Abstract
Chromatin immunoprecipitation (ChIP) is one of the most widely used methods for investigating interactions between proteins and DNA sequences. ChIP plays an important role in the transcriptional regulation study, which can locate the target genes of transcription factors and cofactors or monitor the sequence-specific genomic regions of histone modification. To analyze the interaction between transcription factors and several candidate genes, ChIP coupled with quantitative PCR (ChIP-PCR) assay is a basic tool. With the development of next-generation sequencing technology, ChIP-coupled sequencing (ChIP-seq) can provide the protein-DNA interaction information in a genome-wide dimension, which helps a lot in identifying new target genes. This chapter describes a protocol for performing ChIP-seq of transcription factors from retinal tissues.
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References
Samuel A, Housset M, Fant B, Lamonerie T (2014) Otx2 ChIP-seq reveals unique and redundant functions in the mature mouse retina. PLoS One 9(2):e89110. https://doi.org/10.1371/journal.pone.0089110
Zibetti C, Liu S, Wan J, Qian J, Blackshaw S (2019) Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin. Commun Biol 2:142. https://doi.org/10.1038/s42003-019-0375-9
Popova EY, Barnstable CJ, Zhang SS (2014) Cell type-specific epigenetic signatures accompany late stages of mouse retina development. Adv Exp Med Biol 801:3–8. https://doi.org/10.1007/978-1-4614-3209-8_1
Tao Y, Cao J, Li M, Hoffmann B, Xu K, Chen J et al (2020) PAX6D instructs neural retinal specification from human embryonic stem cell-derived neuroectoderm. EMBO Rep 21(9):e50000. https://doi.org/10.15252/embr.202050000
Liang WJ, Yang HW, Liu HN, Qian W, Chen XL (2020) HMGB1 upregulates NF-kB by inhibiting IKB-alpha and associates with diabetic retinopathy. Life Sci 241:117146. https://doi.org/10.1016/j.lfs.2019.117146
Jorstad NL, Wilken MS, Todd L, Finkbeiner C, Nakamura P, Radulovich N et al (2020) STAT signaling modifies Ascl1 chromatin binding and limits neural regeneration from Muller glia in adult mouse retina. Cell Rep 30(7):2195–2208. e5. https://doi.org/10.1016/j.celrep.2020.01.075
Yu G, Wang LG, He QY (2015) ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31(14):2382–2383. https://doi.org/10.1093/bioinformatics/btv145
Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z et al (2021) clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (N Y) 2(3):100141. https://doi.org/10.1016/j.xinn.2021.100141
Tian B, Yang J, Brasier AR (2012) Two-step cross-linking for analysis of protein-chromatin interactions. Methods Mol Biol 809:105–120. https://doi.org/10.1007/978-1-61779-376-9_7
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Wang, Z., Ji, S., Ma, J.H., Chen, J., Tang, S. (2023). Chromatin Immunoprecipitation Assay in Mouse Retinal Tissue. In: Liu, GS., Wang, JH. (eds) Diabetic Retinopathy. Methods in Molecular Biology, vol 2678. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3255-0_14
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DOI: https://doi.org/10.1007/978-1-0716-3255-0_14
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