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LimiTT: link miRNAs to targets

Julia Bayer, Carsten Kuenne, Jens Preussner, Mario Looso
2016 BMC Bioinformatics  
MicroRNAs (miRNAs) impact various biological processes within animals and plants. They complementarily bind target mRNAs, effecting a post-transcriptional negative regulation on mRNA level. The investigation of miRNA target interactions (MTIs) by high throughput screenings is challenging, as frequently used in silico target prediction tools are prone to emit false positives. This issue is aggravated for niche model organisms, where validated miRNAs and MTIs both have to be transferred from well
more » ... described model organisms. Even though DBs exist that contain experimentally validated MTIs, they are limited in their search options and they utilize different miRNA and target identifiers. Results: The implemented pipeline LimiTT integrates four existing DBs containing experimentally validated MTIs. In contrast to other cumulative databases (DBs), LimiTT includes MTI data of 26 species. Additionally, the pipeline enables the identification and enrichment analysis of MTIs with and without species specificity based on dynamic quality criteria. Multiple tabular and graphical outputs are generated to permit the detailed assessment of results. Conclusion: Our freely available web-based pipeline LimiTT (https://bioinformatics.mpi-bn.mpg.de/) is optimized to determine MTIs with and without species specification. It links miRNAs and/or putative targets with high granularity. The integrated mapping to homologous target identifiers enables the identification of MTIs not only for standard models, but for niche model organisms as well.
doi:10.1186/s12859-016-1070-1 pmid:27170328 pmcid:PMC4866021 fatcat:3hsbie5rznegvpwapct3ud53pu

UROPA GUI: A web platform for genomic region annotation [article]

Hendrik Schultheis, Jens Preussner, Annika Fust, Mette Bentsen, Carsten Kuenne, Mario Looso
2018 bioRxiv   pre-print
The annotation of genomic ranges such as peaks resulting from ChIP-seq/ATAC-seq or other techniques represents a fundamental task of bioinformatics analysis with considerable impact on many downstream analyses. In our previous work, we introduced the Universal Robust Peak Annotator (UROPA), a flexible command line based tool which improves upon the functionality of existing annotation software. In order to reduce the complexity for biologists and clinicians, we have implemented an intuitive
more » ... based graphical user interface (GUI) and fully functional service platform for UROPA. This extension will empower all users to generate annotations for regions of interest interactively. The open source UROPA GUI server was implemented in R Shiny and Python and is available from http://loosolab.mpi-bn.mpg.de. The source code of our App can be downloaded at https://github.molgen.mpg.de/loosolab/UROPA_GUI under the MIT license.
doi:10.1101/302091 fatcat:2vorypkcbje7hm6s4cgfhxzksa

