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Method: Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression
- Di Huang,
- Hanna M. Petrykowska,
- Brendan F. Miller,
- Laura Elnitski,
- and Ivan Ovcharenko
Genome Res. April 2019 29: 657-667; Published in Advance March 18, 2019, doi:10.1101/gr.247007.118
...(posCOR); negatively correlated (negCOR); and uncorrelated (unCOR). negCORs were verified as silencers. (B) Three negCOR silencers in the locus of MEF2A.The negative correlation between negCORs and their neighboring genes does not necessarily indicate that negCORs function as silencers. An alternative...
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Resource: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
...to citations. Additional in-scope elements were identified from targeted searches for elements associated with genes of high biomedical interest (e.g., ACE2, BRCA1, CFTR, HBB and other frequently accessed genes in the NCBI Gene database), from searches for publications that use bulk screening techniques, from...
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LETTER: Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif
- Yong Cheng,
- David C. King,
- Louis C. Dore,
- Xinmin Zhang,
- Yuepin Zhou,
- Ying Zhang,
- Christine Dorman,
- Demesew Abebe,
- Swathi A. Kumar,
- Francesca Chiaromonte,
- Webb Miller,
- Roland D. Green,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2008 18: 1896-1905; Published in Advance September 25, 2008, doi:10.1101/gr.083089.108
...of the binding site motif are particularly interesting in this regard. We note that our biological assay has been confined to GATA1-dependent enhancers in erythroid cells. It will be important to study the phylogenetic extent of motif preservation in other types of CRMs (such as promoters and silencers), using...
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