RNA processing protein complexes and uses thereof

Abstract

The invention provides human protein complexes with endonuclease activity. In particular, the invention provides human protein complexes with tRNA splicing endonuclease activity and/or 3′ end pre-mRNA endonuclease activity. The invention also provides a splice variant of human Sen2, namely human Sen2deltaEx8, and human protein complexes comprising human Sen2deltaEx8. The human Sen2deltaEx8 complexes have pre-tRNA cleavage activity and/or 3′ end pre-mRNA endonuclease activity. The invention also provides human protein complexes with pre-ribosomal RNA cleavage activity. The invention also provides antibodies that immunospecifically bind to a complex described herein or a component thereof, and methods of diagnosing, preventing, treating, managing or ameliorating a disorder utilizing such antibodies. The present invention also provides methods utilizing the complexes described herein, inter alia, in screening, diagnosis, and therapy. The invention further provides methods of preparing and purifying the complexes. The present invention further provides methods of identifying a compound that modulates the expression of a component of a complex described herein, the formation of a complex described herein or the activity of a complex described herein, and methods of preventing, treating, managing or ameliorating a disorder, such as a proliferative disorder, or a symptom thereof utilizing a compound identified in accordance with the methods.

1 . A purified complex, wherein the complex comprises: 
 (i) Sen2 (ACCESSION NO.: NP — 079541), or a protein encoded by a nucleic acid that hybridizes to the Sen2 encoding nucleic acid (ACCESSION NO.: NM — 025265) or its complement under high stringency conditions;    (ii) Sen15 or a protein encoded by a nucleic acid that hybridizes to the Sen15 encoding nucleic acid (ACCESSION NO.:NM — 052965) or its complement under high stringency conditions;    (iii) Sen34 (ACCESSION NO.:NP — 076980), or a protein encoded by a nucleic acid that hybridizes to the Sen34 encoding nucleic acid (ACCESSION NO.:NM — 024075) or its complement under high stringency conditions; and    (iv) Sen54 (ACCESSION NO.:XP — 208944), or a protein encoded by a nucleic acid that hybridizes to the Sen54 encoding nucleic acid (ACCESSION NO.:XM — 208944) or its complement under high stringency conditions,    wherein said high stringency conditions comprise hybridization in a buffer consisting of 6×SSC, 50 mM Tris-HCl (pH=7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 100 μg/ml denatured salmon sperm DNA, for 48 hours at 65° C., washing in a buffer consisting of 2×SSC, 0.01% PVP, 0.01% Ficoll and 0.01% BSA, for 45 minutes at 37° C., and washing in a buffer consisting of 0.1×SSC, for 45 minutes at 50° C.    
     
     
         2 . The complex of  claim 1 , wherein the complex further comprises Clp1 (ACCESSION NO.:NP006822) or a protein encoded by a nucleic acid that hybridizes to the Clp1 encoding nucleic acid (ACCESSION NO.: NM — 006831) or its complement under high stringency conditions.  
     
     
         3 . The complex of  claim 2 , wherein the complex further comprises one or more of the following: 
 (i) Cleavage-Polyadenylation Specificity Factor or proteins encoded by nucleic acids that hybridize to the Cleavage-Polyadenylation Specificity Factor encoding nucleic acids or their complements under high stringency conditions;    (ii) Cleavage Factor I m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor I m  encoding nucleic acid or their complements under high stringency conditions;    (iii) Cleavage Factor II m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor II m  encoding nucleic acids or their complements under high stringency conditions; and    (iv) Cleavage Stimulation Factor or proteins encoded by nucleic acids that hybridize to the Cleavage Stimulation Factor encoding nucleic acids or their complements under high stringency conditions.    
     