UROPA: a tool for Universal RObust Peak Annotation

Maria Kondili, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Mario Looso
2017 Scientific Reports  
The annotation of genomic ranges of interest represents a recurring task for bioinformatics analyses. These ranges can originate from various sources, including peaks called for transcription factor binding sites (TFBS) or histone modification ChIP-seq experiments, chromatin structure and accessibility experiments (such as ATAC-seq), but also from other types of predictions that result in genomic ranges. While peak annotation primarily driven by ChiP-seq was extensively explored, many
more » ... remain simplistic ("most closely located TSS"), rely on fixed pre-built references, or require complex scripting tasks on behalf of the user. An adaptable, fast, and universal tool, capable to annotate genomic ranges in the respective biological context is critically missing. UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for universal genomic range annotation. Based on a configuration file, different target features can be prioritized with multiple integrated queries. These can be sensitive for feature type, distance, strand specificity, feature attributes (e.g. protein_coding) or anchor position relative to the feature. UROPA can incorporate reference annotation files (GTF) from different sources (Gencode, Ensembl, RefSeq), as well as custom reference annotation files. Statistics and plots transparently summarize the annotation process. UROPA is implemented in Python and R. Many bioinformatic analyses result in the definition of genomic regions of interest, generated by a variety of methods. Minimally, they consist of a chromosome, a start position, and an end position, but can also contain a range of additional data such as the strand of the region. For this type of data, the Browser Extensible Data (BED, https://genome.ucsc.edu/FAQ/FAQformat#format1) format became the de facto standard format, and a wide range of tools that are able to handle and produce this datatype were developed. In the context of the extensively used chromatin immunoprecipitation and sequencing (ChIP-seq) method, the regions of interest are commonly referred to as peaks, denoting regions of high coverage of reads produced by the experiment. Peaks are generated by computational tools named "peak callers" (such as MACS2 1 or MUSIC 2 ) and denote potential binding sites of the protein under investigation. Frequently, investigated proteins are transcription factors (TF) or histones with specific modifications. In order to interpret these binding sites, a set of peak annotation tools such as Homer 3 , Goldmine 4 , GREAT 5 or ChIPpeakAnno 6 were developed. As these tools are mainly focused on the assignment of TFs or histone modifications to the corresponding gene, they apply methods to calculate the closest distance of a peak to the transcription start site of genes located in the direct neighborhood. However, annotation of peaks can become complex (Fig. 1A) , especially in regions where multiple genes are located in close proximity or if features are supposed to be treated preferentially based on their category or relative localization. The biological origin of peaks can render the annotation step even more complex. In an epigenetics context, the ChIP-seq method is often used to interpret the state of chromatin by the parallel investigation of a number of different histone modifications such as methylation, acetylation or phosphorylation on distinct sites 7 . These marks of open or condensed chromatin are known to influence transcription regulation. In addition, the combination of such histone marks can be used to identify regulatory regions like enhancers, which can be located up to 1 Mb distant from the gene they regulate, thus requiring special care considering optimal annotation. While ChIP-seq peaks are one-dimensional in relation to the protein of interest, more recently developed methods are intended to produce information about the global structure of the chromatin (ATAC-seq, FAIRE-seq, DNase-seq, Mnase-seq), giving a detailed footprint on regions that are accessible or closed. However, Published: xx xx xxxx OPEN www.nature.com/scientificreports/ 2 Scientific RepoRts | 7: 2593 |
doi:10.1038/s41598-017-02464-y pmid:28572580 pmcid:PMC5453960 fatcat:24mtd3sufrbg3bnz6zhybkofca

WIlsON: Web-based Interactive Omics VisualizatioN

Hendrik Schultheis, Carsten Kuenne, Jens Preussner, Rene Wiegandt, Annika Fust, Mette Bentsen, Mario Looso, Janet Kelso
2018 Bioinformatics  
., 2015) , ADMIRE output (Preussner et al., 2015) based on methylation arrays of patients with pulmonary arterial hypertension (Hautefort et al., 2017) , and Maxquant (Tyanova et al., 2016) proteomics  ... 
doi:10.1093/bioinformatics/bty711 pmid:30535135 pmcid:PMC6419899 fatcat:k5hz37p4zzbyjojca266clfeta

i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics-pipeline Results [article]

Arsenij Ustjanzew, Jens Preussner, Mette Bentsen, Carsten Kuenne, Mario Looso
2020 bioRxiv   pre-print
Data visualization and interactive data exploration are important aspects of illustrating complex concepts and results from analyses of omics data. A suitable visualization has to be intuitive and accessible. Web-based dashboards have become popular tools for the arrangement, consolidation and display of such visualizations. However, the combination of automated data processing pipelines handling omics data and dynamically generated, interactive dashboards is poorly solved. Here, we present
more » ... sh, an R package intended to encapsulate functionality for programmatic creation of customized dashboards. It supports interactive and responsive (linked) visualizations across a set of predefined graphical layouts. i2dash addresses the needs of data analysts for a tool that is compatible and attachable to any R-based analysis pipeline, thereby fostering the separation of data visualization on one hand and data analysis tasks on the other hand. In addition, the generic design of i2dash enables data analysts to generate modular extensions for specific needs. As a proof of principle, we provide an extension of i2dash optimized for single-cell RNA-sequencing analysis, supporting the creation of dashboards for the visualization needs of single-cell sequencing experiments. Equipped with these features, i2dash is suitable for extensive use in large scale sequencing/bioinformatics facilities. Along this line, we provide i2dash as a containerized solution, enabling a straightforward large-scale deployment and sharing of dashboards using cloud services. i2dash is freely available via the R package archive CRAN.
doi:10.1101/2020.07.06.189563 fatcat:4mdnedm6cvb5nexnfp3sdfmjoe

MIRPIPE: quantification of microRNAs in niche model organisms

Carsten Kuenne, Jens Preussner, Mario Herzog, Thomas Braun, Mario Looso
2014 Computer applications in the biosciences : CABIOS  
MicroRNAs (miRNAs) represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here we introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads
more » ... ginating from various sequencing instruments, processing of isomiRs and quantification of detected miRNAs versus public-or user-uploaded reference databases. Availability and implementation: The Web service is freely available at
doi:10.1093/bioinformatics/btu573 pmid:25165094 pmcid:PMC4816158 fatcat:ixrdbhy4pjhmzilhjk2xgt2m3e

