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Electronic Supplementary Material (ESI) for Food & Function. This journal is © The Royal Society of Chemistry 2018 Supplemental Data Supplemental Table S1. LPL induced differential expression listed by fold change. Representative Fold Gene Title Gene Symbol Public ID Change C1q and tumor necrosis factor related protein 3 C1QTNF3 NM_030945 5.2 phosphoglycerate kinase 2 PGK2 AL121974 3.2 BCL2-related protein A1 BCL2A1 NM_004049 3.1 heterogeneous nuclear ribonucleoprotein A1 HNRPA1 AL022097 3.0 caspase 10, apoptosis-related cysteine peptidase CASP10 NM_001230 2.8 excision repair cross-complementing rodent repair deficiency, complementation group 6 ERCC6 NM_000124 2.5 calmodulin 1 (phosphorylase kinase, delta) CALM1 N25325 2.5 oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 AF035776 2.5 ribosomal protein S3A RPS3A AL356115 2.4 Rho GTPase activating protein 24 ARHGAP24 NM_031305 2.4 histamine N-methyltransferase HNMT N40285 2.3 kelch-like 24 (Drosophila) KLHL24 AW006750 2.3 transforming growth factor, beta 2 TGFB2 NM_003238 2.3 zinc finger protein, X-linked ZFX NM_003410 2.2 fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) FSCN1 BC004908 2.2 olfactory receptor, family 2, subfamily A, member 20 pseudogene OR2A20P AA731709 2.2 collagen, type VII, alpha 1 COL7A1 NM_000094 2.2 Hydroxysteroid dehydrogenase like 2 HSDL2 AK023959 2.2 SH2 domain containing 3A SH2D3A N71739 2.2 CDNA: FLJ23194 fis, clone REC00490 --- AK026847 2.2 FAST kinase domains 2 FASTKD2 NM_014929 2.2 IQ motif containing C IQCC NM_018134 2.1 transient receptor potential cation channel, subfamily C, member 1 TRPC1 NM_003304 2.1 SH3 domain binding glutamic acid-rich protein SH3BGR NM_007341 2.1 serine/threonine kinase 3 (STE20 homolog, yeast) STK3 Z25422 2.1 thrombospondin, type I, domain containing 1 THSD1 NM_018676 2.1 nuclear receptor subfamily 2, group F, member 2 NR2F2 AL037401 2.1 chromosome 18 open reading frame 25 C18orf25 W28849 2.1 methionyl-tRNA synthetase MARS AA621558 2.1 furin FURIN NM_002569 2.1 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa NDUFB8 AA723057 2.1 serine/threonine kinase 4 STK4 NM_006282 2.0 oxysterol binding protein-like 10 OSBPL10 NM_017784 2.0 phospholipase A2, group VII PLA2G7 NM_005084 2.0 nuclear factor I/X (CCAAT-binding transcription factor) NFIX U18759 2.0 HLA-B associated transcript 1 BAT1 AL525504 2.0 SNW domain containing 1 SNW1 AL390153 2.0 OTU domain containing 4 OTUD4 NM_014928 2.0 chromosome 21 open reading frame 55 C21orf55 NM_017833 2.0 phosphatidylinositol 4-kinase type II PI4KII H84390 2.0 Supplemental Table S1. LPL induced differential expression listed by fold change. (continued) Representative Fold Gene Title Gene Symbol Public ID Change loss of heterozygosity, 11, chromosomal region 2, gene A LOH11CR2A BC001234 2.0 complement component 3a receptor 1 C3AR1 U62027 2.0 metastasis suppressor 1 MTSS1 NM_014751 2.0 coatomer protein complex, subunit alpha COPA AI621079 -2.0 3'UTR of hypothetical protein (ORF1) --- AL523076 -2.0 vacuolar protein sorting 13 homolog D (S. cerevisiae) VPS13D NM_018156 -2.0 egl nine homolog 3 (C. elegans) EGLN3 NM_022073 -2.0 olfactory receptor, family 1, subfamily D, member 