     
         4 . The complex of  claim 2 , wherein the complex further comprises one or more of the following: 
 (i) CPSF160 or a protein encoded by a nucleic acid that hybridizes to CPSF160 encoding nucleic acid or its complement under high stringency conditions;    (ii) CPSF30 or a protein encoded by a nucleic acid that hybridizes to CPSF30 encoding nucleic acid or its complement under high stringency conditions;    (iii) CstF64 or a protein encoded by a nucleic acid that hybridizes to CstF64 encoding nucleic acid or its complement under high stringency conditions;    (iv) symplekin or a protein encoded by a nucleic acid that hybridizes to symplekin encoding nucleic acid or its complement under high stringency conditions    
     
     
         5 . A purified complex comprising Sen2deltaEx8, or a protein encoded by a nucleic acid that hybridizes under stringent hybridization conditions to a Sen2deltaEx8 encoding nucleic acid.  
     
     
         6 . A purified complex, wherein the complex comprises: 
 (i) Sen2deltaEx8 (SEQ ID NO.: 2), or a protein encoded by a nucleic acid that hybridizes to the Sen2deltaEx8 encoding nucleic acid (SEQ ID NO.: 1) or its complement under high stringency conditions; and    (ii) Sen54 (ACCESSION NO.:XP — 208944), or a protein encoded by a nucleic acid that hybridizes to the Sen54 encoding nucleic acid (ACCESSION NO.:XM — 208944) or its complement under high stringency conditions;    wherein said high stringency conditions comprise hybridization in a buffer consisting of 6×SSC, 50 mM Tris-HCl (pH=7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 100 μg/ml denatured salmon sperm DNA, for 48 hours at 65° C., washing in a buffer consisting of 2×SSC, 0.01% PVP, 0.01% Ficoll and 0.01% BSA, for 45 minutes at 37° C., and washing in a buffer consisting of 0. 1×SSC, for 45 minutes at 50° C.    
     
     
         7 . The purified complex of  claim 6 , wherein the complex further comprises: Clp1 (ACCESSION NO.:NP — 006822) or a protein encoded by a nucleic acid that hybridizes to the Clp1 encoding nucleic acid (ACCESSION NO.: NM — 006831) or its complement under high stringency conditions.  
     
     
         8 . The purified complex of  claim 7 , wherein the complex further comprises one or more of the following: 
 (i) Cleavage-Polyadenylation Specificity Factor or proteins encoded by nucleic acids that hybridize to the Cleavage-Polyadenylation Specificity Factor encoding nucleic acids or their complements under high stringency conditions;    (ii) Cleavage Factor I m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor I m  encoding nucleic acids or their complements under high stringency conditions;    (iii) Cleavage Factor II m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor II m  encoding nucleic acids or their complements under high stringency conditions; and    (iv) Cleavage Stimulation Factor or proteins encoded by nucleic acids that hybridize to the Cleavage Stimulation Factor encoding nucleic acids or their complements under high stringency conditions.    
     
     
         9 . A purified complex, wherein the complex comprises: 
 (i) Sen2deltaEx8 (SEQ ID NO.: 2), or a protein encoded by a nucleic acid that hybridizes to the Sen2deltaEx8 encoding nucleic acid (SEQ ID NO.: 1) or its complement under high stringency conditions; (ii) Sen15 or a protein encoded by a nucleic acid that hybridizes to the Sen15 encoding nucleic acid (ACCESSION NO.:NM — 052965) or its complement under high stringency conditions;    (iii) Sen34 (ACCESSION NO.:NP — 076980), or a protein encoded by a nucleic acid that hybridizes to the Sen34 encoding nucleic acid (ACCESSION NO.:NM — 024075) or its complement under high stringency conditions; and    (iv) Sen54 (ACCESSION NO.:XP — 208944), or a protein encoded by a nucleic acid that hybridizes to the Sen54 encoding nucleic acid (ACCESSION NO.:XM — 208944) or its complement under high stringency conditions,    wherein said high stringency conditions comprise hybridization in a buffer consisting of 6×SSC, 50 mM Tris-HCl (pH=7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 100 μg/ml denatured salmon sperm DNA, for 48 hours at 65° C., washing in a buffer consisting of 2×SSC, 0.01% PVP, 0.01% Ficoll and 0.01% BSA, for 45 minutes at 37° C., and washing in a buffer consisting of 0.1×SSC, for 45 minutes at 50° C.    
     
