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EMBO supports our Practical Course on

EMBO Practical Course: Methods for analysis of circRNAs: From discovery to function

Dates: 13 November 2021 – 19 November 2021

Location: EMBL Heidelberg

We look forward to an impressive line-up of topics and speakers

with hands-on bioinformatics and lab work.


Innovative approaches for cardiology

Prof. Dr. Christoph Dieterich (head of Klaus Tschira Institute for Computational Cardiology) welcomes Jun. Prof. Dr. Sandy Engelhardt (teamleader of the AG Artificial Intelligence in Cardiovascular Medicine) as a speaker.
Alexander Knapstein from INSPIRATIONlabs (Heidelberg) outlines the advantage of augmented reality in the field of cardiological teaching and science.
Prof. Norbert Frey (right) moderated the session about Patient-Centric Molecular Medicine and discussed with Prof. Norbert Hübner (MDC) the topic of cell subtypes at the heart.

DZHK-HiGHmed-Symposium

Heidelberg, 24.09.2020. Experts of the German center for cardiovascular diseases (Deutsches Zentrum für Herz-Kreislauferkrankungen) and the HiGHmed-consortium of the medicine informatics initiative discussed within the first DZHK-HiGHmed-symposium on 21. and 22. of September in Heidelberg about innovative approaches for cardiology.

The link between different data from Imaging, molecular diagnostic, electronic patient record as well as information, which are gathered via wearable sensors like smart watches by the patients, will face huge challenges in the traditional healthcare sector. “Our Aim is to demonstrate the great potential of digitalization and to utilize it for the good of all patients, outlined Prof. Dr. Christoph Dieterich, organizer of the symposium and director of the Klaus Tschira Institute for Computational Cardiology at university hospital Heidelberg at the beginning of the event.

The mutual and ongoing dialogue between medicine and computer science is of utmost importance to reach this goal and to push digitalization towards the next level. Thus, subjects like machine learning concepts within image-based data and medical texts, the use of individual molecular analyses as well as data merging of heterogeneous data sources, were addressed and discussed in detail.

Click here to see the full video footage of the symposium.


New publication: A multi-network comparative analysis of transcriptome and translatome identifies novel hub genes in cardiac remodeling

Posted on October 2020 by Etienne Boileau

In this study, we adopted a systems biology approach to integrate multi-omics data through the use of co-expression networks to highlight higher-order relationships among gene programs that are expressed
in the heart in vivo during the early stages of cardiac remodeling.  Our analysis of 15 mouse left ventricular tissues from experimental models of exercise- and disease-induced cardiac hypertrophy showed, for the first time, the organization of the transcriptome and translatome into networks of biologically meaningful clusters of co-expressed genes. In contrast to differential expression analysis, co-expression and rewiring analysis led us to the identification of yet uncharacterized candidate genes, key to organizing the behaviour of transcriptome and translatome networks. In particular, our results uncovered Fam210a, a novel musculoskeletal modulator, which we hypothesize to regulate the expression of mitochondrial encoded genes; and Psmd12, a regulatory subunit of the 26S proteasome, whose deregulation may act as a pathogenic factor compromising protein quality control in cardiomyocytes. Our results constitute a valuable resource to study in vivo cardiac regulatory networks, and a first step towards the identification and characterization of novel proteins involved in cardiac remodeling, hypertrophy and heart failure.

Link: https://www.frontiersin.org/articles/10.3389/fgene.2020.583124


New publication: Updated and enhanced pig cardiac transcriptome based on long-read RNA sequencing and proteomics

Posted on October 2020 by Etienne Boileau

The pig has emerged as an essential cardiovascular disease model, because its heart, circulatory system, and blood supply are anatomically and functionally similar to that of humans. It is becoming indispensable for cardiovascular research, clinically relevant proof of concept studies and for novel therapeutic interventions. In this work, we employed Nanopore long-read sequencing and in-depth proteomics on top of Illumina RNA-seq to enhance the pig cardiac transcriptome annotation. We predicted coding and non-coding transcripts via an integrated workflow. Our transcriptome assembly is combined with the existing two large databases, Ensembl and NCBI, and validated by a large-scale TMT mass-spectrometry data set, which was collected from 6 adult pig hearts across different left ventricular regions to sample the cardiac proteome diversity. All our data are available for download and are provided as tracks for integration in genome browsers. We deem this resource as highly valuable for molecular research in an increasingly relevant large animal model.

