richard McCulloch1 1. The Wellcome Centre for Molecular Parasitology, University of Glasgow, College of Medical, Veterinary and Life Sciences, Institute of Infection, Immunity and Inflammation, Sir Graeme Davies Building, 120 University Place, Glasgow, G12 8TA, U.K. 2. Glasgow Polyomics, University of Glasgow, Wolfson Wohl Cancer Res Centre, Garscube Estate, Switchback Rd, Bearsden, G61 1QH, U.K. *Correspondence: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/541300; this version posted February 5, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. In every cell ribonucleotides represent a threat to the stability and transmission of the DNA genome. Two types of Ribonuclease H (RNase H) tackle such ribonucleotides, either by excision when they form part of the DNA strand, or by hydrolysing RNA when it base-pairs with DNA, in structures termed R-loops. Loss of either RNase H is lethal in mammals, whereas yeast can prosper in the absence of both enzymes.