     
         10 . The purified complex of  claim 9 , wherein the complex further comprises: Clp1 (ACCESSION NO.:NP — 006822) or a protein encoded by a nucleic acid that hybridizes to the Clp1 encoding nucleic acid (ACCESSION NO.: NM — 00683 1) or its complement under high stringency conditions.  
     
     
         11 . The purified complex of  claim 10 , wherein the complex further comprises: 
 (i) Cleavage-Polyadenylation Specificity Factor or proteins encoded by nucleic acids that hybridize to the Cleavage-Polyadenylation Specificity Factor encoding nucleic acids or their complements under high stringency conditions;    (ii) Cleavage Factor I m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor I m  encoding nucleic acids or their complements under high stringency conditions;    (iii) Cleavage Factor II m  or proteins encoded by nucleic acids that hybridize to the Cleavage Factor II m  encoding nucleic acids or their complements under high stringency conditions; and    (iv) Cleavage Stimulation Factor or proteins encoded by nucleic acids that hybridize to the Cleavage Stimulation Factor encoding nucleic acids or their complements under high stringency conditions.    
     
     
         12 . The complex of  claim 10 , wherein the complex further comprises one or more of the following: 
 (i) CPSF160 or a protein encoded by a nucleic acid that hybridizes to CPSF160 encoding nucleic acid or its complement under high stringency conditions;    (ii) CPSF30 or a protein encoded by a nucleic acid that hybridizes to CPSF30 encoding nucleic acid or its complement under high stringency conditions;    (iii) CstF64 or a protein encoded by a nucleic acid that hybridizes to CstF64 encoding nucleic acid or its complement under high stringency conditions; and    (iv) symplekin or a protein encoded by a nucleic acid that hybridizes to symplekin encoding nucleic acid or its complement under high stringency conditions    
     
     
         13 . A purified complex, wherein the complex comprises: 
 (i) Sen15 or a protein encoded by a nucleic acid that hybridizes to the Sen15 encoding nucleic acid (ACCESSION NO.:NM — 052965) or its complement under high stringency conditions; and    (ii) Sen34 (ACCESSION NO.:NP — 076980), or a protein encoded by a nucleic acid that hybridizes to the Sen34 encoding nucleic acid (ACCESSION NO.:NM — 024075) or its complement under high stringency conditions.    
     
     
         14 . The complex of  claim 1 ,  6 ,  9 , or  13 , wherein at least two proteins of the complex are covalently linked to each other.  
     
     
         15 . The complex of  claim 1 ,  6 ,  9 , or  13 , wherein at least two proteins of the complex are non-covalently linked to each other.  
     
     
         16 . The complex of  claim 1 ,  6 ,  9 , or  13 , wherein at least one protein of the complex is a functionally active derivative, wherein the functionally active derivative is a fusion protein comprising the protein fused to an amino acid sequence different from the protein.  
     
     
         17 . The complex of  claim 1 ,  6 ,  9 , or  13 , wherein the complex comprises at least one fragment of a protein, wherein the fragment binds to one or more other protein components of the complex.  
     
     
         18 . An antibody or a fragment thereof that immunospecifically binds to the complex of  claim 1 ,  6 ,  9 , or  13  with a higher affinity than the affinity of the antibody or antibody fragment to any of the protein components of the complex.  
     
     
         19 . An antibody or a fragment thereof that immunospecifically binds to Sen2 (Accession No.:NP — 079541), Sen15 (Accession No.:NP — 443197), Sen34 (Accession No.:NP — 076980) or Sen54 (Accession No.:XP — 208944).  
     
     
         20 . A method for generating an antibody comprising immunizing an animal with the complex of  claim 1 ,  6 ,  9 , or  13 .  
     
     
         21 . A purified nucleic acid, wherein the nucleic acid encodes a protein comprising the amino acid sequence of SEQ ID NO.:12.  
     
     
         22 . A purified nucleic acid, wherein the nucleic acid comprises the nucleic acid sequence of SEQ ID NO.:11.  
     
