The 3′ Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

Abstract

Non-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3′-end processing factors for RDH genes are enriched; however, this association’s role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs’ association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)–Cap binding complex (CBC)–Negative elongation factor (NELF), components of CBs, interferes with CBs’ association with HLBs and 3′ Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator’s involvement in CBs’ association with HLBs to facilitate 3′ Pol II pausing and subsequent 3′-end processing of RDH genes by supplying 3′-end processing factors.

TDP-43 and NEAT long non-coding RNA: Roles in neurodegenerative disease

“…Interestingly, early work showed CB interactions with replication-dependent histone (RDH) loci ( Shopland et al, 2001 ). These histone locus bodies (HLBs) have now been linked to the formation of a ternary complex with CB and RNA polymerase II, facilitating 3′-end processing of RDH genes ( Imada et al, 2021 ; Suzuki et al, 2022 ). The dependence of these HLBs on histone pre-mRNA transcripts has led to the histone pre-mRNA transcripts being classified as architectural or scaffolding RNAs ( Shevtsov and Dundr, 2011 ; Chujo and Hirose, 2017 ).…”

MED26‐containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies

“…In these mutant cell lines, Pol II TPP at RDH genes was drastically abolished, resulting in increases in the levels of aberrant unprocessed RDH gene transcripts. [ 27 ] Knockdown of NELF and CBC components also significantly abolished Pol II TPP at RDH genes, [ 27 ] indicating that CBC–NELF is involved in TPP at RDH genes. Thus, the interaction of Mediator with LEC–CBC–NELF is required for TPP to inhibit readthrough of Pol II at RDH genes (Figure 4A).…”

“…In contrast, LSM11 localizes between CBs and HLBs. [ 27 ] In D. melanogaster , HLBs have a core‐shell structure in which the internal core contains actively transcribed RDH genes. The N‐terminal region of Mxc, a D. melanogaster homologue of human NPAT, is enriched in the HLB core.…”

Molecular determinants for the layering and coarsening of biological condensates

“…Besides the above examples, other biological condensates, including paraspeckles, [65] anisosomes, [66] Cajal bodies, [67,68] and mitochondrial transcriptional condensates, [69,70] have been known to display complex organization as well. While the physical and biological implications of these structures have been discussed and remain of interest for future studies, [44,49,52,71] how these organizations emerge from molecular level descriptions of the system has not been adequately reviewed.…”