Presentation:

My research focuses on understanding how alternative RNA splicing and post-transcriptional regulation shape gene expression programs in human cells. I integrate long-read transcriptomics with chromatin and nuclear regulatory mechanisms to decipher transcriptome complexity in hematological diseases. My work aims to identify pathogenic RNA signatures and develop therapeutic strategies based on transcriptome reprogramming.

Projects:

My research program investigates how RNA processing shapes gene expression in hematopoiesis and how transcriptome reprogramming can drive therapeutic innovation. After several years at Institut Pasteur studying alternative splicing and gene regulation, I joined Institut IMAGINE five years ago to work with Pr Olivier Hermine on hematological and immune disorders. This transition allowed me to develop an integrated research program at the crossroads of RNA biology, molecular hematology, and translational medicine.

• Deep analysis of RNA-processing regulation during erythropoiesis – We seek to understand how alternative splicing and polyadenylation shape gene expression throughout human erythropoiesis, establishing a reference framework to interpret RNA-processing alterations in red-cell disorders.

• Splicing factor mutations in systemic mastocytosis and associated myelodysplastic syndromes – We examine how mutations in core splicing regulators and apoptosis-related genes (e.g., SF3B1, SRSF2, FAS) rewire signaling networks in mastocytosis, myelodysplastic syndromes, and immune dysregulation.

• Activation of fetal hemoglobin in β-hemoglobinopathies through transcriptome reprogramming – We investigate selective modulation of RNA isoform balance, particularly in BCL11A, to restore HbF expression and develop safer therapeutic strategies for β-hemoglobinopathies.

• Oncogenic transcriptome rewiring in T-cell leukemia – We explore how aberrant splicing generates cryptic isoforms and proteoforms that sustain leukemic proliferation and uncover new therapeutic vulnerabilities.

Together, we seek to better understand how RNA isoform diversity constitutes a central regulatory layer controlling hematopoietic differentiation, oncogenic transformation, and immune dysregulation. By combining mechanistic insight with functional perturbation and translational validation, we aim to transform transcriptomic complexity into actionable therapeutic strategies.

Selected publications:
Base editing of β0-thalassemia mutations as a therapeutic strategy for severe β-hemoglobinopathies.
Hardouin G, Martinucci P, Scaramuzza S, Antoniou P, Corradi F, Tachtsidi A, Corre G, Mombled M, Chermont J, Manceau S, Rouillon C, Masson C, Joseph L, Thuret I, Badens C, Szepetowsky S, Allemand E, Amendola M, Romano O, Ferrari G, Miccio A.
Science Translational Medicine. 2025.
PMID: https://pubmed.ncbi.nlm.nih.gov/41296828/

VEXAS anemia is a mosaic erythroblastopenia.
Rodrigues F, Hardouin G, El Hoss S, Ghoul A, Gautier EF, Dussiot M, Lizarralde-Iragorri MA, Santini A, Peltier S, Amireault P, Soldan V, Miccio A, Debili M, Jachiet V, Trovati Maciel T, Rossignol J, Allemand E, Mékinian AM, Georgin-Lavialle SA, Salma M, Soler E, Gleizes PE, O'Donohue MF, Kosmider O, Rodriguez MS, Hermine O.
Blood. 2025.
PMID: https://pubmed.ncbi.nlm.nih.gov/40971475/

Identification of CaVβ1 Isoforms Required for Neuromuscular Junction Formation and Maintenance.
Vergnol A, Bourguiba A, Bauché S, Traoré M, Gelin M, Gentil C, Pezet S, Saillard L, Meunier P, Lemaitre M, Perronnet J, Tores F, Gautier C, Guesmia Z, Allemand E, Batsché E, Pietri-Rouxel F, Falcone S.
Cells. 2025.
PMID: https://pubmed.ncbi.nlm.nih.gov/40801641/

Dissecting the epigenetic regulation of the fetal hemoglobin genes to unravel a novel therapeutic approach for β-hemoglobinopathies.
Amistadi S, Fontana L, Magnoni C, Felix T, Charvin MK, Martinucci P, Gautier C, Greau L, Bessières B, Antoniou P, Romano O, Allemand E, Mussolino C, Miccio A.
Nucleic Acids Research. 2025.
PMID: https://pubmed.ncbi.nlm.nih.gov/40637230/

Exchange of subtelomeric regions between chromosomes 4q and 10q reverts the FSHD genotype and phenotype.
Ma Y, Schwager Karpukhina A, Dib C, Gautier C, Hermine O, Allemand E*, Vassetzky YS*,.
Science Advances. 2024.
PMID: https://pubmed.ncbi.nlm.nih.gov/38691604/

Transcription-induced domains form the elementary constraining building blocks of bacterial chromosomes.
Bignaud A, Cockram C, Borde C, Groseille J, Allemand E, Thierry A, Marbouty M, Mozziconacci J, Espéli O, Koszul R.
Nature Structural & Molecular Biology. 2024.
PMID: https://pubmed.ncbi.nlm.nih.gov/38177686/

TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer.
Smith C, Goyal A, Weichenhan D, Allemand E, Mayakonda A, Toprak U, Riedel A, Balducci E, Manojkumar M, Pejkovska A, Mücke O, Sollier E, Bakr A, Breuer K, Lutsik P, Hermine O, Spicuglia S, Asnafi V, Plass C, Touzart A.
Haematologica. 2023.
PMID: https://pubmed.ncbi.nlm.nih.gov/36632736/

Analysis of Splicing Regulation by Third-Generation Sequencing.
Allemand E*,, Ango F*,.
Methods in Molecular Biology. 2022.
PMID: https://pubmed.ncbi.nlm.nih.gov/35895260/

Complex regulation of Gephyrin splicing is a determinant of inhibitory postsynaptic diversity.
Dos Reis R, Kornobis E, Pereira A, Tores F, Carrasco J, Gautier C, Jahannault-Talignani C, Nitschké P, Muchardt C, Schlosser A, Maric HM, Ango F*,, Allemand E*,.
Nature Communications. 2022.
PMID: https://pubmed.ncbi.nlm.nih.gov/35717442/

An RNA-Binding Protein Secreted by a Bacterial Pathogen Modulates RIG-I Signaling.
Pagliuso A, Tham TN, Allemand E, Robertin S, Dupuy B, Bertrand Q, Bécavin C, Koutero M, Najburg V, Nahori MA, Tangy F, Stavru F, Bessonov S, Dessen A, Muchardt C, Lebreton A, Komarova AV, Cossart P.
Cell Host & Microbe. 2019.
PMID: https://pubmed.ncbi.nlm.nih.gov/31761719/

A Broad Set of Chromatin Factors Influences Splicing.
Allemand E, Myers MP, Garcia-Bernardo J, Harel-Bellan A, Krainer AR, Muchardt C.
PLoS Genetics. 2016.
PMID: https://pubmed.ncbi.nlm.nih.gov/27662573/

Alternative splicing regulates the expression of G9A and SUV39H2 methyltransferases, and dramatically changes SUV39H2 functions.
Mauger O, Klinck R, Chabot B, Muchardt C, Allemand E*,, Batsché E*,.
Nucleic Acids Research. 2015.
PMID: https://pubmed.ncbi.nlm.nih.gov/25605796/

Expression and purification of splicing proteins from mammalian cells.
Allemand E*,, Hastings ML*,.
Methods in Molecular Biology. 2014.
PMID: https://pubmed.ncbi.nlm.nih.gov/24549667/