Protein phosphorylation in transcription and co-transcriptional processes

Protein phosphorylation is an essential post-translational modification in the regulation of transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA cleavage and polyadenylation. Interestingly, the RNA polymerase (pol) II, via its carboxyl-terminal domain (CTD), is a major protein involved in the crosstalk between transcription and co-transcriptional processes. In human cells, the pol II CTD is composed of 52 repeats of the Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptapeptide, which can be phosphorylated on Tyr, Ser, and Thr residues. The pol II CTD phosphorylation pattern and level changes dynamically during transcription and participates in the recruitment of proteins involved in co-transcriptional processes. Numerous transcriptional kinases, including cyclin-dependent kinases (CDKs), and phosphatases regulate phosphorylation of the pol II CTD and of other transcriptional and co-transcriptional proteins.

We are interested in understanding how phosphorylation of the pol II CTD and of transcriptional and co-transcriptional proteins regulate the coordination between transcription and co-transcriptional processes, coordination which is required for the production of mature mRNAs but also for splice site selection and poly(A) site usage. We are employing a combination of analog-sensitive kinases, targeted degradation approach (dTAG), genome-wide techniques, (phospho-)proteomics, and microscopy approaches.


Tellier M et al. CDK9 and PP2A regulate the link between RNA polymerase II transcription termination and RNA maturation. EMBO Reports. 2022.

Tellier M et al. CDK12 globally promotes RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation. Nucleic Acids Research, 2020.

Tellier M et al. Transcription and splicing: a two-way street. WIREs RNA, 2020.

Transcription of a protein-coding gene in human cells is regulated at different steps, including transcription initiation, pol II pausing and pause release, transcription elongation, and transcription termination. Kinases (CDK7, 8, 9, 11, 12, 13) and phosphatases (PP1, PP2A) play major regulatory roles at the different transcriptional steps.

Protein phosphorylation in R-loop biology

A consequence of transcription is the formation of RNA/DNA hybrids called R-loops, which if not resolved can produce genomic instability. Resolution of R-loops can be performed by different cellular mechanisms, including RNA helicases to unwind RNA/DNA hybrids, RNA-binding proteins, such as splicing factors and mRNA export factors, to limit R-loop formation, and, more drastically, degradation of R-loops by RNaseH proteins (RNaseH1 and RNaseH2).

While several kinases and phosphatases have been found to interact with R-loop structures, the roles of protein phosphorylation in R-loop biology remain poorly understood. Kinases and phosphatases are frequently dysregulated or mutated in disease while unresolved R-loops are associated with genomic instability. We want therefore to understand how protein phosphorylation regulates R-loop biology and whether dysregulation of R-loop-associated kinases and phosphatases promote R-loop accumulation and thus genomic instability. In addition, we want to determine how R-loop resolution is associated/coordinated with transcription and co-transcriptional processes, as some of the kinases and phosphatases found to interact with R-loops are also involved in transcription and pre-mRNA splicing.


Cristini A, Tellier M et al. RNase H2, mutated in Aicardi‐Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation. Nature Communications. 2022.

McCann JL*, Cristini A*, Law EK#, Yun Lee S#, Tellier M et al. R-loop homeostasis and cancer mutagenesis promoted by the DNA cytosine deaminase APOBEC3B. bioRxiv. 2021.

Nojima T*, Tellier M* et al. Deregulated Expression of Mammalian lncRNA through Loss of SPT6 Induces R-Loop Formation, Replication Stress, and Cellular Senescence. Molecular Cell, 2018.

R-loops can be resolved by different cellular pathways, including RNA helicases, association of RNA-binding proteins, and degradation of the R-loop structure by RNaseH proteins.

Dysregulation of protein phosphorylation in disease

Mutations and/or dysregulation of kinases (CDK8, CDK10, CDK12, CDK13, etc) and phosphatases (PTEN, PTPRC, PP3, CTDP1, PP2A, etc) are associated with several developmental diseases but also with cancer. We want to understand the effects of mutations on the activities of kinases/phosphatases and the consequences on transcription, co-transcriptional processes, and transcription-associated processes such as R-loops. In addition, we are interested in the development of novel small molecule inhibitors and small molecule degraders (PROTACs, molecular glues) for kinases and phosphatases known to be dysregulated in cancers for therapeutic purposes.