     
         23 . A purified nucleic acid comprising a contiguous open reading frame which encodes a polypeptide comprising amino acid 280 to amino acid 330 of SEQ ID NO:12.  
     
     
         24 . A purified nucleic acid which hybridizes over its full length to the complement of a nucleic acid comprising SEQ ID NO:11 under high stringency conditions, wherein said high stringency conditions comprise hybridization in a buffer consisting of 6×SSC, 50 mM Tris-HCl (pH=7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 100 μg/ml denatured salmon sperm DNA, for 48 hours at 65° C., washing in a buffer consisting of 2×SSC, 0.01% PVP, 0.01% Ficoll and 0.01% BSA, for 45 minutes at 37° C., and washing in a buffer consisting of 0.1×SSC, for 45 minutes at 50° C.  
     
     
         25 . The nucleic acid of  claim 24 , wherein the nucleic acid encodes a polypeptide that has RNA nucleolytic activity.  
     
     
         26 . The nucleic acid of  claim 22 ,  23 , or  24 , further comprising a heterologous nucleic acid sequence.  
     
     
         27 . A vector comprising the nucleic acid of  claim 21 ,  22 ,  23 , or  24 .  
     
     
         28 . A host cell comprising the vector of  claim 27 .  
     
     
         29 . A host cell comprising the nucleic acid of  claim 21 ,  22 ,  23 , or  24 .  
     
     
         30 . A method for producing a polypeptide comprising culturing the host cell of  claim 28 .  
     
     
         31 . A method for producing a polypeptide comprising culturing the host cell of  claim 29 .  
     
     
         32 . A purified polypeptide comprising the amino acid sequence of SEQ ID NO:12, or the amino acid sequence encoded by a nucleic acid sequence that hybridizes over its full length to the complement of SEQ ID NO:11 under high stringency conditions, wherein said high stringency conditions comprise hybridization in a buffer consisting of 6×SSC, 50 mM Tris-HCl (pH=7.5), 1 mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA and 100 μg/ml denatured salmon sperm DNA, for 48 hours at 65° C., washing in a buffer consisting of 2×SSC, 0.01% PVP, 0.01% Ficoll and 0.01% BSA, for 45 minutes at 37° C., and washing in a buffer consisting of 0.1×SSC, for 45 minutes at 50° C.  
     
     
         33 . The polypeptide of  claim 32  further comprising a heterologous amino acid sequence.  
     
     
         34 . An antibody or fragment thereof that immunospecifically binds to the polypeptide of  claim 32 .  
     
     
         35 . The antibody or antibody fragment of  claim 34 , wherein the antibody does not bind to Sen2 (ACCESSION NO.: NP — 079541).  
     
     
         36 . A method for purifying the complex of  claim 1 ,  6 ,  9 , or  13 , wherein the method comprises: 
 (a) preparing a cell extract or a nuclear extract from a cell, wherein the cell expresses all protein components of the complex and wherein at least one of the protein components is fused to a peptide tag; and    (b) purifying the complex by virtue of the peptide tag.    
     
     
         37 . A pharmaceutical composition comprising the complex of  claim 1 ,  6 ,  9 , or  13  and a pharmaceutically acceptable carrier.  
     
     
         38 . A pharmaceutical composition comprising the antibody of  claim 34 .  
     
     
         39 . A method of identifying a compound that modulates the formation of a complex, wherein the method comprises the following steps: 
 (a) contacting a cell with a compound, wherein the cell comprises all components of the complex of  claim 1 ,  6 ,  9 , or  13 ; and    (b) measuring the amount of the complex of formed in the cell.    
     
     
         40 . The method of  claim 39  wherein the cell is a human cell.  
     
     
         41 . The method of  claim 40 , wherein the cell is a 293T, HeLa, MCF7, Wi-38, SkBr3, Jurkat, CEM, or a THP1 cell.  
     
     
         42 . The method of  claim 39 , wherein the method comprises isolating the complex of  claim 1 ,  6 ,  9 , or  13  from the cell.  
     