2 OR1D2 NM_002548 -2.0 paxillin PXN NM_002859 -2.0 low density lipoprotein receptor-related protein 3 LRP3 NM_002333 -2.0 guanine nucleotide binding protein (G protein), gamma 11 GNG11 NM_004126 -2.0 thrombospondin 1 THBS1 NM_003246 -2.0 similar to cell recognition molecule CASPR3 RP11-138L21.1 NM_024879 -2.1 tubulin, alpha 3c TUBA3C L11645 -2.1 differentially expressed in FDCP 6 homolog (mouse) DEF6 NM_022047 -2.1 Clone 23605 mRNA sequence --- AF007136 -2.1 solute carrier family 35, member C2 SLC35C2 NM_015945 -2.1 L-2-hydroxyglutarate dehydrogenase L2HGDH NM_024884 -2.2 GREB1 protein GREB1 NM_014668 -2.2 RUN and FYVE domain containing 2 RUFY2 NM_017987 -2.2 BTB and CNC homology 1, basic leucine zipper transcription factor 2 BACH2 NM_021813 -2.2 heparan sulfate proteoglycan 2 HSPG2 AI991033 -2.2 interleukin 1 receptor accessory protein IL1RAP AF167343 -2.3 mucin 1, cell surface associated MUC1 NM_002456 -2.3 Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1 GNB2L1 AA443762 -2.3 zinc finger, FYVE domain containing 9 ZFYVE9 NM_004799 -2.3 nucleoporin 205kDa NUP205 AW206115 -2.4 SP110 nuclear body protein SP110 NM_004510 -2.4 steroid-5-alpha-reductase, alpha polypeptide 1 (3- oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1) SRD5A1 NM_001047 -2.4 Ribosomal protein S11 RPS11 BF680255 -2.6 MON2 homolog (S. cerevisiae) MON2 BG548738 -2.7 zinc finger protein 324B ZNF324B AI744673 -2.7 leucine rich repeat containing 40 LRRC40 AL390149 -4.4 catenin, beta interacting protein 1 CTNNBIP1 NM_020248 -5.0 Supplemental Table S2. TGRL induced differential expression listed by fold change. Representative Fold Gene Title Gene Symbol Public ID Change C1q and tumor necrosis factor related protein 3 C1QTNF3 NM_030945 4.4 melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor) MC1R BG034972 2.8 syntrophin, alpha 1 (dystrophin-associated protein A1, 59kDa, acidic component) SNTA1 NM_003098 2.7 oxidized low density lipoprotein (lectin-like) receptor 1 OLR1 AF035776 2.7 SH3 domain binding glutamic acid-rich protein SH3BGR NM_007341 2.6 HLA-B associated transcript 1 BAT1 AL525504 2.6 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa NDUFB8 AA723057 2.6 methionyl-tRNA synthetase MARS AA621558 2.6 calcium/calmodulin-dependent protein kinase kinase 2, beta CAMKK2 AK024748 2.6 required for meiotic nuclear division 5 homolog B (S. cerevisiae) RMND5B AW131783 2.6 stimulated by retinoic acid gene 6 homolog (mouse) STRA6 AF352728 2.4 F11 receptor F11R AF154005 2.4 tripartite motif-containing 66 TRIM66 AW271713 2.4 heterogeneous nuclear ribonucleoprotein A1 HNRPA1 AL022097 2.3 ras homolog gene family, member T2 RHOT2 BC004327 2.3 receptor (G protein-coupled) activity modifying protein 1 RAMP1 NM_005855 2.3 B-cell CLL/lymphoma 6 (zinc finger protein 51) BCL6 NM_001706 2.3 BCL2-antagonist of cell death BAD U66879 2.3 chromosome 8 open reading frame 60 C8orf60 NM_024984 2.3 solute carrier family 7 (cationic amino acid transporter, y+ system), member 8 SLC7A8 AL365347 2.3 RAB11B, member RAS oncogene family RAB11B X79780 2.3 BCL2-like 11 (apoptosis facilitator) BCL2L11 AA629050 2.3 pyrin and HIN domain family, member 1 PYHIN1 AK024890 2.3 DBF4 homolog B (S. cerevisiae) DBF4B NM_025104 2.3 