Maria Carmo-Fonseca Lab

RNA & Gene Regulation

Gene regulation is central to all biology. RNA molecules, with their ability to both encode information and exert catalytic activities, play a key role in the regulation of gene expression.

Our group aims to discover molecular pathways and mechanisms implicating RNA in human health and disease. More specifically, we study RNA splicing and its role in the regulation of gene expression in cancer and genetic diseases, and we are exploring new medical applications for RNA.

Science Dissemination:

• The peaks and valleys of the nascent transcriptome in Drosophila embryos by Rosina Savisaar - Here

Research Team

Research Areas

• RNA Biology
• Gene Regulation
• Splicing
• RNA in Disease

Ongoing Research Projects

2022/2026 Cardiac splicing as a therapeutic target. Participant: Maria Carmo-Fonseca. Funding Agency: LEDUCQ Foundation for Cardiovascular Research.

2022/2025 CANCERNA: RNA processing for anti-cancer immunotherapy. Participant: Maria Carmo-Fonseca. Funding Agency: EU-Horizon Europe.

2022/2024 Impact of the Portuguese BRCA2 founder mutation on transcription and tissue stem cell identity. Coordinator: Maria Carmo-Fonseca. Funding Agency: Fundação para a Ciência e a Tecnologia.

2020/2023 spliceHCM - RNA mis-splicing in hypertrophic cardiomyopathy: opportunities for diagnosis and therapy. Coordinator: Maria Carmo-Fonseca. Funding Agency: “la Caixa” Foundation Health Research.

2019/2023 RNA in disease – RiboMed. Coordinator: Maria Carmo-Fonseca. Funding Agency: European Commission.

2017/2024 The Discoveries CTR: Implementation of the discoveries centre for regenerative and precision medicine, a new centre of excellence in Portugal. Coordinator: Maria Carmo-Fonseca. Funding Agency: European Commission.

Previous Research Projects

2020/2022 From co-transcriptional splicing kinetics to the evolutionary impact of exon and intron definition. Coordinator: Rosina Savisaar. Funding Agency: European Commission.

2020/2021 Exploring new therapeutic strategies for Angelman syndrome: A disease modelling approach based on 3D cerebellar organoids derived from patient iPSCs. Coordinators: Simão Teixeira da Rocha and Evguenia Bekman. Funding Agency: Fundação Amélia de Mello.

2020/2021 Assessing response to splicing inhibitor sulfonamides in cultured primary human AML cells. Coordinator: Maria Carmo-Fonseca. Funding Agency: Gilead Sciences.

2020/2021 AbbVie Inc - Material Transfer Agreement. Coordinator: Maria Carmo-Fonseca. Funding Agency: AbbVie Inc.

2018/2021 O papel dos RNAs não-codificantes longos (lncRNAs) na adaptação molecular e metabólica do cancro da mama (LISBOA-01-0145-FEDER-028534). Coordinator: Bruno Jesus. Funding Agency: Fundação para a Ciência e a Tecnologia and PT2020.

2018/2021 CEREBREX: Desenvolvimento de organóides cerebelares para investigação de ataxias (LISBOA-01-0145-FEDER-029298). Coordinator: Maria Carmo-Fonseca. Funding Agency: Fundação para a Ciência e a Tecnologia and PT2020.

2018/2021 BRCA_RNA: Organóides com edição génica para estudar o impacto funcional de mutações BRCA1 e BRCA2 (LISBOA-01-0145-FEDER-029469). Coordinator: Maria Carmo-Fonseca. Funding Agency: Fundação para a Ciência e a Tecnologia and PT2020.

2018/2021 As barreiras epigenéticas do envelhecimento na reprogramação celular. Coordinator: Simão Rocha. Funding Agency: Fundação para a Ciência e a Tecnologia.

2017/2021 LysoMod: Genetic and small molecule modifiers of Lysomomal Function. Coordinator: Maria Carmo-Fonseca. Funding Agency: European Commission. Marie Skłodowska-Curie Actions Staff Exchanges - Know more here.

2016/2021 Precise - Promoção do avanço significativo do conhecimento na área de medicina de precisão e sua translação para benefício da sociedade. Coordinator: Maria Carmo-Fonseca. Funding Agency: Fundação para a Ciência e a Tecnologia.

Awards

2020 Elected President of the RNA Society 2021/22.

2018 Prémio Aboim Sande Lemos - Identidade Portuguesa.

2013 Prémio D. Antónia Ferreira (Portuguese award for Entrepreneurial women).

2010 Prémio Pessoa (Portuguese award in Culture, Art and Sciences).

2007 Gulbenkian Science Award (Fundação Calouste Gulbenkian, Portugal).

2006 Amélia da Silva de Mello Prize for Health Sciences "Altered BMP signalling in a cellular model of Oculopharyngeal Muscular Dystrophy" (awarded to P. Calado, S. Caldeira, A. Gomes, A. R. Grosso, N. Thorne, M. Carmo-Fonseca).

2005 Best poster presentation in the 5º Meeting of the European Light Microscopy Initiative (ELMI 2005) (awarded to J. Rino).

2005 Young Investigator Award (Sociedade Portuguesa de Genética Humana) (awarded to P. Calado).

2004 Estímulo à Ciência Award (Fundação Ciência e Tecnologia).

2004 Young Investigator Award (Sociedade Portuguesa de Genética Humana) (awarded to A. Gomes).

2004 L'Oreal Portugal/Unesco Award For Women in Science (awarded to M. Gama-Carvalho).

Selected Publications

Carmo-Fonseca M. (2023). Sweet splicing. Cell 186(1):10-11. doi: 10.1016/j.cell.2022.11.025.

Carmo-Fonseca M. (2023). A twist to splicing regulation in haematopoiesis. Nature Cell Biology 25(4):516-517. doi: 10.1038/s41556-022-01043-2.

Tammer L; Hameiri O; Keydar I; Roy VR; Ashkenazy-Titelman A; Custódio N; Sason I; Shayevitch R; Rodriguez-Vaello V; Rino J; Maor GL; Leader Y; Khair D; Aiden EL; Elkon R; Irimia M; Sharan R; Shav-Tal Y; Carmo-Fonseca M; Ast G. (2022). Gene architecture directs splicing outcome in separate nuclear spatial regions. Molecular Cell. 82 5 1021-1034.e8.

Sousa-Luís R, Carmo-Fonseca M. (2022) Pseudouridylation: A new player in co-transcriptional splicing regulation. Molecular Cell 82(3):495-496.

Sousa-Luis R, Dujardin G, Zukher I, Kimura H, Carmo-Fonseca M, Proudfoot NJ, Nojima T (2021). POINT Technology illuminates the processing of polymerase-associated intact nascent transcripts. Molecular Cell 81(9):1935-1950.

Nojima T, Rebelo K, Gomes T, Grosso AR, Proudfoot NJ, Carmo-Fonseca M (2018). RNA Polymerase II phosphorylated on CTD Serine 5 interacts with the spliceosome during co-transcriptional splicing. Molecular Cell 72(2):369-379.

Bernardes de Jesus B, Matinho SP, Barros S, Sousa-Franco A, Alves-Vale C, Carvalho T, Carmo-Fonseca M (2018) Silencing of the lncRNA Zeb2-NAT facilitates reprogramming of aged fibroblasts and safegards stem cell pluripotency. Nature Commun. 9(1):94.

Vaz-Drago R, Custódio N, Carmo-Fonseca M, (2017) Deep intronic mutations and human disease. Hum Genet. 136: 1093-1111.

Nojima T, Gomes T, Grosso AR, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, Proudfoot N (2015). Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161(3):526-540.

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