Inviting an author to review:
Find an author and click ‘Invite to review selected article’ near their name.
Search for authorsSearch for similar articles
22
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      MicroRNAs are deeply linked to the emergence of the complex octopus brain

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.

          Abstract

          Abstract

          The ancestors of octopuses and squids have expanded their small RNA toolkit which enabled the evolution of complex brains.

          Related collections

          Most cited references80

          • Record: found
          • Abstract: found
          • Article: not found

          STAR: ultrafast universal RNA-seq aligner.

          Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Minimap2: pairwise alignment for nucleotide sequences

            Heng Li (2018)
            Recent advances in sequencing technologies promise ultra-long reads of ∼100 kb in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 Mb in length. Existing alignment programs are unable or inefficient to process such data at scale, which presses for the development of new alignment algorithms.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Complex heatmaps reveal patterns and correlations in multidimensional genomic data.

              Parallel heatmaps with carefully designed annotation graphics are powerful for efficient visualization of patterns and relationships among high dimensional genomic data. Here we present the ComplexHeatmap package that provides rich functionalities for customizing heatmaps, arranging multiple parallel heatmaps and including user-defined annotation graphics. We demonstrate the power of ComplexHeatmap to easily reveal patterns and correlations among multiple sources of information with four real-world datasets.
                Bookmark

                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing - original draftRole: Writing - review & editing
                Role: InvestigationRole: MethodologyRole: Writing - original draft
                Role: MethodologyRole: ResourcesRole: ValidationRole: Writing - review & editing
                Role: MethodologyRole: ResourcesRole: Validation
                Role: Data curationRole: Formal analysisRole: InvestigationRole: Visualization
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: Resources
                Role: InvestigationRole: Resources
                Role: ResourcesRole: Writing - review & editing
                Role: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing - original draftRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                November 2022
                25 November 2022
                : 8
                : 47
                : eadd9938
                Affiliations
                [ 1 ]Laboratory of Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str 28, 10115 Berlin, Germany.
                [ 2 ]Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
                [ 3 ]Universitat Pompeu Fabra (UPF), Barcelona, Spain.
                [ 4 ]UiT The Arctic University of Norway, Tromsø, Norway.
                [ 5 ]SciLifeLab, Stockholm University, Stockholm, Sweden.
                [ 6 ]Department of Biology, University of Naples Federico II, Naples, Italy.
                [ 7 ]Dartmouth College, Hanover, NH, USA.
                [ 8 ]School of Earth Sciences, University of Bristol, Bristol, UK.
                [ 9 ]School of Biological Sciences, University of Bristol, Bristol, UK.
                [ 10 ]Laboratory of Developmental Neurobiology, Department of Biology, KU Leuven, Leuven, Belgium.
                [ 11 ]Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy.
                Author notes
                [* ]Corresponding author. Email: rajewsky@ 123456mdc-berlin.de (N.R.); kevin.j.peterson@ 123456dartmouth.edu (K.J.P.)
                Author information
                https://orcid.org/0000-0002-3971-3070
                https://orcid.org/0000-0003-0352-3037
                https://orcid.org/0000-0002-8984-5215
                https://orcid.org/0000-0001-5043-8922
                https://orcid.org/0000-0002-6322-7769
                https://orcid.org/0000-0002-1452-8063
                https://orcid.org/0000-0001-6001-3346
                https://orcid.org/0000-0002-3584-9616
                https://orcid.org/0000-0002-5287-8830
                https://orcid.org/0000-0002-1018-9957
                https://orcid.org/0000-0002-6780-0964
                https://orcid.org/0000-0002-4785-4332
                Article
                add9938
                10.1126/sciadv.add9938
                9699675
                36427315
                baa2aed0-3032-4993-8b89-81960097c316
                Copyright © 2022 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 18 July 2022
                : 27 October 2022
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100016934, Tromsø Forskningsstiftelse;
                Award ID: 20_SG_BF “MIRevolution”
                Funded by: FundRef http://dx.doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft;
                Award ID: RA 838/5-1
                Funded by: FundRef http://dx.doi.org/10.13039/501100001862, Swedish Research Council Formas;
                Funded by: Italian Ministry of Education, Universities and Research;
                Funded by: Italian Ministry of Education, Universities and Research;
                Funded by: Italian Ministry of Education, Universities and Research;
                Funded by: Carlsberg Foundation;
                Categories
                Research Article
                Biomedicine and Life Sciences
                SciAdv r-articles
                Evolutionary Biology
                Organismal Biology
                Organismal Biology
                Custom metadata
                SEF RIO

                Comments

                Comment on this article

                scite_
                0
                0
                0
                0
                Smart Citations
                0
                0
                0
                0
                Citing PublicationsSupportingMentioningContrasting
                View Citations

                See how this article has been cited at scite.ai

                scite shows how a scientific paper has been cited by providing the context of the citation, a classification describing whether it supports, mentions, or contrasts the cited claim, and a label indicating in which section the citation was made.

                Similar content459

                Cited by13

                Most referenced authors1,312