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MiR-92a targets Gene Evidence category miRTarBase ID Gene Evidence category miRTarBase ID ITGA5 Strong MIRT003031 CAMKV Weak MIRT048955 ARID4B Strong MIRT004089 QTRT1 Weak MIRT048956 HIPK3 Strong MIRT004090 ASAH1 Weak MIRT048957 MYLIP Strong MIRT004091 SAP30BP Weak MIRT048958 TP63 Strong MIRT004281 RORA Weak MIRT048959 KAT2B Strong MIRT004331 ELAC2 Weak MIRT048960 ESR2 Strong MIRT004563 HNRNPLL Weak MIRT048961 TGFBR2 Strong MIRT004737 ETV6 Weak MIRT048962 BMPR2 Strong MIRT004932 PRRC2B Weak MIRT048963 CPEB2 Strong MIRT005590 LY6G5B Weak MIRT048964 CDH1 Strong MIRT006029 ALKBH4 Weak MIRT048965 BCL2L11 Strong MIRT006148 DAZAP1 Weak MIRT048966 KLF2 Strong MIRT006372 IPO7 Weak MIRT048967 OSBPL2 Strong MIRT049254 CTC1 Weak MIRT048968 MAPRE1 Strong MIRT049331 CHCHD10 Weak MIRT048969 STAT3 Strong MIRT049359 BSG Weak MIRT048970 HIPK1 Strong MIRT049450 RABGAP1 Weak MIRT048971 RFFL Strong MIRT049627 NMD3 Weak MIRT048972 OSBPL8 Strong MIRT049706 MRPL32 Weak MIRT048973 PCGF5 Strong MIRT049737 RPL11 Weak MIRT048974 PHLPP1 Strong MIRT052970 WEE1 Weak MIRT048975 NR1H4 Strong MIRT054133 BAK1 Weak MIRT048976 PTEN Strong MIRT054327 MYH2 Weak MIRT048977 SOCS5 Strong MIRT054643 INSIG1 Weak MIRT048978 RGS5 Strong MIRT437943 GARNL3 Weak MIRT048979 MAPK8 Strong MIRT437964 HMGCR Weak MIRT048980 MAP2K4 Strong MIRT437965 TUBB2B Weak MIRT048981 DUSP10 Strong MIRT438170 RPL24 Weak MIRT048982 CCL8 Strong MIRT438289 HELQ Weak MIRT048983 DNMT1 Strong MIRT438805 MAPK1IP1L Weak MIRT048984 UVRAG Weak MIRT001199 PLA2G4F Weak MIRT048985 THBS1 Weak MIRT005628 HERC1 Weak MIRT048986 SMAD4 Weak MIRT005632 RASAL2 Weak MIRT048987 TPD52L3 Weak MIRT048915 RAD23B Weak MIRT048988 TXLNA Weak MIRT048916 PSMD11 Weak MIRT048989 NDST1 Weak MIRT048917 TALDO1 Weak MIRT048990 EFNB1 Weak MIRT048918 CCDC6 Weak MIRT048991 RPL39 Weak MIRT048919 RNF128 Weak MIRT048992 TMF1 Weak MIRT048920 CLNS1A Weak MIRT048993 KCTD7 Weak MIRT048921 NUCB1 Weak MIRT048994 VBP1 Weak MIRT048922 POTEG Weak MIRT048995 TPT1 Weak MIRT048923 DCAF12 Weak MIRT048996 TRAPPC13 Weak MIRT048924 USP9X Weak MIRT048997 NEK2 Weak MIRT048925 BLMH Weak MIRT048998 CYP7A1 Weak MIRT048926 DCP2 Weak MIRT048999 SLC25A3 Weak MIRT048927 SEC14L1 Weak MIRT049000 UCHL1 Weak MIRT048928 EIF3I Weak MIRT049001 RPS24 Weak MIRT048929 NCL Weak MIRT049002 FAM83G Weak MIRT048930 MAP1B Weak MIRT049003 BCS1L Weak MIRT048931 GOLIM4 Weak MIRT049004 DTWD2 Weak MIRT048932 EEF2 Weak MIRT049005 SLC20A1 Weak MIRT048933 RASA1 Weak MIRT049006 C1orf174 Weak MIRT048934 PLEKHB1 Weak MIRT049007 CUX1 Weak MIRT048935 CCNI Weak MIRT049008 DDX23 Weak MIRT048936 RPS25 Weak MIRT049009 PON2 Weak MIRT048937 FYCO1 Weak MIRT049010 STK4 Weak MIRT048938 AHCYL2 Weak MIRT049011 CHST9 