Supplementary Table I. mRNAs regulated in cells depleted of GW182 or AGO1. 987 mRNAs (992 probe sets) at least 2-fold upregulated or downregulated in AGO1 or GW182 depleted cells (in two replicates, normalized to control cells). Expression levels are given as fold changes (averages of two the experiments). 37 mRNAs (37 probe sets) at least 2-fold upregulated or downregulated in GFP dsRNA treated cells (in two replicates, normalized to control cells) are highlighted by grey shading . 5 mRNAs represented by 2 probe sets each are highlighted in italics. All other mRNAs were represented by one probe set only. Probe Set ID Gene Title Gene Symbol Representative GO Biological Process DescriptionGO Molecular Function DescriptionGO Cellular Component DescriptionInterPro Description AGO1 depletionGW182 Public ID depletion 1622898_a_at mitochondrial mRpS10 CG4247-RA protein biosynthesis structural constituent of ribosome mitochondrial ribosome /// --- -2.8 -2.5 ribosomal mitochondrial small ribosomal subunit protein S10 1622903_s_at --- CG1841 CG1841-RB --- protein binding --- BTB/POZ domain 2.6 2.6 1622928_at --- CG7940 CG7940-RA cytoskeleton organization and structural constituent of cytoskeletonactin filament Actin/actin-like 2.7 2.3 biogenesis 1622943_s_at --- CG2371 CG2371-RA --- --- --- --- -2.0 -1.8 1622968_at --- p115 CG1422-RA vesicle docking during exocytosis ///protein transporter activity Golgi stack /// endoplasmic reticulumUso1/p1 15 like vesicle tethering 3.2 3.8 intracellular protein transport /// membrane protein, C-terminal /// Uso1/p115 like vesicle tethering protein, head region 1622971_at --- CG15087 CG15087-RA --- --- --- --- 2.2 2.2 1622973_at --- CG8031 CG8031-RA --- --- --- Protein of unknown function DUF522.8 3.3 1622981_at ultraspiracle usp CG4380-RA dendrite morphogenesis /// border juvenile hormone binding /// ligand-polytene chromosome /// nucleus ///Ligand-binding domain of nuclear 2.4 2.2 follicle cell migration (sensu Insecta)dependent /// nuclear receptor activityecdysone /// receptor holocomplex /// hormone receptor /// Zn-finger, C4- positive regulation of transcription ///ecdysteroid hormone receptor activitynucleus /// nucleus type steroid receptor signal transduction /// regulation of/// DNA binding /// protein binding /// transcription from RNA polymerasetranscription II factor activity /// ligand- promoter /// lipid metabolism /// dependent nuclear receptor activity /// regulation of development, ecdysteroid hormone receptor activity heterochronic /// negative regulation of transcription, DNA-dependent /// negative regulation of cell differentiation /// metamorphosis /// ecdysone-mediated induction of salivary gland cell death /// neuron remodeling 1622984_at Superoxide Sod2 CG8905-RA defense response /// removal of metal ion binding /// manganese mitochondrial matrix /// mitochondrialManganese and iron superoxide -2.2 -1.9 dismutase 2 superoxide radicals /// superoxide superoxide dismutase activity /// matrix dismutase (Mn) metabolism /// determination of adultsuperoxide dismutase activity /// life span /// determination of adult antioxidantlife activity /// manganese span superoxide dismutase activity 1622995_at mitochondrial mRpS17 CG4326-RA protein biosynthesis nucleic acid binding /// structural mitochondrial small ribosomal subunit--- -2.3 -1.8 ribosomal constituent of ribosome protein S17 1622999_at Septin-1 38596.0 CG1403-RA mitosis /// cytokinesis /// cellularizationGTPase activity /// structural ring canal (sensu Insecta) /// septinCell division/GTP binding protein 2.9 2.5 /// cytokinesis constituent of cytoskeleton /// ring GTPase activity /// GTP binding /// protein binding 1623012_at mitochondrial mRpL55 CG14283-RA --- structural constituent of ribosome ///mitochondrial large ribosomal subunit--- -3.1 -3.1 ribosomal mRNA binding /// transcription factor/// mitochondrion /// nucleolus /// protein L55 activity nucleus 1623025_at --- CG3457 CG3457-RA --- --- --- --- 12.9 11.6 1623045_at Intronic ProteinIp259 /// RpS27A CG5277-RA ribosome biogenesis /// response tonucleic acid binding /// structural nucleus /// cytoplasm /// ribosome ///Ribosomal protein S8E /// Ribosomal2.5 3.2 259 /// stress /// regulation of transcription, constituent of ribosome /// structuralcytosolic small ribosomal subunit protein S27a /// Ubiquitin Ribosomal DNA-dependent /// establishment constituent of ribosome /// protein (sensu Eukaryota) protein S27A and/or maintenance of chromatin binding architecture /// ATP-dependent proteolysis /// ubiquitin cycle /// protein modification /// ubiquitin-dependent protein catabolism /// protein biosynthesis 1623058_at --- CG32676 CG32676-RA cellular physiological process --- --- Ubiquitin 2.2 2.0 1623109_at --- CG4593 CG4593-RA --- --- --- Protein of unknown