Publications

Check out our recent work below!

Graphical Abstracts

Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster ...

A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo...

Hierarchical length and sequence preferences establish a single major piRNA 3'-end.

Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of...

Cellular abundance shapes function in piRNA-guided genome defense.

Decoding the 5' nucleotide bias of PIWI-interacting RNAs.

PIWI-interacting RNAs who, what, when, where, why, and how.

Themes and variations on piRNA-guided transposon control.

An introduction to PIWI-interacting RNAs (piRNAs) in the context of metazoan small RNA silencing ...

Aberrant expression of select piRNA-pathway genes does not reactivate piRNA silencing in cancer c...

The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis.

Select Publications

• Pachytene piRNAs define a conserved program of meiotic gene regulation
  Loubalova Z., Ahrend, F., Stoyko, D., Cosby, R., Ralls, S., Meister, G., Macfarlan, T., Haase, A.D. bioRxiv
• Protocol for assembling, prioritizing, and characterizing piRNA clusters using the piRNA Cluster Builder
  Ahrend F., Konstantinidou P., Loubalova Z., Wang Y., Lorenzi H., Meister G., Macfarlan T., Haase A.D. Cell STAR Protocols
• A comparative roadmap of PIWI-interacting RNAs across seven species reveals insights into de novo piRNA-precursor formation in mammals.
  Konstantinidou P, Loubalova Z, Ahrend F, Friman A, Almeida MV, Poulet A, Horvat F, Wang Y, Losert W, Lorenzi H, Svoboda P, Miska EA, van Wolfswinkel JC, Haase AD. Cell Rep. 2024;43(10):114777.
• Hierarchical length and sequence preferences establish a single major piRNA 3'-end.
  Stoyko D, Genzor P, Haase AD. iScience. 2022;25(6):104427.
• Functional editing of endogenous genes through rapid selection of cell pools (Rapid generation of endogenously tagged genes in Drosophila ovarian somatic sheath cells).
  Meng Q, Stoyko D, Andrews CM, Konstantinidou P, Genzor P, O T, Elchert AR, Benner L, Sobti S, Katz EY, Haase AD. Nucleic Acids Res. 2022;50(15):e90.
• Cellular abundance shapes function in piRNA-guided genome defense.
  Genzor P, Konstantinidou P, Stoyko D, Manzourolajdad A, Marlin Andrews C, Elchert AR, Stathopoulos C, Haase AD. Genome Res. 2021;31(11):2058-2068.
• Decoding the 5' nucleotide bias of PIWI-interacting RNAs.
  Stein CB, Genzor P, Mitra S, Elchert AR, Ipsaro JJ, Benner L, Sobti S, Su Y, Hammell M, Joshua-Tor L, Haase AD. Nat Commun. 2019;10(1):828.

