Vinther Lab
The Vinther Lab studies RNA based mechanisms involved in the control of cellular processes.
Personal website: vintherlab.dk
Over the last years, our group has contributed to the further development of methods for detection of RNA modifications and for probing RNA structure. Historically, these methods have been restricted to the analysis of one RNA molecule at the time, but by adapting the experiments for modern sequencing technology and developing novel computational tools, we have increased the throughput of such experiments by several orders of magnitude to make transcriptome wide analysis possible. Our methods give us a unique possibility to identify RNA structural and regulatory changes inside cells.
J. Vinther, No Evidence for N7-Methylation of Guanosine (m(7)G) in Human let-7e. Molecular cell 79, 199-200 (2020). https://www.ncbi.nlm.nih.gov/pubmed/32679072
Enroth C, Poulsen LD, Iversen S, Kirpekar F, Albrechtsen A, Vinther J. Detection of internal N7-methylguanosine (m7G) RNA modifications by mutational profiling sequencing, Nucleic Acids Res, (2019). https://www.ncbi.nlm.nih.gov/pubmed/31504776
Poulsen LD, Vinther J. RNA-Seq for Bacterial Gene Expression, Curr Protoc Nucleic Acid Chem 73, e55 (2018). https://www.ncbi.nlm.nih.gov/pubmed/29927111
Kielpinski LJ, Hagedorn PH, Lindow M, Vinther J. RNase H sequence preferences influence antisense oligonucleotide efficiency, Nucleic Acids Res45, 12932-12944 (2017). https://www.ncbi.nlm.nih.gov/pubmed/29126318
Rukov JL, Hagedorn PH, Hoy IB, Feng Y, Lindow M, Vinther J. Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs, Nucleic Acids Res 43, 8476-8487 (2015). https://www.ncbi.nlm.nih.gov/pubmed/26220183
Poulsen LD, Kielpinski LJ, Salama SR, Krogh A, Vinther J. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data, RNA 21, 1042-1052 (2015). https://www.ncbi.nlm.nih.gov/pubmed/25805860
Kielpinski LJ, Sidiropoulos N, Vinther J. Reproducible Analysis of Sequencing-Based RNA Structure Probing Data with User-Friendly Tools, Methods Enzymol 558, 153-180 (2015). https://www.ncbi.nlm.nih.gov/pubmed/26068741
Rukov JL, Wilentzik R, Jaffe I, Vinther J, Shomron N. Pharmaco-miR: linking microRNAs and drug effects, Brief Bioinform 15, 648-659 (2014). https://www.ncbi.nlm.nih.gov/pubmed/23376192
Kielpinski LJ, Vinther J. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility, Nucleic Acids Res 42, e70 (2014). https://www.ncbi.nlm.nih.gov/pubmed/24569351
Kielpinski LJ, Boyd M, Sandelin A, Vinther J. Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing, Methods Mol Biol 1038, 213-231 (2013). https://www.ncbi.nlm.nih.gov/pubmed/23872978
Rukov JL, Vinther J, Shomron N. Pharmacogenomics genes show varying perceptibility to microRNA regulation, Pharmacogenet Genomics 21, 251-262 (2011). https://www.ncbi.nlm.nih.gov/pubmed/21499217
Glahder JA, Kristiansen K, Durand M, Vinther J, Norrild B. The early noncoding region of human papillomavirus type 16 is regulated by cytoplasmic polyadenylation factors, Virus Res 149, 217-223 (2010). https://www.ncbi.nlm.nih.gov/pubmed/20144904
Rosenstierne MW, Vinther J, Mittler G, Larsen L, Mann M, Norrild B. Conserved CPEs in the p53 3' untranslated region influence mRNA stability and protein synthesis, Anticancer Res 28, 2553-2559 (2008). https://www.ncbi.nlm.nih.gov/pubmed/19035278
Irimia M, Rukov JL, Penny D, Vinther J, Garcia-Fernandez J, Roy SW. Origin of introns by 'intronization' of exonic sequences, Trends Genet 24, 378-381 (2008). https://www.ncbi.nlm.nih.gov/pubmed/18597887
Irimia M, Rukov JL, Penny D, Garcia-Fernandez J, Vinther J, Roy SW. Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis, Mol Biol Evol 25, 375-382 (2008). https://www.ncbi.nlm.nih.gov/pubmed/18048400
Gardner PP, Vinther J. Mutation of miRNA target sequences during human evolution, Trends Genet 24, 262-265 (2008). https://www.ncbi.nlm.nih.gov/pubmed/18472179
Boyerinas B, Park SM, Shomron N, Hedegaard MM, Vinther J, Andersen JS, Feig C, Xu J, Burge CB, Peter ME. Identification of let-7-regulated oncofetal genes, Cancer Res 68, 2587-2591 (2008). https://www.ncbi.nlm.nih.gov/pubmed/18413726
Weile C, Gardner PP, Hedegaard MM, Vinther J. Use of tiling array data and RNA secondary structure predictions to identify noncoding RNA genes, BMC Genomics 8, 244 (2007). https://www.ncbi.nlm.nih.gov/pubmed/17645787
Rukov JL, Irimia M, Mork S, Lund VK, Vinther J, Arctander P. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae, Mol Biol Evol 24, 909-917 (2007). https://www.ncbi.nlm.nih.gov/pubmed/17272679
