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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.

Publications

2023

Bhat, P., Cabrera-Quio, LE., Herzog, VA., Fasching, N., Pauli, A., Ameres, SL. (2023)

SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis.

Corresponding preprint Cell Rep. 42(2):112070
Leesch, F., Lorenzo-Orts, L., Pribitzer, C., Grishkovskaya, I., Roehsner, J., Chugunova, A., Matzinger, M., Roitinger, E., Belačić, K., Kandolf, S., Lin, TY., Mechtler, K., Meinhart, A., Haselbach, D., Pauli, A. (2023)

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

Corresponding preprint Nature.

2022

Wu, SS., Lee, H., Szép-Bakonyi, R., Colozza, G., Boese, A., Gert, KR., Hallay, N., Lee, JH., Kim, J., Zhu, Y., Linssen, MM., Pilat-Carotta, S., Hohenstein, P., Theussl, HC., Pauli, A., Koo, BK. (2022)

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

Corresponding preprint Exp Mol Med.
Stock, J., Kazmar, T., Schlumm, F., Hannezo, E., Pauli, A. (2022)

A self-generated Toddler gradient guides mesodermal cell migration.

Corresponding preprint Sci Adv. 8(37):eadd2488
Kellner, MJ., Ross, JJ., Schnabl, J., Dekens, MPS., Matl, M., Heinen, R., Grishkovskaya, I., Bauer, B., Stadlmann, J., Menéndez-Arias, L., Straw, AD., Fritsche-Polanz, R., Traugott, M., Seitz, T., Zoufaly, A., Födinger, M., Wenisch, C., Zuber, J., Pauli, A., Brennecke, J. (2022)

A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing.

Corresponding preprint Front Mol Biosci. 9:801309
Noda, T., Blaha, A., Fujihara, Y., Gert, KR., Emori, C., Deneke, VE., Oura, S., Panser, K., Lu, Y., Berent, S., Kodani, M., Cabrera-Quio, LE., Pauli, A., Ikawa, M. (2022)

Sperm membrane proteins DCST1 and DCST2 are required for sperm-egg interaction in mice and fish.

Corresponding preprint Commun Biol. 5(1):332
Huth, M., Santini, L., Galimberti, E., Ramesmayer, J., Titz-Teixeira, F., Sehlke, R., Oberhuemer, M., Stummer, S., Herzog, V., Garmhausen, M., Romeike, M., Chugunova, A., Leesch, F., Holcik, L., Weipoltshammer, K., Lackner, A., Schoefer, C., von Haeseler, A., Buecker, C., Pauli, A., Ameres, SL., Smith, A., Beyer, A., Leeb, M. (2022)

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

Corresponding preprint Genes Dev. 36(5-6):348-367
Binner, MI., Kogan, A., Panser, K., Schleiffer, A., Deneke, VE., Pauli, A. (2022)

The Sperm Protein Spaca6 is Essential for Fertilization in Zebrafish.

Corresponding preprint Front Cell Dev Biol. 9:806982

2021

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
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
Stock, J., Pauli, A. (2021)

Self-organized cell migration across scales - from single cell movement to tissue formation.

 Development. 148(7)
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
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
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-printGuo,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

2020

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

Species-specific mechanisms during fertilization.

 Curr Top Dev Biol. 140:121-144

2019

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

2018

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

2017

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
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

2016

Chew, GL., Pauli, A., Schier, AF. (2016)

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.

 Nat Commun. 7:11663
Cabrera-Quio, LE., Herberg, S., Pauli, A. (2016)

Decoding sORF translation - from small proteins to gene regulation.

 RNA Biol. 13(11):1051-1059

2015

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

2014

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
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
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
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

2013

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

2012

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

2011

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
Pauli, A., Rinn, JL., Schier, AF. (2011)

Non-coding RNAs as regulators of embryogenesis.

 Nat Rev Genet. 12(2):136-49

2010

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
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

2008

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

2006

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

2004

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