Schema for Transcription - Transcription
  Database: hg38    Primary Table: bigwig_HEK293T_Control_GRO_Seq_rev    Row Count: 1   Data last updated: 2026-07-26
fieldexampleSQL type info
fileName /data02/chenjy/rloopbase/uc...varchar(255) values

Sample Rows
 
fileName
/data02/chenjy/rloopbase/ucsc/gbdb/hg38/inhouse-tracks/bigwig/gro/Human_HEK293T_Control_GRO-Seq_strand2.bw

Note: all start coordinates in our database are 0-based, not 1-based.

Transcription (transcription_tracks) Track Description
 

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