Mono- and multi-nucleated ventricular cardiomyocytes constitute a transcriptionally homogenous cell population

Michail Yekelchyk, Stefan Guenther, Jens Preussner, Thomas Braun
2019 Basic Research in Cardiology  
Individual adult ventricular cardiomyocytes are either mono- or multi-nucleated and undergo morphological changes during cardiac hypertrophy. However, corresponding transcriptional signatures, reflecting potentially different functions or the ability for cell-cycle entry, are not known. The aim of this study was to determine the transcriptional profile of mono- and multi-nucleated adult cardiomyocytes by single-cell RNA-sequencing (scRNA-seq) and to investigate heterogeneity among
more » ... under baseline conditions and in pressure-induced cardiac hypertrophy. We developed an array-based approach for scRNA-seq of rod-shaped multi-nucleated cardiomyocytes from both healthy and hypertrophic hearts. Single-cell transcriptomes of mono- or multi-nucleated cardiomyocytes were highly similar, although a certain degree of variation was noted across both populations. Non-image-based quality control allowing inclusion of damaged cardiomyocytes generated artificial cell clusters demonstrating the need for strict exclusion criteria. In contrast, cardiomyocytes isolated from hypertrophic heart after transverse aortic constriction showed heterogeneous transcriptional signatures, characteristic for hypoxia-induced responses. Immunofluorescence analysis revealed an inverse correlation between HIF1α+ cells and CD31-stained vessels, suggesting that imbalanced vascular growth in the hypertrophied heart induces cellular heterogeneity. Our study demonstrates that individual mono- and multi-nucleated cardiomyocytes express nearly identical sets of genes. Homogeneity among cardiomyocytes was lost after induction of hypertrophy due to differential HIF1α-dependent responses most likely caused by none-homogenous vessel growth.
doi:10.1007/s00395-019-0744-z pmid:31399804 pmcid:PMC6689038 fatcat:azjxlkuqsfdifbjp3fhq2rwcvi

MOESM6 of ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
2016 Figshare  
Additional file 6. Beta values of protein coding genes with significantly differential methylation between patients with atrial fibrillation and healthy individuals.
doi:10.6084/m9.figshare.c.3638270_d7 fatcat:llttslx7ezdu3ntr4dtzea4rli

MOESM5 of ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
2016 Figshare  
Additional file 5. Absolute difference of methylation in 5 and 10 kB tiling regions in atrial fibrillation reported by ADMIRE. Boxplots give information about the magnitude of methylation change.
doi:10.6084/m9.figshare.c.3638270_d3.v1 fatcat:7kbvd6dkg5cpbdk24nldkc5p64

MOESM1 of ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
2016 Figshare  
Additional file 1. Examples of publication ready graphical overviews.
doi:10.6084/m9.figshare.c.3638270_d8.v1 fatcat:o2tguti2f5h6lnrj6gsuv2l3ia

multicrispr: fast gRNA designer enables prime editing and parallel targeting of thousands of targets [article]

Aditya M Bhagwat, Johannes Graumann, Rene Wiegandt, Mette Bentsen, Carsten Kuenne, Jens Preussner, Thomas Braun, Mario Looso
2020 bioRxiv   pre-print
Targeting the coding genome to introduce single nucleotide deletions/insertions via Crispr/Cas9 technology has become a standard procedure in recent years. Due to the whirlwind pace of evolution of Crispr/Cas9 based methods for which Prime editing, Crispr/Cas9 assisted APEX proximity labeling of proteins, or homology directed repair (HDR) are just innovative recent examples, supporting bioinformatic tools are, however, lagging behind. New methods often require specific guide-RNA (gRNA) design
more » ... nctionality, and a generic gRNA design tool is critically missing. Here we review gRNA designer software and introduce multicrispr, an R based tool intended to design individual gRNAs as well as gRNA libraries targeting a multitude of genomic loci in parallel. The package is easy to use, it detects, scores and filters gRNAs on both efficiency and specificity, it visualizes and aggregates results per target or Crispr/Cas9 sequence, and finally returns both genomic ranges as well as sequences of preferred, off target-free gRNAs. In order to be generic, multicrispr defines and implements a genomic arithmetics framework as a basis for facile adaptation to techniques yet to arise. Its performance and new gRNA design concepts such as target set specific filtering for gRNA libraries render multicrispr the tool of choice when dealing with screening-like approaches.
doi:10.1101/2020.04.15.042861 fatcat:d52n3kzr3ze4xi7dhwssuzacmq

