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      High-throughput identification of dominant negative polypeptides in yeast

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      Author(s): 1 , 1 , 1 , 2
      Publication date (Electronic):
      Journal: Nature methods

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          Abstract

          Dominant negative polypeptides can inhibit protein function by binding to the wild type version or by titrating a ligand. Here, we use high-throughput sequencing of libraries composed of fragments of yeast genes to identify dominant negative polypeptides based on their depletion during cell growth. The method can uncover numerous inhibitory polypeptides for a protein and thereby define these fragments with exquisite resolution, even pinpointing individual residues with critical functional roles.

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          BEDTools: The Swiss-Army Tool for Genome Feature Analysis.

          Aaron Quinlan (2014)
          Technological advances have enabled the use of DNA sequencing as a flexible tool to characterize genetic variation and to measure the activity of diverse cellular phenomena such as gene isoform expression and transcription factor binding. Extracting biological insight from the experiments enabled by these advances demands the analysis of large, multi-dimensional datasets. This unit describes the use of the BEDTools toolkit for the exploration of high-throughput genomics datasets. Several protocols are presented for common genomic analyses, demonstrating how simple BEDTools operations may be combined to create bespoke pipelines addressing complex questions. Curr. Protoc. Bioinform. 47:11.12.1-11.12.34. © 2014 by John Wiley & Sons, Inc. Copyright © 2014 John Wiley & Sons, Inc.
          Article 0 comments Cited 541 times – based on 0 reviews     Review now
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            Functional inactivation of genes by dominant negative mutations.

            I Herskowitz (2015)
            Molecular biologists are increasingly faced with the problem of assigning a function to genes that have been cloned. A new approach to this problem involves the manipulation of the cloned gene to create what are known as 'dominant negative' mutations. These encode mutant polypeptides that when overexpressed disrupt the activity of the wild-type gene. There are many precedents for this kind of behaviour in the literature--some oncogenes might be examples of naturally occurring dominant negative mutations.
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              Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-A resolution.

              Jean-Paul Armache, Alexander Jarasch, Andreas Anger … (2010)
              Protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. Although X-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80S ribosomes are lacking. Using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (Triticum aestivum) 80S ribosome at 5.5-Å resolution. This map, together with a 6.1-Å map of a Saccharomyces cerevisiae 80S ribosome, has enabled us to model ∼98% of the rRNA. Accurate assignment of the rRNA expansion segments (ES) and variable regions has revealed unique ES-ES and r-protein-ES interactions, providing insight into the structure and evolution of the eukaryotic ribosome.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101215604
                Journal ID (pubmed-jr-id): 32338
                Journal ID (nlm-ta): Nat Methods
                Journal ID (iso-abbrev): Nat. Methods
                Title: Nature methods
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Nihms-submitted: 6 March 2019
                Publication date (Electronic): 08 April 2019
                Publication date (Print): May 2019
                Publication date PMC-release: 08 October 2019
                Volume: 16
                Issue: 5
                Pages: 413-416
                Affiliations
                [1 ]Department of Genome Sciences, University of Washington, Seattle, WA 98195
                [2 ]Department of Medicine, University of Washington, Seattle, WA 98195
                Author notes

                Author contributions: M.W.D., C.Q., and S.F. conceived and interpreted experiments. M.W.D., C.Q., and S.F. wrote the manuscript. M.W.D. conducted experiments and data analysis.

                Correspondence to Stanley Fields, fields@ 123456uw.edu , tel 206 616-4522
                Article
                Manuscript ID: NIHMS1523027
                DOI: 10.1038/s41592-019-0368-0
                PMC ID: 6555411
                PubMed ID: 30962621
                SO-VID: d0c40ebe-275e-435e-97e5-856d8806ead9
                License:

                Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

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                ScienceOpen disciplines: Life sciences

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