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Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells

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Cellular Quiescence

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1686))

Abstract

Transcription factors bind to specific DNA sequences and control the transcription rate of nearby genes in the genome. This activation or repression of gene expression is further potentiated by epigenetic modifications of histones with active and silent marks, respectively. Resident adult stem cells in the hematopoietic system, skin, and brain exist in a non-proliferative quiescent resting state. When quiescent stem cells become activated and transition to dividing progenitors and distinct cell types, they can replenish and repair tissue. Thus, determination of the position of transcription factor binding and histone epigenetic modification on the chromatin is an essential step toward understanding the gene regulation of quiescent and proliferative adult stem cells for potential applications in regenerative medicine. Genome-wide transcription factor occupancy and histone modifications on the genome can be obtained by assessing DNA-protein interaction through next-generation chromatin immunoprecipitation sequencing technology (ChIP-seq). This chapter outlines the protocol to perform, analyze, and validate ChIP-seq experiments that can be used to identify protein-DNA interactions and histone marks on the chromatin. The methods described here are applicable to quiescent and proliferative neural stem cells, and a wide range of other cellular systems.

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Acknowledgments

We thank Stephen Johnson, Ralf Kittler, Francois Guillemot, Jane Johnson, Victor Corces, Sean Goetsch, Bradford Casey, Mark Borromeo, Derek Smith, Tulip Nandu, Xin Liu, Caelin Potts, and Benjamin Nelson for helpful advice on the ChIP-seq project. We also thank the UT Southwestern Medical Center next-generation sequencing core facilities (McDermott sequencing core for library preparation of samples, Illumina HiSeq ChIP-sequencing and bioinformatics support. Genomics and Microarray core facility for Bioanalyzer,). Jose Cabrera for graphical support. The ChIP-seq work was supported by US National Institutes of Health grants (R01NS093992, R01NS089770, R01NS081203, and K02AG041815), American Heart Association 15GRNT25750034, Department of Defense W81XWH-15-1-0399, and a grant from the Texas Institute for Brain Injury and Repair.

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Authors and Affiliations

  1. Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9148, USA

    Shradha Mukherjee & Jenny Hsieh

  2. Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390-9148, USA

    Shradha Mukherjee & Jenny Hsieh

Authors
  1. Shradha Mukherjee
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  2. Jenny Hsieh
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Correspondence to Jenny Hsieh .

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Editors and Affiliations

  1. Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA

    H. Daniel Lacorazza

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Mukherjee, S., Hsieh, J. (2018). Genome-Wide Identification of Transcription Factor-Binding Sites in Quiescent Adult Neural Stem Cells. In: Lacorazza, H. (eds) Cellular Quiescence. Methods in Molecular Biology, vol 1686. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7371-2_19

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  • DOI: https://doi.org/10.1007/978-1-4939-7371-2_19

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7370-5

  • Online ISBN: 978-1-4939-7371-2

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