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Research: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...Long-read assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events Marin Volarić1,2, Evelin Despot-Slade1,2, Damira Veseljak1, Brankica Mravinac1 and Nevenka Meštrović1 1Ruđer Bošković Institute, 10000 Zagreb, Croatia...
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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
...‐‐by_distance 100000 1000000 10000000.” For each data set in the Cistrome DB and ReMap2022 data, the contact frequency scores for short range and long range were split between pairs overlapping the data set at both ends or at neither end. Data sets with fewer than 500 regions or with fewer than 50...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...Construction and evaluation of a new rat reference assembly, GRCr8, from long reads and long-range scaffolding Kai Li1, Melissa L. Smith2, J. Chris Blazier3, Kelli J. Kochan3, Jonathan M.D. Wood4, Kerstin Howe4, Anne E. Kwitek5, Melinda R. Dwinell5, Hao Chen6, Julia L. Ciosek1, Patrick Masterson7...
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Research: Long-range promoter–enhancer contacts are conserved during evolution and contribute to gene expression robustness
- Alexandre Laverré,
- Eric Tannier,
- and Anamaria Necsulea
Genome Res. February 2022 32: 280-296; Published in Advance December 20, 2021, doi:10.1101/gr.275901.121
....laverre@gmail.com, anamaria.necsulea@univ-lyon1.frAbstractGene expression is regulated through complex molecular interactions, involving cis-acting elements that can be situated far away from their target genes. Data on long-range contacts between promoters and regulatory elements are rapidly accumulating. However...
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Research: Sir3 mediates long-range chromosome interactions in budding yeast
- Myriam Ruault,
- Vittore F. Scolari,
- Luciana Lazar-Stefanita,
- Antoine Hocher,
- Isabelle Loïodice,
- Romain Koszul,
- and Angela Taddei
Genome Res. March 2021 31: 411-425; Published in Advance February 12, 2021, doi:10.1101/gr.267872.120
...spreading of Sir3 from the telomeres up to the SIR3 locus (Supplemental Fig. S5A).View larger version: In this window In a new window Figure 5. Sir3-bound regions coincide with long-range contacts. (A) Intra-chromosomal ratio plots of Chromosome I, VI, and IV-L contact maps generated in sir3-A2Q OE and SIR3...
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Research: An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells
- Zhizhuo Zhang,
- Kern Rei Chng,
- Shreyas Lingadahalli,
- Zikai Chen,
- Mei Hui Liu,
- Huy Hoang Do,
- Shaojiang Cai,
- Nicola Rinaldi,
- Huay Mei Poh,
- Guoliang Li,
- Ying Ying Sung,
- Charlie L. Heng,
- Leighton J. Core,
- Si Kee Tan,
- Xiaoan Ruan,
- John T. Lis,
- Manolis Kellis,
- Yijun Ruan,
- Wing-Kin Sung,
- and Edwin Cheung
Genome Res. February 2019 29: 223-235; Published in Advance January 3, 2019, doi:10.1101/gr.230243.117
...and transcriptional landscape in prostate cancer cells.ResultsThe AR interactome landscape in ERG-fusion–positive prostate cancer cellsUsing ChIA-PET, we constructed a -wide map of long-range chromatin interactions associated with AR in VCaP cells 2 h after androgen stimulation (Fig. 1A). Nonchimeric and uniquely...
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Research: Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations
- Phillippa C. Taberlay,
- Joanna Achinger-Kawecka,
- Aaron T.L. Lun,
- Fabian A. Buske,
- Kenneth Sabir,
- Cathryn M. Gould,
- Elena Zotenko,
- Saul A. Bert,
- Katherine A. Giles,
- Denis C. Bauer,
- Gordon K. Smyth,
- Clare Stirzaker,
- Sean I. O'Donoghue,
- and Susan J. Clark
Genome Res. June 2016 26: 719-731; Published in Advance April 6, 2016, doi:10.1101/gr.201517.115
...Three-dimensional disorganization of the cancer occurs coincident with long-range genetic and epigenetic alterations Phillippa C. Taberlay1,2,7, Joanna Achinger-Kawecka1,2,7, Aaron T.L. Lun3,4, Fabian A. Buske1, Kenneth Sabir1, Cathryn M. Gould1, Elena Zotenko1,2, Saul A. Bert1, Katherine A. Giles1...
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Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
- Nicholas H. Putnam,
- Brendan L. O'Connell,
- Jonathan C. Stites,
- Brandon J. Rice,
- Marco Blanchette,
- Robert Calef,
- Christopher J. Troll,
- Andrew Fields,
- Paul D. Hartley,
- Charles W. Sugnet,
- David Haussler,
- Daniel S. Rokhsar,
- and Richard E. Green
Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
...MO, et al. 2009. Comprehensive mapping of long-range interactions reveals folding principles of the human . Science 326: 289–293. Marie-Nelly H, Marbouty M, Cournac A, Flot JF, Liti G, Parodi DP, Syan S, Guillen N, Margeot A, Zimmer C, et al. 2014. High-quality (re)assembly using chromosomal contact...
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Resource: The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
- Stefan Schoenfelder,
- Mayra Furlan-Magaril,
- Borbala Mifsud,
- Filipe Tavares-Cadete,
- Robert Sugar,
- Biola-Maria Javierre,
- Takashi Nagano,
- Yulia Katsman,
- Moorthy Sakthidevi,
- Steven W. Wingett,
- Emilia Dimitrova,
- Andrew Dimond,
- Lucas B. Edelman,
- Sarah Elderkin,
- Kristina Tabbada,
- Elodie Darbo,
- Simon Andrews,
- Bram Herman,
- Andy Higgs,
- Emily LeProust,
- Cameron S. Osborne,
- Jennifer A. Mitchell,
- Nicholas M. Luscombe,
- and Peter Fraser
Genome Res. April 2015 25: 582-597; Published in Advance March 9, 2015, doi:10.1101/gr.185272.114
...in the absence of spatial proximity data. Long-range interactions and 3D architectural features Enhancer–promoter units (EPUs) have recently been defined based on the observation that coregulated enhancers and promoters form clusters on the linear genomic map (Shen et al. 2012). As expected, we found...
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Research: A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
- Lei Zhang,
- Anshun He,
- Bohan Chen,
- Jinfang Bi,
- Jun Chen,
- Dianhao Guo,
- Yuyang Qian,
- Wenbin Wang,
- Tengfei Shi,
- Zhongfang Zhao,
- Jiandang Shi,
- Woojin An,
- Frank Attenello,
- and Wange Lu
Genome Res. February 2020 30: 155-163; Published in Advance January 17, 2020, doi:10.1101/gr.251058.119
...suggests a possible bivalent function.Development of high-order chromosome conformation capture techniques has facilitated analysis of long-range DNA interactions and enabled analysis of regulatory elements that enhance or repress gene expression through long-range interactions (Wei et al. 2013; Liu et al...

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