TABLE 1.

List of genes targeted by siRNA pools used in this studya

Primary function and name of geneGenBank accession no.bOMIM no.cProduct name, function(s) and other characteristicsc
Clathrin-mediated endocytosis
    AP1B1NM_001127600157Beta prime subunit of the AP-1 clathrin-associated adaptor protein complex 1, important in the formation of clathrin-coated vesicles; present in late-Golgi/trans-Golgi network and endosomes
    AP1M1NM_032493603535Mu subunit of the AP-1 assembly complex
    AP1M2NM_005498607309Component of the AP-1 complex involved in basolateral sorting of endosomal cargoes
    AP2A1NM_014203601026Alpha subunit of clathrin-assembly complex 2 on endocytic vesicles; links receptors to clathrin
    AP2A2NM_012305607024Variant of above
    AP2B1NM_001030006601025Beta subunit of the clathrin assembly complex 2
    CLTAM20471118960Clathrin light chain A; major structural component of clathrin; one of two major classes of light chain (A and B)
    CLTBM20469118970Clathrin light chain B; major structural component of clathrin; one of two major classes of light chain (A and B)
    CLTCNM_004859118955Clathrin heavy chain; binds to light chain to form the clathrin triskelion
    EPN4NM_014666607265Epsin 4; stimulates clathrin assembly and binds clathrin
    Eps15L1NM_021235See Eps15 600051Eps15-like protein 1; may be involved in the internalization of ligand-inducible receptors of the receptor tyrosine kinase (RTK) type
    ITSN1AF064244602442Intersectin-1; adapter protein that may link clathrin-associated endocytosis of receptors to actin assembly machinery
    ITSN2AF182198604464As above
Caveolin-mediated endocytosis
    CAV2AF035752601048Caveolin-2; coats the cytoplasmic face of caveolae; expressed in many cell types
    CAV3AF043101601253Caveolin-3; expressed predominantly in muscle but also in cells in culture
    FYNM14333137025Tyrosine kinase that may couple receptor signaling to caveolin and clathrin function
General endocytosis
    ARF1M36340103180ADP ribosylation factor 1; involved in protein trafficking among different compartments; modulates COP1 function in vesicle budding and uncoating within the Golgi complex
    DNM1L07807602377Dynamin-1; highly expressed in the brain; involved in pinching off of endocytic vesicles from the plasma membrane
    DNM2L36983602378Dynamin-2; functions as above and also in actin cytoskeleton rearrangement; expressed broadly, highly expressed in muscle
    DNM3AB020627See DNM-1Dynamin-3; as above; may also have special functions in specific endocytic pathways
    EEA1L40157605070Early endosome antigen 1; binds Rab5 and early endosomal membranes
    NEDD4NM_006154602278Neural precursor cell expressed, developmentally downregulated; involved in ubiquitination of receptors prior to endocytosis
    NEDD4LNM_015277606384NEDD4-like; shares a ubiquitin ligase domain; as above
    Rab5aM28215179512RAS-associated protein 5A; required and rate limiting for early endosome formation
    Rab5bX54871179514Closely related to Rab5a; as above
    Rab5cU18420604307As above
    Rab7BNM_177403.3Not availableRAS associated protein 7B; lysosome associated
    SNAP91NM_014841607923Synaptosome-associated protein of 91 kDa; similar to clathrin assembly protein AP180
Exocytosis
    Rab4AM28211179511RAS-associated protein 4A; involved in recycling of endocytic vesicles from the early endosome to the cell surface
    Rab4BAF165522See aboveVariant of Rab4A
    Rab11AX53143605570RAS-associated protein 11A; recycling endosomes to surface and trans-Golgi to surface
    Rab11BX79780604198Variant of Rab11A; as above
    Rab11FIP5NM_015470See 608738Rab11 family-interacting protein 5; rab11-regulating protein
Cytoskeleton and membrane remodeling, including actin rearrangement
    ARFIP2NM_012402601638ADP ribosylation factor-interacting protein 2; binds directly to RAC1 and ARF proteins; modulates membrane ruffling
    CAMK1L41816604998Calcium/calmodulin-dependent protein kinase 1; involved in numerous cellular processes, including transcriptional regulation, hormone production, translational regulation, regulation of actin filament organization, and neurite outgrowth
    CFL1NM_005507601442Cofilin; reversibly controls actin polymerization and depolymerization; stimulated by phosphorylation by LIMK1
    DAB2NM_001343601236Disabled homolog 2; binds and stimulates GRB2 (see below)
    GIT1AF124490608434G protein-coupled receptor kinase-interacting protein 1; associated with and modulates signaling modules controlling vesicle trafficking, adhesion, and cytoskeletal organization
    GRB2NM_002086108355Growth factor receptor-bound protein 2; couples receptor signaling (including those for growth factors) to Rac-actin-modeling pathway
    LIMK1D26309601329LIM kinase domain 1; effector of Rho-induced actin polymerization/depolymerization by phosphorylation of cofilin
    PACSIN1AF242529606512Protein kinase C and casein kinase substrate 1 in neurons; may play a role in vesicle formation and transport; high expression in brain
    PACSIN3AF130979606513Protein kinase C and casein kinase substrate 3 in neurons; binds proteins important in vesicle trafficking, including dynamin 1, synaptojanin, synapsin 1, and N-WASP; ubiquitously expressed
