#transcription elongation

Transcription in Eukaryotes

FACT complex is involved during

FACT, facilitates chromatin transcription, is heterodimeric histone chaperone composed of SPT16 and SSRP1 in humans, Spt16-Pob3 plus Nhp6 in yeast, that remains associated with elongating Pol II during gene body transcription. Nucleosomes present strong barrier to polymerase progression, causing frequent pausing and backtracking requiring rescue. FACT binds both H2A-H2B dimers and H3-H4 tetramers simultaneously via acidic domains, destabilizing nucleosome without displacing octamer completely, allowing passage. Interaction with SPT5 DSIF complex and PAF1 complex tethers FACT to elongating polymerase ensuring rapid reassembly behind transcription machinery.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: FACT complex in elongation; JBC, FACT facilitates transcription-dependent nucleosome alteration

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Transcription in Eukaryotes

Phosphorylation of Ser2 in CTD is associated with

During transition to productive elongation, CDK9 cyclin-dependent kinase of P-TEFb complex and later CDK12 phosphorylate serine two of CTD heptad repeats YSPTSPS, creating high density pattern near three prime end of gene body. Serine2-P CTD recruits histone chaperone FACT, Spt6, chromatin modifier Set2 responsible for H3K36 trimethylation, and cleavage and polyadenylation factors CPSF and CstF for messenger RNA three prime end formation. Exchange from serine five to serine two ensures temporal coupling of elongation, chromatin restoration, and termination. Phosphatase Fcp1 recycles polymerase after termination releasing from DNA.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: Ser2-P marks elongation; J Biol Chem, CTD Ser2 phosphorylation elongation

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Transcription in Prokaryotes

Which region of σ70 acts as RNA mimic and must be ejected for elongation?

Sigma70 comprises domains sigma1.1 through sigma4 connected by linkers. Region 3.2, approximately amino acids 510-520 forming acidic loop between domains sigma2 and sigma4, threads through RNA polymerase active site cleft into RNA exit channel. It acts as a molecular mimic of nascent RNA, positioning initiating nucleotides and stabilizing abortive initiation complexes while preventing extension beyond five to six nucleotides. When RNA grows longer, it collides sterically with this loop, necessitating ejection. Removal of 3.2 linker clears exit path and permits promoter clearance and transition to stable elongation.

Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: Sigma region 3.2 as RNA mimic; PNAS 2013 Structure of sigma70 holoenzyme

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Regulation of chromatin structure

Which histone modification is associated with transcription elongation?

Co-transcriptional histone modifications demarcate functional regions of transcribed units. During elongation, Ser2-phosphorylated C-terminal domain of RNA polymerase II recruits Set2 methyltransferase via interaction with PAF complex and Spt6 chaperone, leading to trimethylation of H3K36 over gene bodies. H3K36me3 suppresses cryptic initiation by recruiting Rpd3S deacetylase and Isw1b remodeler, preserving nucleosome integrity behind polymerase. It also influences alternative splicing by binding MRG15 and splicing regulators. Unlike promoter-associated H3K4me3, H3K36me3 peaks toward 3' ends of active genes, marking productive elongation and preventing spurious transcription.

Ref: NCBI Bookshelf, Molecular Biology of Transcription Elongation, Set2-Mediated H3K36 Methylation, S. cerevisiae Studies

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