Link: https://www.jmmc-online.com/article/S0022-2828(20)30300-X/fulltext#st0120


New publication: Deep Characterization of Circular RNAs from Human Cardiovascular Cell Models and Cardiac Tissue

Posted on July 2020 by Tobias Jakobi

Our new study was undertaken to help to uncover potential functions of circular RNAs (circRNAs) that are relevant in cardiovascular disease (CVD) in cardiac model systems and organisms. The study defines a strongly conserved core set of circRNAs in human heart tissue, human induced pluripotent stem cell-derived cardiac myocytes (hiPSC-CMs), as well as mouse and pig heart. These circRNAs are promising potential targets for further studies because their function is likely conserved and therefore may be important in development and progression of CVD.

We employed a specialized deep sequencing approach to generate comprehensive maps of circRNA exon composition in hiPSC-CMs, human umbilical vein cells (HUVECs), and human hearts, which are required for more confident functional studies.

We identified shared circRNAs across all samples, as well as model-specific circRNA signatures and moreover identified a core set of positionally conserved and expressed circRNAs in human, pig, and mouse hearts. Furthermore, we found that the sequence of circRNAs can deviate from the sequence derived from the genome sequence, an important factor in assessing potential functions. Integration of additional data yielded evidence for m6A-modification of circRNAs, potentially linked to translation as well as circRNAs overlapping with potential Agonaut2 binding sites, indicating potential association with the RISC complex. Moreover, we describe, for the first time in cardiac model systems, a sub class of circRNAs containing the start codon of their primary transcript (AUG circRNAs) and observe an enrichment for m6A-modifications and ribosome association.

Link: https://doi.org/10.3390/cells9071616


New publication: CASC3 promotes transcriptome-wide activation of nonsense-mediated decay by the exon junction complex

 Posted on July 2020 by Thiago Britto Borges

Another publication from our magnificent collaboration with the Gehring lab, from the Institute for Genetics - University of Cologne. CASC3 is a core component of the Exon Junction Complex (EJC), a protein complex that signals whether introns were successfully spliced out from the premature mRNA. Importantly, the EJC can signal aberrant translation when an EJC downstream to stop codon indicates the premature end of the translation. This aberrant protein products are likely truncated, and in the worst case harmful for the cell. In this manuscript, we show that cells that were genetically modified to remove CASC3 have a significant abundance increase in transcripts with premature termination codons. Many of these transcripts are shared with cells showing reduced non-sense mediated RNA decay activity (SMG6 / SMG7 mutants). In the absence of CASC3, EJC composition and EJC-dependent splicing are unchanged. We propose that CASC3 equips the EJC with the persisting ability to communicate with the NMD machinery in the cytoplasm. Collectively, our results characterize CASC3 as a peripheral EJC protein that tailors the transcriptome by promoting the degradation of EJC-dependent NMD substrates. Our work establishes and details the importance of CASC3 on the NMD process, which helps us to better understand the process of RNA degradation and its role in cardiac diseases.

