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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...mutagenesis. Nat Biotechnol 27: 1173–1175. Shen SQ, Myers CA, Hughes AEO, Byrne LC, Flannery JG, Corbo JC. 2016. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res 26: 238– 255. Sievert C. 2020. Interactive Web-based Data Visualization with R, Plotly, and Shiny...
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Research: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo
- Andrew E.O. Hughes,
- Connie A. Myers,
- and Joseph C. Corbo
Genome Res. October 2018 28: 1520-1531; Published in Advance August 29, 2018, doi:10.1101/gr.231886.117
...highlight general mechanisms by which mammalian enhancers encode cis-regulatory activity.As described above, our analysis of the correlation between TF binding sites and native CRE activity confirms a role for several families of TFs known to regulate photoreceptor development (Fig. 2D). One unexpected...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...al. 2007).Because UCEs are often situated in the vicinity of functionally important genes and potentially exert cis-regulatory effects on their expression (Snetkova et al. 2022), we explored the expression patterns of the genes adjacent to our UCEs. Based on 55 transcriptomes covering 11 tissues from...
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Research: Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period
- Juan J. Tena,
- Cristina González-Aguilera,
- Ana Fernández-Miñán,
- Javier Vázquez-Marín,
- Helena Parra-Acero,
- Joe W. Cross,
- Peter W.J. Rigby,
- Jaime J. Carvajal,
- Joachim Wittbrodt,
- José L. Gómez-Skarmeta,
- and Juan R. Martínez-Morales
Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113
...Comparative epigenomics in distantly related teleost species identifies conserved cis -regulatory nodes active during the vertebrate phylotypic period Juan J. Tena 1 , 4 , Cristina González-Aguilera 1 , 4 , Ana Fernández-Miñán 1 , Javier Vázquez...
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Research: CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
- Joseph C. Corbo,
- Karen A. Lawrence,
- Marcus Karlstetter,
- Connie A. Myers,
- Musa Abdelaziz,
- William Dirkes,
- Karin Weigelt,
- Martin Seifert,
- Vladimir Benes,
- Lars G. Fritsche,
- Bernhard H.F. Weber,
- and Thomas Langmann
Genome Res. November 2010 20: 1512-1525; Published in Advance August 6, 2010, doi:10.1101/gr.109405.110
...immunoprecipitation with massively parallel sequencing (ChIP-seq) on CRX to identify thousands of cis -regulatory regions around photoreceptor genes in adult mouse retina. CRX directly regulates downstream photoreceptor transcription factors and their target genes via a network of spatially distributed regulatory...
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Method: Discriminative prediction of mammalian enhancers from DNA sequence
- Dongwon Lee,
- Rachel Karchin,
- and Michael A. Beer
Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
.... 2008). Functional genomics is an experimentally driven approach that utilizes recently developed techniques of microarray hybridization or massively parallel sequencing in combination with chromatin immunoprecipitation (ChIP) on specific transcription factors ( Johnson et al. 2007; Robertson et al...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...transcription factor binding (Hamdi et al. 2016). Future massively parallel reporter assays or CRISPR-Cas9 disruptions of quasi-prime sequences with CRISPR-Cas9 will be interesting to systematically examine the cis-regulatory effects and mechanisms at human quasi-primes loci. These results further validate our...
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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
...and functional identities in different layers of the cortex (Campbell 2005; Götz and Huttner 2005; Luo and O'Leary 2005). These steps are finely tuned by a sophisticated network of cis-regulatory elements (e.g., promoters and enhancers), trans-regulatory factors (e.g., transcriptional factors [TFs] and histone...
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Research: A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease
- Sumantra Chatterjee,
- Kameko M. Karasaki,
- Lauren E. Fries,
- Ashish Kapoor,
- and Aravinda Chakravarti
Genome Res. December 2021 31: 2199-2208; Published in Advance November 15, 2021, doi:10.1101/gr.275667.121
....chakravarti@nyulangone.org, sumantra.chatterjee@nyulangone.orgAbstractThe major genetic risk factors for Hirschsprung disease (HSCR) are three common polymorphisms within cis-regulatory elements (CREs) of the receptor tyrosine kinase gene RET, which reduce its expression during enteric nervous system (ENS) development. These risk...
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Research: CG dinucleotides enhance promoter activity independent of DNA methylation
- Dominik Hartl,
- Arnaud R. Krebs,
- Ralph S. Grand,
- Tuncay Baubec,
- Luke Isbel,
- Christiane Wirbelauer,
- Lukas Burger,
- and Dirk Schübeler
Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
...: dirk@fmi.chAbstractMost mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address...
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