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Resource: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize
- Laura E. Tibbs-Cortes,
- Tingting Guo,
- Carson M. Andorf,
- Xianran Li,
- and Jianming Yu
Genome Res. August 2024 34: 1253-1263; Published in Advance September 13, 2024, doi:10.1101/gr.279027.124
...authors: xianran.li@usda.gov, jmyu@iastate.eduAbstractMaize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region are challenging. In this study, we...
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Research: Sequence determinants of polyadenylation-mediated regulation
- Ilya Vainberg Slutskin,
- Adina Weinberger,
- and Eran Segal
Genome Res. October 2019 29: 1635-1647; Published in Advance September 17, 2019, doi:10.1101/gr.247312.118
...levels may be robust to mutation owing to changes in the cleavage efficiency map.Sequence determinants affecting polyadenylation-mediated regulation of reporter gene expressionThe cleavage and polyadenylation reaction is directed by interaction between trans-acting factors and cis...
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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...Identification of determinants of differential chromatin accessibility through a massively parallel -integrated reporter assay Jennifer Hammelman1,2, Konstantin Krismer2,3, Budhaditya Banerjee4, David K. Gifford2,3,5 and Richard I. Sherwood4,6 1Computational and Systems Biology, Massachusetts...
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Research: Saturation mutagenesis reveals manifold determinants of exon definition
- Shengdong Ke,
- Vincent Anquetil,
- Jorge Rojas Zamalloa,
- Alisha Maity,
- Anthony Yang,
- Mauricio A. Arias,
- Sergey Kalachikov,
- James J. Russo,
- Jingyue Ju,
- and Lawrence A. Chasin
Genome Res. January 2018 28: 11-24; Published in Advance December 14, 2017, doi:10.1101/gr.219683.116
...of short k-mers (Ke et al. 2011; Findlay et al. 2014; Mueller et al. 2015; Rosenberg et al. 2015; Julien et al. 2016). In our previous work, we determined the splicing phenotypes of all 4096 hexamers by inserting such a library into five different positions in two different exons (Ke et al. 2011...
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Research: Sequence determinants of improved CRISPR sgRNA design
- Han Xu,
- Tengfei Xiao,
- Chen-Hao Chen,
- Wei Li,
- Clifford A. Meyer,
- Qiu Wu,
- Di Wu,
- Le Cong,
- Feng Zhang,
- Jun S. Liu,
- Myles Brown,
- and X. Shirley Liu
Genome Res. August 2015 25: 1147-1157; Published in Advance June 10, 2015, doi:10.1101/gr.191452.115
...-Yusa data. The dashed lines represent the threshold chosen to determine efficient and inefficient sgRNAs.To this end, we selected three training sets of sgRNAs, namely “ribosomal,” “nonribosomal,” and “mESC,” for the construction of sequence models (Supplemental Table 1). The differences among these sets...
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Research: Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis
- Ilias Georgakopoulos-Soares,
- Sandro Morganella,
- Naman Jain,
- Martin Hemberg,
- and Serena Nik-Zainal
Genome Res. September 2018 28: 1264-1271; Published in Advance August 13, 2018, doi:10.1101/gr.231688.117
...that are optimal for secondary structure formation. Therefore, there is mounting evidence that secondary structures arising from non-B motifs are not simply associated with increased mutation density—they are possibly causally implicated. Our results suggest that they are determinants of mutagenesis and increase...
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Research: Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
- Matthew J. Rossi,
- William K.M. Lai,
- and B. Franklin Pugh
Genome Res. April 2018 28: 497-508; Published in Advance March 21, 2018, doi:10.1101/gr.229518.117
...in the underrepresentation of binding events in all ChIP-based assays for those proteins possessing only one point of cross-linking to DNA. This underreporting is applicable to ChIP-seq, although the low resolution of the assay does not allow the number of cross-linking points to be determined. Proteins with multiple points...
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Research: Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation
- Christine Roden,
- Jonathan Gaillard,
- Shaveta Kanoria,
- William Rennie,
- Syndi Barish,
- Jijun Cheng,
- Wen Pan,
- Jun Liu,
- Chris Cotsapas,
- Ye Ding,
- and Jun Lu
Genome Res. March 2017 27: 374-384; Published in Advance January 13, 2017, doi:10.1101/gr.208900.116
...and pairing, we observed improvements in enrichment for other features, including apical loop size, CNNC 5-6, basal UG, and apical UGU (Supplemental Fig. S2D). These data are consistent with optimal stem length/pairing as important determinants of miRNA processing.The peak of 36 nt for miRNA stem length...
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Corrigendum: Corrigendum: Unraveling determinants of transcription factor binding outside the core binding site
- Michal Levo,
- Einat Zalckvar,
- Eilon Sharon,
- Ana Carolina Dantas Machado,
- Yael Kalma,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Zohar Yakhini,
- Remo Rohs,
- and Eran Segal
Genome Res. September 2015 25: 1410.2
...: Unraveling determinants of transcription factor binding outside the core binding site Genome Research 25: 655–666 (2015) Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells Jennifer Y. Tan, Tamara Sirey, Frantisek Honti, Bryony Graham, Allison Piovesan...
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Research: Determinants of nucleosome positioning and their influence on plant gene expression
- Ming-Jung Liu,
- Alexander E. Seddon,
- Zing Tsung-Yeh Tsai,
- Ian T. Major,
- Monique Floer,
- Gregg A. Howe,
- and Shin-Han Shiu
Genome Res. August 2015 25: 1182-1195; Published in Advance June 10, 2015, doi:10.1101/gr.188680.114
...pattern reflects the competition between nucleosome formation and RNA polymerase or general TFs binding to core promoter regions (Valouev et al. 2011; Struhl and Segal 2013).There are at least two factors determining nucleosome occupancy in the . The first is intrinsic sequence property. In yeast...

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