Eivind Valen

• Svalastoga, Pernille; Kaci, Alba; Molnes, Janne; Solheim, Marie Holm; Johansson, Bente Berg & Krogvold, Lars [Vis alle 16 forfattere av denne artikkelen] (2023). Characterisation of HNF1A variants in paediatric diabetes in Norway using functional and clinical investigations to unmask phenotype and monogenic diabetes. Diabetologia. ISSN 0012-186X. 66, s. 2226–2237. doi: 10.1007/s00125-023-06012-4. Fulltekst i vitenarkiv
• Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra & Niazi, Adnan Muhammad [Vis alle 11 forfattere av denne artikkelen] (2022). Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nature Methods. ISSN 1548-7091. doi: 10.1038/s41592-022-01714-w.
• Tilahun Bizuayehu, Teshome; Labun, Kornel; Jakubec, Martin; Jefimov, Kirill; Niazi, Adnan Muhammad & Valen, Eivind Dale (2022). Long-read single-molecule RNA structure sequencing using nanopore. Nucleic Acids Research (NAR). ISSN 0305-1048. 50(20). doi: 10.1093/nar/gkac775.
• Kute, Preeti; Soukarieh, Omar; Tjeldnes, Håkon; Trégouët, David-Alexandre & Valen, Eivind Dale (2022). Small Open Reading Frames, How to Find Them and Determine Their Function. Frontiers in Genetics. ISSN 1664-8021. 12. doi: 10.3389/fgene.2021.796060.
• Niazi, Adnan Muhammad; Krause, Maximilian & Valen, Eivind Dale (2021). Transcript Isoform-Specific Estimation of Poly(A) Tail Length by Nanopore Sequencing of Native RNA. Methods in molecular biology. ISSN 1064-3745. 2284, s. 543–567. doi: 10.1007/978-1-0716-1307-8_30.
• Chyzynska, Katarzyna; Labun, Kornel; Jones, Carl Matthew; Grellscheid, Sushma Nagaraja & Valen, Eivind Dale (2021). Deep conservation of ribosome stall sites across RNA processing genes. NAR Genomics and Bioinformatics. ISSN 2631-9268. 3(2), s. 1–13. doi: 10.1093/nargab/lqab038. Vis sammendrag

  The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation.

• Labun, Kornel; Krause, Maximilian; Torres Cleuren, Yamila Nicole & Valen, Eivind Dale (2021). CRISPR Genome Editing Made Easy Through the CHOPCHOP Website. Current Protocols in Bioinformatics. ISSN 1934-3396. 1. doi: 10.1002/cpz1.46.
• Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri & Mamia, Katariina Aino Inkeri [Vis alle 19 forfattere av denne artikkelen] (2021). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. eLIFE. ISSN 2050-084X. 11. doi: 10.7554/eLife.75415. Fulltekst i vitenarkiv Vis sammendrag

  Precision CRISPR gene editing relies on the cellular homology-directed DNA repair (HDR) to introduce custom DNA sequences to target sites. The HDR editing efficiency varies between cell types and genomic sites, and the sources of this variation are incompletely understood. Here, we have studied the effect of 450 DNA repair protein - Cas9 fusions on CRISPR genome editing outcomes. We find the majority of fusions to improve precision genome editing only modestly in a locus- and cell-type specific manner. We identify Cas9-POLD3 fusion that enhances editing by speeding up the initiation of DNA repair. We conclude that while DNA repair protein fusions to Cas9 can improve HDR CRISPR editing, most need to be optimized to the cell type and genomic site, highlighting the diversity of factors contributing to locus-specific genome editing outcomes.

• Tjeldnes, Håkon; Labun, Kornel; Torres Cleuren, Yamila Nicole; Chyzynska, Katarzyna; Swirski, Michal & Valen, Eivind Dale (2021). ORFik: a comprehensive R toolkit for the analysis of translation. BMC Bioinformatics. ISSN 1471-2105. 22, s. 1–16. doi: 10.1186/s12859-021-04254-w.
• Poduval, Deepak; Berge, Elisabet Ognedal; Sichmanovà, Zuzana; Valen, Eivind; Iversen, Gjertrud Titlestad & Minsaas, Laura [Vis alle 8 forfattere av denne artikkelen] (2020). Assessment of tumor suppressor promoter methylation in healthy individuals. Clinical Epigenetics. ISSN 1868-7075. 12:131, s. 1–15. doi: 10.1186/s13148-020-00920-7.
• Pálfy, Máté; Schulze, Gunnar; Valen, Eivind & Vastenhouw, Nadine L. (2020). Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genetics. ISSN 1553-7390. 16(1), s. 1–25. doi: 10.1371/journal.pgen.1008546. Vis sammendrag

  In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here, we generated chromatin accessibility maps with ATAC-seq from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hypertranscribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.

