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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...on Chromosome 10. This is accompanied by de novo interactions correlating not only with elevated MYC expression in T1 and C1 cells but also with enhanced expression of other breast cancer–related genes on both chromosomes. Our FISH analysis supports our Hi-C findings of de novo interactions between MYC...
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Method: Examining the dynamics of three-dimensional genome organization with multitask matrix factorization
- Da-Inn Lee and
- Sushmita Roy
Genome Res. May 2025 35: 1179-1193; Published in Advance March 20, 2025, doi:10.1101/gr.279930.124
...similarity of the input Hi-C matrices measured by stratum-adjusted correlation coefficient (SCC; Methods) (Supplemental Fig. S2; Yang et al. 2017) or a similar distance-stratified metric.TGIF-DB identifies fewer false-positive differential boundaries in simulated and real Hi-C dataTGIF-DB was benchmarked...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...of the three-dimensional (3D) nucleome through Lamin B1 ChIP-seq and in situ Hi-C.ResultsLoss of Suv39-dependent H3K9me3 results in paradoxical gene repressionTo investigate the molecular consequences of heterochromatin loss, we performed RNA-seq on Suv39DKO and littermate control CD4+ CD8+ double-positive (DP...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
.... The reproducibility between the two replicates was represented by the Pearson correlation coefficient and the stratum-adjusted correlation (Yang et al. 2017). Fit-Hi-C (version 2.0.8) was used to determine the significant interactions with the cut off of FDR 0.01 (Ay et al. 2014). The details are available...
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Method: NicE-C efficiently reveals open chromatin–associated chromosome interactions at high resolution
- Zhengyu Luo,
- Ran Zhang,
- Tengfei Hu,
- Yuting Zhu,
- Yueming Wu,
- Wenfei Li,
- Zhi Zhang,
- Xuebiao Yao,
- Haiyi Liang,
- and Xiaoyuan Song
Genome Res. March 2022 32: 534-544; Published in Advance February 1, 2022, doi:10.1101/gr.275986.121
....1 M input cells. (C) Reproducibility analysis of 1 M cells and 0.1 M cells NicE-C data. Reproducibility scores were calculated by HiC-Rep at different resolutions. (D) NicE-C chromatin contact maps of an example region on Chromosome 2 at 1-kb resolution; the top right of the heatmap showed the Nic...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...Methods) (Cazalet et al. 2004). The cells were processed using Hi-C and RNA-seq (see Methods), and the resulting reads aligned against the reference C3 to assess changes in the structure and the host transcription program, respectively. RNA-seq was performed in triplicate and Hi-C in duplicate (see...
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Research: CTCF looping is established during gastrulation in medaka embryos
- Ryohei Nakamura,
- Yuichi Motai,
- Masahiko Kumagai,
- Candice L. Wike,
- Haruyo Nishiyama,
- Yoichiro Nakatani,
- Neva C. Durand,
- Kaori Kondo,
- Takashi Kondo,
- Tatsuya Tsukahara,
- Atsuko Shimada,
- Bradley R. Cairns,
- Erez Lieberman Aiden,
- Shinichi Morishita,
- and Hiroyuki Takeda
Genome Res. June 2021 31: 968-980; Published in Advance May 18, 2021, doi:10.1101/gr.269951.120
...by average total contacts of each row, so that all samples will have the same total contact number. We used Juicer Tools (version 1.7.6) to calculate Pearson's correlation matrices, eigenvectors, and others in what follows.The reproducibility between the replicates was calculated using HiCRep (Yang et al...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...alignment and filtering steps, the data were binned at different resolutions followed by matrix balancing. HiCRep was used to examine the reproducibility (Yang et al. 2017). Biological replicates showed high reproducibility. Therefore, for the downstream analysis, reads obtained from biological replicates...
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Method: Quantitative prediction of enhancer–promoter interactions
- Polina S. Belokopytova,
- Miroslav A. Nuriddinov,
- Evgeniy A. Mozheiko,
- Daniil Fishman,
- and Veniamin Fishman
Genome Res. January 2020 30: 72-84; Published in Advance December 2, 2019, doi:10.1101/gr.249367.119
...; Supplemental Tables S2, S3 for details). To estimate the quality of predictions, we used Pearson's correlation, stratum-adjusted correlation coefficient (SCC) (Yang et al. 2017a), mean squared error (MSE), mean absolute error (MAE), and mean relative error (MRE). As a result, we developed 3DPredictor...

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