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small RNA group Mainz
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The small RNA group represents a research focus of the Institute of Anthropology at the Johannes Gutenberg University. Our work intends to provide insights into function and evolution of small RNA pathways in diverse animal species including human and non-human primates and model systems such as mouse and drosophila, with the emphasis being on the fast evolving Piwi/piRNA system.
We concentrate on comparative analyses of small RNA transcriptomes and the development of new bioinformatic tools such as the piRNA cluster prediction software proTRAC that allow us to reveal functional and evolutionary coherences based on high-throughput sequencing data. We closely collaborate with the Institute of Molecular Biology (IMB), especially with the group of René Ketting (Biology of non-coding RNA). We participate in the IMBs International PhD Program (IPP), International Summer School (ISS) and are part of the research focus GeneRED (Gene Regulation in Evolution and Development).


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NEWS


27/10/2016
Next lecture of the "Introduction to Epigenetics" series: Tuesday, 8 November 2016. The lecture will be held by David Rosenkranz: “Primate piRNA/PIWI: functional aspects and evolution” from 08:15-09:45 am. IMPORTANT: The lecture will be held in the lecture hall 7 (HS 7), Forum 1, JGU Campus. For further information please see the attached poster or visit the IMB homepage.
13/10/2016
A new model organism in our group: The pond snail Lymnaea stagnalis.
01/09/2016
The Lecture Series "Introduction to Epigenetics" starts on Tuesday, 25 October. The lecture series is open for everybody interested. The lecture 'Primate piRNA/PIWI: functional aspects and evolution' will be held on Tuesday, 8 November by David Rosenkranz from 8:15-9:00 a.m. You can download the Lecture Series schedule here.
01/09/2016
We added BED files comprising clustered piRNAs and piRNA clusters for each SRA dataset to piRNA cluster database.
19/04/2016
Candidates of the small RNA group will present their research projects at the smallRNAgroup Mini-Symposium. The Symposium will be held on 18th May, 14:00-15:00 in the Institute of Anthropology, seminar room. The Symposium is aimed at master students that intend to do their master thesis in the group of David Rosenkranz, as well as all other interested Biology/Anthropology students.
31/03/2016
small RNA group Mainz offers a project in the course of the International PhD programm 2016. Registration deadline is 01. May 2016. Application deadline is 08. May 2016. For more information on the IPP 2016 go to the IMB website.
05/02/2016
Apply to the International Summer School programm and become part of the small RNA group Mainz. The application deadline is 10. April 2016. For more information on the ISS 2016 go to the IMB website.
07/12/2015
Use our new PHASER tool to quantify the amount of phased piRNAs. Download the tool here.
17/11/2015
piRNA cluster database paper is published in Nucleic Acids Research. piRNA cluster database: a web resource for piRNA producing loci.
06/10/2015
A new review article is published in Wiley Interdisciplinary Reviews: RNA. RNA-based regulation of transposon expression.
05/10/2015
proTRAC version 2.1 is now available for download at the software section. PNG image output files have been replaced by convenient HTML output files. The Transcription Factor Binding Site search function now includes sequences for three more testis expressed transcription factors (Gata4, SPZ1 and SOX9) involved in testis development and fertility.
17/09/2015
piFETCH, a fetching tool for piRNA cluster database is available for download in the software section.
10/07/2015
'Data in Brief'-paper is available online at Genomics Data. The article provides detailed information on material and methods (applied to generate the according NCBI GEO datasets) for the Roovers et al. paper puplished in Cell Reports 2015.
03/07/2015
Two SRA datasets from chicken were added to the piRNA cluster database. In line with data from fly and fish, and contrasting piRNAs in the mammalian adult male germline, piRNAs in chicken testis are enriched for transposon derived sequences compared to the whole genome situation.
22/06/2015
Datasets from mouse, rat, cow, pig, zebrafish and fruitfly were added to the piRNA cluster database which now comprises more than 33,000 piRNA clusters from 11 species.
07/05/2015
New paper is out in PLoS ONE: piRNAs from Pig Testis Provide Evidence for a Conserved Role of the Piwi Pathway in Post-Transcriptional Gene Regulation in Mammals.

07/05/2015
Marmoset (Callithrix jacchus) and Rhesus monkey (Macaca mulatta) join the piRNA cluster database which now comprises 7558 piRNA clusters from 5 species. We also added heatmaps that refer to piRNA expression of different genomic loci accross different SRA datasets for each species.

24/04/2015
Tree shrew (Tupaia belangeri) joins the piRNA cluster database with 139 piRNA clusters. With ~20% of transposon related sequences (total genome ~36%), piRNA clusters in tree shrew exhibit a very low amount of transposon sequences compared to other mammalian species studied thus far.

piRNA cluster database launch19/04/2015
Launch of piRNA cluster database, a comprehensive database for genomic piRNA clusters. We start with datasets from Homo sapiens and Macaca fascicularis. The database will be under construction until the first full release which is scheduled for the end of June 2015. During this time new datasets will be added bit by bit.

Cell Reports paper26/03/2015
New paper published in Cell Reports: Piwi proteins and piRNAs in mammalian oocytes and early embryos.

RNA paper23/03/2015
New paper published in RNA: Tupaia small RNAs provide insights into function and evolution of  RNAi-based transposon defense in mammals.



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