• Svalastoga, Pernille; Sulen, Åsta Nordsveen; Fehn, Jarle Røneid; Aukland, Stein Magnus; Irgens, Henrik Underthun & Sirnes, Eivind [Vis alle 10 forfattere av denne artikkelen] (2020). Intellectual disability in KATP channel neonatal diabetes. Diabetes Care. ISSN 0149-5992. 43(3), s. 526–533. doi: 10.2337/dc19-1013.
• Giess, Adam; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon; Krause, Maximilian; Bizuayehu, Teshome Tilahun & Hiensch, Senna [Vis alle 9 forfattere av denne artikkelen] (2020). Profiling of Small Ribosomal Subunits Reveals Modes and Regulation of Translation Initiation. Cell reports. ISSN 2211-1247. 31(3). doi: 10.1016/j.celrep.2020.107534. Vis sammendrag

  Translation initiation is often attributed as the rate-determining step of eukaryotic protein synthesis and key to gene expression control. Despite this centrality, the series of steps involved in this process is poorly understood. Here, we capture the transcriptome-wide occupancy of ribosomes across all stages of translation initiation, enabling us to characterize the transcriptome-wide dynamics of ribosome recruitment to mRNAs, scanning across 5′ UTRs and stop codon recognition, in a higher eukaryote. We provide mechanistic evidence for ribosomes attaching to the mRNA by threading the mRNA through the small subunit. Moreover, we identify features that regulate the recruitment and processivity of scanning ribosomes and redefine optimal initiation contexts. Our approach enables deconvoluting translation initiation into separate stages and identifying regulators at each step.

• Danks, Gemma Barbara; Galbiati, Heloisa; Raasholm, Martina; Torres Cleuren, Yamila Nicole; Valen, Eivind & Navratilova, Pavla [Vis alle 7 forfattere av denne artikkelen] (2019). Trans-splicing of mRNAs links gene transcription to translational control regulated by mTOR. BMC Genomics. ISSN 1471-2164. 20(1). doi: 10.1186/s12864-019-6277-x. Fulltekst i vitenarkiv Vis sammendrag

  Background In phylogenetically diverse organisms, the 5′ ends of a subset of mRNAs are trans-spliced with a spliced leader (SL) RNA. The functions of SL trans-splicing, however, remain largely enigmatic. Results We quantified translation genome-wide in the marine chordate, Oikopleura dioica, under inhibition of mTOR, a central growth regulator. Translation of trans-spliced TOP mRNAs was suppressed, consistent with a role of the SL sequence in nutrient-dependent translational control of growth-related mRNAs. Under crowded, nutrient-limiting conditions, O. dioica continued to filter-feed, but arrested growth until favorable conditions returned. Upon release from unfavorable conditions, initial recovery was independent of nutrient-responsive, trans-spliced genes, suggesting animal density sensing as a first trigger for resumption of development. Conclusion Our results are consistent with a proposed role of trans-splicing in the coordinated translational down-regulation of nutrient-responsive genes under growth-limiting conditions.

• Krause, Maximilian; Niazi, Adnan Muhammad; Labun, Kornel; Torres Cleuren, Yamila Nicole; Müller, Florian Sebastian Alexander & Valen, Eivind (2019). tailfindr: Alignment-free poly(A) length measurement for Oxford Nanopore RNA and DNA sequencing. RNA: A publication of the RNA Society. ISSN 1355-8382. 25(10), s. 1229–1241. doi: 10.1261/rna.071332.119. Fulltekst i vitenarkiv Vis sammendrag

  Polyadenylation at the 3′-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3′-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr’s performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.

