Dicer

2EB1, 4NGB, 4NGC, 4NGD, 4NGF, 4NGG, 4NH3, 4NH5, 4NH6, 4NHA, 4WYQ23405192119ENSG00000100697ENSMUSG00000041415Q9UPY3Q8R418NM_001195573NM_001271282NM_001291628NM_030621NM_177438NM_148948NP_001182502NP_001258211NP_001278557NP_085124NP_803187NP_683750Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, is an enzyme that in humans is encoded by the DICER1 gene. Being part of the RNase III family, Dicer cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short single-stranded RNA fragments called small interfering RNA and microRNA, respectively. These fragments are approximately 20-25 base pairs long with a two-base overhang on the 5' ends. Dicer facilitates the activation of the RNA-induced silencing complex (RISC), which is essential for RNA interference. RISC has a catalytic component argonaute, which is an endonuclease capable of degrading messenger RNA (mRNA). Dicer, also known as endoribonuclease Dicer or helicase with RNase motif, is an enzyme that in humans is encoded by the DICER1 gene. Being part of the RNase III family, Dicer cleaves double-stranded RNA (dsRNA) and pre-microRNA (pre-miRNA) into short single-stranded RNA fragments called small interfering RNA and microRNA, respectively. These fragments are approximately 20-25 base pairs long with a two-base overhang on the 5' ends. Dicer facilitates the activation of the RNA-induced silencing complex (RISC), which is essential for RNA interference. RISC has a catalytic component argonaute, which is an endonuclease capable of degrading messenger RNA (mRNA). Dicer was given its name in 2001 by Emily Bernstein, a graduate student in Gregory Hannon's lab at Cold Spring Harbor Laboratory, who sought to discover the enzyme responsible for generating small RNA fragments from double-stranded RNA. Dicer's ability to generate ~22 nucleotide RNA fragments was discovered by separating it from the RISC enzyme complex after initiating the RNAi pathway with dsRNA transfection. This experiment showed that RISC was not responsible for generating the observable small nucleotide fragments. Subsequent experiments testing RNase III family enzymes abilities to create RNA fragments narrowed the search to Drosophila CG4792, now named Dicer. Dicer orthologs are present in many other organisms. In the moss Physcomitrella patens DCL1b, one of four DICER proteins, is not involved in miRNA biogenesis but in dicing miRNA target transcripts. Thus, a novel mechanism for regulation of gene expression, the epigenetic silencing of genes by miRNAs, was discovered. In terms of crystal structure, the first Dicer to be explored was that from the protozoan Giardia intestinalis. A PAZ domain and two RNase III domains were discovered by X-ray crystallography. The protein size is 82 kDa, while it is larger in other organisms; for example, it is 219 kDa in humans. The difference in size from humans to G. intestinalis Dicer is due to at least five different domains being present within human Dicer. These domains are important in Dicer activity regulation, dsRNA processing, and RNA interference protein factor functioning. Human dicer (also known as hsDicer or DICER1) is classified a Ribonuclease III because it contains both helicase and PAZ (Piwi/Argonaute/Zwille) domains. In addition to these domains, hsDicer contains four other functional domains: two RNaseIII domains and two double stranded RNA binding domains (DUF283 and dsRBD). Current research suggests the PAZ domain is capable of binding the 2 nucleotide 3' overhang of dsRNA while the RNaseIII catalytic domains form a pseudo-dimer around the dsRNA to initiate cleavage of the strands. This results in a functional shortening of the dsRNA strand. The distance between the PAZ and RNaseIII domains is determined by the angle of the connector helix and influences the length of the micro RNA product. The dsRBD domain binds the dsRNA, although the specific binding site of the domain has not been defined. It is possible that this domain works as part of a complex with other regulator proteins (TRBP in humans, R2D2, Loqs in Drosophila) in order to effectively position the RNaseIII domains and thus control the specificity of the sRNA products. The helicase domain has been implicated in processing long substrates. RNA interference is a process where the breakdown of RNA molecules into miRNA inhibits gene expression of specific host mRNA sequences. miRNA is produced within the cell starting from primary miRNA (pri-miRNA) in the nucleus. These long sequences are cleaved into smaller precursor miRNA (pre-miRNA), which are usually 70 nucleotides with a hairpin structure. Pri-miRNA are identified by DGCR8 and cleaved by Drosha to form the pre-miRNA, a process that occurs in the nucleus. These pre-miRNA are then exported to the cytoplasm, where they are cleaved by Dicer to form mature miRNA. Small interfering RNA (siRNA) are produced and function in a similar manner to miRNA by cleaving double-stranded RNA with Dicer into smaller fragments, 21 to 23 nucleotides in length. Both miRNAs and siRNAs activate the RNA-induced silencing complex (RISC), which finds the complementary target mRNA sequence and cleaves the RNA using RNase. This in turn silences the particular gene by RNA interference. siRNAs and miRNAs differ in the fact that siRNAs are typically specific to the mRNA sequence while miRNAs aren't completely complementary to the mRNA sequence. miRNAs can interact with targets that have similar sequences, which inhibits translation of different genes. In general, RNA interference is an essential part of normal processes within organisms such as humans, and it is an area being researched as a diagnostic and therapeutic tool for cancer targets. Age related macular degeneration is a prominent cause of blindness in developed countries. Dicer's role in this disease became apparent after it was discovered that affected patients showed decreased levels of Dicer in their retinal pigment epithelium (RPE). Mice with Dicer knocked out, lacking Dicer only in their RPE, exhibited similar symptoms. However, other mice lacking important RNAi pathway proteins like Drosha and Pasha, did not have symptoms of macular degeneration as Dicer-knockout mice. This observation suggested a Dicer specific role in retinal health that was independent of the RNAi pathway and thus not a function of si/miRNA generation. A form of RNA called Alu RNA (the RNA transcripts of alu elements)) was found to be elevated in patients with insufficient Dicer levels. These non coding strands of RNA can loop forming dsRNA structures that would be degraded by Dicer in a healthy retina. However, with insufficient Dicer levels, the accumulation of alu RNA leads to the degeneration of RPE as a result of inflammation.