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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
...of the link between chromatin architecture and gene regulation in disease contexts (Paulsen et al. 2017).Indeed, transcriptional dysregulation has been attributed to alterations in 3D organization in diseases, including cancer (Feng and Pauklin 2020; Osman et al. 2022), yet analysis of multiple cancers shows...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells Johannes Hiltunen1,3, Laura Helminen1,3, Niina Aaltonen1,3, Kaisa-Mari Launonen1, Hanna Laakso1, Marjo Malinen2, Einari A. Niskanen1, Jorma J. Palvimo1 and Ville...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...the endogenous transcriptional activity of ERBS.To determine whether ERBS categories translated into differential gene expression, we linked ERBS to their target genes using ATAC-seq-derived peak-to-gene maps in breast tumors (Corces et al. 2018) and analyzed gene expression after 24 h E2 stimulation in MCF-7...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...methods in transcriptomics and validated many novel, lowly expressed, often times sample-specific transcripts identified by long reads. These molecules represent deviations of the major transcriptional program that were overlooked by short-read sequencing methods but are now captured by the full...
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Resource: A limited set of transcriptional programs define major cell types
- Alessandra Breschi,
- Manuel Muñoz-Aguirre,
- Valentin Wucher,
- Carrie A. Davis,
- Diego Garrido-Martín,
- Sarah Djebali,
- Jesse Gillis,
- Dmitri D. Pervouchine,
- Anna Vlasova,
- Alexander Dobin,
- Chris Zaleski,
- Jorg Drenkow,
- Cassidy Danyko,
- Alexandra Scavelli,
- Ferran Reverter,
- Michael P. Snyder,
- Thomas R. Gingeras,
- and Roderic Guigó
Genome Res. July 2020 30: 1047-1059; Published in Advance July 29, 2020, doi:10.1101/gr.263186.120
...from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components...
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Research: Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
- Aarthi Venkat,
- Maximillian J. Carlino,
- Betty R. Lawton,
- Manju L. Prasad,
- Matthew Amodio,
- Courtney E. Gibson,
- Caroline J. Zeiss,
- Scott E. Youlten,
- Smita Krishnaswamy,
- and Diane S. Krause
Genome Res. June 2024 34: 837-850; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123
...Aarthi Venkat1,10, Maximillian J. Carlino2,3,10, Betty R. Lawton2,3,10, Manju L. Prasad4, Matthew Amodio5,6, Courtney E. Gibson7, Caroline J. Zeiss8, Scott E. Youlten9, Smita Krishnaswamy1,2,5,9,11 and Diane S. Krause2,3,4,11 1Computational Biology and Bioinformatics Program, Yale University, New...
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Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
- Stacey E.P. Joosten,
- Sebastian Gregoricchio,
- Suzan Stelloo,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Kerim Yavuz,
- Maria Donaldson Collier,
- Tunç Morova,
- Umut Berkay Altintaş,
- Yongsoo Kim,
- Sander Canisius,
- Cathy B. Moelans,
- Paul J. van Diest,
- Gozde Korkmaz,
- Nathan A. Lack,
- Michiel Vermeulen,
- Sabine C. Linn,
- and Wilbert Zwart
Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
...—worldwide (Waks and Winer 2019). As such, ESR1 is considered the critical drug target in both the adjuvant and metastatic phase of the disease, but resistance to hormonal treatment is common (Early Breast Cancer Trialists’ Collaborative Group [EBCTCG] 2005). ESR1 serves as a hormone-dependent transcription factor...
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Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
- Jean Fan,
- Hae-Ock Lee,
- Soohyun Lee,
- Da-eun Ryu,
- Semin Lee,
- Catherine Xue,
- Seok Jin Kim,
- Kihyun Kim,
- Nikolaos Barkas,
- Peter J. Park,
- Woong-Yang Park,
- and Peter V. Kharchenko
Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
...transcriptional subpopulations (CCL3/CCL4, antigen presentation) appear independently of the subclonal structure.DiscussionAltogether, our results demonstrate the ability to integrate genetic and transcriptional information using scRNA-seq data to identify and characterize transcriptional programs driving...
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Research: Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis
- Hector L. Franco,
- Anusha Nagari,
- Venkat S. Malladi,
- Wenqian Li,
- Yuanxin Xi,
- Dana Richardson,
- Kendra L. Allton,
- Kaori Tanaka,
- Jing Li,
- Shino Murakami,
- Khandan Keyomarsi,
- Mark T. Bedford,
- Xiaobing Shi,
- Wei Li,
- Michelle C. Barton,
- Sharon Y.R. Dent,
- and W. Lee Kraus
Genome Res. February 2018 28: 159-170; Published in Advance December 22, 2017, doi:10.1101/gr.226019.117
...is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epis...
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Resource: Modeling molecular development of breast cancer in canine mammary tumors
- Kiley Graim,
- Dmitriy Gorenshteyn,
- David G. Robinson,
- Nicholas J. Carriero,
- James A. Cahill,
- Rumela Chakrabarti,
- Michael H. Goldschmidt,
- Amy C. Durham,
- Julien Funk,
- John D. Storey,
- Vessela N. Kristensen,
- Chandra L. Theesfeld,
- Karin U. Sorenmo,
- and Olga G. Troyanskaya
Genome Res. February 2021 31: 337-347; Published in Advance December 23, 2020, doi:10.1101/gr.256388.119
...for isolation of breast cancer stem cells, and analyses of tumor evolution at both the level of mutations and associated transcriptional programs.MethodsEthics statementAnimal work was approved by the University of Pennsylvania Institutional Animal Care and Use Committee (IACUC), listed as protocol 804298...
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