Link: https://doi.org/10.1093/nar/gkaa564


New publication in Molecular Cell: An Insulin-Sensitive Circular RNA That Regulates Lifespan in Drosophila

Posted on June 2020 by Christoph Dieterich

Abstract

Circular RNAs (circRNAs) are abundant and accumulate with age in neurons of diverse species. However, only few circRNAs have been functionally characterized, and their role during aging has not been addressed. Here, we use transcriptome profiling during aging and find that accumulation of circRNAs is slowed down in long-lived insulin mutant flies. Next, we characterize the in vivo function of a circRNA generated by the sulfateless gene (circSfl), which is consistently upregulated, particularly in the brain and muscle, of diverse long-lived insulin mutants. Strikingly, lifespan extension of insulin mutants is dependent on circSfl, and overexpression of circSfl alone is sufficient to extend the lifespan. Moreover, circSfl is translated into a protein that shares the N terminus and potentially some functions with the full-length Sfl protein encoded by the host gene. Our study demonstrates that insulin signaling affects global circRNA accumulation and reveals an important role of circSfl during aging in vivo.

Link: https://pubmed.ncbi.nlm.nih.gov/32592682


Published: RNA Modification Level Estimation with pulseR

Posted on December 11, 2018 by Christoph Dieterich

Abstract

RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m6A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale. Our workflow centers around the pulseR package, which was originally developed for the analysis of metabolic labeling experiments. We demonstrate how to analyze data without external normalization (i.e., in the absence of spike-ins), given high efficiency of separation, and how, alternatively, scaling factors can be derived from unmodified spike-ins. Importantly, our workflow provides an estimate of uncertainty of modification levels in terms of confidence intervals for model parameters, such as gene expression and RNA modification levels. We also compare alternative model parametrizations, log-odds, or the proportion of the modified molecules and discuss the pros and cons of each representation. In summary, our workflow is a versatile approach to RNA modification level estimation, which is open to any read-count-based experimental approach.

https://www.mdpi.com/2073-4425/9/12/619

Posted in Publications


Dieterich Lab is now a member of epitran.eu

Posted on December 5, 2018 by Christoph Dieterich

We are now an official member of the Epitran network (check out: https://epitran.eu )

Posted in General


Accepted: A placental mammal-specific microRNA cluster acts as a natural brake for sociability in mice

Posted on November 26, 2018 by Christoph Dieterich

Did you ever wonder how ncRNAs could influence behavior ?

Then, you would probably like to read on it in our new EMBO reports manuscript by

Lackinger, M., Sungur, A.Ö., Daswani, R., Soutschek, M., Bicker, S., Stemmler, L., Wüst, T., Fiore, R., Dieterich, C., Schwarting, R.K.W., Wöhr, M. and Schratt, G.

Aberrant synaptic function is thought to underlie social deficits in neurodevelopmental disorders such as autism and schizophrenia. microRNAs have been shown to regulate synapse development and plasticity, their potential involvement in the control of social behaviour in mammals however remains unexplored. Here we show that deletion of the large placental mammal-specific miR379-410 cluster in mice unexpectedly leads to hypersocial behaviour, which is accompanied by increased excitatory synaptic transmission and exaggerated expression of ionotropic glutamate receptor complexes in the hippocampus. Bioinformatics further allowed us to identify five “hub” microRNAs whose deletion accounts for a large part of the upregulation of excitatory synaptic genes, including Cnih2, Dlgap3, Prr7 and Src. Thus, miR379-410 is a natural brake for sociability and interfering with specific members of this cluster could represent a therapeutic strategy for social deficits in neurodevelopmental disorders.

Posted in General


CircTools manuscript accepted at Bioinformatics

Posted on November 16, 2018 by Christoph Dieterich

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software has been accepted for publication in Bioinformatics.

Please visit https://github.com/dieterich-lab/circtools for more information.

Posted in Publications, Software


Methods for Analysis of Circular RNAs: No Tautology

Posted on October 24, 2018 by Christoph Dieterich

We are excited to announce funding by EMBO for implementing a workshop on circular RNAs.