Additional Publications

• A deficiency screen identifies genomic regions critical for sperm head-tail connection.
  Galletta BJ, Konstantinidou P, Haase AD, Rusan NM. G3 (Bethesda). 2025 Feb 5;15.
• Activity of the mammalian DNA transposon piggyBat from Myotis lucifugus is restricted by its own transposon ends.
  Hickman AB, Lannes L, Furman CM, Hong C, Franklin L, Ghirlando R, Ghosh A, Luo W, Konstantinidou P, Lorenzi HA, Grove A, Haase AD, Wilson MH, Dyda F. Nat Commun. 2025 Jan 7;16:458.
• PIWI-interacting RNAs who, what, when, where, why, and how.
  Haase AD, Ketting RF, Lai EC, van Rij RP, Siomi M, Svoboda P, van Wolfswinkel JC, Wu PH. EMBO J. 2024 Nov;43:5335-5339.
• A deficiency screen identifies genomic regions critical for sperm head-tail connection.
  Galletta BJ, Konstantinidou P, Haase AD, Rusan NM. bioRxiv. 2024 Aug 21.
• Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.
  Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. bioRxiv. 2024 Apr 1.
• Themes and variations on piRNA-guided transposon control.
  Loubalova Z, Konstantinidou P, Haase AD. Mob DNA. 2023 Sep 2;14:10.
• Transposase N-terminal phosphorylation and asymmetric transposon ends inhibit piggyBac transposition in mammalian cells.
  Luo W, Hickman AB, Genzor P, Ghirlando R, Furman CM, Menshikh A, Haase A, Dyda F, Wilson MH. Nucleic Acids Res. 2022 Dec 9;50:13128-13142.
• CRISPR-Cas9 Genome Editing and Rapid Selection of Cell Pools.
  Stoyko D, O T, Hernandez A, Konstantinidou P, Meng Q, Haase AD. Curr Protoc. 2022 Dec;2:e624.
• An introduction to PIWI-interacting RNAs (piRNAs) in the context of metazoan small RNA silencing pathways.
  Haase AD. RNA Biol. 2022 Jan;19:1094-1102.
• A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol.
  Anastasakis DG, Jacob A, Konstantinidou P, Meguro K, Claypool D, Cekan P, Haase AD, Hafner M. Nucleic Acids Res. 2021 May 7;49:e45.
• Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas.
  Hickman AB, Kailasan S, Genzor P, Haase AD, Dyda F. Elife. 2020 Jan 8;9.
• PiRNAs Rise to Rescue Koalas.
  Haase AD, Macfarlan TS. Cell. 2019 Oct 17;179:582-583.
• Aberrant expression of select piRNA-pathway genes does not reactivate piRNA silencing in cancer cells.
  Genzor P, Cordts SC, Bokil NV, Haase AD. Proc Natl Acad Sci U S A. 2019 Jun 4;116:11111-11112.
• Argonaute-miRNA Complexes Silence Target mRNAs in the Nucleus of Mammalian Stem Cells.
  Sarshad AA, Juan AH, Muler AIC, Anastasakis DG, Wang X, Genzor P, Feng X, Tsai PF, Sun HW, Haase AD, Sartorelli V, Hafner M. Mol Cell. 2018 Sep 20;71:1040-1050.e8.
• A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements.
  Haase AD. Stem Cells Int. 2016;2016:7595791.
• Dephosphorylation of tyrosine 393 in argonaute 2 by protein tyrosine phosphatase 1B regulates gene silencing in oncogenic RAS-induced senescence.
  Yang M, Haase AD, Huang FK, Coulis G, Rivera KD, Dickinson BC, Chang CJ, Pappin DJ, Neubert TA, Hannon GJ, Boivin B, Tonks NK. Mol Cell. 2014 Sep 4;55:782-90.
• The making of a slicer: activation of human Argonaute-1.
  Faehnle CR, Elkayam E, Haase AD, Hannon GJ, Joshua-Tor L. Cell Rep. 2013 Jun 27;3:1901-9.
• The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis.
  Ipsaro JJ, Haase AD, Knott SR, Joshua-Tor L, Hannon GJ. Nature. 2012 Nov 8;491:279-83.
• The structure of human argonaute-2 in complex with miR-20a.
  Elkayam E, Kuhn CD, Tocilj A, Haase AD, Greene EM, Hannon GJ, Joshua-Tor L. Cell. 2012 Jul 6;150:100-10.
• Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.
  Haase AD, Fenoglio S, Muerdter F, Guzzardo PM, Czech B, Pappin DJ, Chen C, Gordon A, Hannon GJ. Genes Dev. 2010 Nov 15;24:2499-504.
• The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs.
  Trabucchi M, Briata P, Garcia-Mayoral M, Haase AD, Filipowicz W, Ramos A, Gherzi R, Rosenfeld MG. Nature. 2009 Jun 18;459:1010-4.
• TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing.
  Haase AD, Jaskiewicz L, Zhang H, Lainé S, Sack R, Gatignol A, Filipowicz W. EMBO Rep. 2005 Oct;6:961-7.
• TIS7 interacts with the mammalian SIN3 histone deacetylase complex in epithelial cells.
  Vietor I, Vadivelu SK, Wick N, Hoffman R, Cotten M, Seiser C, Fialka I, Wunderlich W, Haase A, Korinkova G, Brosch G, Huber LA. EMBO J. 2002 Sep 2;21:4621-31.