Weak MIRT048939 ABL2 Weak MIRT049012 SHISA5 Weak MIRT048940 GANAB Weak MIRT049013 CD3EAP Weak MIRT048941 CRBN Weak MIRT049014 GCHFR Weak MIRT048942 MKI67 Weak MIRT049015 DHX30 Weak MIRT048943 LPIN1 Weak MIRT049016 CEP97 Weak MIRT048944 KDM6B Weak MIRT049017 IPO4 Weak MIRT048945 GPR89A Weak MIRT049018 POLE Weak MIRT048946 CBX6 Weak MIRT049019 SETDB1 Weak MIRT048947 ANKLE2 Weak MIRT049020 GABPA Weak MIRT048948 SCD5 Weak MIRT049021 ATAD3A Weak MIRT048949 NUDCD3 Weak MIRT049022 HSD17B10 Weak MIRT048950 ago-01 Weak MIRT049023 TYMP Weak MIRT048951 PKM Weak MIRT049024 CIT Weak MIRT048952 NUP205 Weak MIRT049025 IK Weak MIRT048953 RASA3 Weak MIRT049026 TFPI Weak MIRT048954 EIF3C Weak MIRT049027 1 Gene Evidence category miRTarBase ID Gene Evidence category miRTarBase ID HADHA Weak MIRT049028 RPL3 Weak MIRT049123 GHITM Weak MIRT049029 CKB Weak MIRT049124 PLEKHH3 Weak MIRT049030 SSX2IP Weak MIRT049125 RCAN1 Weak MIRT049031 PDS5B Weak MIRT049126 UBE2H Weak MIRT049032 WIPF2 Weak MIRT049127 CCSAP Weak MIRT049033 CC2D2A Weak MIRT049128 DHTKD1 Weak MIRT049034 DHCR24 Weak MIRT049129 IER3IP1 Weak MIRT049035 POR Weak MIRT049130 SLAIN1 Weak MIRT049036 EEF1A1 Weak MIRT049131 NPLOC4 Weak MIRT049037 TANC2 Weak MIRT049132 DOT1L Weak MIRT049038 AURKB Weak MIRT049133 TPRN Weak MIRT049039 AIDA Weak MIRT049134 RPL27 Weak MIRT049040 DNAJA3 Weak MIRT049135 ELOVL6 Weak MIRT049041 PXN Weak MIRT049136 DHRS3 Weak MIRT049042 PARK7 Weak MIRT049137 FKBP1A Weak MIRT049043 HDGF Weak MIRT049138 HIST1H3D Weak MIRT049044 LIMD1 Weak MIRT049139 ZNF785 Weak MIRT049045 PTGFRN Weak MIRT049140 ACAT2 Weak MIRT049046 COX18 Weak MIRT049141 ADAMTS1 Weak MIRT049047 MYO19 Weak MIRT049142 SPEN Weak MIRT049048 ZNF276 Weak MIRT049143 TAOK2 Weak MIRT049049 AARS2 Weak MIRT049144 POLRMT Weak MIRT049050 ETFA Weak MIRT049145 EFNA5 Weak MIRT049051 SART3 Weak MIRT049146 SHC3 Weak MIRT049052 TEX10 Weak MIRT049147 POLI Weak MIRT049053 PFN1 Weak MIRT049148 CDK11A Weak MIRT049054 EPHA7 Weak MIRT049149 MAML1 Weak MIRT049055 WDR6 Weak MIRT049150 TUBB3 Weak MIRT049056 UBAP2L Weak MIRT049151 CDK1 Weak MIRT049057 TESK1 Weak MIRT049152 KPNA6 Weak MIRT049058 ZNF503 Weak MIRT049153 FAF1 Weak MIRT049059 DENND5A Weak MIRT049154 RPL7A Weak MIRT049060 PRR12 Weak MIRT049155 EIF2B2 Weak MIRT049061 BTAF1 Weak MIRT049156 DNM2 Weak MIRT049062 MYO5C Weak MIRT049157 ACADS Weak MIRT049063 MRPL3 Weak MIRT049158 EIF3B Weak MIRT049064 CDKN3 Weak MIRT049159 CPSF6 Weak MIRT049065 RBBP7 Weak MIRT049160 PSMB1 Weak MIRT049066 PHACTR4 Weak MIRT049161 PDE4DIP Weak MIRT049067 NPM1 Weak MIRT049162 BTRC Weak MIRT049068 KMT2D Weak MIRT049163 TRIP12 Weak MIRT049069 PKN1 Weak MIRT049164 TRAF4 Weak MIRT049070 MDN1 Weak MIRT049165 SLC25A38 Weak MIRT049071 RPL18A Weak MIRT049166 CEP85 Weak MIRT049072 