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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
....We identified the most enriched domains found in the set of core versus cloud pangenes and observed some distinct patterns of domain types (Fig. 4A). Core pangenes are enriched in domains including S-adenosyl-L-methionine-dependent (SAM) methyltransferase, AP2/ERF, WD40, helix–loop–helix, Myb domain, C2H2 zinc...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
...) and thyroid hormone receptor (THR) proteins directly compete for binding to response elements involved in regulating lipid metabolism, cell growth, and differentiation (Miyamoto et al. 1997). In fungi, a well-known example of competitive TF-DNA binding is that of Saccharomyces cerevisiae basic helix-loop-helix...
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Resource: Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana
- Tom Denyer,
- Pin-Jou Wu,
- Kelly Colt,
- Bradley W. Abramson,
- Zhili Pang,
- Pavel Solansky,
- Allen Mamerto,
- Tatsuya Nobori,
- Joseph R. Ecker,
- Eric Lam,
- Todd P. Michael,
- and Marja C.P. Timmermans
Genome Res. July 2024 34: 1106-1120; Published in Advance July 1, 2024, doi:10.1101/gr.279091.124
.... 2011), is specifically expressed in cells of this supercluster (Fig. 1D). Further, select basic helix–loop–helix (bHLH) and MYB TF genes linked to drought-stress responses are uniquely expressed in cells of the CA supercluster. These include MYB41 and MYB49, which are part of a regulatory circuit...
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Resource: A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
- Jack F. Cazet,
- Stefan Siebert,
- Hannah Morris Little,
- Philip Bertemes,
- Abby S. Primack,
- Peter Ladurner,
- Matthias Achrainer,
- Mark T. Fredriksen,
- R. Travis Moreland,
- Sumeeta Singh,
- Suiyuan Zhang,
- Tyra G. Wolfsberg,
- Christine E. Schnitzler,
- Andreas D. Baxevanis,
- Oleg Simakov,
- Bert Hobmayer,
- and Celina E. Juliano
Genome Res. February 2023 33: 283-298; Published in Advance January 13, 2023, doi:10.1101/gr.277040.122
..., parascleraxis (G017021), is the ancestral ortholog of two paralogous vertebrate basic helix-loop-helix TFs, paraxis/tcf15 and scleraxis, that regulate muscle differentiation (Freitas et al. 2006; Della Gaspera et al. 2022).View larger version: In this window In a new window Figure 4. An updated Hydra single...
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Research: Joint actions of diverse transcription factor families establish neuron-type identities and promote enhancer selectivity
- Angela Jimeno-Martín,
- Erick Sousa,
- Rebeca Brocal-Ruiz,
- Noemi Daroqui,
- Miren Maicas,
- and Nuria Flames
Genome Res. March 2022 32: 459-473; Published in Advance January 24, 2022, doi:10.1101/gr.275623.121
...helix loop helix (bHLH), zinc finger (ZF), basic leucine zipper domain (bZIP), and nuclear hormone receptors (NHR). HD TF members are overrepresented, supporting a key role for this family in the establishment of neuronal identities. These five TF families are also prevalent when considering mutant...
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LETTER: Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data
- David C. King,
- James Taylor,
- Ying Zhang,
- Yong Cheng,
- Heather A. Lawson,
- Joel Martin,
- ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis,
- Francesca Chiaromonte,
- Webb Miller,
- and Ross C. Hardison
Genome Res. June 2007 17: 775-786; doi:10.1101/gr.5592107
...of relationships between genomic function and evolutionary constraint are utilized. We find that sets of putative transcriptional regulatory sequences, defined by ENCODE experimental data, have a wide span of evolutionary histories, ranging from stringent constraint shown by deep phylogenetic comparisons to recent...
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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
...of TF binding sites implicitly detected by gkm-SVM. Consistent with our logistic regression models, the majority of high-scoring PWMs correspond to homeodomain TFs (Supplemental Fig. 4). Furthermore, gkm-SVM detects binding sites for additional TF families (including MADS, zinc finger, basic helix–loop–helix...
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LETTER: Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
- Ali Mortazavi,
- Evonne Chen Leeper Thompson,
- Sarah T. Garcia,
- Richard M. Myers,
- and Barbara Wold
Genome Res. October 2006 16: 1208-1221; Published in Advance September 8, 2006, doi:10.1101/gr.4997306
...Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire Ali Mortazavi 1 , Evonne Chen Leeper Thompson 2 , Sarah T. Garcia 2 , Richard M. Myers 2 , and Barbara Wold 1 , 3...
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Research: Evolution of a genomic regulatory domain: The role of gene co-option and gene duplication in the Enhancer of split complex
- Elizabeth J. Duncan and
- Peter K. Dearden
Genome Res. July 2010 20: 917-928; Published in Advance May 10, 2010, doi:10.1101/gr.104794.109
...of genes including four bearded genes and seven basic helix-loop-helix (bHLH) genes. We examined the evolution of this unusual complex by identifying bearded and bHLH genes in the genome sequences of Arthropods. We find that a four-gene E(spl)-C, containing three bHLH genes and one bearded gene...
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Research: Epigenetic modification and inheritance in sexual reversal of fish
- Changwei Shao,
- Qiye Li,
- Songlin Chen,
- Pei Zhang,
- Jinmin Lian,
- Qiaomu Hu,
- Bing Sun,
- Lijun Jin,
- Shanshan Liu,
- Zongji Wang,
- Hongmei Zhao,
- Zonghui Jin,
- Zhuo Liang,
- Yangzhen Li,
- Qiumei Zheng,
- Yong Zhang,
- Jun Wang,
- and Guojie Zhang
Genome Res. April 2014 24: 604-615; Published in Advance February 2, 2014, doi:10.1101/gr.162172.113
...the helix-loop-helix DNA binding domain that is critical to the binding with other proteins (Fig. 5C), so that ovarian follicles can be formed (Liang et al. 1997; Chaudhary and Skinner 1999). It is interesting that the use of different splicing forms by ovaries and pseudomale testes is strongly associated...

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