kelch-like 24 (Drosophila) KLHL24 AW006750 2.3 zinc finger protein 143 ZNF143 AW162015 2.3 U-box domain containing 5 UBOX5 NM_014948 2.2 hypothetical protein LOC286434 LOC286434 AW452796 2.2 blocked early in transport 1 homolog (S. cerevisiae)- like BET1L NM_016526 2.2 ribosomal protein S3A RPS3A AL356115 2.2 TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated factor, 31kDa TAF9B AF077053 2.2 protein kinase, cAMP-dependent, catalytic, alpha PRKACA NM_002730 2.2 sulfotransferase family, cytosolic, 1B, member 1 SULT1B1 NM_014465 2.2 ribosomal protein S6 kinase, 90kDa, polypeptide 5 RPS6KA5 NM_004755 2.2 mitogen-activated protein kinase kinase 6 MAP2K6 U39657 2.2 epsin 2 EPN2 NM_014964 2.2 major histocompatibility complex, class II, DR beta 1 HLA-DRB1 U66825 2.2 Supplemental Table S2. TGRL induced differential expression listed by fold change. (continued) Representative Fold Gene Title Gene Symbol Public ID Change TRK-fused gene TFG BF057492 2.1 MAP7 domain containing 3 MAP7D3 NM_024765 2.1 fatty acid binding protein 4, adipocyte FABP4 NM_001442 2.1 caspase 10, apoptosis-related cysteine peptidase CASP10 NM_001230 2.1 nuclear receptor co-repressor 1 NCOR1 AW771910 2.1 START domain containing 5 STARD5 T54159 2.1 tRNA aspartic acid methyltransferase 1 TRDMT1 AJ223333 2.1 SH2 domain containing 3A SH2D3A N71739 2.1 protein kinase, AMP-activated, beta 2 non-catalytic subunit PRKAB2 NM_005399 2.1 PTPRF interacting protein, binding protein 1 (liprin beta 1) PPFIBP1 NM_003622 2.1 rhomboid 5 homolog 2 (Drosophila) RHBDF2 NM_024599 2.1 protein phosphatase 2A activator, regulatory subunit 4 PPP2R4 X86428 2.1 melanophilin MLPH NM_024101 2.0 olfactory receptor, family 7, subfamily E, member 47 pseudogene OR7E47P AF065854 2.0 ribonuclease L (2',5'-oligoisoadenylate synthetase- dependent) RNASEL NM_021133 2.0 collagen, type XXI, alpha 1 COL21A1 NM_030820 2.0 ectodermal-neural cortex (with BTB-like domain) ENC1 AF010314 2.0 protein tyrosine phosphatase type IVA, member 1 PTP4A1 BF576710 -2.0 La ribonucleoprotein domain family, member 4 LARP4 AI743740 -2.0 ribosomal protein S6 kinase, 70kDa, polypeptide 1 RPS6KB1 NM_003161 -2.0 phosphatidic acid phosphatase type 2A PPAP2A AF014403 -2.0 basic leucine zipper nuclear factor 1 (JEM-1) BLZF1 NM_003666 -2.0 proliferation-associated 2G4, 38kDa PA2G4 AL136460 -2.0 Bardet-Biedl syndrome 10 BBS10 NM_024685 -2.0 chromosome 10 open reading frame 97 C10orf97 NM_024948 -2.0 huntingtin (Huntington disease) HD NM_002111 -2.0 zinc finger, DHHC-type containing 3 ZDHHC3 NM_016598 -2.0 AT hook, DNA binding motif, containing 1 AHDC1 NM_015699 -2.0 B-cell CLL/lymphoma 3 BCL3 NM_005178 -2.1 KIAA1641 KIAA1641 AB046861 -2.1 similar to Putative S100 calcium-binding protein A11 pseudogene LOC729659 NM_021039 -2.1 Centrosomal protein 152kDa CEP152 AK025247 -2.1 zinc finger protein 257 ZNF257 AF070651 -2.1 KIAA1009 KIAA1009 AK023613 -2.1 tumor necrosis factor, alpha-induced protein 6 TNFAIP6 NM_007115 -2.1 MRNA; cDNA DKFZp564F133 (from clone DKFZp564F133) --- AL049263 -2.1 alpha 1,4-galactosyltransferase (globotriaosylceramide synthase) A4GALT NM_017436 -2.1
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    Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.
