Biology subjects

LOUBIERE, V.

Publications and source records attributed to LOUBIERE, V..

3 recordsLinked to original sources

bioRxiv2023

Enhancer cooperativity can compensate for loss of activity over large genomic distances

Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements is not well understood. Here, we developed a novel synthetic platform that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and revealed that the strength of an enhancer determines how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances.

molecular biology↗

bioRxiv2023

Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila

Genomic enhancers are key transcriptional regulators which, upon the binding of sequence-specific transcription factors, activate their cognate target promoters. Although enhancers have been extensively studied in isolation, a substantial number of genes have more than one simultaneously active enhancer, and it remains unclear how these cooperate to regulate transcription. Using Drosophila melanogaster S2 cells as a model, we assay the activities of more than a thousand individual enhancers and a million enhancer pairs towards housekeeping and developmental core promoters with STARR-seq. We report that housekeeping and developmental enhancers show distinct modes of enhancer-enhancer cooperativity: while housekeeping enhancers are additive such that their combined activity mirrors the sum of their individual activities, developmental enhancers are synergistic and follow a multiplicative model of cooperativity. This developmental enhancer synergy is promiscuous and neither depends on the enhancers endogenous genomic contexts nor on specific transcription factor motif signatures, but it saturates for the highest levels of enhancer activity. These results have important implications for our understanding of gene-regulation in complex multi-enhancer loci and genomically clustered housekeeping genes, providing a rationale for strong and mild transcriptional effects of mutations within enhancer regions.

genomics↗

bioRxiv2023

Transient loss of Polycomb components induces an epigenetic cancer fate

Cell fate depends on genetic, epigenetic and environmental inputs that are interconnected, making it difficult to disentangle their respective contributions to cell fate decisions1-3, and epigenetic reprogramming is a major contributor to tumor plasticity and adaptation4-6. Although cancer initiation and progression are generally associated with the accumulation of somatic mutations7,8, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility9-18, suggesting that genetic mechanisms alone may not be sufficient to drive malignant transformations19-23. However, whether purely non-genetic reprogramming mechanisms are sufficient to initiate tumorigenesis irrespective of mutations is unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb-Group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including JNK and JAK-STAT signalling pathways and zfh1, the fly homolog of the ZEB1 oncogene, which we show to be a necessary driver of the cancer fate. These data show that a reversible perturbation of Polycomb-Group protein levels can induce cancer in the absence of driver mutations and suggest that this is achieved through epigenetic inheritance of altered cell fates.

developmental biology↗