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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...regulation can be inferred from experimentally measured changes in chromatin accessibility at carefully selected gene loci. For this purpose, Förster resonance energy transfer combined with fluorescence in situ hybridization (FRET-FISH) was recently developed (Mota et al. 2022). This method takes advantage...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...for shorter interactions, a variety of technical factors complicate distance measurements by imaging methods. Imaging studies require probes to measure DNA. Often probes hybridize a DNA carrying a fluorescent tag to nuclear DNA to identify the position of the enhancer and/or promoter. These probes often lie...
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Resource: A high-resolution map of small-scale inversions in the gibbon genome
- Ludovica Mercuri,
- Donato Palmisano,
- Alberto L'Abbate,
- Pietro D'Addabbo,
- Francesco Montinaro,
- Claudia Rita Catacchio,
- Patrick Hasenfeld,
- Mario Ventura,
- Jan O. Korbel,
- Ashley D. Sanders,
- Flavia Angela Maria Maggiolini,
- and Francesca Antonacci
Genome Res. October 2022 32: 1941-1951; Published in Advance September 30, 2022, doi:10.1101/gr.276960.122
....ResultsStrand-seq data analysisTo detect inversions between the s of human and gibbon, we sequenced an NSI individual using Strand-seq. We selected the same individual from the genus Nomascus whose was well characterized using extensive fluorescence in situ hybridization (FISH) analyses to create a synteny block...
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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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Method: Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome
- Yueying He,
- Yue Xue,
- Jingyao Wang,
- Yupeng Huang,
- Lu Liu,
- Yanyi Huang,
- and Yi Qin Gao
Genome Res. August 2023 33: 1354-1368; Published in Advance July 25, 2023, doi:10.1101/gr.277737.123
...of the . CTG aims to recover a steady genomic structural geometry excluding any stochastic sources.One way to test whether a sequencing-based method such as Hi-C can faithfully reproduce geometric structure information is to make a comparison with fluorescence in situ hybridization (FISH) imaging data (Su et...
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Method: Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing
- Shilin Zhang,
- Yichen Wang,
- Lin Jia,
- Xue Wen,
- Zhonghua Du,
- Cong Wang,
- Yajing Hao,
- Dehai Yu,
- Lei Zhou,
- Naifei Chen,
- Jingcheng Chen,
- Huiling Chen,
- Hui Zhang,
- Ilkay Celik,
- Günhan Gülsoy,
- Jianjun Luo,
- Baoming Qin,
- Xueling Cui,
- Zhonghui Liu,
- Songling Zhang,
- Miguel A. Esteban,
- Ferhat Ay,
- Wei Xu,
- Runsheng Chen,
- Wei Li,
- Andrew R. Hoffman,
- Ji-Fan Hu,
- and Jiuwei Cui
Genome Res. September 2019 29: 1521-1532; Published in Advance July 17, 2019, doi:10.1101/gr.244996.118
...activity of functional genes. However, the mechanisms by which the lncRNAs govern spatial chromatin positioning in stem cells are not well understood. In this study, we have developed a CRIST-seq approach to map lncRNA interactions in the Sox2 promoter. This assay combines the simplicity of lncRNA in situ...
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Method: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
- Brendan F. Miller,
- Dhananjay Bambah-Mukku,
- Catherine Dulac,
- Xiaowei Zhuang,
- and Jean Fan
Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
...transcriptomic data. We applied MERINGUE to a variety of spatially resolved transcriptomic data sets including multiplexed error-robust fluorescence in situ hybridization (MERFISH), spatial transcriptomics, Slide-seq, and aligned in situ hybridization (ISH) data. We anticipate that such statistical analysis...
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Resource: A spatial and temporal map of C. elegans gene expression
- W. Clay Spencer,
- Georg Zeller,
- Joseph D. Watson,
- Stefan R. Henz,
- Kathie L. Watkins,
- Rebecca D. McWhirter,
- Sarah Petersen,
- Vipin T. Sreedharan,
- Christian Widmer,
- Jeanyoung Jo,
- Valerie Reinke,
- Lisa Petrella,
- Susan Strome,
- Stephen E. Von Stetina,
- Menachem Katz,
- Shai Shaham,
- Gunnar Rätsch,
- and David M. Miller III
Genome Res. February 2011 21: 325-341; Published in Advance December 22, 2010, doi:10.1101/gr.114595.110
...reflect the persistence of maternally provided transcripts in Z2 and Z3. To distinguish between maternal loading and zygotic transcription, we manually examined existing in situ hybridization images (NextDB; http://nematode.lab.nig.ac.jp) for genes in the core Z2/Z3 list (Supplemental Table S6).We found...
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Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
- Marta Farré,
- Jaebum Kim,
- Anastasia A. Proskuryakova,
- Yang Zhang,
- Anastasia I. Kulemzina,
- Qiye Li,
- Yang Zhou,
- Yingqi Xiong,
- Jennifer L. Johnson,
- Polina L. Perelman,
- Warren E. Johnson,
- Wesley C. Warren,
- Anna V. Kukekova,
- Guojie Zhang,
- Stephen J. O'Brien,
- Oliver A. Ryder,
- Alexander S. Graphodatsky,
- Jian Ma,
- Harris A. Lewin,
- and Denis M. Larkin
Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
.... 2017). In this study, combining in silico (DESCHRAMBLER) and fluorescence in situ hybridization (FISH) techniques, we described four ancestral karyotypes in the lineage leading to cattle: Cetartiodactyl, Ruminant, Pecoran, and Bovidae. The aim of this study was to utilize these reconstructed ancestral...
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Method: Single-cell-level spatial gene expression in the embryonic neural differentiation niche
- Yi Huang,
- Xiaoming Yu,
- Na Sun,
- Nan Qiao,
- Yaqiang Cao,
- Jerome D. Boyd-Kirkup,
- Qin Shen,
- and Jing-Dong J. Han
Genome Res. April 2015 25: 570-581; Published in Advance January 9, 2015, doi:10.1101/gr.181966.114
...in situ hybridization images of E14.5 mouse embryos at single-cell resolution for more than 1600 telencephalon-expressed genes from the Eurexpress database. Using this pipeline, we derived the spatial gene expression profiles at single-cell resolution across the cortical layers to gain insight...

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