small RNA group Mainz
The small RNA group is embedded in the Institute of Organismic and Molecular Evolution
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 unitas
, a universal tool for convenient annotation of small RNAs, or
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)
particularly with the group of René
Ketting (Biology of non-coding RNA)
but also with other groups from Europe, Canada, China and the USA.
We participate in the IMBs
International PhD Program (IPP)
Summer School (ISS)
and are part of the research focus GeneRED
(Gene Regulation in Evolution and Development)
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Our new paper on PIWI genes and piRNAs in mollusks is now available at Communications Biology
. "PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation"
. Check it out here
An updated version (1.5.2) of unitas is available for download here
. It uses the latest releases from Ensembl (92) Ensembl Genomes (32) miRBase (22) and SILVA (132).
That means 1193 supported species, more rRNA, more tRFs, more miRNAs...
Check out our new paper in RNA Biology, a solicited point-of-view: Isabel Fast & David Rosenkranz (2018) Temperature-dependent small RNA expression in Drosophila melanogaster, RNA Biology, DOI: 10.1080/15476286.2018.1429881.
A limited number of free reprints is available here
Updated version of proTRAC
(2.4.0) and unitas
(1.5.0) are available for download. proTRAC
now calculates the amount of repetitive DNA for each cluster separately
and all clusters together, compared to the genomic amount of repetitive DNA. unitas
now includes updated internal web links according to the new Ensembl
release 91 and SILVA release 132. We further added some piRNA ping pong analysis steps and fixed minor bugs.
Announcement: The 2nd smallRNAgroup Mini-Symposium will take place on Monday, 4th December in the Seminarraum Anthropologie
Candidates of the group will present their projects in short talks. Following this: Discussion and Glühwein
. Anyone interested is welcome to attend!
New paper puplished in RNA
Temperature-responsive miRNAs in Drosophila orchestrate adaptation to different ambient temperatures
We show that small RNA profiles critically depend on the ambient temperature and that Drosophila
utilizes miRNAs for global changes in gene expression
as a physiologic answer to changes in ambient temperature. Further, changes in ambient temperature affect piRNA ping-pong amplification rates which is presumably
driven by less stable secondary structures of transposon transcripts at higher temperatures.
The paper will be published as a Report in the upcoming RNA September issue 23 (9)
unitas update (1.1.0)
is out now. Minor bugs were removed and new
functionality was included, e.g., the '-riborase' option for most sensitive detection of rRNA fragments using a complete set of rRNA reference sequences from NCBI
First unitas update (1.0.1)
is out now. With the new Ensembl release 88,
Ensemble Genomes release 35 and SILVA rRNA database releas 128, the number of supported species grows to 835. The total available reference RNA data for small RNA
annotation (synchronized on our server) comes up to more than 9 GB.
update (2.3.0) is out now. GD image files are
disabled, which means that proTRAC no longer requires the GD module (installation of GD on some computers may be difficult for cryptic reasons).
Input SAM files no longer need to be sorted and sequence data used to create SAM files must not be collapsed any longer.
In the course of a reorganization of working groups within the Biological Faculty, the former Institute of Anthropology is taken up in the
newly formed Institute of Organismic and Molecular Evolutionary Biology
New paper puplished in Reproduction
Bovine piRNA-like RNAs are associated with both mobile elements and mRNAs
Stewart J. Russell and coworkers show that piRNAs target both transposons and mRNAs in the early bovine embryo and that target-mRNA expression negatively
correlates with piRNA expression, suggesting a role for piRNAs beyond transposon silencing in early embryogenesis.
The new proTRAC
version (2.2.0) is out now. Finally,
proTRAC accepts SAM files as input which means you can now use a more popular aligner such as Bowtie or STAR if you think sRNAmapper is
to slow. BUT NOTE: SAM files must be sorted according to chromosome coordinates and FASTA/FASTQ files still must be collapsed! You should
also make sure to allow multi-mapping.
For those who want to keep things easy, we still recommend to use sRNAmapper
as it produces an appropriate map file when using the default settings.
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
A new model organism in our group: The pond snail Lymnaea stagnalis
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
We added BED files comprising clustered piRNAs and piRNA clusters for each SRA dataset to piRNA cluster database
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.
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
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
Use our new PHASER tool to quantify the amount of phased piRNAs. Download the tool
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.
piFETCH, a fetching tool for piRNA cluster database
is available for download in the software section.
'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
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.
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.
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.
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.
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.