    PAK1BC050377602590p21/CDC42/RAC1-activated kinase 1; activity results in depolymerization of F-actin; also acts on Jun N-terminal protein kinase 1 pathway; substrate of Rac1 and CDC42
    RhoAX05026165930RAS homolog gene family member A; involved in triggering actin cytoskeleton rearrangement
    TNIKAF172264610005TRAF2 and NCK interacting kinase; stress-activated serine/threonine kinase promotes actin depolymerization
ARP2/3 complex involved in nucleating actin polymerization
    ACTR2NM_005722604221Actin-related protein 2; component of the ARP2/3 complex that promotes actin polymerization in lamellipodia
    ACTR3NM_005721604222Actin-related protein 3; one of the seven proteins that comprise the ARP2/3 complex; see ACTR2
    ARPC1BNM_005720604223Actin-related protein 2/3 complex subunit 1b; see ACTR2
    ARPC2NM_152862604224Actin related protein 2/3 complex subunit 2; see ACTR2
    ARPC3NM_005719604225Actin-related protein 2/3 complex subunit 3; see ACTR2
    ARPC4NM_005718604226Actin-related protein 2/3 complex subunit 4; see ACTR2
    ARPC5NM_005717604227Actin-related protein 2/3 complex subunit 5; see ACTR2
    DDEF2AB007860603817Development and differentiation-enhancing factor 2; regulates the formation of post-Golgi vesicles and modulates constitutive secretion and phagocytosis; modulates ARF1 and -5
    PIP5K1AU78576603275Phosphatidylinositol-4-phosphate 5-kinase 1A; involved in actin cytoskeleton modulation
    ROCK1U43195601702Rho-associated coiled-coil-containing protein kinase 1; downstream effector of RhoA, phosphorylating LIMK1 to regulate the actin cytoskeleton
    ROCK2D87931604002Rho-associated coiled-coil-containing protein kinase 2; isozyme of ROCK1; see ROCK1
    WASF1AF134303605035Wiskott-Aldrich syndrome protein family member 1; (WAVE1); transmits signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton; involved in filopodium formation; effector of RAC1
    WASF2AB026542605875Wiskott-Aldrich syndrome protein family member 2; homolog of WASF1
    WASF3AB026543605068Wiskott-Aldrich syndrome protein family member 3; homolog of WASF1
Others
    ARRB1NM_004041107940β-Arrestin 1; targets receptors to clathrin-coated vesicles; binds SRC
    ARRB2NM_004313107941β-Arrestin 2; homolog of ARRB1; promotes receptor internalization
    ATMU33841607585Ataxia-telangiectasia mutated gene; checkpoint control in DNA repair; may play a role in vesicle and/or protein transport by binding beta adaptin
    ATP6V0A1NM_005177192130ATPase, H+ transporting, lysosomal V0 subunit A1; component of the vacuolar ATPase proton pump involved in endosomal acidification
    BIN1AF004015601248Bridging interactor 1; binds integrins; associated with CAV3 in muscle
    CBLNM_005188165360CAS-BR-M murine ecotropic retroviral-transforming sequence homolog; regulates receptor tyrosine kinase degradation and possibly endocytosis through ubiquitination
    CBLBNM_170662604491CAS-BR-M murine ecotropic retroviral-transforming sequence B; related to CBL
    CBLCNM_012116608453CAS-BR-M murine ecotropic retroviral-transforming sequence C; interacts with PI3K, FYN, and GRB2; may alter EGFR endocytosis
    GORASP1NM_031899606867Golgi reassembly stacking protein-1; Golgi structural protein
    IHPK3NM_054111606993Inositol hexaphosphate kinase 3; may regulate inositol phosphate-stimulated vesicle formation and trafficking
    MAP4K2U07349603166Mitogen-activated protein kinase 2; associated with Rab8 and may control protein secretion
    MAPK8IP1NM_005456604641Mitogen-activated protein kinase 8-interacting protein 1; accumulates in cell surface projections and interacts with proteins affecting the Jun N-terminal kinase pathway
    MAPK8IP2NM_012324607755Mitogen-activated protein kinase 8-interacting protein 2; as above
    MAPK8IP3NM_015133605431Mitogen-activated protein kinase 8-interacting protein 3; as above; binds kinesin; acts as a molecular scaffold for Jun N-terminal kinase pathway proteins
    PSCD3NM_004227605081Pleckstrin homology, SEC7, and coiled-coil domain protein 3; regulates ARF proteins to control vesicle trafficking
    STAUNM_004602601706Staufen homolog; cross-links cytoskeleton and RNA
    SYNJ1NM_003895604297Synaptojanin 1; binds Eps15 and is localized to clathrin-coated vesicles; high levels in neurons
    SYNJ2NM_003898609410Synaptohanin 2; ubiquitously expressed; effector or RAC1 in actin regulation and lamellipodium formation and clathrin-mediated endocytosis
    SYT1M55047185605Synaptotagmin 1; important in exocytosis and endocytosis in neurons
    SYT2NM_177402600104Synaptotagmin 1; as above
  • a These are a subset of the Dharmacon Membrane Trafficking siRNA library. Each is ordered by reported primary function and then alphabetically.

  • b GenBank database 2006 (http://www.ncbi.nlm.nih.gov/).

  • c The description of gene function is summarized from Online Mendelian Inheritance in Man (OMIM), McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD), and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), as of October 2006. http://www.ncbi.nlm.nih.gov/omim/.