• Labun, Kornel; Montague, Tessa G.; Krause, Maximilian; Torres Cleuren, Yamila Nicole; Tjeldnes, Håkon & Valen, Eivind (2019). CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Research (NAR). ISSN 0305-1048. 47(W1), s. W171–W174. doi: 10.1093/nar/gkz365. Fulltekst i vitenarkiv Vis sammendrag

  The CRISPR–Cas system is a powerful genome editing tool that functions in a diverse array of organisms and cell types. The technology was initially developed to induce targeted mutations in DNA, but CRISPR–Cas has now been adapted to target nucleic acids for a range of purposes. CHOPCHOP is a web tool for identifying CRISPR–Cas single guide RNA (sgRNA) targets. In this major update of CHOPCHOP, we expand our toolbox beyond knockouts. We introduce functionality for targeting RNA with Cas13, which includes support for alternative transcript isoforms and RNA accessibility predictions. We incorporate new DNA targeting modes, including CRISPR activation/repression, targeted enrichment of loci for long-read sequencing, and prediction of Cas9 repair outcomes. Finally, we expand our results page visualization to reveal alternative isoforms and downstream ATG sites, which will aid users in avoiding the expression of truncated proteins. The CHOPCHOP web tool now supports over 200 genomes and we have released a command-line script for running larger jobs and handling unsupported genomes. CHOPCHOP v3 can be found at https://chopchop.cbu.uib.no

• Labun, Kornel; Guo, Xiaoge; Chavez, Alejandro; Church, George; Gagnon, James A. & Valen, Eivind (2019). Accurate analysis of genuine CRISPR editing events with ampliCan. Genome Research. ISSN 1088-9051. 29(5), s. 843–847. doi: 10.1101/gr.244293.118. Fulltekst i vitenarkiv Vis sammendrag

  We present ampliCan, an analysis tool for genome editing that unites highly precise quantification and visualization of genuine genome editing events. ampliCan features nuclease-optimized alignments, filtering of experimental artifacts, event-specific normalization, and off-target read detection and quantifies insertions, deletions, HDR repair, as well as targeted base editing. It is scalable to thousands of amplicon sequencing–based experiments from any genome editing experiment, including CRISPR. It enables automated integration of controls and accounts for biases at every step of the analysis. We benchmarked ampliCan on both real and simulated data sets against other leading tools, demonstrating that it outperformed all in the face of common confounding factors.

• Birkeland, Åsmund; Chyzynska, Katarzyna & Valen, Eivind (2018). Shoelaces: An interactive tool for ribosome profiling processing and visualization. BMC Genomics. ISSN 1471-2164. 19. doi: 10.1186/s12864-018-4912-6. Fulltekst i vitenarkiv Vis sammendrag

  Background The emergence of ribosome profiling to map actively translating ribosomes has laid the foundation for a diverse range of studies on translational regulation. The data obtained with different variations of this assay is typically manually processed, which has created a need for tools that would streamline and standardize processing steps. Results We present Shoelaces, a toolkit for ribosome profiling experiments automating read selection and filtering to obtain genuine translating footprints. Based on periodicity, favoring enrichment over the coding regions, it determines the read lengths corresponding to bona fide ribosome protected fragments. The specific codon under translation (P-site) is determined by automatic offset calculations resulting in sub-codon resolution. Shoelaces provides both a user-friendly graphical interface for interactive visualisation in a genome browser-like fashion and a command line interface for integration into automated pipelines. We process 79 libraries and show that studies typically discard excessive amounts of quality data in their manual analysis pipelines. Conclusions Shoelaces streamlines ribosome profiling analysis offering automation of the processing, a range of interactive visualization features and export of the data into standard formats. Shoelaces stores all processing steps performed in an XML file that can be used by other groups to exactly reproduce the processing of a given study. We therefore anticipate that Shoelaces can aid researchers by automating what is typically performed manually and contribute to the overall reproducibility of studies. The tool is freely distributed as a Python package, with additional instructions, tutorial and demo datasets available at https://bitbucket.org/valenlab/shoelaces.