Organizers: Vladimir Benes (main), Irene Bozzoni, Marie-Laure Baudet and
Christoph Dieterich
Category: EMBO Practical Course
Title: EMBO Practical Course: Methods for analysis of circular RNAs: No tautology
Dates: 17 November 2019 – 22 November 2019
Location: DE–Heidelberg

https://www.embl.de/training/events/2019/CIR19-01/index.html

 

Posted in Conference, General


Advanced Training with Oxford Nanopore Technologies

Posted on October 17, 2018 by Christoph Dieterich

Join us for an advanced training experience using the Oxford Nanopore Technologies (ONT) platform. We will start with an introduction into ONT technology and devices, with the goal of covering end to end workflows for the preparation and analysis of human and yeast samples using whole genome and barcoded cDNA sequencing approaches. This course will cover the wet lab preparation of libraries from genomic DNA and total RNA, with a focus on the critical steps and potential pitfalls and understanding what constitutes a ‘good’ sample for purpose of best results using the technology. The training includes an overview of the MinKNOW GUI for GridION and MinION devices. We then cover methods available for basecalling and analysis of samples for structural variants and differential gene expression, using both Oxford Nanopore and open source tools.

More information and application at https://www.embl.de/training/events/2019/NAN19-01/index.html

Posted in Conference


Guardians of the transcriptome

Posted on October 11, 2018 by Christoph Dieterich

Our new article on “Exon junction complexes suppress spurious splice sites to safeguard transcriptome integrity” is in press and will appear in Molecular Cell beginning of November. Congratulations to the team of authors: 

Volker Boehm1, Thiago Britto-Borges2,3, Anna-Lena Steckelberg1,4, Kusum K. Singh1,5, Jennifer V. Gerbracht1, Elif Gueney1, Lorea Blazquez6,7, Janine Altmüller8,9,10, Christoph Dieterich2,3, Niels H. Gehring1,11

Productive splicing of human pre-mRNAs requires the correct selection of authentic splice sites (SS) from the large pool of potential SS. Although SS consensus sequence and splicing regulatory proteins are known to influence SS usage, the mechanisms ensuring the effective suppression of cryptic SS are insufficiently explored. Here, we find that many aberrant exonic SS are efficiently silenced by the exon junction complex (EJC), a multi-protein complex that is deposited on spliced mRNA near the exon-exon junction. Upon depletion of EJC proteins, cryptic SS are de-repressed, leading to the mis-splicing of a broad set of mRNAs. Mechanistically, the EJC-mediated recruitment of the splicing regulator RNPS1 inhibits cryptic 5′SS usage, while the deposition of the EJC core directly masks reconstituted 3′SS, thereby precluding transcript disintegration. Thus, the EJC protects the transcriptome of mammalian cells from inadvertent loss of exonic sequences and safeguards the expression of intact, full length mRNAs.

Posted in General, Publications


PostDoc Start-up Grants awarded

Congratulation to Tobias Jakobi, Heidelberg/Mannheim.

He received a PostDoc Start-up grant for:
"Investigating roles of dynamic RNA editing in the endoplasmic reticulum stress response in the heart"


Our book on circular RNAs is out (Springer Press)

Circular RNAs (series: Methods in Molecular Biology) has been published.
Editor: Christoph Dieterich & Argyris Papantonis




pulseR: Versatile computational analysis of RNA turnover from metabolic labeling experiments

Motivation:

High throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. read more…

 


Flexbar 3.0 – SIMD and multicore parallelization

Motivation:

High throughput sequencing machines can process many samples in a single run. For Illumina systems, sequencing reads are barcoded with an additional DNA tag that is contained in the respective sequencing adapters. The recognition of barcode and adapter sequences is hence commonly needed for the analysis of next generation sequencing data. Flexbar performs demultiplexing based on barcodes and adapter trimming for such data. read more…