  • Prediction of Meiosis-Essential Genes Based Upon the Dynamic Proteomes Responsive to Spermatogenesis

    Prediction of Meiosis-Essential Genes Based Upon the Dynamic Proteomes Responsive to Spermatogenesis

    bioRxiv preprint doi: https://doi.org/10.1101/2020.02.05.936435; this version posted February 6, 2020. 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-NC 4.0 International license. Prediction of meiosis-essential genes based upon the dynamic proteomes responsive to spermatogenesis Kailun Fang1,2,3,8, Qidan Li3,4,5,8, Yu Wei2,3,8, Jiaqi Shen6,8, Wenhui Guo3,4,5,7,8, Changyang Zhou2,3,8, Ruoxi Wu1, Wenqin Ying2, Lu Yu1,2, Jin Zi5, Yuxing Zhang3,4,5, Hui Yang2,3,9*, Siqi Liu3,4,5,9*, Charlie Degui Chen1,3,9* 1. State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China. 2. State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. 3. University of the Chinese Academy of Sciences, Beijing 100049, China. 4. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China. 5. BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China. 6. United World College Changshu China, Jiangsu 215500, China. 7. Malvern College Qingdao, Shandong, 266109, China 8.
  • Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer Stephen Shang1, Jiekun Yang1, Amir A

    Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer Stephen Shang1, Jiekun Yang1, Amir A

    Published OnlineFirst July 29, 2019; DOI: 10.1158/0008-5472.CAN-19-0215 Cancer Genome and Epigenome Research Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer Stephen Shang1, Jiekun Yang1, Amir A. Jazaeri2, Alexander James Duval1, Turan Tufan1, Natasha Lopes Fischer1, Mouadh Benamar1,3, Fadila Guessous3, Inyoung Lee1, Robert M. Campbell4, Philip J. Ebert4, Tarek Abbas1,3, Charles N. Landen5, Analisa Difeo6, Peter C. Scacheri6, and Mazhar Adli1 Abstract Chemoresistance is driven by unique regulatory net- tance, our findings identified SOX9 as a critical SE-regulated works in the genome that are distinct from those necessary transcription factor that plays a critical role in acquiring for cancer development. Here, we investigate the contri- and maintaining the chemoresistant state in ovarian cancer. bution of enhancer elements to cisplatin resistance in The approach and findings presented here suggest that ovarian cancers. Epigenome profiling of multiple cellular integrative analysis of epigenome and transcriptional pro- models of chemoresistance identified unique sets of distal grams could identify targetable key drivers of chemoresis- enhancers, super-enhancers (SE), and their gene targets tance in cancers. that coordinate and maintain the transcriptional program of the platinum-resistant state in ovarian cancer. Pharma- Significance: Integrative genome-wide epigenomic and cologic inhibition of distal enhancers through small- transcriptomic analyses of platinum-sensitive and -resistant molecule epigenetic inhibitors suppressed the expression ovarian lines identify key distal regulatory regions and of their target genes and restored cisplatin sensitivity in vitro associated master regulator transcription factors that can be and in vivo. In addition to known drivers of chemoresis- targeted by small-molecule epigenetic inhibitors.