Stem Cell Transcriptional Networks: Methods and Protocols

283 Pages·2014·8.072 MB·English

by  Benjamin L. Kidder (eds.)

Methods in
Molecular Biology 1150
Benjamin L. Kidder Editor
Stem Cell
Transcriptional
Networks
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life Sciences
University of Hertfordshire
Hat fi eld, Hertfordshire, AL10 9AB, UK
For further volumes:
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Stem Cell Transcriptional
Networks
Methods and Protocols
Edited by
Benjamin L. Kidder
Systems Biology Center, National Heart, Lung, and Blood Institute,
National Institutes of Health, Bethesda, MD, USA
Editor
Benjamin L. K idder
Systems Biology Center
National Heart, Lung, and Blood Institute
National Institutes of Health
Bethesda, MD, USA
ISSN 1064-3745 ISSN 1940-6029 (electronic)
ISBN 978-1-4939-0511-9 ISBN 978-1-4939-0512-6 (eBook)
DOI 10.1007/978-1-4939-0512-6
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Prefa ce
Research in stem cell biology has generated immense interest recently due to the potential
of stem cells to treat human diseases such as neurodegenerative disease, cardiovascular
disease, and cancer. Advancements in stem cell research aid our understanding of genetics
and developmental biology, and, because stem cells have the ability to repopulate tissues,
there is an expectation that stem cells research will translate into clinical therapies. However,
much work is required to understand the underlying transcriptional programs of stem cells
that promote self-renewal vs. differentiation. Investigating how epigenetic and transcrip-
tional landscapes are patterned in stem cells and committed lineages will provide insight
into how these features regulate unique cellular expression programs during development,
and contribute to the diverse cellular repertoire that exists in mammals. Next-generation
sequencing technologies have recently been used to survey global expression and protein–
DNA binding interactions at nucleotide resolution in stem cells. Use of these emerging
technologies has shed light on stem cell transcriptional networks that defi ne primitive vs.
committed epigenetic landscapes. Moreover, recent advancements in reprogramming and
transdifferentiation have armed stem cell biologists with additional tools to develop solu-
tions for regenerative medicine purposes. The aim of this volume is to provide a resource
for biologists to interrogate stem cell transcriptional networks.
Bethesda, MD, USA Benjamin L. Kidder
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
PART I NEXT-GENERATION SEQUENCING LIBRARY PREPARATION
AND DATA ANALYSIS
1 Efficient Library Preparation for Next-Generation Sequencing
Analysis of Genome-Wide Epigenetic and Transcriptional
Landscapes in Embryonic Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Benjamin L. K idder and Keji Zhao
2 Analysis of Next-Generation Sequencing Data Using Galaxy . . . . . . . . . . . . . . 21
Daniel Blankenberg and J ennifer H illman-Jackson
3 e dgeR for Differential RNA-seq and ChIP-seq Analysis:
An Application to Stem Cell Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Olga Nikolayeva and Mark D. Robinson
4 U se Model-Based Analysis of ChIP-Seq (MACS)
to Analyze Short Reads Generated by Sequencing Protein–DNA
Interactions in Embryonic Stem Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 1
Tao Liu
5 Spatial Clustering for Identification of ChIP-Enriched
Regions (SICER) to Map Regions of Histone Methylation
Patterns in Embryonic Stem Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Shiliyang X u, S ean G rullon, Kai G e, and Weiqun Peng
PART II V ISUAL ANALYSIS AND INTERPRETATION OF LARGE-SCALE
INTERACTION NETWORKS
6 Identifying Stem Cell Gene Expression Patterns and Phenotypic
Networks with AutoSOME. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Aaron M. N ewman and James B. C ooper
7 V isualization and Clustering of High-Dimensional Transcriptome
Data Using GATE . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 31
Patrick S . S tumpf and B en D. M acArthur
8 I nterpreting and Visualizing ChIP-seq Data
with the seqMINER Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Tao Ye, Sarina R avens, A rnaud R . K rebs, and L àszlò T ora
9 A Description of the Molecular Signatures Database (MSigDB) Web Site . . . . 1 53
Arthur Liberzon
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viii Contents
PART III TRANSCRIPTIONAL NETWORKS IN EMBRYONIC AND ADULT STEM CELL
10 Use of Genome-Wide RNAi Screens to Identify Regulators
of Embryonic Stem Cell Pluripotency and Self-Renewal . . . . . . . . . . . . . . . . . 1 63
Xiaofeng Z heng and Guang H u
