Pathway: MicroRNA (miRNA) biogenesis
Reactions in pathway: MicroRNA (miRNA) biogenesis :
MicroRNA (miRNA) biogenesis
Biogenesis of microRNAs (miRNAs) can be summarized in five steps (reviewed in Ketting 2011, Nowotny and Yang 2009, Kim et al. 2009, Chua et al. 2009, Hannon and He 2004):
1. Transcription. miRNA transcripts may come from autonomously transcribed genes, they may be contained in cotranscripts with other genes, or they may be located in introns of host genes. Most miRNAs are transcribed by RNA polymerase II, however a few miRNAs originate as RNA polymerase III cotranscripts with neighboring repetitive elements. The initial transcript, termed a primary microRNA (pri-miRNA), contains an imperfectly double-stranded region within a hairpin loop. Longer sequences extend from the 5' and 3' ends of the hairpin and may also contain double-stranded regions.
2. Cleavage by DROSHA. The 5' and 3' ends of the pri-miRNA are removed during endoribonucleolytic cleavage by the DROSHA nuclease in a complex with the RNA-binding protein DGCR8 (the Microprocessor complex). The cleavage product is a short hairpin of about 60 to 70 nt called the pre-microRNA (pre-miRNA).
3. Nuclear export by Exportin-5. The resulting pre-miRNA is bound by Exportin-5 in a complex with Ran and GTP. The complex translocates the pre-miRNA through the nuclear pore into the cytoplasm.
4. Cleavage by DICER1. Once in the cytoplasm the pre-miRNA is bound by the RISC loading complex which contains DICER1, an Argonaute protein and either TARBP2 or PRKRA. DICER1 cleaves the pre-miRNA to yield an imperfectly double-stranded miRNA of about 21 to 23 nucleotides. At this stage the double-stranded miRNA has protruding single-stranded 3' ends of 2-3 nt.
5. Incorporation into RNA-Induced Silencing Complex (RISC) and strand selection. The double-stranded miRNA is passed to a Argonaute protein contained in the RISC loading complex. One strand, the passenger strand, will be removed and degraded; the other strand, the guide strand, will be retained and will guide the Argonaute:miRNA complex (RISC) to target mRNAs.
The human genome encodes 4 Argonaute proteins (AGO1 (EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4)), however only AGO2 (EIF2C2) can cleave target mRNAs with perfect or nearly perfect complementarity to the guide miRNA. For complexes that contain AGO2, cleavage of the passenger strand of the double-stranded miRNA accompanies removal of the passenger strand. Complexes containing other Argonautes may use a helicase to remove the passenger strand but this is not fully known. The resulting miRNA-loaded AGO2 is predominantly located in complexes with TARBP2 or PRKRA at the cytosolic face of the rough endoplasmic reticulum. AGO2, TARBP2, and DICER1 are also observed in the nucleus.
1. Transcription. miRNA transcripts may come from autonomously transcribed genes, they may be contained in cotranscripts with other genes, or they may be located in introns of host genes. Most miRNAs are transcribed by RNA polymerase II, however a few miRNAs originate as RNA polymerase III cotranscripts with neighboring repetitive elements. The initial transcript, termed a primary microRNA (pri-miRNA), contains an imperfectly double-stranded region within a hairpin loop. Longer sequences extend from the 5' and 3' ends of the hairpin and may also contain double-stranded regions.
2. Cleavage by DROSHA. The 5' and 3' ends of the pri-miRNA are removed during endoribonucleolytic cleavage by the DROSHA nuclease in a complex with the RNA-binding protein DGCR8 (the Microprocessor complex). The cleavage product is a short hairpin of about 60 to 70 nt called the pre-microRNA (pre-miRNA).
3. Nuclear export by Exportin-5. The resulting pre-miRNA is bound by Exportin-5 in a complex with Ran and GTP. The complex translocates the pre-miRNA through the nuclear pore into the cytoplasm.
4. Cleavage by DICER1. Once in the cytoplasm the pre-miRNA is bound by the RISC loading complex which contains DICER1, an Argonaute protein and either TARBP2 or PRKRA. DICER1 cleaves the pre-miRNA to yield an imperfectly double-stranded miRNA of about 21 to 23 nucleotides. At this stage the double-stranded miRNA has protruding single-stranded 3' ends of 2-3 nt.
5. Incorporation into RNA-Induced Silencing Complex (RISC) and strand selection. The double-stranded miRNA is passed to a Argonaute protein contained in the RISC loading complex. One strand, the passenger strand, will be removed and degraded; the other strand, the guide strand, will be retained and will guide the Argonaute:miRNA complex (RISC) to target mRNAs.
The human genome encodes 4 Argonaute proteins (AGO1 (EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4)), however only AGO2 (EIF2C2) can cleave target mRNAs with perfect or nearly perfect complementarity to the guide miRNA. For complexes that contain AGO2, cleavage of the passenger strand of the double-stranded miRNA accompanies removal of the passenger strand. Complexes containing other Argonautes may use a helicase to remove the passenger strand but this is not fully known. The resulting miRNA-loaded AGO2 is predominantly located in complexes with TARBP2 or PRKRA at the cytosolic face of the rough endoplasmic reticulum. AGO2, TARBP2, and DICER1 are also observed in the nucleus.
In this module, the biology of various types of regulatory non-coding RNAs are described. Biogenesis and functions of small interfering RNAs (siRNAs) and microRNAs (miRNAs) are annotated. Biogenesis of PIWI-interacting small RNAs (piRNAs) and tRNA-derived small RNAs (tsRNAs) are also annotated.
Gene expression encompasses transcription and translation and the regulation of these processes. RNA Polymerase I Transcription produces the large preribosomal RNA transcript (45S pre-rRNA) that is processed to yield 18S rRNA, 28S rRNA, and 5.8S rRNA, accounting for about half the RNA in a cell. RNA Polymerase II transcription produces messenger RNAs (mRNA) as well as a subset of non-coding RNAs including many small nucleolar RNAs (snRNA) and microRNAs (miRNA). RNA Polymerase III Transcription produces transfer RNAs (tRNA), 5S RNA, 7SL RNA, and U6 snRNA. Transcription from mitochondrial promoters is performed by the mitochondrial RNA polymerase, POLRMT, to yield long transcripts from each DNA strand that are processed to yield 12S rRNA, 16S rRNA, tRNAs, and a few RNAs encoding components of the electron transport chain. Regulation of gene expression can be divided into epigenetic regulation, transcriptional regulation, and post-transcription regulation (comprising translational efficiency and RNA stability). Epigenetic regulation of gene expression is the result of heritable chemical modifications to DNA and DNA-binding proteins such as histones. Epigenetic changes result in altered chromatin complexes that influence transcription. Gene Silencing by RNA mostly occurs post-transcriptionally but can also affect transcription. Small RNAs originating from the genome (miRNAs) or from exogenous RNA (siRNAs) are processed and transferred to the RNA-induced silencing complex (RISC), which interacts with complementary RNA to cause cleavage, translational inhibition, or transcriptional inhibition.