Structural Biochemistry/Nucleic Acid/RNA/RNA modification/snRNP

Small Nuclear Ribonucleoprotein Particles (snRNPs)
Small Nuclear RiboNucleoprotein Particles (snRNPs) are the secondary molecules made of small nuclear RNAs (snRNAs) and specific proteins. snRNP molecules make up the larger splicosome molecules. U1 snRNP recognizes the binding site on the 5’ end and the six-nucleotide sequence of the U1 snRNA binds to the splice site on the pre-mRNA. From this, the spliceosome will assemble along the pre-mRNA molecule. The U2 snRNP will bind to the branch site on the intron with its complementary sequence between the U2 snRNA sequence and the pre-mRNA. The U4, U5, and U6 snRNPS then bind with the U1 and U2 complexes and form the necessary spliceosome. The splicing process itself begins with the U5 interaction with the exon sequence on the 5’ splice site. The U6 goes through intramoleculear reorganization after breaking from U4, which allows U2 to base pair and interact with the 5’ end of the intron, taking U1 out of the spliceosome. The U2-U6 complex forms a helix that forms the center of the spliceosome itself. U4 prevents U6 from splicing until the splice sites are correctly aligned. Once alignment has occurred, the transesterification reaction cuts the 5’ exon at the phosphodiester bond and produces a lariat intermediate. Splicing continues with rearrangements with the spliceosome that will then produce the next transesterification reaction on the pre-mRNA. In the rearrangement, the U5 aligns with the 5’ exon so that it is easier to attack the 3’ splice site to produce another spliced product. To finish the splicing process, the U2, U5, and U6 release itself from the lariat intron.

snRNP Biogenesis Cycle
The biogenesis of snRNPs begin with the transcription of a monomethyl-guanosine (m7G)capped snRNA-precursor using RNA polymerase II. Following its transcription, the snRNA is exported out of the nucleas to react with Sm proteins, which combine to form the Sm core domain. This then triggers the hypermethylation of them7G-cap, thereby generatingthe trimethylguanosine (TMG)m^(2,2,7)3G-cap. The two-part nuclear localization signal (NLS) consisting of the Sm core domain and the TMG cap causes the relocation of the snRNP back to the nucleus. Before re-entering the nucleus, the snRNP undergoes completion of the biogenesis cycle in subnuclear domains called Cajal bodies. It is still relatively unknown as to which proteins join the snRNP at which stages of the biogenesis cycle. The U6snRNP does not follow the above stated steps and is speculated to carry out its biogenesis within the nucleoplasm.

snRNP Assembly Factors
Current work on snRNPs have demonstrated cellular assembly strategies for RNA-protein complexes. snRNPs form in vivo by the synchronized action of a complex assembly line containing assembly chaperones, scaffolding proteins, and catalysts. RNP assembly factors satisfy two functions. One, they augment assembly efficiency by helping the accumulation of higher order building blocks and second, they hinder the collection of Sm proteins and the assembly of snNRP centers that contain wrong RNA, or RNAs that do not entertain an Sm site. Various reports have spoken of the ‘proofreading’ function of the assembly machinery. These new strategies employ affinity to those used by protein complexes and also admit the explanation of common rules on how molecular machines are made in vivo.