Transcription Track Settings

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Transcription (All R-loopBase Data tracks)

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All	*Cell Line*	3T3-L1	MEFs	mES
*Technology*
GRO-seq

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	Cell Line^↓1	Technology^↓2	Strand^↓3	Rep^↓4	Track Name^↓5
full Configure	3T3-L1	GRO-seq	fwd	1	GRO-seq_3T3-L1.fwd	Schema
full Configure	3T3-L1	GRO-seq	rev	1	GRO-seq_3T3-L1.rev	Schema
full Configure	MEFs	GRO-seq	fwd	1	GRO-seq_MEFs.fwd	Schema
full Configure	MEFs	GRO-seq	rev	1	GRO-seq_MEFs.rev	Schema
full Configure	mES	GRO-seq	no	1	GRO-seq_mES_1	Schema
full Configure	mES	GRO-seq	no	2	GRO-seq_mES_2	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

Li Z, Duan S, Hua X et al, Asymmetric distribution of parental H3K9me3 in S phase silences L1 elements. Nature. 2023 Nov;623(7987):643-651. PMID: 37938774

Wei C, Xiao R, Chen L et al, RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes. Mol Cell. 2016 Jun 16;62(6):875-889. PMID: 27211866

Cardamone MD, Tanasa B, Cederquist CT et al, Mitochondrial Retrograde Signaling in Mammals Is Mediated by the Transcriptional Cofactor GPS2 via Direct Mitochondria-to-Nucleus Translocation. Mol Cell. 2018 Mar 1;69(5):757-772.e7. PMID: 29499132