Background

Eukaryotic RNA polymerase II (RNAPII) is a complex enzyme that plays a central role in synthesizing both protein-coding mRNAs and non-coding RNAs. As RNAPII transcribes DNA into RNA through chromatin, it induces changes in the composition and modification of nucleosomes. These transcriptional activities are closely linked to co-transcriptional processes like capping, splicing, and polyadenylation, all of which feed back into the nascent transcript. However, the precise nature of these interconnections remains poorly understood (Fig. 1A).

Traditionally, transcription is described as a three-step process involving RNAPII: initiation, elongation, and termination, all of which are primarily regulated by the association of transcription factors. While much of the focus has been on initiation and elongation, termination is increasingly recognized as a crucial regulatory step. It not only determines the final fate of the transcript but also influences chromatin modifications (Fig. 1B). Moreover, deficiencies in transcription termination play a role in several key physiological stress responses, such as heat, oxidative stress, osmotic stress, and are implicated in cellular senescence, viral infections, and certain cancers.

Figure 1. Schematic representations of the long-term research problem addressed in our group. (A) Complex feedback mechanisms involved in the regulation of transcriptional output. (B) Graphical abstract of the transcriptional termination-driven chromatin modifications paradigm previously described.

Research Interests

Our research focuses on understanding how transcription and co-transcriptional processes interact to shape the chromatin environment. To explore these mechanisms, we use Arabidopsis thaliana as a model system, taking advantage of the well-characterized FLOWERING LOCUS C (FLC) gene.

FLC encodes a MADS-box transcription factor that represses a group of floral integrators, thereby halting the transition from vegetative to reproductive growth. This regulatory function is broadly conserved across plant species (Figure 2). The quantitative variation of FLC plays a crucial role in Arabidopsis adaptation to diverse climates, ranging from near the Arctic Circle to the equator, likely reason why its transcriptional control is tightly controlled.

Figure 2. FLC transcriptional output is key for the reproductive transition. (A) Schematic representation of the different pathways influencing FLC transcriptional output. Green ovals surrounding FRI (FRIGIDA), a transcriptional activator of FLC. The vernalization pathway, represented by a blue snowflake, represses FLC expression and reduces the amount of active FRI. Pale orange ovals represent a group of generic transcriptional regulators found to genetically cluster with FCA to repress FLC expression. The FCA-pathway also represses the antisense (COOLAIR) pathway. (B) Architecture of the FLC locus, with a representation of the sense and main antisense transcripts.

My recent research has uncovered new insights into the transcription-coupled repression mechanism at FLC, linking co-transcriptional processing with chromatin modifications. We identified a plant-specific version of the CPF module (LD-TOPP4-APRF1), which is conserved across species—from yeast (Ref2-Glc7-Swd2) to humans (PNUTS-PP1-WDR82). This module modulates RNAPII termination and interacts with the Arabidopsis chromatin modifier FLD, a homolog of the human LSD1 (Figure 3).

Additionally, by integrating experimental data with mathematical modeling, we revealed how FLD’s function is connected to PRC2-mediated epigenetic silencing. Our findings show that transcription-coupled repression regulates the degree of transcriptional antagonism to PRC2, which in turn dictates the timing of the epigenetic switch to PRC2-H3K27me3 silencing. Therefore, the CPF-FLD interaction establishes a framework for understanding how polyadenylation, termination, and graded transcriptional repression drive chromatin changes that influence the timing of the Polycomb switch.

Figure 3. CPF phosphatase module conservation among species and CPF-FLD framework connecting termination and silencing. (A) Matching colours indicate orthologs. Dashed and black lines indicate proteins with unknown or unrelated orthologs. (B) Early termination events led to changes in chromatin environment that reinforces subsequent early termination events. This feedback reduces transcription allowing PRC2 nucleation and epigenetic silencing.

We are currently delving deeper into the mechanistic details of these processes, employing a multidisciplinary approach that includes molecular biology, genetics, biochemistry, and a wide range of sequencing technologies. Our research aims to uncover fundamental principles that explain how transcription termination shapes the surrounding chromatin environment. These findings have the potential to unlock new opportunities in biotechnology, synthetic biology, and agriculture, as well as implications for advancing human health.