• Ndah, Elvis; Jonckheere, Veronique; Giess, Adam; Valen, Eivind; Menschaert, Gerben & Van Damme, Petra (2017). REPARATION: ribosome profiling assisted (re-) annotation of bacterial genomes. Nucleic Acids Research (NAR). ISSN 0305-1048. 45(20). doi: 10.1093/nar/gkx758. Vis sammendrag

  Prokaryotic genome annotation is highly dependent on automated methods, as manual curation cannot keep up with the exponential growth of sequenced genomes. Current automated methods depend heavily on sequence context and often underestimate the complexity of the proteome. We developed REPARATION (RibosomeE Profiling Assisted (Re-)AnnotaTION), a de novo algorithm that takes advantage of experimental protein translation evidence from ribosome profiling (Ribo-seq) to delineate translated open reading frames (ORFs) in bacteria, independent of genome annotation. REPARATION evaluates all possible ORFs in the genome and estimates minimum thresholds based on a growth curve model to screen for spurious ORFs. We applied REPARATION to three annotated bacterial species to obtain a more comprehensive mapping of their translation landscape in support of experimental data. In all cases, we identified hundreds of novel (small) ORFs including variants of previously annotated ORFs. Our predictions were supported by matching mass spectrometry (MS) proteomics data, sequence composition and conservation analysis. REPARATION is unique in that it makes use of experimental translation evidence to perform de novo ORF delineation in bacterial genomes irrespective of the sequence context of the reading frame.

• Giess, Adam; Jonckheere, Veronique; Ndah, Elvis; Chyzynska, Katarzyna; Van Damme, Petra & Valen, Eivind (2017). Ribosome signatures aid bacterial translation initiation site identification. BMC Biology. ISSN 1741-7007. 15:76, s. 1–14. doi: 10.1186/s12915-017-0416-0. Vis sammendrag

  Background While methods for annotation of genes are increasingly reliable, the exact identification of translation initiation sites remains a challenging problem. Since the N-termini of proteins often contain regulatory and targeting information, developing a robust method for start site identification is crucial. Ribosome profiling reads show distinct patterns of read length distributions around translation initiation sites. These patterns are typically lost in standard ribosome profiling analysis pipelines, when reads from footprints are adjusted to determine the specific codon being translated. Results Utilising these signatures in combination with nucleotide sequence information, we build a model capable of predicting translation initiation sites and demonstrate its high accuracy using N-terminal proteomics. Applying this to prokaryotic translatomes, we re-annotate translation initiation sites and provide evidence of N-terminal truncations and extensions of previously annotated coding sequences. These re-annotations are supported by the presence of structural and sequence-based features next to N-terminal peptide evidence. Finally, our model identifies 61 novel genes previously undiscovered in the Salmonella enterica genome. Conclusions Signatures within ribosome profiling read length distributions can be used in combination with nucleotide sequence information to provide accurate genome-wide identification of translation initiation sites.

• Valen, Eivind; Labun, Kornel; Montague, Tessa G.; Gagnon, James A. & Thyme, Summer B. (2016). CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering. Nucleic Acids Research (NAR). ISSN 0305-1048. 44. doi: 10.1093/nar/gkw398. Vis sammendrag

  In just 3 years CRISPR genome editing has transformed biology, and its popularity and potency continue to grow. New CRISPR effectors and rules for locating optimum targets continue to be reported, highlighting the need for computational CRISPR targeting tools to compile these rules and facilitate target selection and design. CHOPCHOP is one of the most widely used web tools for CRISPR- and TALEN-based genome editing. Its overarching principle is to provide an intuitive and powerful tool that can serve both novice and experienced users. In this major update we introduce tools for the next generation of CRISPR advances, including Cpf1 and Cas9 nickases. We support a number of new features that improve the targeting power, usability and efficiency of CHOPCHOP. To increase targeting range and specificity we provide support for custom length sgRNAs, and we evaluate the sequence composition of the whole sgRNA and its surrounding region using models compiled from multiple large-scale studies. These and other new features, coupled with an updated interface for increased usability and support for a continually growing list of organisms, maintain CHOPCHOP as one of the leading tools for CRISPR genome editing. CHOPCHOP v2 can be found at http://chopchop.cbu.uib.no.