function DUF814-3.4 -2.6 1623160_at Matrix Mmp1 CG4859-RA proteolysis and peptidolysis /// anti-zinc ion binding /// structural moleculeextracellular matrix (sensu Metazoa)Peptidase M10A and M12B, matrixin2.5 2.8 metalloproteina apoptosis /// dorsal trunk growth /// activity /// metalloendopeptidase and adamalysin /// Hemopexin repeat se 1 larval development (sensu Insecta) activity/// /// metalloendopeptidase tracheal system development (sensuactivity /// metalloendopeptidase Insecta) /// salivary gland cell death activity/// autophagic cell death 1623200_at fringe fng CG10580-RA segment specification /// receptor binding /// Golgi apparatus /// endoplasmic Fringe-like 5.9 2.6 neurogenesis /// ectoderm acetylglucosaminyltransferase activityreticulum /// Golgi stack /// integral to development /// oogenesis (sensu /// transferase activity, transferring membrane /// Golgi apparatus /// Golgi Insecta) /// cell fate specification /// glycosyl groups /// apparatus regulation of Notch signaling pathwayacetylglucosaminyltransferase activity /// negative regulation of Notch /// acetylglucosaminyltransferase signaling pathway /// regulation of activity /// UDP-glycosyltransferase Notch signaling pathway /// activity /// transferase activity, dorsal/ventral lineage restriction, transferring glycosyl groups imaginal disc /// Notch signaling pathway /// positive regulation of Notch signaling pathway /// regulation of Notch signaling pathway /// egg chamber formation (sensu Insecta) /// Notch signaling pathway /// fucose metabolism /// leg segmentation /// leg joint morphogenesis /// eye morphogenesis (sensu Endopterygota) /// wing morphogenesis /// wing morphogenesis /// dorsal/ventral pattern formation, imaginal disc /// wing margin morphogenesis 1623216_s_at --- CG9629 CG9629-RA metabolism aldehyde dehydrogenase (NAD) --- Aldehyde dehydrogenase -6.6 -5.9 activity 1623225_s_at --- CG7611 CG7611-RE --- --- --- G-protein beta WD-40 repeat 2.1 1.9 1623252_a_at --- l(1)G0030 CG3861-RB tricarboxylic acid cycle lyase activity /// citrate (Si)-synthasemitochondrial matrix Citrate synthase -2.1 -2.6 activity 1623287_at --- CG13921 CG13921-RA --- --- --- --- 38.2 17.4 1623293_at --- CG4042 CG4042-RA --- --- --- --- -3.1 -2.9 1623300_at /// CG18586 /// CG18586-RA metabolism ligase activity /// 4-coumarate-CoA --- AMP-dependent synthetase and 4.1 3.8 CG5568 ligase activity ligase 1623312_s_at --- CG11836 CG11836-RB proteolysis and peptidolysis /// trypsin activity /// serine-type --- Peptidase S1, chymotrypsin 2.8 3.0 defense response endopeptidase activity /// chymotrypsin activity 1623327_at --- --- S.C2R001709 --- --- --- --- 2.1 4.2 1623364_at --- CG4250 CG4250-RA --- --- --- --- -9.0 -2.9 1623388_at --- CG15861 CG15861-RA --- --- --- --- -4.7 -5.9 1623408_s_at /// CG2947 /// CG2947-RB protein folding Hsc70 protein regulator activity --- TPR repeat 2.6 2.8 CG32789 1623424_a_at baboon babo CG8224-RB dendrite morphogenesis /// skeletalA TP binding /// plasma membrane /// activin receptorProtein kinase /// TGF-beta 3.0 2.4 development /// mesoderm hematopoietin/interferon-class (D200-complex /// activin receptor complexreceptor/activin receptor, type I/II development /// cytokine and domain) cytokine receptor activity /// chemokine mediated signaling protein kinase activity /// type I pathway /// positive regulation of bodytransforming growth factor beta size /// mushroom body developmentreceptor activity /// protein /// eye-antennal disc metamorphosisserine/threonine kinase activity /// type /// protein amino acid phosphorylationI transforming growth factor beta /// transforming growth factor beta receptor activity /// type I activin receptor signaling pathway /// signalreceptor activity /// activin binding /// G- transduction /// protein amino acidprotein coupled receptor kinase phosphorylation activity 1623436_a_at bunched bun CG5461-RC regulation of transcription from RNAtranscription factor activity /// RNA cytoplasm /// nucleus /// cytoplasm TSC-22 / Dip / Bun 2.0 1.6 polymerase II promoter /// salivary polymerase II transcription factor gland cell death /// autophagic cell activity /// protein homodimerization death /// ovarian follicle cell activity development (sensu Insecta) /// peripheral nervous system development /// oogenesis (sensu Insecta) /// eye morphogenesis (sensu Endopterygota) /// dorsal appendage formation /// cell fate determination /// negative regulation of cell fate specification /// eggshell formation (sensu Insecta) /// dorsal appendage formation /// eye photoreceptor cell differentiation (sensu Endopterygota) /// decapentaplegic receptor signaling pathway /// segmentation 1623459_at Serine Spn4 CG9453-RC proteolysis and peptidolysis serine-type endopeptidase inhibitor--- Serpin 4.5 4.4 protease activity