Computational Biology of Non-Coding RNA: Methods and Protocols

454 Pages·2019·11.099 MB·English

by  Xin Lai, Shailendra K. Gupta, Julio Vera

Methods in
Molecular Biology 1912
Xin Lai
Shailendra K. Gupta
Julio Vera Editors
Computational
Biology of Non-
Coding RNA
Methods and Protocols
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire,AL109AB,UK
Forfurther volumes:
http://www.springer.com/series/7651
Computational Biology
of Non-Coding RNA
Methods and Protocols
Edited by
Xin Lai
Department of Dermatology, Erlangen University Hospital, Erlangen, Germany
Shailendra K. Gupta
Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
Julio Vera
Department of Dermatology, Erlangen University Hospital, Erlangen, Germany
Editors
XinLai ShailendraK.Gupta
DepartmentofDermatology DepartmentofSystemsBiology
ErlangenUniversityHospital andBioinformatics
Erlangen,Germany UniversityofRostock
Rostock,Germany
JulioVera
DepartmentofDermatology
ErlangenUniversityHospital
Erlangen,Germany
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8981-2 ISBN978-1-4939-8982-9 (eBook)
https://doi.org/10.1007/978-1-4939-8982-9
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Preface
NoncodingRNAs(ncRNAs)haveemergedasamajorclassofregulatorygenesforadiverse
rangeofbiologicalfunctions.ncRNAsexerttheireffectinthecontextofcomplexregulatory
networks by targeting protein-coding genes, as well as other ncRNAs. Computational
methods, such as high-throughput sequencing data analysis, biochemical network recon-
struction and analysis, and kinetic modeling, have been applied to provide the functional
characterization and annotation of ncRNAs. The aim of this volume is to review current
knowledge, novel methods, and open challenges in understanding the regulatory role of
ncRNAs in biomedicine. In particular, this volume offers a collection of state-of-the-art
methodsincludingtheidentificationofnovelncRNAsandtheir targets,functionalannota-
tion,anddiseaseassociationindifferentbiologicalcontexts.
The book is divided into five parts: (1) Overview of Disease-Specific ncRNAs,
(2) Computational Methods and Workflows for ncRNA Discovery and Annotation Based
onHigh-ThroughputSequencingData,(3)BioinformaticsToolsandDatabasesforncRNA
Analyses,(4)Network-BasedMethodsforCharacterizingncRNAFunction,and(5)Kinetic
Modeling of ncRNA-Mediated Gene Regulation. In the first part, Schulte et al. discuss in
detail the current knowledge on the role of regulatory microRNAs (miRNAs) and long
ncRNA (lncRNA) in inflammatory and infectious diseases (Chapter 1). In Chapter 2,
Logotheti, Marquardt, and Pu¨tzer discuss the cross-talk between p73 and miRNAs in
realizingthecancer metastasisphenotype.Thischapteralsohighlightstranslationaloppor-
tunitiesandresearchchallengesforthep73/miRNAcancernetworkinthecontextofcancer
metastasis.
Thesubsequentfivechaptersdescribeexperimentalandcomputationalmethods,work-
flows that are useful for identification and functional annotation of circular RNAs (cir-
cRNAs), lncRNAs, and miRNAs. In Chapter 3, Sharma et al. describe software and
workflows to identify circRNAs from RNA sequencing (RNA-seq) data as well as a step-
by-step procedure to experimentally validate in silico identified circRNAs. Chapter 4 by
Mathew et al. presents methods and pipelines for the discovery of novel lncRNAs from
RNA-seq data of zebrafish. In Chapter 5, Wolfien et al. review and discuss state-of-the-art
experimental and computational workflows for the identification and characterization of
ncRNAs, and they emphasize the use of transcriptome-wide association studies, molecular
network analyses, and artificial intelligence-guided predictions. They also propose a
promising strategy for developing reproducible and sharable computational workflows for
the study of ncRNAs using RNA-seq data. In Chapter 6, Nigita et al. review methods and
resourcesforgenome-widedetectionofRNAeditinginncRNAsanddiscussthefeaturesof
ncRNA editing associated with their function as well as with the onset of human diseases.
