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. Author manuscript; available in PMC: 2024 Jul 20.
Published in final edited form as: Mol Cell. 2023 Jul 3;83(14):2449–2463.e13. doi: 10.1016/j.molcel.2023.06.012

Figure 1. Transcription factor binding to RNA in cells.

Figure 1.

(A) Schematic of DNA-binding and effector domains in transcription factors from different families (PDB accession numbers in Methods).

(B) Experimental scheme for RBR-ID in human K562 cells. 4SU-labeled RNAs are crosslinked to proteins with UV light. RNA-binding peptides are identified by comparing the levels of crosslinked and unbound peptides by mass spectrometry.

(C) Volcano plot of TF peptides in RBR-ID for human K562 cells with select highlighted TFs (dotted line at p=0.05). Each marker represents the peptide with maximum RBR-ID score for each protein.

(D) Volcano plot of all detected peptides in RBR-ID for human K562 cells with select highlighted RBPs (dotted line at p=0.05). Each marker represents the peptide with maximum RBR-ID score for each protein.

(E) ChIP-seq and CLIP signal for GATA2 at the HINT1 locus in K562 cells.

(F) Meta-gene analysis of input-subtracted CLIP signal centered on GATA2 or RUNX1 ChIP-seq peaks in K562 cells.