RPA-ChIP Track Settings
 
RPA-ChIP   (All R-loopBase Data tracks)

Maximum display mode:       Reset to defaults   
Select data type (Help):
Coverage ▾       Peak      
Select subtracks by cell line and technology:
 All Cell Line HeLa 
Technology
pRPA2-ChIP 
RPA2-ChIP 
RPA1-ChIP 
Select subtracks further by: (select multiple categories and items - help)
Replicate:

List subtracks: only selected/visible    all    ()
  Cell Line↓1 Technology↓2 Replicate↓3   Track Name↓4  
hide
 HeLa  pRPA2-ChIP  1  bigwig_HeLa_Control_pRPA2ChIP_1   Schema 
hide
 Configure 		 HeLa  pRPA2-ChIP  1  bigwig_HeLa_Control_pRPA2ChIP_1   Schema 
hide
 HeLa  RPA1-ChIP  1  bigwig_HeLa_Control_RPA1ChIP_1   Schema 
hide
 Configure 		 HeLa  RPA1-ChIP  1  bigwig_HeLa_Control_RPA1ChIP_1   Schema 
hide
 HeLa  RPA2-ChIP  1  bigwig_HeLa_Control_RPA2ChIP_1   Schema 
hide
 Configure 		 HeLa  RPA2-ChIP  1  bigwig_HeLa_Control_RPA2ChIP_1   Schema 
hide
 HeLa  RPA2-ChIP  2  bigwig_HeLa_Control_RPA2ChIP_2   Schema 
hide
 Configure 		 HeLa  RPA2-ChIP  2  bigwig_HeLa_Control_RPA2ChIP_2   Schema 
    

Description

This track integrates RPA1, RPA2 and pRPA2 ChIP-seq datasets. The RPA complex (RPA1/RPA2/RPA3) has high affinity for ssDNA and is recruited to the displaced strand of R-loops, therefore providing a complementary readout to direct RNA:DNA hybrid mapping. In contrast, pRPA2 (the ATR-phosphorylated form of RPA2 at serine 33) specifically reports the activation of the replication stress response. Phosphorylation of RPA2 by ATR occurs when R-loops physically interfere with replication fork progression, primarily at transcription termination sites (TTS) that are replicated in a head-on orientation relative to transcription. Thus, while RPA1/RPA2 indicate the presence of R-loop-associated ssDNA, pRPA2 distinguishes which R-loop regions cause replication fork stalling and ATR activation.

Reference

Zhang H, Gan H, Wang Z, RPA interacts with HIRA and regulates H3.3 deposition at gene regulatory elements in mammalian cells. Mol Cell. 2017 Jan 19;65(2):272-284. PMID: 28107649

Promonet A, Padioleau I, Liu Y et al, Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites. Nat Commun. 2020 Aug 7;11(1):3940. PMID: 32769985