List of Publications

Pliota, P., Marvanova, H., Koreshova, A (...) Ben-David, E., Burga, A. (2024). Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature.

Yelagandula, R., Stecher, K., Novatchkova, M (...) Brennecke, J., Bell, O. (2023). ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers. Nat Cell Biol.

L Baumgartner, JJ Ipsaro, U Hohmann, D Handler, A Schleiffer, P Duchek, J Brennecke (2023). Evolutionary adaptation of the chromodomain of the HP1-protein Rhino allows the integration of chromatin and DNA sequence signals BioRxiv.

Baumgartner, L., Handler, D., Platzer, SW (...) Duchek, P., Brennecke, J. (2022). The <i>Drosophila</i> ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters. Elife. 11

Andreev, VI., Yu, C., Wang, J (...) Patel, DJ., Brennecke, J. (2022). Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. Nat Struct Mol Biol. 29(2):130-142

Kellner, MJ., Ross, JJ., Schnabl, J (...) Pauli, A., Brennecke, J. (2022). A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing. Front Mol Biosci. 9:801309

ElMaghraby, MF., Tirian, L., Senti, KA., Meixner, K., Brennecke, J. (2021). A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary. Genetics.

Schnabl, J., Wang, J., Hohmann, U (...) Patel, DJ., Brennecke, J. (2021). Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex. Genes Dev. 35(5-6):392-409

Kellner 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

Grentzinger, T., Oberlin, S., Schott, G (...) Brennecke, J., Voinnet, O. (2020). A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Res. 48(14):e79

Xie, W., Sowemimo, I., Hayashi, R (...) Ameres, SL., Patel, DJ. (2020). Structure-function analysis of microRNA 3'-end trimming by Nibbler. Proc Natl Acad Sci U S A. 117(48):30370-30379

Pühringer, T., Hohmann, U., Fin, L (...) Brennecke, J., Plaschka, C. (2020). Structure of the human core transcription-export complex reveals a hub for multivalent interactions. Elife. 9

Batki, J., Schnabl, J., Wang, J (...) Patel, DJ., Brennecke, J. (2019). The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Nat Struct Mol Biol. 26(8):720-731

ElMaghraby, MF., Andersen, PR., Pühringer, F (...) Tirian, L., Brennecke, J. (2019). A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production. Cell. 178(4):964-979.e20

Andersen, PR., Tirian, L., Vunjak, M., Brennecke, J. (2017). A heterochromatin-dependent transcription machinery drives piRNA expression. Nature. 549(7670):54-59

Hayashi, R., Schnabl, J., Handler, D (...) Ameres, SL., Brennecke, J. (2016). Genetic and mechanistic diversity of piRNA 3'-end formation. Nature. 539(7630):588-592

Mohn, F., Handler, D., Brennecke, J. (2015). Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science. 348(6236):812-817

Sienski, G., Batki, J., Senti, KA (...) Meixner, K., Brennecke, J. (2015). Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. Genes Dev. 29(21):2258-71

Senti, KA., Jurczak, D., Sachidanandam, R., Brennecke, J. (2015). piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire. Genes Dev. 29(16):1747-62

Marinov, GK., Wang, J., Handler, D (...) Brennecke, J., Toth, KF. (2015). Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell. 32(6):765-71

Hayashi, R., Handler, D., Ish-Horowicz, D., Brennecke, J. (2014). The exon junction complex is required for definition and excision of neighboring introns in Drosophila. Genes Dev. 28(16):1772-85

Mohn, F., Sienski, G., Handler, D., Brennecke, J. (2014). The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell. 157(6):1364-1379

Handler, D., Meixner, K., Pizka, M (...) Gruber, FS., Brennecke, J. (2013). The genetic makeup of the Drosophila piRNA pathway. Mol Cell. 50(5):762-77

Dönertas, D., Sienski, G., Brennecke, J. (2013). Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev. 27(15):1693-705

Sienski, G., Dönertas, D., Brennecke, J. (2012). Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell. 151(5):964-80

Malone, C., Brennecke, J., Czech, B., Aravin, A., Hannon, GJ. (2012). Preparation of small RNA libraries for high-throughput sequencing. Cold Spring Harb Protoc. 2012(10):1067-77