     
         43 . The method of  claim 39 , wherein the amount of complex is measured by FRET.  
     
     
         44 . The method of  claim 39 , wherein the cell is engineered to express at least one of the protein components of the complex.  
     
     
         45 . A method of identifying a compound that modulates the formation of a complex, wherein the method comprises the following steps: 
 (a) incubating (i) Sen2 (ACCESSION NO.: NP — 079541), or a protein encoded by a nucleic acid that hybridizes to the Sen2 encoding nucleic acid (ACCESSION NO.:    NM — 025265) or its complement under high stringency conditions;    (ii) Sen15 or a protein encoded by a nucleic acid that hybridizes to the Sen15 encoding nucleic acid (ACCESSION NO.:NM — 052965) or its complement under high stringency conditions;    (iii) Sen34 (ACCESSION NO.:NP — 076980), or a protein encoded by a nucleic acid that hybridizes to the Sen34 encoding nucleic acid (ACCESSION NO.:NM — 024075) or its complement under high stringency conditions; and    (iv) Sen54 (ACCESSION NO.:XP — 208944), or a protein encoded by a nucleic acid that hybridizes to the Sen54 encoding nucleic acid (ACCESSION NO.:XM — 208944) or its complement under high stringency conditions;    in the presence of a compound under conditions conducive to formation of a complex comprising the proteins; and    (b) determining the amount of the complex,    wherein a difference in the amount of the complex determined in step (b) relative to the amount of the complex determined in the absence of the compound indicates that the compound modulates the formation of the complex.    
     
     
         46 . The method of  claim 45 , wherein Clp1 (ACCESSION NO.:NP — 006822) or a protein encoded by a nucleic acid that hybridizes to the Clp1 encoding nucleic acid (ACCESSION NO.: NM — 006831) or its complement under high stringency conditions is also incubated in step (a).  
     
     
         47 . A method of identifying a compound that modulates the formation of a complex, wherein the method comprises the following steps: 
 (a) incubating 
 (i) Sen2deltaEx8 (SEQ ID NO.: 2), or a protein encoded by a nucleic acid that hybridizes to the Sen2deltaEx8 encoding nucleic acid (SEQ ID NO.: 1) or its complement under high stringency conditions;  
 (ii) Sen15 or a protein encoded by a nucleic acid that hybridizes to the Sen15 encoding nucleic acid (ACCESSION NO.:NM — 052965) or its complement under high stringency conditions;  
 (iii) Sen34 (ACCESSION NO.:NP — 076980), or a protein encoded by a nucleic acid that hybridizes to the Sen34 encoding nucleic acid (ACCESSION NO.:NM — 024075) or its complement under high stringency conditions; and  
 (iv) Sen54 (ACCESSION NO.:XP — 208944), or a protein encoded by a nucleic acid that hybridizes to the Sen54 encoding nucleic acid (ACCESSION NO.:XM — 208944) or its complement under high stringency conditions;  
 in the presence of a compound under conditions conducive to formation of a complex comprising the proteins; and  
   (b) determining the amount of the complex,    wherein a difference in the amount of the complex determined in step (b) relative to the amount of the complex determined in the absence of the compound indicates that the compound modulates the formation of the complex.    
     
     
         48 . The method of  claim 47 , wherein Clp1 (ACCESSION NO.:NP — 006822) or a protein encoded by a nucleic acid that hybridizes to the Clp1 encoding nucleic acid (ACCESSION NO.: NM — 006831) or its complement under high stringency conditions is also incubated in step (a).  
     
     
         49 . A method of identifying a compound that modulates the stability of a complex, wherein the method comprises the following steps: 
 (a) incubating the complex of  claim 1 ,  6 ,  9 , or  13  in the presence of a compound under conditions conducive to maintaining the complex; and    (b) determining the amount of the complex,    wherein a difference in the amount of the complex determined in step (b) relative to the amount of the complex determined in the absence of the compound indicates that the compound modulates the stability of the complex.    
     
     
         50 . The method of  claim 45  or  46 , wherein the method further comprises the step of comparing the ratio between the formed complex relative to the amount of the individual proteins.  
     