Finally, Demirci, Yousef, and Allmer present computational methodologies allowing the
identification and validation of functional miRNA-mRNA interactions and discuss key
pointsforinvestigatingmiRNAsasbiomarkersofhumandiseases(Chapter7).
ThenextthreechapterspresentbioinformaticstoolsanddatabasesforncRNAanalyses.
In Chapter 8, Bagnacani et al. present a strategy that makes use of community effort to
develop sharable and reusable computational workflows using the Galaxy platform. The
conceptisexemplifiedwithadatabasefor theidentificationandcharacterizationofcooper-
ative miRNA regulation of gene expression. In Chapter 9, Monga and Kumar provide a
v
vi Preface
comprehensive review of in silico miRNA resources and databases. They present tools for
miRNA annotation, miRNA-disease association and identification and characterization of
miRNA variants. In Chapter 10, Maracaja-Coutinho et al. present an up-to-date review
about229databasesrelatedwithncRNAresearchwithparticularemphasisonbiomedicine,
including ncRNA databases for cancer, cardiovascular, nervous systems, pathogens, and
otherdiseases.
Chapters11–13highlightnetwork-basedmethodsforcharacterizingncRNAfunctions.
In Chapter 11, Nacher and Akutsu review the current research on network controllability
methods.TheauthorsalsopresentatripartitenetworkmodelincludingncRNA-targetand
protein-disease layers and analyze the network with controllability methods to identify the
subsetofcriticalcontrolncRNAsassociatedwithhumandiseases.PiroandMarsicosumma-
rize recent developments in lncRNA function prediction and lncRNA-disease associations
using methods based on network analysis and competing endogenous RNAs (ceRNAs)
function prediction (Chapter 12). Paul presents a mutual information-based Maximum-
RelevanceMaximum-SignificancealgorithmtoidentifymiRNA-mRNAregulatorymodules
frominteractionnetworksinacasestudyongynecologiccancer(Chapter13).
The last four chapters of this book showcase the use of kinetic modeling for providing
quantitative understanding about mechanisms of ncRNA-mediated regulation of gene
expression. In Chapter 14, Bocci et al. review and discuss kinetic models that investigate
the ability of miRNA-mediated feedback loops in provoking bistability in gene expression.
They link this phenomenon with the switch of cellular phenotypes and the control of
intrinsic and extrinsic signaling noise. In Chapter 15, Martirosyan et al. review kinetic
models that describe competition and depletion of shared miRNAs by ceRNAs, showing
the importance of ceRNA effect in processing gene expression noise. In Chapter 16, Tian
et al. demonstrated the use of kinetic modeling to explain the emerging properties asso-
ciatedwithmiRNA-mRNAreciprocalregulationandshowthatsuchregulationcanleadto
bistableswitchesingeneexpressiondirectingcellfatedecision.Inthelastchapter,Rabajante
andRosariodiscussmathematicalmodelingframeworksforstudyinglncRNAregulationof
the mammalian cell cycle. They also present a model of ordinary differential equations to
simulateandanalyzecellcycleregulationinresponsetoDNAdamage.
Takentogether,allchapterspresentedinthisbookprovideastate-of-the-artcollection
ofcomputational methods and approaches that willbeof valueto researchersinterested in
thencRNAfield.Computationalbiology-basedmethodsfor theidentificationandanalyses
of ncRNAs in the context of biomedicine are rapidly growing with both challenges and
opportunities to identify ncRNA biomarkers and to develop ncRNA therapeutics. We
believe that this volume is a valuable and useful resource for addressing many of these
exciting challenges in ncRNA research and hope it will be of interest to many peers. This
book is also dedicated to the loss of Dr. Baltazar D. Aguda who has made numerous and
important contribution to improve our understanding of ncRNA-mediated regulation of
geneexpressionusingmathematicalmodels.
