Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

Southall, Tony D.; Gold, Katrina S.; Egger, Boris; Davidson, Catherine M.; Caygill, Elizabeth E.; Marshall, Owen J.; Brand, Andrea H.

doi:10.1016/j.devcel.2013.05.020

Title: Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

Journal Article · Mon Jul 01 00:00:00 EDT 2013 · Developmental Cell

DOI:https://doi.org/10.1016/j.devcel.2013.05.020· OSTI ID:1623657

Southall, Tony D. ^[1]; Gold, Katrina S. ^[1]; Egger, Boris ^[1]; Davidson, Catherine M. ^[1]; Caygill, Elizabeth E. ^[1]; Marshall, Owen J. ^[1]; Brand, Andrea H. ^[1]

Univ. of Cambridge (United Kingdom). The Gurdon Inst. and Dept. of Physiology, Development and Neuroscience

Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed ‘‘TaDa,’’ a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transcribed genes in a celltype-specific manner with considerable temporal precision, enabling the identification of differential gene expression between neuroblasts and the neuroepithelial cells from which they derive. We profile the genome-wide binding of RNA polymerase II in these adjacent, clonally related stem cells within intact Drosophila brains. Our data reveal expression of specific metabolic genes in neuroepithelial cells, but not in neuroblasts, and highlight gene regulatory networks that may pattern neural stem cell fates.

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Research Organization:: Univ. of Cambridge (United Kingdom)

Sponsoring Organization:: Wellcome Trust

DOE Contract Number:: 068055; 092545

OSTI ID:: 1623657

Journal Information:: Developmental Cell, Vol. 26, Issue 1; ISSN 1534-5807

Publisher:: Cell Press - Elsevier

Country of Publication:: United States

Language:: English

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Nuclear Lamin is required for Winged Eye‐mediated transdetermination of Drosophila imaginal disc Masuko, Keita; Furuhashi, Hirofumi; Komaba, Kanae Genes to Cells, Vol. 23, Issue 8 https://doi.org/10.1111/gtc.12608	journal	July 2018
Dynamic neurotransmitter specific transcription factor expression profiles during Drosophila development Estacio-Gómez, Alicia; Hassan, Amira; Walmsley, Emma Biology Open https://doi.org/10.1101/830315	posted_content	April 2020
Early stem cell aging in the mature brain. Ibrayeva, Albina; Bay, Maxwell; Pu, Elbert Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.66347	text	January 2021
Chromatin regulators in neurodevelopment and disease: Analysis of fly neural circuits provides insights: Networks of chromatin regulators and transcription factors underlie Drosophila neurogenesis and cognitive defects in intellectual disability and neuro Taniguchi, Hiroaki; Moore, Adrian W. BioEssays, Vol. 36, Issue 9 https://doi.org/10.1002/bies.201400087	journal	July 2014
Mushroom Body Specific Transcriptome Analysis Reveals Dynamic Regulation of Learning and Memory Genes After Acquisition of Long-Term Courtship Memory in Drosophila Jones, Spencer G.; Nixon, Kevin C. J.; Chubak, Melissa C. G3 Genes\|Genomes\|Genetics, Vol. 8, Issue 11 https://doi.org/10.1534/g3.118.200560	journal	November 2018
Adipocyte nuclei captured from VAT and SAT Ambati, Suresh; Yu, Ping; McKinney, Elizabeth C. BMC Obesity, Vol. 3, Issue 1 https://doi.org/10.1186/s40608-016-0112-6	journal	July 2016
The Drosophila fussel gene is required for bitter gustatory neuron differentiation acting within an Rpd3 dependent chromatin modifying complex Rass, Mathias; Oestreich, Svenja; Guetter, Severin PLOS Genetics https://doi.org/10.1101/481721	posted_content	November 2018
Context-dependent gene regulation by transcription factor complexes Kribelbauer, Judith F.; Loker, Ryan E.; Feng, Siqian https://doi.org/10.1101/706473	posted_content	July 2019
DamID as a versatile tool for understanding gene regulation Aughey, Gabriel N.; Cheetham, Seth W.; Southall, Tony D. Development, Vol. 146, Issue 6 https://doi.org/10.1242/dev.173666	journal	March 2019
Neuroblast-specific chromatin landscapes allow integration of spatial and temporal cues to generate neuronal diversity in Drosophila Sen, Sonia Q.; Chanchani, Sachin; Southall, Tony D. BioRxiv https://doi.org/10.1101/485193	posted_content	January 2018
Initiated by CREB: Resolving Gene Regulatory Programs in Learning and Memory: Switch in Cofactors and Transcription Regulators between Memory Consolidation and Maintenance Network Kaldun, Jenifer C.; Sprecher, Simon G. BioEssays, Vol. 41, Issue 8 https://doi.org/10.1002/bies.201900045	journal	June 2019
Distinct gene-selective roles for a network of core promoter factors in Drosophila neural stem cell identity Neves, Alexandre; Eisenman, Robert N. Biology Open, Vol. 8, Issue 4 https://doi.org/10.1242/bio.042168	journal	April 2019
The female gametophyte: an emerging model for cell type-specific systems biology in plant development Schmid, Marc W.; Schmidt, Anja; Grossniklaus, Ueli Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.00907	journal	November 2015
Generation of mechanosensory neurons in adult Drosophila Fernández-Hernández, Ismael; Marsh, Evan B.; Bonaguidi, Michael A. Development https://doi.org/10.1101/812057	posted_content	June 2020
Generation of mechanosensory neurons in adult Drosophila Fernández-Hernández, Ismael; Marsh, Evan; Bonaguidi, Michael A. TAGC 2020 https://doi.org/10.6084/m9.figshare.12151101.v1	image	January 2020
Mechanosensory neuron regeneration in adult Drosophila Fernández-Hernández, Ismael; Marsh, Evan B.; Bonaguidi, Michael A. Development, Vol. 148, Issue 5 https://doi.org/10.1242/dev.187534	journal	March 2021

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