     
         51 . The method of  claim 45  or  46 , wherein the proteins are incubated in step (a) in equimolar amounts.  
     
     
         52 . A method for identifying a compound that modulates human tRNA splicing endonuclease activity, said method comprising: 
 (a) contacting a member of a library of compounds with a the complex of  claim 1  and a nucleic acid comprising a reporter gene, wherein the reporter gene comprises a tRNA intron, and wherein all factors required for gene expression are present; and    (b) detecting the expression of said reporter gene, wherein a compound that modulates tRNA splicing endonuclease activity is identified if the expression of said reporter gene in the presence of a compound is altered relative to the expression of said reporter gene in the absence of said compound or the presence of a control.    
     
     
         53 . A method for identifying a compound that modulates 3′ end pre-mRNA endonuclease cleavage activity, said method comprising: 
 (a) contacting a member of a library of compounds with a the complex of  claim 1  or  9  and a nucleic acid comprising a reporter gene and a cleavage site for a 3′ end pre-mRNA endonuclease, wherein the reporter gene is located 3′ of the cleavage site for a 3′ end pre-mRNA endonuclease, and wherein all factors required for gene expression are present; and    (b) detecting the expression of said reporter gene, wherein a compound that modulates 3′ end pre-mRNA endonuclease cleavage activity is identified if the expression of said reporter gene in the presence of a compound is altered relative to the expression of said reporter gene in the absence of said compound or the presence of a control.    
     
     
         54 . A method of identifying a compound that modulates human tRNA splicing endonuclease activity, said method comprising: 
 (a) contacting the complex of  claim 1  with a substrate of a tRNA splicing endonuclease and a member of a library of compounds, wherein the substrate is labeled at the 5′ end with a fluorophore and at the 3′ end with a quencher; and    (b) measuring the activity of the tRNA splicing endonuclease, wherein a compound that modulates tRNA splicing activity is identified if a fluorescent signal is altered in the presence of the compound relative to the absence of the compound or the presence of a control.    
     
     
         55 . A method of identifying a compound that modulates human 3′ end pre-mRNA endonuclease cleavage activity, said method comprising: 
 (a) contacting the complex of  claim 1  or  9  with a substrate of a 3′ end pre-mRNA endonuclease and a member of a library of compounds, wherein the substrate is labeled at the 5′ end with a fluorophore and at the 3′ end with a quencher; and    (b) measuring the activity of the 3′ end pre-mRNA endonuclease, wherein a compound that modulates 3′ end pre-mRNA endonuclease activity is identified if a fluorescent signal is altered in the presence of the compound relative to the absence of the compound or the presence of a control.    
     
     
         56 . A method of identifying a compound that modulates human tRNA splicing endonuclease activity, said method comprising: 
 (a) contacting the complex of  claim 1  with a substrate of a tRNA splicing endonuclease and a member of a library of compounds, wherein said substrate is labeled at the 5′ end with a fluorescent donor moiety and labeled at the 3′ end with a fluorescent acceptor moiety; and    (b) measuring the activity of the tRNA splicing endonuclease, wherein a compound that modulates tRNA splicing activity is identified if the fluorescence emission of the fluorescent acceptor moiety at the wavelength of the fluorescent donor moiety in the presence of the compound is altered relative to the absence of the compound or the presence of a control.    
     
     
         57 . A method of identifying a compound that modulates human 3′ end pre-mRNA endonuclease cleavage activity, said method comprising: 
 (a) contacting the complex of  claim 1  or  9  with a substrate of a 3′ end pre-mRNA endonuclease and a member of a library of compounds, wherein said substrate is labeled at the 5′ end with a fluorescent donor moiety and labeled at the 3′ end with a fluorescent acceptor moiety; and    (b) measuring the activity of the 3′ end pre-mRNA endonuclease, wherein a compound that modulates 3′ end pre-mRNA endonuclease activity is identified if the fluorescence emission of the fluorescent acceptor moiety at the wavelength of the fluorescent donor moiety in the presence of the compound is altered relative to the absence of the compound or the presence of a control.    
     
