Biology subjects

Wickramasinghe, V.

Publications and source records attributed to Wickramasinghe, V..

3 recordsLinked to original sources

bioRxiv2026

Cell cycle dependent regulation of mRNA export in response to replication stress

Nuclear export of mRNA is extensively coupled to transcription and processing of mRNA. How mRNA export is mechanistically regulated remains poorly understood. Here, we uncover a physical checkpoint at nuclear speckles that regulates mRNA export during DNA replication in S-phase of the cell cycle. Unbiased screening approaches identify WEE1 and CHK1 as novel mRNA export regulators. mRNA export complexes are recruited to sites of replication stress in S-phase. WEE1 inhibition prematurely activates CDK1 and PLK1, leading to accumulation of R-loop associated mRNA in large nuclear speckles, with late markers of replication stress present around their periphery. This recruitment is dependent on CDK1 activity. Phosphorylation of ALYREF by CDK1 and PLK1 regulates nuclear speckle accumulation of mRNA following replication stress. mRNA export factors including ALYREF are subsequently mis-localised from these speckles, preventing nuclear export of R-loop associated mRNA. Thus, WEE1, CDK1 and PLK1 enforce a cell cycle regulated checkpoint at nuclear speckles that serves to protect the cell from major sources of genome instability by ensuring that R-loop associated mature mRNA is not exported to the cytoplasm.

molecular biology↗

bioRxiv2026

Termination dynamics set RNAPII elongation rate and gate the response to CDK12 inactivation

The transcriptional fidelity of RNA polymerase II (RNAPII) is governed by a tight equilibrium between elongation and termination activities, a balance frequently disrupted in human diseases such as cancer. The transcriptional cyclin-dependent kinase 12 (CDK12) maintains RNAPII elongation rate and processivity throughout the gene body. Inactivation of CDK12 disrupts this homeostatic balance and causes elongation stress, slowing RNAPII and triggering premature termination at intronic polyadenylation sites (IPAs). Despite this, the precise executors of intronic premature termination under CDK12-inactivation-induced elongation stress remain poorly understood. Using genome-wide CRISPR screening combined with chemical-genetic approach, we identified a pro-termination mechanism at intronic checkpoints; upon CDK12 inactivation, SCAF4 recruits the cleavage and polyadenylation (CPA) complex through its catalytic endonuclease CPSF3 to execute premature cleavage at IPAs. Disruption of SCAF4-CPA axis prevents early termination, restores full length transcription and confers resistance to CDK12/cyclin K inhibition. Genetic loss of SCAF4 restores the RNAPII elongation rate under CDK12 inhibition, revealing that termination dynamics actively shape the rate of transcription. Supporting this model, we uncovered an anti-termination mechanism driven by KHDRBS1/SAM68, whose depletion promotes proximal termination and sensitises cells to CDK12 targeting. Our findings mechanistically couple elongation and termination activities at intronic checkpoints as joint contributors to both the processivity and elongation rate of RNAPII. This establishes termination dynamics as an active and tractable axis of the cellular response to elongation stress.

molecular biology↗

bioRxiv2018

Transcriptome-wide profiling of mammalian spliceosome and branchpoints with iCLIP

Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we employed spliceosome iCLIP, which immunoprecipitates SmB along with snRNPs and auxiliary RNA binding proteins (RBPs), to map human spliceosome engagement with snRNAs and pre-mRNAs. This identified over 50,000 branchpoints (BPs) that have canonical sequence and structural features. Moreover, it revealed 7 binding peaks around BPs and splice sites, each precisely overlapping with binding profiles of specific splicing factors. We show how the binding patterns of these RBPs are affected by the position and strength of BPs. For example, strong or proximally located BPs preferentially bind SF3 rather than U2AF complex. Notably, these effects are partly neutralized during spliceosomal assembly in a way that depends on the core spliceosomal protein PRPF8. These insights exemplify spliceosome iCLIP as a broadly applicable method for transcriptomic studies of splicing mechanisms.

genomics↗