Vinther J, Hedegaard MM, Gardner PP, Andersen JS, Arctander P. Identification of miRNA targets with stable isotope labeling by amino acids in cell culture, Nucleic Acids Res 34, e107 (2006). https://www.ncbi.nlm.nih.gov/pubmed/16945957
Vinther J, Rosenstierne MW, Kristiansen K, Norrild B. The 3' region of human papillomavirus type 16 early mRNAs decrease expression, BMC Infect Dis 5, 83 (2005). https://www.ncbi.nlm.nih.gov/pubmed/16225671
Vinther J, Norrild B. Clearance of cervical human papillomavirus infections, Int J Cancer 104, 255-256 (2003). https://www.ncbi.nlm.nih.gov/pubmed/12569584
Rosenstierne MW, Vinther J, Hansen CN, Prydsoe M, Norrild B. Identification and characterization of a cluster of transcription start sites located in the E6 ORF of human papillomavirus type 16, J Gen Virol 84, 2909-2920 (2003). https://www.ncbi.nlm.nih.gov/pubmed/14573795
Glahder JA, Hansen CN, Vinther J, Madsen BS, Norrild B. A promoter within the E6 ORF of human papillomavirus type 16 contributes to the expression of the E7 oncoprotein from a monocistronic mRNA, J Gen Virol 84, 3429-3441 (2003). https://www.ncbi.nlm.nih.gov/pubmed/14645924
We are extremely grateful that the following grant agencies support our research:
Danish Council for Independent Research
Innovation Fund Denmark:
NextProd: Next generation cell factories for industrial production by non-coding RNA manipulation.
Novo Nordisk Fonden
m7G-MaP-seq: our method for mapping of N7-methyl-guanosine RNA modifications. Publication. Tools.
RNA-seq protocol: Publication. Tools.
RNAprobR: R-package for analysis of Reverse Transcription termination data, including RNA structure probing data. Publication. Tools. R-package.
I teach a yearly course in Fundamental Bioinformatics (Blok 3). The course is taught in english and is open to students with a background in molecular and cellular biology.
The description of the last version of the course can be found at https://kurser.ku.dk/course/nbib15021u/2021-2022
Our group studies RNA based mechanisms involved in the control of cellular processes. Currently, we have a particular interest in answering the following questions:
- How prevalent are noncanonical 5’ RNA capping in different species?
- What are the functional consequences of noncanonical RNA capping?
- How does RNA oxidation influence the regulation of mRNAs in bacterial, yeast and human cells?
- Can we improve methods for detection of noncanonical RNA capping and RNA oxidation?
We answer these questions using molecular and biochemical methods as well as high throughput methods based on sequencing. We have the computational tools and know-how required to analyse the sequencing data and if the project involves sequencing, the student can choose whether they want to be involved in the computational analysis of the data. Master and bachelor projects are available within the topics listed above. The specific projects depend on the status of the research projects. Thus, if you are interested in doing a project in our group, you should contact Associate Professor Jeppe Vinther to hear more about the current project possibilities. Please attach CV and course/grade transcript with your email.
Working in the Vinther Lab
The reason we work here is to do excellent science and this is our main focus. At the same time the lab should be a good and inspiring place to work.
We will therefore always treat each other with respect and try to help each other whenever possible, both with practical issues and by discussing the science and relevance of our projects.
Gabriele Indrisiunaite (Postdoc)
Klara Marie Andersen (MSc)
Sesilie Weiss (MSc)
Line Dahl Poulsen (PhD, Postdoc)
Agnieszka Podolska-Charlery (Postdoc)
Lasse Votborg Novél (MSc)
Lisa Marie Simon (MSc)
Thorsten Brodersen (MSc)
Søren Iversen (MSc)
Lukasz Jan Kielpinski (PhD, Postdoc)
Jakob Lewin Rukov (PhD, Postdoc)
Signe Olivarius (MSc, PhD)
Isabel Bro Høy (MSc)
Mads Marquardt Hedegaard
Ditte Lindschouw (MSc)
Kirsten Reichwald (MSc)
Christian Weile (MSc)
Members
| Name | Title | Phone | |
|---|---|---|---|
| Amal Al-Chaer | Laboratory Technician | +4535330238 | |
| Anna Sherwood | Assistant Professor | +4535331490 | |
| Jeppe Vinther | Associate Professor |
Contact
Associate Professor Jeppe Vinther
Computational and RNA Biology
Ole Maaløes Vej 5, 3.1.11
2200 Copenhagen N
jvinther@bio.ku.dk
Phone: +45 22 84 07 80
News @VintherLab