• Thyme, Summer B.; Akhmetova, Laila; Montague, Tessa G.; Valen, Eivind & Schier, Alexander F. (2016). Internal guide RNA interactions interfere with Cas9-mediated cleavage. Nature Communications. ISSN 2041-1723. 7:11750. doi: 10.1038/ncomms11750. Vis sammendrag

  The CRISPR/Cas system uses guide RNAs (gRNAs) to direct sequence-specific DNA cleavage. Not every gRNA elicits cleavage and the mechanisms that govern gRNA activity have not been resolved. Low activity could result from either failure to form a functional Cas9-gRNA complex or inability to recognize targets in vivo. Here we show that both phenomena influence Cas9 activity by comparing mutagenesis rates in zebrafish embryos with in vitro cleavage assays. In vivo, our results suggest that genomic factors such as CTCF inhibit mutagenesis. Comparing near-identical gRNA sequences with different in vitro activities reveals that internal gRNA interactions reduce cleavage. Even though gRNAs containing these structures do not yield cleavage-competent complexes, they can compete with active gRNAs for binding to Cas9. These results reveal that both genomic context and internal gRNA interactions can interfere with Cas9-mediated cleavage and illuminate previously uncharacterized features of Cas9-gRNA complex formation.

• Merkle, Florian T.; Neuhausser, Werner M.; Santos, David; Valen, Eivind; Gagnon, James A. & Maas, Kristi [Vis alle 9 forfattere av denne artikkelen] (2015). Efficient CRISPR-Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus. Cell reports. ISSN 2211-1247. 11(6), s. 875–883. doi: 10.1016/j.celrep.2015.04.007. Fulltekst i vitenarkiv Vis sammendrag

  The CRISPR-Cas9 system has the potential to revolutionize genome editing in human pluripotent stem cells (hPSCs), but its advantages and pitfalls are still poorly understood. We systematically tested the ability of CRISPR-Cas9 to mediate reporter gene knockin at 16 distinct genomic sites in hPSCs. We observed efficient gene targeting but found that targeted clones carried an unexpectedly high frequency of insertion and deletion (indel) mutations at both alleles of the targeted gene. These indels were induced by Cas9 nuclease, as well as Cas9-D10A single or dual nickases, and often disrupted gene function. To overcome this problem, we designed strategies to physically destroy or separate CRISPR target sites at the targeted allele and developed a bioinformatic pipeline to identify and eliminate clones harboring deleterious indels at the other allele. This two-pronged approach enables the reliable generation of knockin hPSC reporter cell lines free of unwanted mutations at the targeted locus.

• Andersson, Robin; Refsing Andersen, Peter; Valen, Eivind; Core, Leighton J.; Bornholdt, Jette & Boyd, Mette [Vis alle 8 forfattere av denne artikkelen] (2014). Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nature Communications. ISSN 2041-1723. 5:5336. doi: 10.1038/ncomms6336. Vis sammendrag

  Mammalian genomes are pervasively transcribed, yielding a complex transcriptome with high variability in composition and cellular abundance. Although recent efforts have identified thousands of new long non-coding (lnc) RNAs and demonstrated a complex transcriptional repertoire produced by protein-coding (pc) genes, limited progress has been made in distinguishing functional RNA from spurious transcription events. This is partly due to present RNA classification, which is typically based on technical rather than biochemical criteria. Here we devise a strategy to systematically categorize human RNAs by their sensitivity to the ribonucleolytic RNA exosome complex and by the nature of their transcription initiation. These measures are surprisingly effective at correctly classifying annotated transcripts, including lncRNAs of known function. The approach also identifies uncharacterized stable lncRNAs, hidden among a vast majority of unstable transcripts. The predictive power of the approach promises to streamline the functional analysis of known and novel RNAs.

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• Valen, Eivind (2022). Nye CRISPR-metoder og mer presis presisjonsmedisin. Tidsskrift for Den norske legeforening. ISSN 0029-2001. 142(17). doi: 10.4045/tidsskr.22.0689.
• Reint, Ganna; Li, Zhuokun; Labun, Kornel; Keskitalo, Salla; Soppa, Inkeri & Mamia, Katariina Aino Inkeri [Vis alle 19 forfattere av denne artikkelen] (2022). Rapid genome editing by CRISPR-Cas9-POLD3 fusion. .
• Mamia, Katariina Aino Inkeri; Saarela, Janna Saija; Li, Zhuokun; Reint, Ganna; Fatkhutdinov, Nail & Haugen, Frida Høsøien [Vis alle 13 forfattere av denne artikkelen] (2022). CRISPR-Cas9 T cell editing pipeline for Finnish founder diseases.
• Giess, Adam & Valen, Eivind (2019). Understanding translational landscapes through the footprints of ribosomes. Universitetet i Bergen. ISSN 978-82-308-3514-2.

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