DNA double-strand break end synapsis by DNA loop extrusion

Yang, Jin; Brandão, Hugo B.; Hansen, Anders S.

doi:10.1101/2021.10.20.465154

Cited by 5 publications

(7 citation statements)

References 104 publications

(175 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…3A and (20, 74)) may mediate mutual regulation, possibly facilitating the spreading of histone marks and transcription factors. Linear scanning by cohesin in gene regulation would be consistent with cohesin’s proposed role in other contexts, including V(D)J recombination (22, 82–85), alternative protocadherin choice (23), and double strand break repair (86, 87). Furthermore, since moving RNAP extrusion barriers are transcription-dependent, chromosomal interactions could be rapidly modulated in a locus-specific manner.…”

Section: Discussionsupporting

confidence: 73%

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Banigan

Tang

Berg

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Cohesin organizes mammalian interphase chromosomes by reeling chromatin fibers into dynamic loops (Banigan and Mirny, 2020; Davidson et al., 2019; Kim et al., 2019; Yatskevich et al., 2019). "Loop extrusion" is obstructed when cohesin encounters a properly oriented CTCF protein (Busslinger et al., 2017; de Wit et al., 2015; Fudenberg et al., 2016; Nora et al., 2017; Sanborn et al., 2015; Wutz et al., 2017), and recent work indicates that other factors, such as the replicative helicase MCM (Dequeker et al., 2020), can also act as barriers to loop extrusion. It has been proposed that transcription relocalizes (Busslinger et al., 2017; Glynn et al., 2004; Lengronne et al., 2004) or interferes with cohesin (Heinz et al., 2018; Jeppsson et al., 2020; Valton et al., 2021; S. Zhang et al., 2021), and that active transcription start sites function as cohesin loading sites (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), but how these effects, and transcription in general, shape chromatin is unknown. To determine whether transcription can modulate loop extrusion, we studied cells in which the primary extrusion barriers could be removed by CTCF depletion and cohesin's residence time and abundance on chromatin could be increased by Wapl knockout. We found evidence that transcription directly interacts with loop extrusion through a novel "moving barrier" mechanism, but not by loading cohesin at active promoters. Hi-C experiments showed intricate, cohesin-dependent genomic contact patterns near actively transcribed genes, and in CTCF-Wapl double knockout (DKO) cells (Busslinger et al., 2017), genomic contacts were enriched between sites of transcription-driven cohesin localization ("cohesin islands"). Similar patterns also emerged in polymer simulations in which transcribing RNA polymerases (RNAPs) acted as "moving barriers" by impeding, slowing, or pushing loop-extruding cohesins. The model predicts that cohesin does not load preferentially at promoters and instead accumulates at TSSs due to the barrier function of RNAPs. We tested this prediction by new ChIP-seq experiments, which revealed that the "cohesin loader" Nipbl (Ciosk et al., 2000) co-localizes with cohesin, but, unlike in previous reports (Busslinger et al., 2017; Kagey et al., 2010; Zhu et al., 2021; Zuin et al., 2014), Nipbl did not accumulate at active promoters. We propose that RNAP acts as a new type of barrier to loop extrusion that, unlike CTCF, is not stationary in its precise genomic position, but is itself dynamically translocating and relocalizes cohesin along DNA. In this way, loop extrusion could enable translocating RNAPs to maintain contacts with distal regulatory elements, allowing transcriptional activity to shape genomic functional organization.

show abstract

Section: Discussionsupporting

confidence: 73%

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Banigan

Tang

Berg

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…In addition to these functions, we reveal a new cohesin role in tethering DSB ends. Cohesin's first contribution, early after DSB formation is independent of MRX and Exo1 and likely relies on cohesin-dependent genome looping, as predicted by recent theoretical work (2). Later, cohesin-dependent DSB end-tethering requires de novo cohesin loading, acts in cooperation with Exo1 and Smc5/6, is independent of sister chromatid cohesion and loop formation, and relies on cohesin oligomerization.…”

Section: Discussionmentioning

confidence: 70%

“…Repair mechanisms, such as NHEJ and homologous recombination are essential for restoring chromosome continuity by directly rejoining DSB ends or using a donor homologous template ( 1 ). However, before these repair processes can occur, it is imperative to bring DSB ends together, a task unlikely achieved through passive diffusion ( 2 ). Instead, active DSB end-tethering mechanisms have been identified, and represent a critical step in preventing joining or recombination events between unrelated chromosome loci, which could lead to harmful translocations.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks

Phipps,

Toulouze,

Ducrot

et al. 2023

Preprint

View full text Add to dashboard Cite

DNA double-strand breaks (DSB) must be repaired to ensure genome stability. Crucially, DSB ends must be kept together for timely repair. InSaccharomyces cerevisiae, two poorly understood pathways mediate DSB end-tethering. One employs the Mre11-Rad50-Xrs2 (MRX) complex to physically bridge DSB ends. Another requires the conversion of DSB ends into single-strand DNA (ssDNA) by Exo1, but the bridging proteins are unknown. We uncover that cohesin, its loader and Smc5/6 act with Exo1 to tether DSB ends. Remarkably, cohesin specifically impaired in oligomerization fails to tether DSB ends, revealing a new function for cohesin oligomerization. In addition to the known importance of sister chromatid cohesion, microscopy-based microfluidic experiments unveil a new role for cohesin in repair by ensuring DSB end-tethering. Altogether, our findings demonstrate that oligomerization of cohesin prevents DSB end separation and promotes DSB repair, revealing a novel mode of action and role for cohesin in safeguarding genome integrity.

show abstract

“…In addition, HS-AFM imaging shows both forward and reserve steps, suggesting that cohesin-NIPBL can switch DNA strands during DNA loop extrusion. It is highly likely that surface anchoring of DNA and cohesin-NIPBL increases the frequency of strand switching and DNA loop extrusion pausing (40,(60)(61)(62)(63)(64)(65)(66)(67).…”

Section: Dna Loop Extrusion Dynamics By Cohesin-nipbl Despite Recent ...mentioning

confidence: 99%

DNA capture and loop extrusion dynamics by cohesin-NIPBL

Kaur

Shi

et al. 2022

Preprint

View full text Add to dashboard Cite

3D chromatin organization plays a critical role in regulating gene expression, DNA replication, recombination, and repair. While initially discovered for its role in sister chromatid cohesion, emerging evidence suggests that the cohesin complex (SMC1, SMC3, RAD21, and SA1/SA2), facilitated by NIPBL, mediates topologically associating domains (TADs) and chromatin loops through DNA loop extrusion. However, information on how conformational changes of cohesin-NIPBL drive its loading onto DNA, initiation, and growth of DNA loops is still lacking. Using high-speed AFM (HS-AFM) imaging, we show that cohesin-NIPBL captures DNA through arm extension, followed by transfer of DNA to its globular domain and DNA loop initiation independent of ATPase hydrolysis. Additional shorter protrusions (feet) from cohesin-NIPBL transiently bind to DNA, facilitating its loading onto DNA. Furthermore, HS-AFM imaging reveals distinct forward and reverse DNA loop extrusion steps by cohesin-NIPBL. These results provide critical missing links in our understanding of DNA binding and loop extrusion by cohesin-NIPBL.

show abstract

DNA double-strand break end synapsis by DNA loop extrusion

Cited by 5 publications

References 104 publications

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Transcription shapes 3D chromatin organization by interacting with loop extrusion

Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks

DNA capture and loop extrusion dynamics by cohesin-NIPBL

Contact Info

Product

Resources

About