ISM2 Weak MIRT049167 CD59 Weak MIRT049073 QSOX2 Weak MIRT049168 RPA2 Weak MIRT049074 SHMT2 Weak MIRT049169 B4GALT2 Weak MIRT049075 RIOK1 Weak MIRT049170 MLX Weak MIRT049076 ARID1A Weak MIRT049171 SELRC1 Weak MIRT049077 IGSF1 Weak MIRT049172 CXorf56 Weak MIRT049078 PPIB Weak MIRT049173 KDM3B Weak MIRT049079 PPP1CC Weak MIRT049174 USP10 Weak MIRT049080 CHCHD2 Weak MIRT049175 TRMT61A Weak MIRT049081 NFIB Weak MIRT049176 ENO1 Weak MIRT049082 STARD7 Weak MIRT049177 PPP1R3G Weak MIRT049083 DYNC1H1 Weak MIRT049178 SNF8 Weak MIRT049084 FNDC3B Weak MIRT049179 EBP Weak MIRT049085 SRSF5 Weak MIRT049180 NTPCR Weak MIRT049086 KIFC1 Weak MIRT049181 LRRC37A2 Weak MIRT049087 EARS2 Weak MIRT049182 TNRC18 Weak MIRT049088 MCM3 Weak MIRT049183 SRPRB Weak MIRT049089 TUSC2 Weak MIRT049184 RCC1 Weak MIRT049090 CLDND1 Weak MIRT049185 PFDN6 Weak MIRT049091 BRCC3 Weak MIRT049186 CMTM6 Weak MIRT049092 ACTR1A Weak MIRT049187 PBX2 Weak MIRT049093 DHX16 Weak MIRT049188 MRPL9 Weak MIRT049094 KIAA0100 Weak MIRT049189 KLHL15 Weak MIRT049095 DUSP11 Weak MIRT049190 RPS15 Weak MIRT049096 ARRB1 Weak MIRT049191 SPTLC1 Weak MIRT049097 ATP1A1 Weak MIRT049192 HDAC1 Weak MIRT049098 VARS Weak MIRT049193 MINK1 Weak MIRT049099 ITPR3 Weak MIRT049194 HSP90B1 Weak MIRT049100 AXIN1 Weak MIRT049195 SKI Weak MIRT049101 RPL13A Weak MIRT049196 NXN Weak MIRT049102 STX3 Weak MIRT049197 SACM1L Weak MIRT049103 GLOD4 Weak MIRT049198 TCOF1 Weak MIRT049104 U2AF2 Weak MIRT049199 NFKB1 Weak MIRT049105 KCTD5 Weak MIRT049200 DDX17 Weak MIRT049106 GSTP1 Weak MIRT049201 PSMC3 Weak MIRT049107 GOT2 Weak MIRT049202 HIP1R Weak MIRT049108 COL18A1 Weak MIRT049203 CCAR1 Weak MIRT049109 NOC2L Weak MIRT049204 TUBA1C Weak MIRT049110 USP31 Weak MIRT049205 SNX9 Weak MIRT049111 RBX1 Weak MIRT049206 KPNA2 Weak MIRT049112 SCML2 Weak MIRT049207 CSDE1 Weak MIRT049113 ARPP19 Weak MIRT049208 YBX3 Weak MIRT049114 CCDC86 Weak MIRT049209 CHAF1A Weak MIRT049115 P4HB Weak MIRT049210 APOLD1 Weak MIRT049116 LMBR1L Weak MIRT049211 PDIK1L Weak MIRT049117 CDK9 Weak MIRT049212 C9orf64 Weak MIRT049118 BCL9L Weak MIRT049213 RANBP2 Weak MIRT049119 TUFM Weak MIRT049214 CDC25A Weak MIRT049120 RPL15 Weak MIRT049215 NACC2 Weak MIRT049121 ALMS1 Weak MIRT049216 TRIM28 Weak MIRT049122 MLLT4 Weak MIRT049217 2 Gene Evidence category miRTarBase ID Gene Evidence category miRTarBase ID CUL5 Weak MIRT049218 SIN3A Weak MIRT049314 KPNB1 Weak MIRT049219 MDM2 Weak MIRT049315 MYO1C Weak MIRT049220 MAP4 Weak MIRT049316 TLR10 Weak MIRT049221 MAVS Weak MIRT049317 COX4I1 Weak MIRT049222 CBFB Weak MIRT049318 SF3B3 Weak MIRT049223 CTLA4 Weak MIRT049319 CTNNBL1 Weak MIRT049224 PCNXL4 Weak MIRT049320 YWHAQ Weak MIRT049225 SIN3B Weak MIRT049321 BRD2 Weak MIRT049226 NPC2 Weak MIRT049322 PFKM Weak MIRT049227 POLR2I