Erlangen,Germany XinLai
Rostock,Germany ShailendraK.Gupta
Erlangen,Germany JulioVera
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I OVERVIEW OF DISEASE-SPECIFIC NCRNAS
1 ncRNAsinInflammatoryandInfectiousDiseases........................... 3
LeonN.Schulte,WilhelmBertrams,ChristinaStielow,
andBerndSchmeck
2 p73-GovernedmiRNANetworks:TranslatingBioinformatics
ApproachestoTherapeuticSolutionsforCancerMetastasis.................. 33
StellaLogotheti,StephanMarquardt,andBrigitteM.Pu¨tzer
PART II COMPUTATIONAL METHODS AND WORKFLOWS FOR NCRNA
DISCOVERY AND ANNOTATION BASED ON HIGH-THROUGHPUT
SEQUENCING DATA
3 MethodsforAnnotationandValidationofCircularRNAs
fromRNAseqData...................................................... 55
DishaSharma,ParasSehgal,JudithHariprakash,SridharSivasubbu,
andVinodScaria
4 MethodstoStudyLongNoncodingRNAExpression
andDynamicsinZebrafishUsingRNASequencing......................... 77
SamathaMathew,AmbilySivadas,ParasSehgal,KritiKaushik,
ShamsudheenK.Vellarikkal,VinodScaria,andSridharSivasubbu
5 WorkflowDevelopmentfor theFunctionalCharacterizationofncRNAs....... 111
MarkusWolfien,DavidLeonBrauer,AndreaBagnacani,
andOlafWolkenhauer
6 ncRNAEditing:FunctionalCharacterizationandComputational
Resources.............................................................. 133
GiovanniNigita,GioacchinoP.Marceca,LuisaTomasello,
RosarioDistefano,FedericaCalore,DarioVeneziano,GiuliaRomano,
SergePatrickNana-Sinkam,MarioAcunzo,andCarloM.Croce
7 ComputationalPredictionofFunctionalMicroRNA–mRNA
Interactions ............................................................ 175
Mu¨s¸errefDuyguSac¸arDemirci,MalikYousef,andJensAllmer
PART III BIOINFORMATICS TOOLS AND DATABASES FOR NCRNA ANALYSES
8 ToolsforUnderstandingmiRNA–mRNAInteractionsforReproducible
RNAAnalysis........................................................... 199
AndreaBagnacani,MarkusWolfien,andOlafWolkenhauer
vii
viii Contents
9 ComputationalResourcesforPredictionandAnalysisofFunctional
miRNAandTheirTargetome ............................................ 215
IshaMongaandManojKumar
10 NoncodingRNAsDatabases:CurrentStatusandTrends .................... 251
ViniciusMaracaja-Coutinho,AlexandreRossiPaschoal,
Jose´CarlosCaris-Maldonado,PedroVinı´ciusBorges,
AlmirJose´Ferreira,andAlanMitchellDurham
PART IV NETWORK-BASED METHODS FOR CHARACTERIZING
NCRNA FUNCTION
11 ControllabilityMethodsforIdentifyingAssociationsBetween
CriticalControlncRNAsandHumanDiseases ............................. 289
JoseC.NacherandTatsuyaAkutsu
12 Network-BasedMethodsandOtherApproachesforPredicting
lncRNAFunctionsandDiseaseAssociations ............................... 301
RosarioMichaelPiro andAnnalisaMarsico
13 IntegrationofmiRNAandmRNAExpressionData
forUnderstandingEtiologyofGynecologicCancers ........................ 323
SushmitaPaul
PART V KINETIC MODELING OF NCRNA-MEDIATED GENE REGULATION
14 QuantitativeCharacteristicofncRNARegulationinGene
RegulatoryNetworks.................................................... 341
FedericoBocci,MohitKumarJolly,HerbertLevine,
andJose´NelsonOnuchic
