Rde 4 sandbox: Difference between revisions

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==Introduction==

RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. <ref>DOI: 10.~~1042~~/~~BJ20131347~~</ref> (Yellow Citation)

RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. <ref name=first>DOI: 10.1261/rna.2338706</ref> (Yellow Citation)

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== Function ==

In C. elegans, exogenous dsRNA is detected and bound by RDE-4, which stimulates dicer activity. RDE-4 initiates the siRNA pathway by binding to long dsRNA and assisting Dcr-1, a Dicer1 homologue, to facilitate siRNA production. RDE-4 interacts with Dcr-1, RDE-1, DRH-1 (Dicer-related helicase 1) and long dsRNA, which thereby suggests that RDE-4 is required only for the initiation of the RNAi pathway to generate siRNA, although high levels of dsRNA abrogate RDE-4’s role in the RNAi initiation. RDE-4 co- operatively binds to long dsRNA with nanomolar affinity, but exhibits micromolar affinity for short dsRNA, and the enhanced affinity arises from binding of several RDE-4 molecules to a single long dsRNA. (Blue citation) The C-terminal region of RDE-4 is necessary and sufficient to induce homodimerization RDE-4 linker– dsRBD2 are absolutely essential in C. elegans gene silencing and RDE-4 dsRBD1 and the C-terminal domain do not have any primary role in vivo. RDE-4 recognizes the A-form of nucleic acid structure adopted by dsRNA and the interaction is sequence-independent. (Purple citation) RDE-4 dimerization is important for the assembly of active RDE-4/Dicer complexes via one of two proposed scenarios, proper Dicer recruitment to dsRNA, or facilitating Dicer dimerization. (Yellow citation)

In C. elegans, exogenous dsRNA is detected and bound by RDE-4, which stimulates dicer activity. RDE-4 initiates the siRNA pathway by binding to long dsRNA and assisting Dcr-1, a Dicer1 homologue, to facilitate siRNA production. RDE-4 interacts with Dcr-1, RDE-1, DRH-1 (Dicer-related helicase 1) and long dsRNA, which thereby suggests that RDE-4 is required only for the initiation of the RNAi pathway to generate siRNA, although high levels of dsRNA abrogate RDE-4’s role in the RNAi initiation. RDE-4 co- operatively binds to long dsRNA with nanomolar affinity, but exhibits micromolar affinity for short dsRNA, and the enhanced affinity arises from binding of several RDE-4 molecules to a single long dsRNA. (Blue citation) The C-terminal region of RDE-4 is necessary and sufficient to induce homodimerization RDE-4 linker– dsRBD2 are absolutely essential in C. elegans gene silencing and RDE-4 dsRBD1 and the C-terminal domain do not have any primary role in vivo. RDE-4 recognizes the A-form of nucleic acid structure adopted by dsRNA and the interaction is sequence-independent. (Purple citation) RDE-4 dimerization is important for the assembly of active RDE-4/Dicer complexes via one of two proposed scenarios, proper Dicer recruitment to dsRNA, or facilitating Dicer dimerization. <ref name=first/> (Yellow citation)

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@@ Line 1: / Line 1: @@
 ==Introduction==
-RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. <ref>DOI: 10.1042/BJ20131347</ref> (Yellow Citation)
+RDE-4 was identified through a genome-wide screening as a gene responsible for greatly reducing or abolishing RNAi in C. elegans. In organisms ranging from Arabidopsis to humans, Dicer requires dsRNA-binding proteins (dsRBPs) to carry out its roles in RNA interference (RNAi) and micro-RNA (miRNA) processing. In Caenorhabditis elegans, the dsRBP RDE-4 acts with Dicer during the initiation of RNAi, when long dsRNA is cleaved to small interfering RNAs (siRNAs). RDE-4 is not sequence-specific, however, RDE-4 binds with higher affinity to long dsRNA. Interestingly, RDE- 4 is the only protein that exhibits micromolar affinity for dsRNA in the absence of co-operativity. In addition, RDE-4 is a homodimer in solution. <ref name=first>DOI: 10.1261/rna.2338706</ref> (Yellow Citation)
   <Structure load='2LTR' size='350' frame='true' align='right' caption='Structure of RDE-4 (pdb code 2LTR) scene='Insert optional scene name here' />
@@ Line 13: / Line 13: @@
 == Function ==
-In C. elegans, exogenous dsRNA is detected and bound by RDE-4, which stimulates dicer activity. RDE-4 initiates the siRNA pathway by binding to long dsRNA and assisting Dcr-1, a Dicer1 homologue, to facilitate siRNA production. RDE-4 interacts with Dcr-1, RDE-1, DRH-1 (Dicer-related helicase 1) and long dsRNA, which thereby suggests that RDE-4 is required only for the initiation of the RNAi pathway to generate siRNA, although high levels of dsRNA abrogate RDE-4’s role in the RNAi initiation. RDE-4 co- operatively binds to long dsRNA with nanomolar affinity, but exhibits micromolar affinity for short dsRNA, and the enhanced affinity arises from binding of several RDE-4 molecules to a single long dsRNA. (Blue citation) The C-terminal region of RDE-4 is necessary and sufficient to induce homodimerization RDE-4 linker– dsRBD2 are absolutely essential in C. elegans gene silencing and RDE-4 dsRBD1 and the C-terminal domain do not have any primary role in vivo. RDE-4 recognizes the A-form of nucleic acid structure adopted by dsRNA and the interaction is sequence-independent. (Purple citation) RDE-4 dimerization is important for the assembly of active RDE-4/Dicer complexes via one of two proposed scenarios, proper Dicer recruitment to dsRNA, or facilitating Dicer dimerization. (Yellow citation)
+In C. elegans, exogenous dsRNA is detected and bound by RDE-4, which stimulates dicer activity. RDE-4 initiates the siRNA pathway by binding to long dsRNA and assisting Dcr-1, a Dicer1 homologue, to facilitate siRNA production. RDE-4 interacts with Dcr-1, RDE-1, DRH-1 (Dicer-related helicase 1) and long dsRNA, which thereby suggests that RDE-4 is required only for the initiation of the RNAi pathway to generate siRNA, although high levels of dsRNA abrogate RDE-4’s role in the RNAi initiation. RDE-4 co- operatively binds to long dsRNA with nanomolar affinity, but exhibits micromolar affinity for short dsRNA, and the enhanced affinity arises from binding of several RDE-4 molecules to a single long dsRNA. (Blue citation) The C-terminal region of RDE-4 is necessary and sufficient to induce homodimerization RDE-4 linker– dsRBD2 are absolutely essential in C. elegans gene silencing and RDE-4 dsRBD1 and the C-terminal domain do not have any primary role in vivo. RDE-4 recognizes the A-form of nucleic acid structure adopted by dsRNA and the interaction is sequence-independent. (Purple citation) RDE-4 dimerization is important for the assembly of active RDE-4/Dicer complexes via one of two proposed scenarios, proper Dicer recruitment to dsRNA, or facilitating Dicer dimerization. <ref name=first/> (Yellow citation)