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Andrea Pauli

Fertilisation marks the beginning of life of any sexually reproducing organism. It also initiates a series of events that result in the large-scale remodelling of the arrested egg cell into metabolically and functionally distinct embryonic cells. Both of these events occur during the oocyte-to-embryo transition, which comprises one of the most dramatic yet remarkably mysterious developmental transition. In the Pauli lab, we aim to gain mechanistic insights into the molecular control of fertilisation and the oocyte-to-embryo transition by employing genetic, molecular, cellular, biochemical and genomics approaches in zebrafish embryos.



Bhat, P., Burkard, TR., Herzog, VA., Pauli, A., Ameres, SL. (2021)

Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.

Methods Enzymol. 655:205-223
Pre-printBinner,MI., Kogan,A., Panser,K., Schleiffer, A., Deneke,VE., Pauli, A. (2021)

The sperm protein Spaca6 is essential for fertilization in zebrafish

bioRxiv . 2021.11.19.469324
Cabrera-Quio, LE., Schleiffer, A., Mechtler, K., Pauli, A. (2021)

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition.

PLoS Genet. 17(2):e1009390
Deneke, VE., Pauli, A. (2021)

The Fertilization Enigma: How Sperm and Egg Fuse.

Annu Rev Cell Dev Biol.
Fujihara, Y., Herberg, S., Blaha, A., Panser, K., Kobayashi, K., Larasati, T., Novatchkova, M., Theussl, HC., Olszanska, O., Ikawa, M., Pauli, A. (2021)

The conserved fertility factor SPACA4/Bouncer has divergent modes of action in vertebrate fertilization.

Corresponding preprint Proc Natl Acad Sci U S A. 118(39)
Pre-printGert,KR., Cabrera Quio,LE., Novatchkova,M., Guo,Y., Cairns,BR., Pauli,A. (2021)

Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

bioRxiv . 2021.11.03.467109
Guo,Y., Gert,KR., Lebedeva,S., Potok,ME., Wike,CL., Grow,EJ., Ketting,RF., Pauli,A., Cairns,B. (2021)

Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos

bioRxiv . 2021.11.03.467172
Pre-printKellner MJ, Matl M, Ross JJ, Schnabl J, Handler D, Heinen R, Schaeffer J, Hufnagl P, Indra A, Dekens MPS, Fritsche-Polanz R, Födinger M, Zuber J, Vienna Covid-19 Detection Initiative (VCDI), Allerberger F, Pauli A, Brennecke J (2021)

Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics.

medRxiv. 2021.01.19.21250079
Pre-printLeesch,KF., Lorenzo-Orts,L., Pribitzer,C., Grishkovskaya,I., Matzinger,M., Roitinger,E., Belacic,K., Kandolf,S., Lin, TY., Mechtler,K., Meinhart,A., Haselbach,D., Pauli,A. (2021)

A molecular network of conserved factors keeps ribosomes dormant in the egg

bioRxiv . 2021.11.03.467131
Pre-printNoda T, Blaha A, Fujihara Y, Gert KR, Emori C, Deneke VE, Oura S, Berent S, Kodani M, Panser K, Cabrera-Quio LE, Pauli A, Ikawa M (2021)

Sperm membrane proteins DCST1 and DCST2 are required for the sperm-egg fusion process in mice and fish

bioRxiv . 2021.04.18.440256
Stock,S., Kazmar,T., Schlumm,S., Hannezo,E., Pauli,A. (2021)

A self-generated Toddler gradient guides mesodermal cell migration

bioRxiv . 2021.12.16.472981
Pre-printWu, S-HS, Szep-Bakonyi R, Lee H, Colozza G, Boese A, Gert KR, Hallay N, Kim J, Zhu Y, Pilat-Carotta S, Theussl H-C, Pauli A, Koo B-K. (2021)

SCON - A Short Conditional intrON for conditional knockout with one-step zygote injection

bioRxiv . 2021.05.09.443220


Pre-printGalimberti E, Sehlke R, Huth M, Garmhausen M, Romeike M, Ramesmayer J, Stummer S, Titz-Teixeira F, Herzog V, Chugunova A, Leesch KF, Holcik L, Weipoltshammer K, Santini L, Lackner A, von Haeseler A, Bücker C, Pauli A, Schoefer C, Ameres SL, Smith A, Beyer A, Leeb M. (2020)

NMD is required for timely cell fate transitions by fine-tuning gene expression and controlling translation

bioRxiv . 2020.07.07.180133
Gert, KR., Pauli, A. (2020)

Species-specific mechanisms during fertilization.

Curr Top Dev Biol. 140:121-144
Pre-printKellner MJ, Ross JJ, Schnabl J, Dekens MPS, Heinen R, Grishkovskaya I, Bauer B, Stadlmann J, Menéndez-Arias L, Fritsche-Polanz R, Traugott M, Seitz T, Zoufaly A, Födinger M, Wenisch C, Zuber J, Vienna Covid-19 Detection Initiative (VCDI), Pauli A, Brennecke J (2020)

A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing

bioRxiv . 2020.06.23.166397


Kamieniarz-Gdula, K., Gdula, MR., Panser, K., Nojima, T., Monks, J., Wiśniewski, JR., Riepsaame, J., Brockdorff, N., Pauli, A., Proudfoot, NJ. (2019)

Selective Roles of Vertebrate PCF11 in Premature and Full-Length Transcript Termination.

Mol Cell. 74(1):158-172.e9


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