8 public questions tagged with this topic.
RNA polymerase III is responsible for transcribing **tRNA and some small RNAs** in eukaryotes.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
Poly-A polymerase adds a poly-A tail to mRNA to enhance its stability and regulate translation.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance DNA Replication - Semiconservative and Machinery
Removal of noncoding introns from precursor messenger RNA and ligation of coding exons is termed splicing, essential step generating continuous open reading frame for translation. Carried out by spliceosome, dynamic ribonucleoprotein complex assembling on consensus signals GU at five prime splice site, branch point adenosine near three prime end, and AG at three prime splice site. Two transesterification reactions without ATP for chemistry, ATP used for helicase remodeling, excise intron as lariat and join exons. Alternative splicing produces multiple isoforms from single gene expanding proteome complexity in metazoans significantly.
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Intron removal called splicing; Lodish 9th ed., Pre-mRNA splicing overview
Polyadenylate polymerase is classified as template-independent terminal nucleotidyltransferase, lacking ability to read DNA or RNA template for base selection. Instead specificity arises from intrinsic preference for ATP binding pocket and interactions with CPSF and PABPN1. Therefore polyadenine sequence is not encoded in genome but added post-transcriptionally forming uniform adenine homopolymer essential for stability. This contrasts with DNA polymerases, RNA polymerases that are template dependent. Other template independent polymerases include CCA-adding enzyme for transfer RNA and terminal deoxynucleotidyl transferase TdT in immunoglobulin gene rearrangement adding N-nucleotides.
Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: Poly(A) polymerase template independent; Lodish 9th ed., Terminal nucleotidyltransferase family
Polyadenylation signal in nascent messenger RNA consists of highly conserved hexamer AAUAAA located ten to thirty nucleotides upstream of CA dinucleotide cleavage site. Recognized by WDR33 and CPSF30 subunits of cleavage and polyadenylation specificity factor CPSF through base stacking in zinc finger pockets. Mutation of AAUAAA to AAGAAA drastically reduces cleavage efficiency and causes read-through transcription. Auxiliary upstream sequence elements USE enriched in uridine and downstream GU-rich downstream sequence element DSE bound by CstF enhance recognition. Identical DNA motif is AATAAA.
Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: Poly(A) signal AAUAAA; Lodish 9th ed., CPSF recognition of AAUAAA hexamer
Polyadenylation of eukaryotic messenger RNA occurs exclusively at three prime end, downstream of AAUAAA signal where nascent RNA is cleaved by endonuclease CPSF73. Polyadenylate polymerase PAP adds continuous stretch of adenine residues to new three hydroxyl group in template-independent manner using ATP. Location exclusively three prime is critical for defining messenger RNA orientation, promoting nuclear export, protecting against three prime to five prime exosome decay, and enhancing translation initiation via interaction between polyadenine binding protein PABPC and eIF4G that circularizes mRNA. Replication-dependent histone mRNAs are exception lacking polyadenylation.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Polyadenylation at 3' end; Alberts 7th ed., Poly(A) tail addition site
Five prime cap shields messenger RNA from rapid degradation mediated by highly processive five prime to three prime exonucleases. Without cap, uncapped pre-mRNAs bearing five prime monophosphate are substrates for nuclear Xrn2 Rat1 and cytoplasmic Xrn1 surveillance pathways that degrade aberrant or decapped transcripts as part of quality control. Cap physically blocks entry into exonuclease active site channel and recruits cap binding complex CBP20-CBP80 that sterically occludes end. It also masks RNA from innate immune sensors RIG-I and IFIT that detect exposed five prime triphosphates of viral RNAs.
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: 5' cap protects from 5'-3' exonucleases; Lodish 9th ed., Mechanism of mRNA stability
Nucleosome core particle contains one hundred forty-seven base pairs of DNA wrapped around octamer of histones with central H3-H4 tetramer and two peripheral H2A-H2B dimers. To transcribe through chromatin, RNA polymerase II needs partial disassembly. FACT binds to nucleosome and destabilizes dimer-tetramer contacts, causing transient eviction of one H2A-H2B dimer converting nucleosome to hexasome, unwrapping approximately thirty base pairs of entry DNA. This reduction lowers mechanical barrier, decreasing polymerase crossing time measured by optical tweezers. FACT then acts as chaperone to redeposit dimer after passage.
Ref: PubMed 2003 FACT removes H2A-H2B dimer during Pol II passage; Nature 2020 Structural visualization of FACT-mediated nucleosome reorganization