15 KineticModellingofCompetitionandDepletionofShared
miRNAsbyCompetingEndogenousRNAs................................ 367
AraksMartirosyan,MarcoDelGiudice,ChiaraEnricoBena,
AndreaPagnani,CarlaBosia,andAndreaDeMartino
16 ModelingncRNA-MediatedCircuitsinCellFateDecision................... 411
Xiao-JunTian,ManuelaVanegasFerro,andHanahGoetz
17 ModelingLongncRNA-MediatedRegulationintheMammalian
CellCycle.............................................................. 427
JomarF.RabajanteandRicardoC.H.delRosario
Index ...................................................................... 447
Contributors
MARIOACUNZO (cid:1) DivisionofPulmonaryDiseasesandCriticalCareMedicine,Virginia
CommonwealthUniversity,Richmond,VA,USA
TATSUYAAKUTSU (cid:1) BioinformaticsCenter,InstituteforChemicalResearch,KyotoUniversity,
Kyoto,Japan
JENS ALLMER (cid:1) AppliedBioinformatics,Bioscience,WageningenUniversity&Research,
Wageningen,TheNetherlands
ANDREA BAGNACANI (cid:1) DepartmentofSystemsBiologyandBioinformatics, Institute
ofComputerScience,UniversityofRostock,Rostock,Germany
CHIARAENRICO BENA (cid:1) DISAT,PolitecnicodiTorino,Turin,Italy;ItalianInstitutefor
GenomicMedicine,Turin,Italy
WILHELMBERTRAMS (cid:1) InstituteforLungResearch,UniversitiesofGiessenandMarburg
LungCenter,MemberoftheGermanCenterforLungResearch(DZL),Philipps-University
Marburg,Marburg,Germany
FEDERICO BOCCI (cid:1) Center forTheoreticalBiologicalPhysics,RiceUniversity,Houston,TX,
USA;DepartmentofChemistry,RiceUniversity,Houston,TX,USA
PEDRO VINI´CIUSBORGES (cid:1) DepartmentofComputerScience,BioinformaticsGraduation
Program(PPGBIOINFO),FederalUniversityofTechnology—Parana´,Corne´lioProc(cid:1)opio,
Brazil
CARLABOSIA (cid:1) DISAT,PolitecnicodiTorino,Turin,Italy;ItalianInstituteforGenomic
Medicine,Turin,Italy
DAVIDLEONBRAUER (cid:1) DepartmentofSystemsBiologyandBioinformatics,Institute
ofComputerScience,UniversityofRostock,Rostock,Germany
FEDERICA CALORE (cid:1) DepartmentofCancerBiologyandGenetics,ComprehensiveCancer
Center,TheOhioStateUniversity,Columbus,OH,USA
JOSE´ CARLOSCARIS-MALDONADO (cid:1) AdvancedCenter forChronicDiseases—ACCDiS,
FacultaddeCienciasQuı´micasyFarmace´uticas,UniversidaddeChile,Santiago,Chile
CARLOM.CROCE (cid:1) DepartmentofCancerBiologyandGenetics,ComprehensiveCancer
Center,TheOhioStateUniversity,Columbus,OH,USA
ROSARIODISTEFANO (cid:1) DepartmentofCancerBiologyandGenetics,ComprehensiveCancer
Center,TheOhioStateUniversity,Columbus,OH,USA
ALANMITCHELLDURHAM (cid:1) ComputerScienceDepartment,InstitutodeMatema´tica
eEstatı´stica,UniversidadedeSa˜oPaulo,Sa˜oPaulo,Brazil
ALMIRJOSE´ FERREIRA (cid:1) ComputerScienceDepartment,InstitutodeMatema´ticaeEstatı´stica,
UniversidadedeSa˜oPaulo,Sa˜oPaulo,Brazil
MARCODELGIUDICE (cid:1) DISAT,PolitecnicodiTorino,Turin,Italy;ItalianInstitutefor
GenomicMedicine,Turin,Italy
HANAHGOETZ (cid:1) SchoolofBiologicalandHealthSystemsEngineering,ArizonaState
University,Tempe,AZ,USA
JUDITHHARIPRAKASH (cid:1) G.N.RamachandranKnowledgeCenter forBioinformatics,CSIR
InstituteofGenomicsandIntegrativeBiology(CSIR-IGIB),Delhi,India
