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Kahiapo JK, Monahan K. Chromatin Immunoprecipitation from Formaldehyde Cross-Linked Olfactory Sensory Neurons. Methods Mol Biol 2023; 2710:71-82. [PMID: 37688725 DOI: 10.1007/978-1-0716-3425-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Chromatin immunoprecipitation (ChIP) allows a researcher to determine the genomic occupancy of nuclear proteins, providing insight into the roles of transcription factors, chromatin modifiers, histone modifications, and other factors bound to DNA. Protein-DNA interactions are first fixed in vivo by chemical cross-linking, and then a target protein is captured together with any associated DNA by an antibody mediated pull-down. The co-immunoprecipitated DNA can then be assayed by quantitative PCR or deep sequencing. Here, we demonstrate this technique using murine olfactory sensory neurons (OSNs) purified using fluorescence-activated cell sorting (FACS) and antibodies for the ubiquitous chromatin protein CTCF.
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Affiliation(s)
- Jerome K Kahiapo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Shayya HJ, Kahiapo JK, Duffié R, Lehmann KS, Bashkirova L, Monahan K, Dalton RP, Gao J, Jiao S, Schieren I, Belluscio L, Lomvardas S. ER stress transforms random olfactory receptor choice into axon targeting precision. Cell 2022; 185:3896-3912.e22. [PMID: 36167070 PMCID: PMC9588687 DOI: 10.1016/j.cell.2022.08.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
Olfactory sensory neurons (OSNs) convert the stochastic choice of one of >1,000 olfactory receptor (OR) genes into precise and stereotyped axon targeting of OR-specific glomeruli in the olfactory bulb. Here, we show that the PERK arm of the unfolded protein response (UPR) regulates both the glomerular coalescence of like axons and the specificity of their projections. Subtle differences in OR protein sequences lead to distinct patterns of endoplasmic reticulum (ER) stress during OSN development, converting OR identity into distinct gene expression signatures. We identify the transcription factor Ddit3 as a key effector of PERK signaling that maps OR-dependent ER stress patterns to the transcriptional regulation of axon guidance and cell-adhesion genes, instructing targeting precision. Our results extend the known functions of the UPR from a quality-control pathway that protects cells from misfolded proteins to a sensor of cellular identity that interprets physiological states to direct axon wiring.
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Affiliation(s)
- Hani J Shayya
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Medical Scientist Training Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jerome K Kahiapo
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Katherine S Lehmann
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa Bashkirova
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kevin Monahan
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Ryan P Dalton
- The Miller Institute for Basic Research in Science, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joanna Gao
- Barnard College, New York, NY 10025, USA
| | - Song Jiao
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Leonardo Belluscio
- Developmental Neural Plasticity Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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