Olivieri, D., Senti, KA., Subramanian, S., Sachidanandam, R., Brennecke, J. (2012). The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila. Mol Cell. 47(6):954-69

Handler, D., Olivieri, D., Novatchkova, M (...) Sachidanandam, R., Brennecke, J. (2011). A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J. 30(19):3977-93

Ni, JQ., Zhou, R., Czech, B (...) Hannon, GJ., Perrimon, N. (2011). A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods. 8(5):405-7

Olivieri, D., Sykora, MM., Sachidanandam, R., Mechtler, K., Brennecke, J. (2010). An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J. 29(19):3301-17

Senti, KA., Brennecke, J. (2010). The piRNA pathway: a fly's perspective on the guardian of the genome. Trends Genet. 26(12):499-509

Zhou, R., Czech, B., Brennecke, J (...) Perrimon, N., Hannon, GJ. (2009). Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA. 15(10):1886-95

Czech, B., Zhou, R., Erlich, Y (...) Perrimon, N., Hannon, GJ. (2009). Hierarchical rules for Argonaute loading in Drosophila. Mol Cell. 36(3):445-56

Malone, CD., Brennecke, J., Dus, M (...) Sachidanandam, R., Hannon, GJ. (2009). Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 137(3):522-35

Bushati, N., Stark, A., Brennecke, J., Cohen, SM. (2008). Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol. 18(7):501-6

Stark, A., Bushati, N., Jan, CH (...) Cohen, SM., Kellis, M. (2008). A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22(1):8-13

Olson, AJ., Brennecke, J., Aravin, AA., Hannon, GJ., Sachidanandam, R. (2008). Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput. :126-36

Czech, B., Malone, CD., Zhou, R (...) Hannon, GJ., Brennecke, J. (2008). An endogenous small interfering RNA pathway in Drosophila. Nature. 453(7196):798-802

Brennecke, J., Malone, CD., Aravin, AA (...) Stark, A., Hannon, GJ. (2008). An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 322(5906):1387-92

Müller, MS., Brennecke, JF., Porter, ET., Ottinger, MA., Anderson, DJ. (2008). Perinatal androgens and adult behavior vary with nestling social system in siblicidal boobies. PLoS One. 3(6):e2460

Brennecke, J., Aravin, AA., Stark, A (...) Sachidanandam, R., Hannon, GJ. (2007). Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128(6):1089-103

Aravin, AA., Hannon, GJ., Brennecke, J. (2007). The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 318(5851):761-4

Stark, A., Lin, MF., Kheradpour, P (...) Gelbart, WM., Kellis, M. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450(7167):219-32

Stark, A., Kheradpour, P., Parts, L (...) Hannon, GJ., Kellis, M. (2007). Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17(12):1865-79

Rehwinkel, J., Natalin, P., Stark, A (...) Cohen, SM., Izaurralde, E. (2006). Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol. 26(8):2965-75

Cohen, SM., Brennecke, J., Stark, A. (2006). Denoising feedback loops by thresholding--a new role for microRNAs. Genes Dev. 20(20):2769-72

Cohen, SM., Brennecke, J. (2006). Developmental biology. Mixed messages in early development. Science. 312(5770):65-6

Stark, A., Brennecke, J., Bushati, N., Russell, RB., Cohen, SM. (2005). Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell. 123(6):1133-46

Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005). Principles of microRNA-target recognition. PLoS Biol. 3(3):e85

Brennecke, J., Stark, A., Cohen, SM. (2005). Not miR-ly muscular: microRNAs and muscle development. Genes Dev. 19(19):2261-4

Güttinger, S., Mühlhäusser, P., Koller-Eichhorn, R., Brennecke, J., Kutay, U. (2004). Transportin2 functions as importin and mediates nuclear import of HuR. Proc Natl Acad Sci U S A. 101(9):2918-23

Brennecke, J., Cohen, SM. (2003). Towards a complete description of the microRNA complement of animal genomes. Genome Biol. 4(9):228

Brennecke, J., Hipfner, DR., Stark, A., Russell, RB., Cohen, SM. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell. 113(1):25-36

Stark, A., Brennecke, J., Russell, RB., Cohen, SM. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1(3):E60

Gritzan, U., Weiss, C., Brennecke, J., Bohmann, D. (2002). Transrepression of AP-1 by nuclear receptors in Drosophila. Mech Dev. 115(1-2):91-100