Research interests of my group are centered on the characterization of molecular transactions ruling healthy/disease gene expression programs. We aim for better fundamental understanding of essential chromatin/cellular processes ruling RNA polymerase II transcription initiation and elongation at protein coding- and non-coding- (lncRNAs, eRNAs…), how genomic DNA sequences integrity is guaranteed in the face of environmental and genetic perturbations, and what might be the impact of defined gene regulatory networks (GRNs) on cells commitment in developmental or pathogenic (de)differentiation lineages.
We apply 4D (time and space) -resolution biochemical and Next Generation Sequencing (NGS) protocols as well as bioinformatics analyses/simulations to decipher gene control mechanisms at the molecular/multi-molecular and cellular/multicellular levels. Using human cell lines, mouse models or available data, we resolve chromatin status (ChIP-seq, ATAC-seq), protein complexes (IP, RIP, ChIP-western), transcription machinery binding sites (ChIP-seq, Cut-and-Run), DNA topology (4C-seq, HiC), DNA integrity (damage/repaired DNA patterns), nascent/mature RNA levels and synthesis rate (EU-seq, mRNA-seq, quant-seq). We also rely on single cell (sc) (scRNA-seq and scATAC-seq) approaches to establish transcriptional and chromatin regulatory networks and show what is their effect on cellular differentiation trajectories. Overall, the variety of wet and dry techniques we routinely develop are integrated to infer transcriptional and epigenetic principles and pinpoint when/how they might go eerie in disease.
Armaka M, Konstantopoulos D, Tzaferis C, Lavigne MD, Sakkou M, Liakos A, Sfikakis PP, Dimopoulos MA, Fousteri M, Kollias G. (2022) Single-cell multimodal analysis identifies common regulatory programs in synovial fibroblasts of rheumatoid arthritis patients and modeled TNF-driven arthritis. Genome Med. 14:78.
Liakos A, Konstantopoulos D, Lavigne MD, Fousteri M. (2020) Continuous transcription initiation guarantees robust repair of all transcribed genes and regulatory regions. Nat Commun. 11:916.
Liakos A, Lavigne MD, Fousteri M. (2017) Nucleotide Excision Repair: From Neurodegeneration to Cancer. Adv Exp Med Biol. 1007:17-39.
Lavigne MD, Konstantopoulos D, Ntakou-Zamplara KZ, Liakos A, Fousteri M. (2017) Global unleashing of transcription elongation waves in response to genotoxic stress restricts somatic mutation rate. Nat Commun. 8:2076.
Lavigne MD, Vatsellas G, Polyzos A, Mantouvalou E, Sianidis G, Maraziotis I, Agelopoulos M, Thanos D. (2015) Composite macroH2A/NRF-1 nucleosomes suppress noise and generate robustness in gene expression. Cell Rep. 11:1090-1101.
For complete list click here: https://pubmed.ncbi.nlm.nih.gov/?term=Lavigne+MD&sort=date