Cargando…

Experimental characterization of the human non-sequence-specific nucleic acid interactome

BACKGROUND: The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual...

Descripción completa

Detalles Bibliográficos
Autores principales: Dürnberger, Gerhard, Bürckstümmer, Tilmann, Huber, Kilian, Giambruno, Roberto, Doerks, Tobias, Karayel, Evren, Burkard, Thomas R, Kaupe, Ines, Müller, André C, Schönegger, Andreas, Ecker, Gerhard F, Lohninger, Hans, Bork, Peer, Bennett, Keiryn L, Superti-Furga, Giulio, Colinge, Jacques
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053969/
https://www.ncbi.nlm.nih.gov/pubmed/23902751
http://dx.doi.org/10.1186/gb-2013-14-7-r81
_version_ 1782320478940037120
author Dürnberger, Gerhard
Bürckstümmer, Tilmann
Huber, Kilian
Giambruno, Roberto
Doerks, Tobias
Karayel, Evren
Burkard, Thomas R
Kaupe, Ines
Müller, André C
Schönegger, Andreas
Ecker, Gerhard F
Lohninger, Hans
Bork, Peer
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
author_facet Dürnberger, Gerhard
Bürckstümmer, Tilmann
Huber, Kilian
Giambruno, Roberto
Doerks, Tobias
Karayel, Evren
Burkard, Thomas R
Kaupe, Ines
Müller, André C
Schönegger, Andreas
Ecker, Gerhard F
Lohninger, Hans
Bork, Peer
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
author_sort Dürnberger, Gerhard
collection PubMed
description BACKGROUND: The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. RESULTS: We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. CONCLUSIONS: The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms.
format Online
Article
Text
id pubmed-4053969
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-40539692014-06-12 Experimental characterization of the human non-sequence-specific nucleic acid interactome Dürnberger, Gerhard Bürckstümmer, Tilmann Huber, Kilian Giambruno, Roberto Doerks, Tobias Karayel, Evren Burkard, Thomas R Kaupe, Ines Müller, André C Schönegger, Andreas Ecker, Gerhard F Lohninger, Hans Bork, Peer Bennett, Keiryn L Superti-Furga, Giulio Colinge, Jacques Genome Biol Research BACKGROUND: The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. RESULTS: We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. CONCLUSIONS: The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms. BioMed Central 2013 2013-07-31 /pmc/articles/PMC4053969/ /pubmed/23902751 http://dx.doi.org/10.1186/gb-2013-14-7-r81 Text en Copyright © 2013 Dürnberger et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Dürnberger, Gerhard
Bürckstümmer, Tilmann
Huber, Kilian
Giambruno, Roberto
Doerks, Tobias
Karayel, Evren
Burkard, Thomas R
Kaupe, Ines
Müller, André C
Schönegger, Andreas
Ecker, Gerhard F
Lohninger, Hans
Bork, Peer
Bennett, Keiryn L
Superti-Furga, Giulio
Colinge, Jacques
Experimental characterization of the human non-sequence-specific nucleic acid interactome
title Experimental characterization of the human non-sequence-specific nucleic acid interactome
title_full Experimental characterization of the human non-sequence-specific nucleic acid interactome
title_fullStr Experimental characterization of the human non-sequence-specific nucleic acid interactome
title_full_unstemmed Experimental characterization of the human non-sequence-specific nucleic acid interactome
title_short Experimental characterization of the human non-sequence-specific nucleic acid interactome
title_sort experimental characterization of the human non-sequence-specific nucleic acid interactome
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053969/
https://www.ncbi.nlm.nih.gov/pubmed/23902751
http://dx.doi.org/10.1186/gb-2013-14-7-r81
work_keys_str_mv AT durnbergergerhard experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT burckstummertilmann experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT huberkilian experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT giambrunoroberto experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT doerkstobias experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT karayelevren experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT burkardthomasr experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT kaupeines experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT mullerandrec experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT schoneggerandreas experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT eckergerhardf experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT lohningerhans experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT borkpeer experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT bennettkeirynl experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT supertifurgagiulio experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome
AT colingejacques experimentalcharacterizationofthehumannonsequencespecificnucleicacidinteractome