Weak MIRT049323 PPP6C Weak MIRT049228 HIST1H2AM Weak MIRT049324 NFE2L1 Weak MIRT049229 RNF123 Weak MIRT049325 SHOC2 Weak MIRT049230 WDR18 Weak MIRT049326 KIAA1671 Weak MIRT049231 RPS28 Weak MIRT049327 HIST1H1E Weak MIRT049232 FAM129B Weak MIRT049328 R3HDM4 Weak MIRT049233 ZCCHC2 Weak MIRT049329 SURF4 Weak MIRT049234 EPB41L3 Weak MIRT049330 METTL16 Weak MIRT049235 NT5DC3 Weak MIRT049332 ZNF420 Weak MIRT049236 AHCYL1 Weak MIRT049333 ARPC2 Weak MIRT049237 KLC2 Weak MIRT049334 RRP9 Weak MIRT049238 ZBTB22 Weak MIRT049335 HEATR1 Weak MIRT049239 TSR1 Weak MIRT049336 HSPA1B Weak MIRT049240 NUP155 Weak MIRT049337 PTP4A2 Weak MIRT049241 HIST2H2AA3 Weak MIRT049338 MACF1 Weak MIRT049242 DDX39A Weak MIRT049339 HNRNPF Weak MIRT049243 CAMTA2 Weak MIRT049340 VCPIP1 Weak MIRT049244 RNF40 Weak MIRT049341 CORO7 Weak MIRT049245 NCAPH Weak MIRT049342 UNC13B Weak MIRT049246 MYO1D Weak MIRT049343 PSMD3 Weak MIRT049247 APOBEC3C Weak MIRT049344 DDAH1 Weak MIRT049248 GSK3B Weak MIRT049345 MKNK2 Weak MIRT049249 SARS2 Weak MIRT049346 HS3ST3A1 Weak MIRT049250 C17orf51 Weak MIRT049347 ALKBH5 Weak MIRT049251 RAB11A Weak MIRT049348 TKT Weak MIRT049252 EIF4B Weak MIRT049349 DLX6 Weak MIRT049253 OTUD6A Weak MIRT049350 CDC37 Weak MIRT049255 CERS1 Weak MIRT049351 CLTC Weak MIRT049256 ENOPH1 Weak MIRT049352 TUT1 Weak MIRT049257 CAD Weak MIRT049353 GLO1 Weak MIRT049258 KIAA1549 Weak MIRT049354 ZC3H18 Weak MIRT049259 CELSR1 Weak MIRT049355 HMGCS1
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  • Eef3 Promotes Late Stages of Trna Translocation on the Ribosome

    Eef3 Promotes Late Stages of Trna Translocation on the Ribosome

    bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182105; this version posted July 1, 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-ND 4.0 International license. eEF3 promotes late stages of tRNA translocation on the ribosome Namit Ranjan1,6,*, Agnieszka A. Pochopien2,3,6, Colin Chih-Chien Wu4,6, Bertrand Beckert3, Sandra Blanchet1, Rachel Green4,5,*, Marina V. Rodnina1,*, Daniel N. Wilson2,3,7,* 1 Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany. 2 Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Feodor-Lynenstr. 25, 81377 Munich, Germany 3 Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin- Luther-King-Platz 6, 20146 Hamburg, Germany 4 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, MD21205 Baltimore, United States. 5 Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, MD21205 Baltimore, United States. 6 These authors contributed equally *Correspondence: [email protected], [email protected], [email protected], [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.01.182105; this version posted July 1, 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.
  • Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass

    Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass

    cancers Review Ubiquitin and Ubiquitin-Like Proteins Are Essential Regulators of DNA Damage Bypass Nicole A. Wilkinson y, Katherine S. Mnuskin y, Nicholas W. Ashton * and Roger Woodgate * Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA; [email protected] (N.A.W.); [email protected] (K.S.M.) * Correspondence: [email protected] (N.W.A.); [email protected] (R.W.); Tel.: +1-301-435-1115 (N.W.A.); +1-301-435-0740 (R.W.) Co-first authors. y Received: 29 August 2020; Accepted: 29 September 2020; Published: 2 October 2020 Simple Summary: Ubiquitin and ubiquitin-like proteins are conjugated to many other proteins within the cell, to regulate their stability, localization, and activity. These modifications are essential for normal cellular function and the disruption of these processes contributes to numerous cancer types. In this review, we discuss how ubiquitin and ubiquitin-like proteins regulate the specialized replication pathways of DNA damage bypass, as well as how the disruption of these processes can contribute to cancer development. We also discuss how cancer cell survival relies on DNA damage bypass, and how targeting the regulation of these pathways by ubiquitin and ubiquitin-like proteins might be an effective strategy in anti-cancer therapies. Abstract: Many endogenous and exogenous factors can induce genomic instability in human cells, in the form of DNA damage and mutations, that predispose them to cancer development. Normal cells rely on DNA damage bypass pathways such as translesion synthesis (TLS) and template switching (TS) to replicate past lesions that might otherwise result in prolonged replication stress and lethal double-strand breaks (DSBs).
  • Genetic Features of Myelodysplastic Syndrome and Aplastic Anemia in Pediatric and Young Adult Patients

    Genetic Features of Myelodysplastic Syndrome and Aplastic Anemia in Pediatric and Young Adult Patients

    Bone Marrow Failure SUPPLEMENTARY APPENDIX Genetic features of myelodysplastic syndrome and aplastic anemia in pediatric and young adult patients Siobán B. Keel, 1* Angela Scott, 2,3,4 * Marilyn Sanchez-Bonilla, 5 Phoenix A. Ho, 2,3,4 Suleyman Gulsuner, 6 Colin C. Pritchard, 7 Janis L. Abkowitz, 1 Mary-Claire King, 6 Tom Walsh, 6** and Akiko Shimamura 5** 1Department of Medicine, Division of Hematology, University of Washington, Seattle, WA; 2Clinical Research Division, Fred Hutchinson Can - cer Research Center, Seattle, WA; 3Department of Pediatric Hematology/Oncology, Seattle Children’s Hospital, WA; 4Department of Pedi - atrics, University of Washington, Seattle, WA; 5Boston Children’s Hospital, Dana Farber Cancer Institute, and Harvard Medical School, MA; 6Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA; and 7Department of Laboratory Medicine, University of Washington, Seattle, WA, USA *SBK and ASc contributed equally to this work **TW and ASh are co-senior authors ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol. 2016.149476 Received: May 16, 2016. Accepted: July 13, 2016. Pre-published: July 14, 2016. Correspondence: [email protected] or [email protected] Supplementary materials Supplementary methods Retrospective chart review Patient data were collected from medical records by two investigators blinded to the results of genetic testing. The following information was collected: date of birth, transplant, death, and last follow-up,
  • Understanding Brassicaceae Evolution Through Ancestral

    Understanding Brassicaceae Evolution Through Ancestral

    Understanding Brassicaceae evolution through ancestral genome reconstruction Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero Villanueva, Richard Cooke, Hadi Quesneville, Hugues Roest Crollius, Jerome Salse To cite this version: Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero Villanueva, Richard Cooke, et al.. Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biology, BioMed Central, 2015, 16 (262), 10.1186/s13059-015-0814-y. hal-01281832 HAL Id: hal-01281832 https://hal.archives-ouvertes.fr/hal-01281832 Submitted on 2 Mar 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Murat et al. Genome Biology (2015) 16:262 DOI 10.1186/s13059-015-0814-y RESEARCH Open Access Understanding Brassicaceae evolution through ancestral genome reconstruction Florent Murat1†, Alexandra Louis2,3,4†, Florian Maumus5†, Alix Armero1, Richard Cooke6, Hadi Quesneville5, Hugues Roest Crollius2,3,4 and Jerome Salse1* Abstract Background: Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed. Results: We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula.