Structural robustness of mammalian transcription factor networks reveals plasticity across development

Scientific Reports
J L Caldu-PrimoJosé Dávila-Velderrain

Abstract

Network biology aims to understand cell behavior through the analysis of underlying complex biomolecular networks. Inference of condition-specific interaction networks from epigenomic data enables the characterization of the structural plasticity that regulatory networks can acquire in different tissues of the same organism. From this perspective, uncovering specific patterns of variation by comparing network structure among tissues could provide insights into systems-level mechanisms underlying cell behavior. Following this idea, here we propose an empirical framework to analyze mammalian tissue-specific networks, focusing on characterizing and contrasting their structure and behavior in response to perturbations. We structurally represent the state of the cell/tissue by condition specific transcription factor networks generated using DNase-seq chromatin accessibility data, and we profile their systems behavior in terms of the structural robustness against random and directed perturbations. Using this framework, we unveil the structural heterogeneity existing among tissues at different levels of differentiation. We uncover a novel and conserved systems property of regulatory networks underlying embryonic stem cells (ESCs): in ...Continue Reading

References

Oct 16, 1999·Science·A L Barabasi, R Albert
Aug 10, 2000·Nature·R AlbertA L Barabasi
Jan 3, 2001·Physical Review Letters·D S CallawayD J Watts
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
May 28, 2004·Briefings in Functional Genomics & Proteomics·Sui Huang
Oct 6, 2005·Proceedings of the National Academy of Sciences of the United States of America·John C DoyleWalter Willinger
Mar 15, 2006·Journal of Molecular Biology·M Madan BabuL Aravind
May 25, 2006·Annual Review of Genomics and Human Genetics·Glenn A MastonMichael R Green
May 26, 2006·Nature Reviews. Molecular Cell Biology·Eran Meshorer, Tom Misteli
Mar 17, 2007·Nature Reviews. Genetics·Mikhail Spivakov, Amanda G Fisher
Apr 7, 2007·Developmental Biology·Sui HuangTariq Enver
May 9, 2008·Cell Stem Cell·Bryan M Turner
Mar 24, 2009·Nature Methods·Jay R HesselberthJohn A Stamatoyannopoulos
May 30, 2009·PloS One·Zhihua Zhang, Jianzhi Zhang
Dec 15, 2010·Trends in Genetics : TIG·Joseph X Zhou, Sui Huang
Jul 6, 2011·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sui Huang
May 1, 2012·Cell·Hendrik MarksHendrik G Stunnenberg
May 12, 2012·Bioinformatics·Shane NephJohn A Stamatoyannopoulos
Sep 11, 2012·Cell·Shane NephJohn A Stamatoyannopoulos
Dec 4, 2012·Current Opinion in Genetics & Development·Jordi Garcia-Ojalvo, Alfonso Martinez Arias
Mar 5, 2013·Nature Biotechnology·Ines ThieleBernhard Ø Palsson
Aug 6, 2013·Cell·Ben D MacArthur, Ihor R Lemischka
Oct 25, 2013·Scientific Reports·Christopher R S BanerjiAndrew E Teschendorff
Nov 21, 2014·Nature·Andrew B StergachisJohn A Stamatoyannopoulos
Feb 20, 2015·Nature·UNKNOWN Roadmap Epigenomics ConsortiumManolis Kellis
May 9, 2015·Frontiers in Genetics·Jose Davila-VelderrainElena R Alvarez-Buylla
May 26, 2015·Frontiers in Physiology·Sergi ValverdeJordi Garcia-Ojalvo
Jun 18, 2015·Nature·Jason D BuenrostroWilliam J Greenleaf
Nov 21, 2015·Nucleic Acids Research·Ivan V KulakovskiyVsevolod J Makeev
Feb 26, 2016·Nature Methods·Jeff Vierstra, John A Stamatoyannopoulos
Jan 10, 2017·Nature Communications·Tiago A SchieberMartín G Ravetti
Jun 2, 2017·Nature Communications·Andrew E Teschendorff, Tariq Enver

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Methods Mentioned

BETA
footprinting
PCA
DNA-seq

Software Mentioned

Roadmap ChromHMM
igraph
R environment

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