MOHITKUMARJOLLY (cid:1) Center forTheoreticalBiologicalPhysics,RiceUniversity,Houston,
TX,USA
ix
x Contributors
KRITIKAUSHIK (cid:1) GenomicsandMolecularMedicine,CSIRInstituteofGenomicsand
IntegrativeBiology(CSIR-IGIB),Delhi,India;AcademyofScientificandInnovative
Research(AcSIR),NewDelhi,India
MANOJKUMAR (cid:1) BioinformaticsCentre,InstituteofMicrobialTechnology,Council
ofScientificandIndustrialResearch,Chandigarh,India
HERBERTLEVINE (cid:1) Center forTheoreticalBiologicalPhysics,RiceUniversity,Houston,TX,
USA;DepartmentofChemistry,RiceUniversity,Houston,TX,USA;Department
ofBioengineering,RiceUniversity,Houston,TX,USA;DepartmentofPhysicsand
Astronomy,RiceUniversity,Houston,TX,USA
STELLA LOGOTHETI (cid:1) InstituteofExperimentalGeneTherapyandCancerResearch,Rostock
UniversityMedicalCenter,Rostock,Germany
VINICIUS MARACAJA-COUTINHO (cid:1) AdvancedCenter forChronicDiseases—ACCDiS,
FacultaddeCienciasQuı´micasyFarmace´uticas,UniversidaddeChile,Santiago,Chile
GIOACCHINOP.MARCECA (cid:1) DepartmentofCancerBiologyandGenetics,Comprehensive
CancerCenter,TheOhioStateUniversity,Columbus,OH,USA;DepartmentofClinical
andExperimentalMedicine,UniversityofCatania,Catania,CT,Italy
STEPHANMARQUARDT (cid:1) InstituteofExperimentalGeneTherapyandCancerResearch,
RostockUniversityMedicalCenter,Rostock,Germany
ANNALISAMARSICO (cid:1) Max-Planck-Institutfu¨r molekulareGenetik,Berlin,Germany;
Institutfu¨rInformatik,FreieUniversita€tBerlin,Berlin,Germany
ANDREADEMARTINO (cid:1) Soft&LivingMatterLab,CNR-NANOTEC,Rome,Italy;Italian
InstituteforGenomicMedicine,Turin,Italy
ARAKSMARTIROSYAN (cid:1) LaboratoryofGliaBiology,VIB-KULeuvenCenter forBrainand
DiseaseResearch,Leuven,Belgium;KULeuvenDepartmentofNeuroscience,Leuven,
Belgium
SAMATHAMATHEW (cid:1) GenomicsandMolecularMedicine,CSIRInstituteofGenomicsand
IntegrativeBiology(CSIR-IGIB),Delhi,India;AcademyofScientificandInnovative
Research(AcSIR),NewDelhi,India
ISHAMONGA (cid:1) BioinformaticsCentre,InstituteofMicrobialTechnology,CouncilofScientific
andIndustrialResearch,Chandigarh,India
JOSEC.NACHER (cid:1) FacultyofScience,DepartmentofInformationScience,TohoUniversity,
Chiba,Japan
SERGEPATRICKNANA-SINKAM (cid:1) DivisionofPulmonaryDiseasesandCriticalCareMedicine,
VirginiaCommonwealthUniversity,Richmond,VA,USA
GIOVANNI NIGITA (cid:1) DepartmentofCancerBiologyandGenetics,ComprehensiveCancer
Center,TheOhioStateUniversity,Columbus,OH,USA
JOSE´ NELSONONUCHIC (cid:1) CenterforTheoreticalBiologicalPhysics,RiceUniversity,Houston,
TX,USA;DepartmentofChemistry,RiceUniversity,Houston,TX,USA;Department
ofPhysicsandAstronomy,RiceUniversity,Houston,TX,USA;DepartmentofBiosciences,
RiceUniversity,Houston,TX,USA
ANDREAPAGNANI (cid:1) DISAT,PolitecnicodiTorino,Turin,Italy;ItalianInstituteforGenomic
Medicine,Turin,Italy
ALEXANDREROSSIPASCHOAL (cid:1) DepartmentofComputerScience,BioinformaticsGraduation
Program(PPGBIOINFO),FederalUniversityofTechnology—Parana´,Corne´lioProc(cid:1)opio,
Brazil
SUSHMITAPAUL (cid:1) DepartmentofBioscience&Bioengineering,IndianInstituteofTechnology
Jodhpur,Jodhpur,Rajasthan,India