A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses – New paper

Abstract: Synaptic downscaling is a homeostatic mechanism that allows neurons to reduce firing rates during chronically elevated network activity. Although synaptic downscaling is important in neural circuit development and epilepsy, the underlying mechanisms are poorly described. We performed small RNA profiling in picrotoxin (PTX)-treated hippocampal neurons, a model of synaptic downscaling. Thereby, we identified eight microRNAs (miRNAs) that were increased in response to PTX, including miR-129-5p, whose inhibition blocked synaptic downscaling in vitro and reduced epileptic seizure severity in vivo Using transcriptome, proteome, and bioinformatic analysis, we identified the calcium pump Atp2b4 and doublecortin (Dcx) as miR-129-5p targets. Restoring Atp2b4 and Dcx expression was sufficient to prevent synaptic downscaling in PTX-treated neurons. Furthermore, we characterized a functional crosstalk between miR-129-5p and the RNA-binding protein (RBP) Rbfox1. In the absence of PTX, Rbfox1 promoted the expression of Atp2b4 and Dcx. Upon PTX treatment, Rbfox1 expression was downregulated by miR-129-5p, thereby allowing the repression of Atp2b4 and Dcx. We therefore identified a novel activity-dependent miRNA/RBP crosstalk during synaptic scaling, with potential implications for neural network homeostasis and epileptogenesis.

Find me on Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/28487411

 


Great Gordon Research Conference on RNA editing

One week of beautiful RNA modification science in Ventura / California.


Rp-bp is published in NAR

[Translate to English:] Wir haben eine weitere Publikation zur Identifizierung von translatierten RNA-Regionen aus Ribosom-Fußdruckdaten in Nucleic Acids Research.

Hier finden Sie alle weiteren Details: https://www.ncbi.nlm.nih.gov/pubmed/28126919


New publication

Ivan Kel; Zisong Chang; Nadia Galluccio; Margherita Romeo; Stefano Beretta; Luisa Diomede; Alessandra Mezzelani; Luciano Milanesi; Christoph Dieterich; Ivan Merelli. SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans


JACUSA is accepted for publication

JACUSA: Site-specific identification of RNA editing events from replicate sequencing data

 

https://www.ncbi.nlm.nih.gov/pubmed/28049429

Two new publications are out

Somatic increase of CCT8 mimics proteostasis of human pluripotent stem cells and extends C. elegans lifespan.

Noormohammadi A, Khodakarami A, Gutierrez-Garcia R, Lee HJ, Koyuncu S, König T, Schindler C, Saez I, Fatima A, Dieterich C, Vilchez D.

Nat Commun. 2016 Nov 28;7:13649. doi: 10.1038/ncomms13649.

PMID: 27892468

Reducing RBM20 activity improves diastolic dysfunction and cardiac atrophy.

Hinze F, Dieterich C, Radke MH, Granzier H, Gotthardt M.

J Mol Med (Berl). 2016 Nov 26. [Epub ahead of print]

PMID: 27889803

Unser Team hat sich weiter vergrößert

Wir begrüßen Ralf Hauenschild und Parisa Rezaee Borj in unserem Team!

New publication is out

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.

 

Our team extended

We welcome Ralf Hauenschild and Parisa Rezaee Borj into our team!

Talk at GCB 2016 in Berlin

Our software contribution

FUCHS – Towards full circular RNA characterization using RNAseq

has been selected for a talk at GCB2016

You will find a preprint at https://peerj.com/preprints/2418/

Neue Publikation

Le HQ, Ghatak S, Yeung CC, Tellkamp F,Günschmann C, Dieterich C, Yeroslaviz A, Habermann B, Pombo A, Niessen CM, Wickström SA.
Mechanical regulation of transcription controls Polycomb-mediated gene silencing during lineage commitment.

Compute Cluster

Our compute cluster ready for operation.

Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals

Title: Mondo complexes regulate TFEB via TOR inhibition to promote longevity in response to gonadal signals

Authors: Shuhei Nakamura, Özlem Karalay, Philipp S. Jäger, MakotoHorikawa, Corinna Klein, Kayo Nakamura, Christian Latza, Sven E. Templer, Christoph Dieterich & Adam Antebi

Joint work with our dear colleagues from the MPI-AGE was accepted for publication
in Nature Communications.

New Compute Cluster is ordered

Our new compute cluster is ordered and we are eagerly awaiting our Christmas gift.

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