     
         58 . The method of  claim 39 , wherein the compound is tested for inhibition of the formation of the complex.  
     
     
         59 . The method of  claim 45  or  46 , wherein the compound is tested for inhibition of the formation of the complex.  
     
     
         60 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 58 .  
     
     
         61 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 59 .  
     
     
         62 . The method of  claim 52 ,  54  or  56 , wherein the compound is tested for inhibition of human tRNA splicing endonuclease activity.  
     
     
         63 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 62 .  
     
     
         64 . The method of  claim 53 , wherein the compound is tested for inhibition of human 3′ end pre-mRNA endonuclease activity.  
     
     
         65 . The method of  claim 55 , wherein the compound is tested for inhibition of human 3′ end pre-mRNA endonuclease activity  
     
     
         66 . The method of  claim 57 , wherein the compound is tested for inhibition of human 3′ end pre-mRNA endonuclease activity  
     
     
         67 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 64 .  
     
     
         68 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 65 .  
     
     
         69 . A method of treating, preventing, or managing a proliferative disorder comprising administering a pharmaceutically acceptable amount of a compound identified by the method of  claim 66 .  
     
     
         70 . The method of  claim 52 ,  54  or  56 , wherein the compound enhances tRNA splicing endonuclease activity.  
     
     
         71 . The method of  claim 53 , wherein the compound enhances 3′ end pre-mRNA endonuclease activity.  
     
     
         72 . The method of  claim 55 , wherein the compound enhances 3′ end pre-mRNA endonuclease activity.  
     
     
         73 . The method of  claim 57 , wherein the compound enhances 3′ end pre-mRNA endonuclease activity.  
     
     
         74 . The method of  claim 52 ,  54  or  56 , wherein the method further comprises determining the structure of the compound.  
     
     
         75 . The method of  claim 53 , wherein the method further comprises determining the structure of the compound.  
     
     
         76 . The method of  claim 55 , wherein the method further comprises determining the structure of the compound.  
     
     
         77 . The method of  claim 57 , wherein the method further comprises determining the structure of the compound.  
     
     
         78 . The method of  claim 45 ,  47 ,  52 ,  54 , or  56 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         79 . The method of  claim 39 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         80 . The method of  claim 49 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         81 . The method of  claim 53 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         82 . The method of  claim 55 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         83 . The method of  claim 57 , wherein the compound is selected from a combinatorial library of compounds comprising peptoids; random biooligomers; diversomers such as hydantoins, benzodiazepines and dipeptides; vinylogous polypeptides; nonpeptidal peptidomimetics; oligocarbamates; peptidyl phosphonates; peptide nucleic acid libraries; antibody libraries; carbohydrate libraries; and small organic molecule libraries.  
     
     
         84 . The method of  claim 52 ,  54 , or  56 , wherein the compound directly binds the complex.  
     
     
         85 . The method of claim 39 , wherein the compound directly binds the complex.  
     
     
         86 . The method of  claim 49 , wherein the compound directly binds the complex.  
     
     
         87 . A method for diagnosing a proliferative disorder in a subject, wherein the method comprises (a) contacting a sample from the subject with an antibody or fragment thereof that immunospecifically binds to a protein selected from the group selected of Sen2, Sen15, Sen34, Sen54, Clp1, SenΔ8Ex, CPSF, CFI m , CFII m , and CstF; and (b) detecting the antibody of fragment thereof, wherein a reduced level of the protein compared to the level of the protein in a subject without a proliferative disorder indicates that the subject has a proliferative disorder.  
     
     
         88 . A method for diagnosing a proliferative disorder in a subject, wherein the method comprises (a) contacting a sample from the subject with an antibody or fragment thereof that immunospecifically binds to the complex of  claim 1 ,  6 ,  9 , or  13 ; and (b) detecting the antibody of fragment thereof, wherein a reduced level of the complex compared to the level of the complex in a subject without a proliferative disorder indicates that the subject has a proliferative disorder.