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Transcription (All R-loopBase Data tracks)

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	Cell Line^↓1	Technology^↓2	Treatment^↓3	Strand^↓4	Track Name^↓5
full Configure	HEK293T	GRO-seq	Control	fwd	HEK293T_Control_GRO-seq.fwd	Schema
full Configure	HEK293T	GRO-seq	Control	rev	HEK293T_Control_GRO-seq.rev	Schema
full Configure	HEK293T	PRO-seq	Control	fwd	HEK293T_Control_PRO-seq.fwd	Schema
full Configure	HEK293T	PRO-seq	Control	rev	HEK293T_Control_PRO-seq.rev	Schema
full Configure	HeLa	GRO-seq	Control	fwd	HeLa_Control_GRO-seq.fwd	Schema
full Configure	HeLa	GRO-seq	Control	rev	HeLa_Control_GRO-seq.rev	Schema
full Configure	HeLa	PRO-seq	Control	fwd	HeLa_Control_PRO-seq.fwd	Schema
full Configure	HeLa	PRO-seq	Control	rev	HeLa_Control_PRO-seq.rev	Schema
full Configure	hESCs	GRO-seq	Control	fwd	hESCs_Control_GRO-seq.fwd	Schema
full Configure	hESCs	GRO-seq	Control	rev	hESCs_Control_GRO-seq.rev	Schema
full Configure	K562	GRO-seq	Control	fwd	K562_Control_GRO-seq.fwd	Schema
full Configure	K562	GRO-seq	Control	rev	K562_Control_GRO-seq.rev	Schema
full Configure	MCF-7	GRO-seq	Control	fwd	MCF7_Control_GRO-seq.fwd	Schema
full Configure	MCF-7	GRO-seq	Control	rev	MCF7_Control_GRO-seq.rev	Schema

Description

GRO-seq (Global Run-On sequencing) and PRO-seq (Precision Run-On sequencing) capture nascent RNA by labeling and sequencing actively elongating RNA polymerases, providing a high-resolution, strand-specific map of ongoing transcription. Since R-loop formation is coupled to active transcription, regions with high nascent RNA output are frequently hotspots for R-loop formation.

Reference

Chen L, Chen JY, Zhang X et al, R-ChIP Using Inactive RNase H Reveals Dynamic Coupling of R-loops with Transcriptional Pausing at Gene Promoters. Mol Cell. 2017 Nov 16;68(4):745-757. PMID: 29104020

Fei J, Ishii H, Hoeksema MA et al, NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev. 2018 May 1;32(9-10):682-694. PMID: 29759984

Estarás C, Benner C, Jones KA, SMADs and YAP compete to control elongation of ß-catenin:LEF-1-recruited RNAPII during hESC differentiation. Mol Cell. 2015 Jun 4;58(5):780-93. PMID: 25936800

Core LJ, Martins AL, Danko CG et al, Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014 Dec;46(12):1311-20. PMID: 25383968

Bi M, Zhang Z, Jiang YZ et al, Enhancer reprogramming driven by high-order assemblies of transcription factors promotes phenotypic plasticity and breast cancer endocrine resistance. Nat Cell Biol. 2020 Jun;22(6):701-715. PMID: 32424275

Wang K, Wang H, Li C et al, Genomic profiling of native R loops with a DNA-RNA hybrid recognition sensor. Sci Adv. 2021 Feb 17;7(8):eabe3516. PMID: 33597247

Nilson KA, Lawson CK, Mullen NJ et al, Oxidative stress rapidly stabilizes promoter-proximal paused Pol II across the human genome. Nucleic Acids Res. 2017 Nov 2;45(19):11088-11105. PMID: 28977633