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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...unique ChIP-seq DAP targets in HepG2 and nine histone modifications. This expanded catalog of DAPs and associated gene regulatory data sets provides a rich resource to characterize and understand the functional impact of DAP binding on gene regulation.DAP associations at cCREs reveal the interaction...
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RESEARCH: A High-Resolution Physical and Transcript Map of the Cri du Chat Region of Human Chromosome 5p
- Deanna M. Church,
- Julie Yang,
- Maureen Bocian,
- Rita Shiang,
- and John J. Wasmuth
Genome Res. August 1, 1997 7: 787-801; doi:10.1101/gr.7.8.787
....A. , Long K.R. , Murell J.R. , Stotler C.J. , Gusella J.F. , Buckler A.J. ( 1995 ) An expression independent catalog of genes from human chromosome 22. Genome Res. 5 : 214 – 224 . ↵ Vaisberg E.A. , Grissom P.M. , McIntosh J.R. ( 1996 ) Mammalian cells express three distinct dynein heavy chains...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...(Janky et al. 2014). Additionally, 94 promoters of housekeeping genes (HKG) were selected as control regions, assuming that they drive stable reporter gene expression independent of any perturbation (Eisenberg and Levanon 2013). Also, 66 negative control regions in the were selected (Methods; Yip et al...
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Research: Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance
- Jingfeng Li,
- Keiko Akagi,
- Yongjun Hu,
- Anna L. Trivett,
- Christopher J.W. Hlynialuk,
- Deborah A. Swing,
- Natalia Volfovsky,
- Tamara C. Morgan,
- Yelena Golubeva,
- Robert M. Stephens,
- David E. Smith,
- and David E. Symer
Genome Res. May 2012 22: 870-884; Published in Advance February 23, 2012, doi:10.1101/gr.130740.111
...combinations of restriction enzymes and degenerate primers (Supplemental Table 1). Thismethod reidentified 1538 out of 1665 (92.4%) of the youngestmappable ERV (IAPLTR1) integrants in the reference B6 at;14-fold sequencing coverage. To validate these results, we compared chromosomal distributions of identified...
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12 Drosophila Genomes/Letter: Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
- J. Graham Ruby,
- Alexander Stark,
- Wendy K. Johnston,
- Manolis Kellis,
- David P. Bartel,
- and Eric C. Lai
Genome Res. December 2007 17: 1850-1864; Published in Advance November 7, 2007, doi:10.1101/gr.6597907
...the constituent miRNAs of each labeled subcluster indicate that the two subclusters were expressed independently ( Fig. 6E ). Although most of the novel miRNA genes closely resembled those previously annotated, three of the hairpin precursors were much larger than those observed previously in animals...
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Methods: Predicting tissue-specific enhancers in the human genome
- Len A. Pennacchio,
- Gabriela G. Loots,
- Marcelo A. Nobrega,
- and Ivan Ovcharenko
Genome Res. February 2007 17: 201-211; Published in Advance January 8, 2007, doi:10.1101/gr.5972507
...with low expression (independently performed for each tissue; see Methods). We named this approach Enhancer Identification (or EI) and its application allowed us to select candidate tissue-specific enhancers from the pool of conserved noncoding elements in loci of genes highly expressed in a given tissue...
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