Maria Carmo-Fonseca - Selected Publications#

Prudêncio P, Savisaar R, Rebelo K, Martinho RG, Carmo-Fonseca M (2021). Transcription and splicing dynamics during early Drosophila development. RNA (in press). Using NET-seq, we found distinct patterns of transcription termination in early and late Drosophila embryos. We further detected highly heterogeneous splicing kinetics, irrespective of intron size.

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. Mol Cell 81(9):1935-1950. A new methodology to purify and sequence RNA polymerase II-associated intact nascent transcripts reveals the kinetics of co-transcriptional splicing at a single molecule level. Cited by 10.

Desterro J, Bak-Gordon P, Carmo-Fonseca M (2020). Targeting mRNA processing as an anticancer strategy. Nature Reviews Drug Discovery 19:112-129. This commissioned review testifies Carmo-Fonseca’s recognition in the field of splicing and its medical implications. Cited by 51.

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. Mol Cell 72(2):369-379. Genome-wide analysis of nascent RNA complexes using NET-seq revealed unanticipated dynamic links between Pol II and the spliceosome. Cited by 81.

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. Nat Commun. 9(1):94. This study highlights the physiological importance of antisense transcription in fine tuning the expression of a protein coding gene. We identified the transcription factor Zeb2 as a novel age-associated barrier to reprogramming. We show that forcing Zeb2 downregulation may help improve reprogramming efficiency, and we uncovered a long non-coding RNA that is overlapping and antisense to the Zeb2 locus as a target to achieve robust Zeb2 downregulation. Cited by 39.

Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M. (2017) Pharmacological inhibition of the spliceosome subunit SF3b triggers EJC-independent NMD. J Cell Sci. 130 (9): 1519-1531. This study not only shows that cytoplasmic pre-mRNAs evoke an EJC-independent NMD pathway response when splicing is blocked, but also provides insights into the effects of a set of potential anti-cancer drugs on the stability and transport of mRNAs. Cited by 21.

Vaz-Drago R, Custódio N, Carmo-Fonseca M, (2017) Deep intronic mutations and human disease. Hum Genet. 136: 1093-1111. This review highlights the importance of studying variation in deep intronic sequence as a cause of monogenic disorders as well as hereditary cancer syndromes. Cited by 222.

Nojima T, Gomes T, Grosso AR, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, and Proudfoot N. (2015) Mammalian NET-seq reveals genome-wide nascent transcription coupled to RNA processing. Cell 161(3): 526-540. This study provides the first genome-wide analysis of co-transcriptional RNA splicing at single-nucleotide resolution. Cited by 396.

~10,000 citations (h index 54)