Untargeted CUT&Tag and BG4 CUT&Tag Are Both Enriched at G-quadruplexes and Accessible Chromatin

Overview

Journal bioRxiv

Date 2024 Oct 10

PMID 39386625

Authors

Matthew Thompson

Alicia Byrd

Affiliations

Soon will be listed here.

Abstract

G-quadruplex DNA structures (G4s) form within single-stranded DNA in nucleosome-free chromatin. As G4s modulate gene expression and genomic stability, genome-wide mapping of G4s has generated strong research interest. Recently, the Cleavage Under Targets and Tagmentation (CUT&Tag) method was performed with the G4-specific BG4 antibody to target Tn5 transposase to G4s. While this method generated a novel high-resolution map of G4s, we unexpectedly observed a strong correlation between the genome-wide signal distribution of BG4 CUT&Tag and accessible chromatin. To examine whether untargeted Tn5 cutting at accessible chromatin contributes to BG4 CUT&Tag signal, we examined the genome-wide distribution of signal from untargeted (i.e. negative control) CUT&Tag datasets. We observed that untargeted CUT&Tag signal distribution was highly similar to both that of accessible chromatin and of BG4 CUT&Tag. We also observed that BG4 CUT&Tag signal increased at mapped G4s, but this increase was accompanied by a concomitant increase in untargeted CUT&Tag at the same loci. Consequently, enrichment of BG4 CUT&Tag over untargeted CUT&Tag was not increased at mapped G4s. These results imply that either the vast majority of accessible chromatin regions contain mappable G4s or that the presence of G4s within accessible chromatin cannot reliably be determined using BG4 CUT&Tag alone.

References

Wang G, Vasquez K . Dynamic alternative DNA structures in biology and disease. Nat Rev Genet. 2022; 24(4):211-234. PMC: 11634456. DOI: 10.1038/s41576-022-00539-9. View

Lago S, Nadai M, Cernilogar F, Kazerani M, Dominiguez Moreno H, Schotta G . Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome. Nat Commun. 2021; 12(1):3885. PMC: 8222265. DOI: 10.1038/s41467-021-24198-2. View

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R . Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):e1003118. PMC: 3738458. DOI: 10.1371/journal.pcbi.1003118. View

Skene P, Henikoff S . An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife. 2017; 6. PMC: 5310842. DOI: 10.7554/eLife.21856. View

Kaya-Okur H, Janssens D, Henikoff J, Ahmad K, Henikoff S . Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc. 2020; 15(10):3264-3283. PMC: 8318778. DOI: 10.1038/s41596-020-0373-x. View

Chambers V, Marsico G, Boutell J, Di Antonio M, Smith G, Balasubramanian S . High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat Biotechnol. 2015; 33(8):877-81. DOI: 10.1038/nbt.3295. View

Buenrostro J, Giresi P, Zaba L, Chang H, Greenleaf W . Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013; 10(12):1213-8. PMC: 3959825. DOI: 10.1038/nmeth.2688. View

Kaya-Okur H, Wu S, Codomo C, Pledger E, Bryson T, Henikoff J . CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat Commun. 2019; 10(1):1930. PMC: 6488672. DOI: 10.1038/s41467-019-09982-5. View

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

10.

Marsico G, Chambers V, Sahakyan A, McCauley P, Boutell J, Di Antonio M . Whole genome experimental maps of DNA G-quadruplexes in multiple species. Nucleic Acids Res. 2019; 47(8):3862-3874. PMC: 6486626. DOI: 10.1093/nar/gkz179. View

11.

Dahan D, Tsirkas I, Dovrat D, Sparks M, Singh S, Galletto R . Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures. Nucleic Acids Res. 2018; 46(22):11847-11857. PMC: 6294490. DOI: 10.1093/nar/gky1065. View

12.

Edgar R, Domrachev M, Lash A . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2001; 30(1):207-10. PMC: 99122. DOI: 10.1093/nar/30.1.207. View

13.

Henikoff S, Henikoff J, Kaya-Okur H, Ahmad K . Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation. Elife. 2020; 9. PMC: 7721439. DOI: 10.7554/eLife.63274. View

14.

Nordin A, Zambanini G, Pagella P, Cantu C . The CUT&RUN suspect list of problematic regions of the genome. Genome Biol. 2023; 24(1):185. PMC: 10416431. DOI: 10.1186/s13059-023-03027-3. View

15.

Meier-Stephenson V . G4-quadruplex-binding proteins: review and insights into selectivity. Biophys Rev. 2022; 14(3):635-654. PMC: 9250568. DOI: 10.1007/s12551-022-00952-8. View

16.

Meers M, Tenenbaum D, Henikoff S . Peak calling by Sparse Enrichment Analysis for CUT&RUN chromatin profiling. Epigenetics Chromatin. 2019; 12(1):42. PMC: 6624997. DOI: 10.1186/s13072-019-0287-4. View

17.

Zhang H, Lu T, Liu S, Yang J, Sun G, Cheng T . Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. NAR Genom Bioinform. 2021; 3(4):lqab094. PMC: 8557372. DOI: 10.1093/nargab/lqab094. View

18.

Stoltenburg R, Krafcikova P, Viglasky V, Strehlitz B . G-quadruplex aptamer targeting Protein A and its capability to detect Staphylococcus aureus demonstrated by ELONA. Sci Rep. 2016; 6:33812. PMC: 5030626. DOI: 10.1038/srep33812. View

19.

Hon J, Martinek T, Zendulka J, Lexa M . pqsfinder: an exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics. 2017; 33(21):3373-3379. DOI: 10.1093/bioinformatics/btx413. View

20.

Li L, Williams P, Ren W, Wang M, Gao Z, Miao W . YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression. Nat Chem Biol. 2020; 17(2):161-168. PMC: 7854983. DOI: 10.1038/s41589-020-00695-1. View