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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
...in any eukaryotic organism, TSSPlant (Shahmuradov et al. 2017) designed for plant TSS prediction, and machine learning-enhanced options like DeePromoter (Oubounyt et al. 2019) designed exclusively for mammalian TSSs. Newer CamoTSS specifically calls TSS from actual RNA-seq data (Hou et al. 2023).Most...
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Research: Dynamic modulation of genomic enhancer elements in the suprachiasmatic nucleus, the site of the mammalian circadian clock
- Akanksha Bafna,
- Gareth Banks,
- Michael H. Hastings,
- and Patrick M. Nolan
Genome Res. May 2023 33: 673-688; Published in Advance May 8, 2023, doi:10.1101/gr.277581.122
...with changing transcriptional output in the SCN, as noted with the rhythmic expression of the core-clock genes Per2 and Cry1. About 50% of the differing histone acetylation levels perfectly correlated (Pearson's correlation (r) = 1) with the host gene expression (Supplemental Fig. S4E). To our knowledge...
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Research: Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation
- Jack A. Collora and
- Ya-Chi Ho
Genome Res. June 9, 2023 gr.277698.123; Published in Advance June 9, 2023, doi:10.1101/gr.277698.123
...16 et al. 1994; Weintraub et al. 2017), have been shown to interact with the HIV-1 LTR through intermediary 17 proteins and are associated with 3D chromatin looping. We postulate that HIV-1 increases host gene 18 expression beyond the transcription unit by increasing host chromatin accessibility...
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Resource: Dynamics of microRNA expression during mouse prenatal development
- Sorena Rahmanian,
- Rabi Murad,
- Alessandra Breschi,
- Weihua Zeng,
- Mark Mackiewicz,
- Brian Williams,
- Carrie A. Davis,
- Brian Roberts,
- Sarah Meadows,
- Dianna Moore,
- Diane Trout,
- Chris Zaleski,
- Alex Dobin,
- Lei-Hoon Sei,
- Jorg Drenkow,
- Alex Scavelli,
- Thomas R. Gingeras,
- Barbara J. Wold,
- Richard M. Myers,
- Roderic Guigó,
- and Ali Mortazavi
Genome Res. November 2019 29: 1900-1909; Published in Advance October 23, 2019, doi:10.1101/gr.248997.119
..., Willingham AT, Duttagupta R, Dumais E, et al. 2009. Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs. Nature 457: 1028–1032. doi:10.1038/nature07759 ↵Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19...
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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
...and conserved changes contribute to converting the host intranuclear environment to a suitable circumstance for efficient viral replication and transcription. However, how these alterations of chromatin state affect gene expression and infection progression remains poorly explored. Therefore, it is fundamental...
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Research: Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation
- Maria Warnefors,
- Katharina Mössinger,
- Jean Halbert,
- Tania Studer,
- John L. VandeBerg,
- Isa Lindgren,
- Amir Fallahshahroudi,
- Per Jensen,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1961-1973; Published in Advance October 27, 2017, doi:10.1101/gr.225391.117
..., Sweden Corresponding authors: maria.warnefors@gmail.com, h.kaessmann@zmbh.uni-heidelberg.deAbstractSexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set...
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Research: MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum
- Maria Ninova,
- Matthew Ronshaugen,
- and Sam Griffiths-Jones
Genome Res. January 2016 26: 85-96; Published in Advance October 30, 2015, doi:10.1101/gr.193367.115
...MicroRNA evolution, expression, and function during short germband development in Tribolium castaneum Maria Ninova , Matthew Ronshaugen and Sam Griffiths-Jones Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, United Kingdom...
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Resource: Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
- Tsung-Cheng Chang,
- Mihaela Pertea,
- Sungyul Lee,
- Steven L. Salzberg,
- and Joshua T. Mendell
Genome Res. September 2015 25: 1401-1409; Published in Advance August 19, 2015, doi:10.1101/gr.193607.115
...and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours. Nat Commun 2: 4802. Rodriguez A, Griffiths-Jones S, Ashurst JL, Bradley A. 2004. Identification of mammalian microRNA host genes and transcription units. Genome Res 14: 1902–1910. Roush S, Slack FJ. 2008. The let-7 family...
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Method: Identification of microRNA-regulated gene networks by expression analysis of target genes
- Vincenzo Alessandro Gennarino,
- Giovanni D'Angelo,
- Gopuraja Dharmalingam,
- Serena Fernandez,
- Giorgio Russolillo,
- Remo Sanges,
- Margherita Mutarelli,
- Vincenzo Belcastro,
- Andrea Ballabio,
- Pasquale Verde,
- Marco Sardiello,
- and Sandro Banfi
Genome Res. June 2012 22: 1163-1172; Published in Advance February 15, 2012, doi:10.1101/gr.130435.111
...Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA. Abstract MicroRNAs (miRNAs) and transcription factors control eukaryotic cell proliferation, differentiation, and metabolism through their specific gene regulatory networks. However, differently from transcription...
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Research: Widespread context dependency of microRNA-mediated regulation
- Florian Erhard,
- Jürgen Haas,
- Diana Lieber,
- Georg Malterer,
- Lukasz Jaskiewicz,
- Mihaela Zavolan,
- Lars Dölken,
- and Ralf Zimmer
Genome Res. June 2014 24: 906-919; Published in Advance March 25, 2014, doi:10.1101/gr.166702.113
.... Expression of genes is not only regulated at the level of transcription but also post-transcriptionally in various ways, of which regulation mediated by microRNAs is one of the most prevalent (He andHannon 2004). MicroRNAs are 20- to 24-nt long noncoding RNAs that have been found in animals and plants...

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