Genome-wide analysis using ChIP to identify isoform-specific gene targets.

Journal of Visualized Experiments : JoVE
Michael L BeshiriElizaveta V Benevolenskaya

Abstract

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the protein domains that bind to specific histone modifications. One such domain is the plant homeodomain (PHD), found in several chromatin-binding proteins. The epigenetic factor RBP2 has multiple PHD domains, however, they have different functions (Figure 4). In particular, the C-terminal PHD domain, found in a RBP2 oncogenic fusion in human leukemia, binds to trimethylated lysine 4 in histone H3 (H3K4me3). The transcript corresponding to the RBP2 isoform containing the C-terminal PHD accumulates during differentiation of promonocytic, lymphoma-derived, U937 cells into monocytes. Consistent with both sets of data, genome-wide analysis showed that in differentiated U937 cells, the RBP2 protein gets localized to genomic regions highly enriched for H3K4me3. Localization of RBP2 to its targets correlates with a decrease in H3K4me3 due to RBP2 histone demethylase activity and a decrease in transcriptional activity. In contrast, two other PHDs of RBP2 are unable to bind H3K4me3. Notably, the C-terminal domain PHD of RBP2 is absent in the smaller RBP2 isoform. It is conceivable that the sm...Continue Reading

References

Feb 28, 2004·Science·Duncan T OdomRichard A Young
Jun 14, 2005·Molecular Cell·Elizaveta V BenevolenskayaWilliam G Kaelin
Aug 24, 2007·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Elizaveta V Benevolenskaya
Jan 15, 2009·Genes & Development·Matthew G GuentherRichard A Young

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Citations

Oct 12, 2011·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Doris M SeilerAnna A Friedl
Jan 10, 2013·The Journal of Biological Chemistry·Meghan E McGee-LawrenceJennifer J Westendorf
Nov 30, 2013·Developmental Cell·Aaron M AmbrusMaxim V Frolov
Jan 26, 2018·Cell Death & Disease·Marianna HalasiAndrei L Gartel
Nov 13, 2015·The Journal of Biological Chemistry·Marianna HalasiAndrei L Gartel
Mar 14, 2021·Nature Communications·Alexandre F AissaElizaveta V Benevolenskaya

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Methods Mentioned

BETA
PCR
ChIP-Seq

Software Mentioned

illumina
Ensembl

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