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Andrea Pauli

Recent genome-wide analyses have spurred the notion of ‘pervasive translation’ outside of known protein-coding genes. Some of these translated regions have been predicted to encode short, conserved proteins, while others lack signatures of protein conservation and might have regulatory roles. We aim to identify functions for these newly discovered short translated open reading frames (ORFs) during embryogenesis by employing genetic, molecular, cellular and genomics approaches in zebrafish embryos.



Herberg, S., Gert, KR., Schleiffer, A., Pauli, A. (2018)The Ly6/uPAR protein Bouncer is necessary and sufficient for species-specific fertilization. Science. 361(6406):1029-1033


Freyer, L., Hsu, CW., Nowotschin, S., Pauli, A., Ishida, J., Kuba, K., Fukamizu, A., Schier, AF., Hoodless, PA., Dickinson, ME., Hadjantonakis, AK. (2017)Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives. Cell Rep. 20(9):2116-2130
Norris, ML., Pauli, A., Gagnon, JA., Lord, ND., Rogers, KW., Mosimann, C., Zon, LI., Schier, AF. (2017)Toddler signaling regulates mesodermal cell migration downstream of Nodal signaling. Elife. 6
Rogers, KW., Lord, ND., Gagnon, JA., Pauli, A., Zimmerman, S., Aksel, DC., Reyon, D., Tsai, SQ., Joung, JK., Schier, AF. (2017)Nodal patterning without Lefty inhibitory feedback is functional but fragile. Elife. 6


Cabrera-Quio, LE., Herberg, S., Pauli, A. (2016)Decoding sORF translation - from small proteins to gene regulation. RNA Biol. 13(11):1051-1059
Chew, GL., Pauli, A., Schier, AF. (2016)Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun. 7:11663


Pauli, A., Montague, TG., Lennox, KA., Behlke, MA., Schier, AF. (2015)Antisense Oligonucleotide-Mediated Transcript Knockdown in Zebrafish. PLoS One. 10(10):e0139504
Pauli, A., Valen, E., Schier, AF. (2015)Identifying (non-)coding RNAs and small peptides: challenges and opportunities. Bioessays. 37(1):103-12


Gagnon, JA., Valen, E., Thyme, SB., Huang, P., Akhmetova, L., Ahkmetova, L., Pauli, A., Montague, TG., Zimmerman, S., Richter, C., Schier, AF. (2014)Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs. PLoS One. 9(5):e98186
Pauli, A., Norris, ML., Valen, E., Chew, GL., Gagnon, JA., Zimmerman, S., Mitchell, A., Ma, J., Dubrulle, J., Reyon, D., Tsai, SQ., Joung, JK., Saghatelian, A., Schier, AF. (2014)Toddler: an embryonic signal that promotes cell movement via Apelin receptors. Science. 343(6172):1248636
Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, DJ., Pauli, A., Hacohen, N., Schier, AF., Blackshear, PJ., Friedman, N., Amit, I., Regev, A. (2014)High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies. Cell. 159(7):1698-710
Zhang, Y., Vastenhouw, NL., Feng, J., Fu, K., Wang, C., Ge, Y., Pauli, A., van Hummelen, P., Schier, AF., Liu, XS. (2014)Canonical nucleosome organization at promoters forms during genome activation. Genome Res. 24(2):260-6


Chew, GL., Pauli, A., Rinn, JL., Regev, A., Schier, AF., Valen, E. (2013)Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development. 140(13):2828-34


Pauli, A., Valen, E., Lin, MF., Garber, M., Vastenhouw, NL., Levin, JZ., Fan, L., Sandelin, A., Rinn, JL., Regev, A., Schier, AF. (2012)Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res. 22(3):577-91


Pauli, A., Rinn, JL., Schier, AF. (2011)Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet. 12(2):136-49
Strübbe, G., Popp, C., Schmidt, A., Pauli, A., Ringrose, L., Beisel, C., Paro, R. (2011)Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proc Natl Acad Sci U S A. 108(14):5572-7


Oliveira, RA., Hamilton, RS., Pauli, A., Davis, I., Nasmyth, K. (2010)Cohesin cleavage and Cdk inhibition trigger formation of daughter nuclei. Nat Cell Biol. 12(2):185-92
Pauli, A., van Bemmel, JG., Oliveira, RA., Itoh, T., Shirahige, K., van Steensel, B., Nasmyth, K. (2010)A direct role for cohesin in gene regulation and ecdysone response in Drosophila salivary glands. Curr Biol. 20(20):1787-98


Pauli, A., Althoff, F., Oliveira, RA., Heidmann, S., Schuldiner, O., Lehner, CF., Dickson, BJ., Nasmyth, K. (2008)Cell-type-specific TEV protease cleavage reveals cohesin functions in Drosophila neurons. Dev Cell. 14(2):239-51


Panse, VG., Kressler, D., Pauli, A., Petfalski, E., Gnädig, M., Tollervey, D., Hurt, E. (2006)Formation and nuclear export of preribosomes are functionally linked to the small-ubiquitin-related modifier pathway. Traffic. 7(10):1311-21


Marhold, J., Rothe, N., Pauli, A., Mund, C., Kuehle, K., Brueckner, B., Lyko, F. (2004)Conservation of DNA methylation in dipteran insects. Insect Mol Biol. 13(2):117-23