11 C orrelating Histone Modification Patterns with Gene Expression
Data During Hematopoiesis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 75
Gangqing H u and Keji Z hao
PART IV EMBRYO CULTURE AND DERIVATION OF STEM CELLS
12 In Vitro Maturation and In Vitro Fertilization
of Mouse Oocytes and Preimplantation Embryo Culture. . . . . . . . . . . . . . . . . 191
Benjamin L. K idder
13 Derivation and Manipulation of Trophoblast Stem Cells
from Mouse Blastocysts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Benjamin L. K idder
PART V TRANSCRIPTIONAL PROGRAMS THAT PROMOTE SELF-RENEWAL,
REPROGRAMMING, AND TRANSDIFFERENTIATION
14 Conversion of Epiblast Stem Cells to Embryonic Stem Cells
Using Growth Factors and Small Molecule Inhibitors . . . . . . . . . . . . . . . . . . . 2 15
Jyoti Rao and B oris G reber
15 G eneration of Induced Pluripotent Stem Cells Using Chemical
Inhibition and Three Transcription Factors. . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Benjamin L. Kidder
16 T ransdifferentiation of Mouse Fibroblasts and Hepatocytes
to Functional Neurons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Samuele Marro and Nan Y ang
17 D irect Lineage Conversion of Pancreatic Exocrine
to Endocrine Beta Cells In Vivo with Defined Factors. . . . . . . . . . . . . . . . . . . 247
Claudia Cavelti-Weder, W eida Li, G ordon C. Weir, and Q iao Zhou
18 D irect Reprogramming of Cardiac Fibroblasts
to Cardiomyocytes Using MicroRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 63
Tilanthi J ayawardena, M aria M irotsou, and V ictor J. Dzau
19 Reprogramming Somatic Cells into Pluripotent
Stem Cells Using miRNAs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 73
Frederick A nokye-Danso
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 83
Contributors
FREDERICK ANOKYE-DANSO • Department of Medicine, P erelman School of Medicine,
University of Pennsylvania , P hiladelphia, PA, USA
DANIEL BLANKENBERG • Department of Biochemistry and Molecular Biology,
Penn State University , U niversity Park, P A, USA
CLAUDIA CAVELTI-WEDER • Section on Islet Cell and Regenerative Biology , J oslin Diabetes
Center Boston , Boston, MA, USA
JAMES B. COOPER • Department of Molecular, Cellular, and Developmental Biology,
University of California at Santa Barbara , Santa Barbara, C A , U SA
VICTOR J. DZAU • Division of Cardiology, Department of Medicine, Mandel Center
for Hypertension and Atherosclerosis Research, and the Cardiovascular Research Center ,
Duke University Medical Center , D urham, NC , U SA
KAI GE • Laboratory of Endocrinology and Receptor Biology, Adipocyte Biology and Gene
Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases,
National Institutes of Health , Bethesda, M D , U SA
BORIS G REBER • Max Planck Institute for Molecular Biomedicine , M ünster, G ermany ;
Chemical Genomics Centre of the Max Planck Society , D ortmund, Germany
SEAN GRULLON • Department of Physics, T he George Washington University , W ashington,
DC, U SA ; Laboratory of Endocrinology and Receptor Biology, Adipocyte Biology
and Gene Regulation Section, N ational Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes of Health , B ethesda, MD , U SA
JENNIFER HILLMAN-JACKSON • Department of Biochemistry and Molecular Biology,
Penn State University , U niversity Park, P A , U SA
GANGQING HU • Systems Biology Center , N ational Heart, Lung, and Blood Institute,
National Institutes of Health , B ethesda, MD , U SA
GUANG HU • Laboratory of Molecular Carcinogenesis , N ational Institute of Environmental
Health Sciences , Research Triangle Park, N C, U SA
TILANTHI JAYAWARDENA • Division of Cardiology, Department of Medicine, Mandel Center
for Hypertension and Atherosclerosis Research, and the Cardiovascular Research Center ,
Duke University Medical Center , D urham, NC, U SA
BENJAMIN L. KIDDER • Systems Biology Center , National Heart, Lung, and Blood Institute,
National Institutes of Health , Bethesda, M D , U SA
ARNAUD R . KREBS • Friedrich Miescher Institut for Biomedical Research , Basel, S witzerland
WEIDA LI • Department of Stem Cell and Regenerative Biology , H arvard Stem Cell
Institute, Harvard University , C ambridge, M A, USA
ARTHUR LIBERZON • Broad Institute of MIT and Harvard , C ambridge, MA, U SA
TAO L IU • Department of Biochemistry , University at Buffalo-COEBLS , B uffalo, N Y , U SA
BEN D. MACARTHUR • School of Mathematics and Institute for Life Sciences,
University of Southampton , Southampton, U K
SAMUELE M ARRO • Department of Pathology, Institute for Stem Cell Biology
and Regenerative Medicine, Stanford University School of Medicine , S tanford , C A , U SA
ix