SIROCCO

Hairpin transcription does not necessarily lead to efficient triggering of the RNAi pathway.

Aileen Hogan — Wed, 21 Jul 2010 10:27:37 +0000

Dalakouras A, Tzanopoulou M, Tsagris M, Wassenegger M, Kalantidis K. Hairpin transcription does not necessarily lead to efficient triggering of the RNAi pathway. Transgenic Res. 2010 Jun 26. [Epub ahead of print]

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana.

Aileen Hogan — Tue, 20 Jul 2010 13:36:39 +0000

Todesco M, Balasubramanian S, Hu TT, Traw MB, Horton M, Epple P, Kuhns C, Sureshkumar S, Schwartz C, Lanz C, Laitinen RA, Huang Y, Chory J, Lipka V, Borevitz JO, Dangl JL, Bergelson J, Nordborg M, Weigel D. Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature. 2010 Jun 3;465(7298):632-6.

Utilization of unlocked nucleic acid (UNA) to enhance siRNA performance in vitro and in vivo.

Aileen Hogan — Tue, 20 Jul 2010 13:34:08 +0000

Laursen MB, Pakula MM, Gao S, Fluiter K, Mook OR, Baas F, Langklaer N, Wengel SL, Wengel J, Kjems J, Bramsen JB. Utilization of unlocked nucleic acid (UNA) to enhance siRNA performance in vitro and in vivo. Mol Biosyst. 2010 May 10;6(5):862-70. Epub 2010 Feb 9.

The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa.

Aileen Hogan — Tue, 20 Jul 2010 13:31:56 +0000

Braun JE, Tritschler F, Haas G, Igreja C, Truffault V, Weichenrieder O, Izaurralde E. The C-terminal alpha-alpha superhelix of Pat is required for mRNA decapping in metazoa. EMBO J. 2010 Jun 11. [Epub ahead of print]

MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems.

Aileen Hogan — Tue, 20 Jul 2010 13:28:26 +0000

Herranz H, Cohen SM. MicroRNAs and gene regulatory networks: managing the impact of noise in biological systems. Genes Dev. 2010 Jul 1;24(13):1339-44. Review.

A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing.

Aileen Hogan — Tue, 20 Jul 2010 13:23:29 +0000

Martí E, Pantano L, Bañez-Coronel M, Llorens F, Miñones-Moyano E, Porta S, Sumoy L, Ferrer I, Estivill X. A myriad of miRNA variants in control and Huntington’s disease brain regions detected by massively parallel sequencing. Nucleic Acids Res. 2010 Jun 30. [Epub ahead of print]

Postdoc at EMBL Monterotondo: Control of Argonaute-bound small-RNA stability in vivo

Rishi — Tue, 20 Jul 2010 10:01:45 +0000

SELECTION 2010

Short Title: Control of Argonaute-bound small-RNA stability in vivo
Coordinator: D. O’Carroll
Partner: A. Enright

miRNA expression is tightly controlled in space and time. Appropriate miRNA expression
is required for animal development and physiology. While a number of studies have
identified transcriptional regulators of miRNA expression, post-transcriptional control of
miRNA expression is a new and emerging area of research. We will focus on the
regulation of miRNA biogenesis and stability through RNA modifying enzymes. Our
starting point will be a class of poly(U) polymerase enzymes that have recently been
shown to modify miRNAs and their precursors in vitro. To this end we propose to explore
the function of controlled miRNA stability through the analysis of poly(U) polymerase Tut4
in the development and homeostasis of the miRNA-dependant hematopoietic system and
male germ cells.

This project will couple state-of-the-art mouse genetic strategies, high throughput
sequencing (HTS) and bioinformatic approaches. We will generate a conditional allele for
the Tut4 poly(U) polymerase in the mouse. Specific Cre alleles we be used to delete in
Tut4 in hematopoietic and germ cells. We propose to use HTS genomic approaches
(small-RNA seq, HTS-CLIP, RNA Seq) to relate the phenotype to a molecular mechanism.
Key to this endeavor is bioinformatic analysis and integration of large distinct genomic
data sets.

The successful candidate will join the O’Carroll lab at the EMBL Mouse Biology Unit in
Monterotondo, and interact frequently with the Enright group at EMBL-EBI. The post
holder will benefit from the mentorship of both group leaders to design investigative
approaches. This arrangement will provide an excellent opportunity for career
development, taking advantage of the resources and expertise of both EMBL laboratories
to execute this multidisciplinary project.

For more information see http://www.embl.it

New Partners Join the SIROCCO Consortium

Rishi — Thu, 15 Jul 2010 13:45:31 +0000

The SIROCCO consortium welcomes three new partners selected by competitive call who will participate for the remainder of the project

Anton Enright at the EBI and Jaak Vilo at Quretec are developing computational methods for the analysis of sRNA datasets produced in the consortium, as well as improved data submission and management tools.

Markus Stoffel at ETHZ is developing technologies to substitute, overexpress or silence sRNAs in vivo using knockout mouse models.

miR-375 maintains normal pancreatic alpha- and beta-cell mass.

Rishi — Thu, 15 Jul 2010 13:37:09 +0000

Poy MN, Hausser J, Trajkovski M, Braun M, Collins S, Rorsman P, Zavolan M, Stoffel M. miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5813-8. Epub 2009 Mar 16.

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.

Rishi — Thu, 15 Jul 2010 13:32:18 +0000

Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM. Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res. 2010 Apr 12. [Epub ahead of print]