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso
2015 Epigenetics & Chromatin  
DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and a wide range of diseases. Cytosine bases of the DNA are converted to 5-methylcytosine by the methyltransferase enzyme, acting as a reversible regulator of gene expression. Due to its outstanding importance in the epigenetic field, a number of lab techniques were developed to interrogate DNA methylation on a global range. Besides whole-genome bisulfite sequencing, the Infinium
more » ... thylation450 Assay represents a versatile and cost-effective tool to investigate genome-wide changes of methylation patterns.
doi:10.1186/s13072-015-0045-1 pmid:26628921 pmcid:PMC4666223 fatcat:uspz5qcrdjdaxkgvmgrf7s73l4

Connect-four: genomic analyses of regenerating stem cells identifies zygotic Dux factors as tumor initiators

Jens Preussner, Jiasheng Zhong, Mario Looso, Thomas Braun, Johnny Kim
2019 Molecular & Cellular Oncology  
How, if and in which cell types embryonic gene expression programs are elicited to induce tumor formation remains poorly understood. Through genomic analyses of regenerating, p53 deficient muscle stem cells we identified various oncogenomic amplifications, including but not limited to, the zygotic transcription factor Duxbl/DUXB to initiate tumorigenic transformation.
doi:10.1080/23723556.2019.1565469 pmid:31131298 pmcid:PMC6512926 fatcat:76ikc22cwvdhhmivtmbcb4x6gy

Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation [article]

Mette Bentsen, Philipp Goymann, Hendrik Schultheis, Anastasiia Petrova, Kathrin Klee, Annika Fust, Jens Preussner, Carsten Kuenne, Thomas Braun, Johnny Kim, Mario Looso
2019 bioRxiv   pre-print
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational method implementing both footprinting, visualization and downstream analysis has hindered the widespread application of this method. Here we present TOBIAS, a comprehensive footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TF simultaneously. As a proof-of-concept, we illustrate how TOBIAS can unveil
more » ... mplex TF dynamics during zygotic genome activation (ZGA) in both humans and mice, and explore how the TF Dux activates cascades of TF, binds to repeat elements and induces expression of novel genetic elements. TOBIAS is freely available at: https://github.com/loosolab/TOBIAS.
doi:10.1101/869560 fatcat:hyyvqrlqyneejb6cjofp5t7rey

The Histone Demethylase PHF8 Is Essential for Endothelial Cell Migration

Lunda Gu, Juliane Hitzel, Franziska Moll, Christoph Kruse, Randa Abdel Malik, Jens Preussner, Mario Looso, Matthias S. Leisegang, Dieter Steinhilber, Ralf P. Brandes, Christian Fork, Tim Thomas
2016 PLoS ONE  
Epigenetic marks critically control gene expression and thus the cellular activity state. The functions of many epigenetic modifiers in the vascular system have not yet been studied. We screened for histone modifiers in endothelial cells and observed a fairly high expression of the histone plant homeodomain finger protein 8 (PHF8). Given its high expression, we hypothesize that this histone demethylase is important for endothelial cell function. Overexpression of PHF8 catalyzed the removal of
more » ... thyl-groups from histone 3 lysine 9 (H3K9) and H4K20, whereas knockdown of the enzyme increased H3K9 methylation. Knockdown of PHF8 by RNAi also attenuated endothelial proliferation and survival. As a functional readout endothelial migration and tube formation was studied. PHF8 siRNA attenuated the capacity for migration and developing of capillary-like structures. Given the impact of PHF8 on cell cycle genes, endothelial E2F transcription factors were screened, which led to the identification of the gene repressor E2F4 to be controlled by PHF8. Importantly, PHF8 maintains E2F4 but not E2F1 expression in endothelial cells. Consistently, chromatin immunoprecipitation revealed that PHF8 reduces the H3K9me2 level at the E2F4 transcriptional start site, demonstrating a direct function of PHF8 in endothelial E2F4 gene regulation. Conclusion: PHF8 by controlling E2F4 expression maintains endothelial function.
doi:10.1371/journal.pone.0146645 pmid:26751588 pmcid:PMC4713448 fatcat:m4r45nlta5ab7jierod7iowbyy
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