RNA Biology

E-mail: julius.brennecke(at)imba.oeaw.ac.at
Phone: 0043 1 79044
Research Group: www.imba.oeaw.ac.at/research/julius-brennecke
Institution: IMBA

Full member of the DoktoratsKolleg RNA Biology since 2014 and of the SFB RNA Reg since 2011.

PhD students within/associated to the DK:

Jakob Schnabl
Mostafa Elmaghraby
Lisa Baumgartner
Veselin Andreev

DK RNA Biology alumni & their PhD theses:

Julia Batki: “Nuclear small RNA-guided silencing of transposable elements in Drosophila melanogaster”

For complete list of group members please visit the Brennecke group website.

Joint SFB research project J. Brennecke and A. Stark:

We propose to perform an unbiased study of RNA-abundance and post-transcriptional regulation in the female Drosophila germ line. Drosophila oogenesis serves as a paradigm for regulation of gene expression at the RNA-level, as all 3 known small RNA pathways (miRNAs, siRNAs, PiRNAs) are employed and it is the key system in which control of RNA localization, translation and transport have been established and are actively studied.

Specifically, we will establish and employ ribosome foot-printing (Ingolia et al. 2009) to determine ribosome occupancy and translation rates of mRNAs and RNA-PAR-CLIP (Hafner et al, 2010) to identify the specific target RNAs of three key protein factors involved in post-transcriptional regulation (Pumilio, Staufen, and Argonaute 1). We will couple these genom-wide approaches to bioninformatics analyses established in our or the Hofacker groups to determine the cis-regulatory motifs of RNAs at the level of sequence and secondary structure. We anticipate gaining significant insight into the post-transcriptional control of RNA fate in a complex in vivo context.

In a broader perspective, both technologies will proof extremely useful for the scientific progress within the Brennecke/Stark labs, which are focusing on small RNAs and cis-regulatory motifs. Finally, we believe that multiple groups within this SFB (e.g. Kiebler, Dorner, Mochizuki, Martinez) and a number of labs at the Vienna Biocenter Campus will benefit strongly from the establishment of the two technologies.

 

Publications: (since 2011)

A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production.
ElMaghraby MF, Andersen PR, Pühringer F, Hohmann U, Meixner K, Lendl T, Tirian L, Brennecke J.
Cell. 2019 Aug 8;178(4):964-979.e20.

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J.
Nat Struct Mol Biol. 2019 Aug;26(8):720-731. Epub 2019 Aug 5.

A heterochromatin-dependent transcription machinery drives piRNA expression.
Andersen PR, Tirian L, Vunjak M, Brennecke J.
Nature. 2017 Sep 7;549(7670):54-59.

Genetic and mechanistic diversity of piRNA 3′-end formation.
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J.
Nature. 2016 Nov 24;539(7630):588-592.

Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.
Sienski G, Batki J, Senti KA, Dönertas D, Tirian L, Meixner K, Brennecke J.
Genes Dev. 2015 Nov 1;29(21):2258-71.

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.
Senti KA, Jurczak D, Sachidanandam R, Brennecke J.
Genes Dev. 2015 Aug 15;29(16):1747-62.

Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.
Mohn F, Handler D, Brennecke J.
Science. 2015 May 15;348(6236):812-817.

Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi’s genomic targets still not identified.
Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF.
Dev Cell. 2015 Mar 23;32(6):765-71.

The exon junction complex is required for definition and excision of neighboring introns in Drosophila.
Hayashi R, Handler D, Ish-Horowicz D, Brennecke J.
Genes Dev. 2014 Aug 15;28(16):1772-85.

Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex.
Dönertas D, Sienski G, Brennecke J.
Genes Dev. 2013 Aug 1;27(15):1693-705.

The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila.
Mohn F, Sienski G, Handler D, Brennecke J.
Cell. 2014 Jun 5;157(6):1364-79.

The genetic makeup of the Drosophila piRNA pathway.
Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber FS, Brennecke J.
Mol Cell. 2013 Jun 6;50(5):762-77.

Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression.
Sienski G, Dönertas D, Brennecke J.
Cell. 2012 Nov 21;151(5):964-80.

Preparation of small RNA libraries for high-throughput sequencing.
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ.
Cold Spring Harb Protoc. 2012 Oct 1;2012(10):1067-77.

The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.
Olivieri D, Senti KA, Subramanian S, Sachidanandam R, Brennecke J.
Mol Cell. 2012 Sep 28;47(6):954-69.

A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors.
Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J.
EMBO J. 2011 Aug 23;30(19):3977-93.

A genome-scale shRNA resource for transgenic RNAi in Drosophila.
Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N.
Nat Methods. 2011 May;8(5):405-7.