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Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- Piotr J. Balwierz,
- Mikhail Pachkov,
- Phil Arnold,
- Andreas J. Gruber,
- Mihaela Zavolan,
- and Erik van Nimwegen
Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
...collection of mammalian regulatory motifs, TFBS predictions for all motifs across all promoters, and predicted target transcripts of miRNAs (Fig. 1A). Additionally, we developed a substantial number of analysis procedures in order to automatically process and normalize the raw input data (Fig. 1B...
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Research: Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
.... It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulatory element; however, the mechanism by which this occurs is unclear. We report here a periodic poly-thymine motif, which we term T...
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Research: Nucleotide composition-linked divergence of vertebrate core promoter architecture
- Simon J. van Heeringen,
- Waseem Akhtar,
- Ulrike G. Jacobi,
- Robert C. Akkers,
- Yutaka Suzuki,
- and Gert Jan C. Veenstra
Genome Res. March 2011 21: 410-421; Published in Advance January 10, 2011, doi:10.1101/gr.111724.110
...in the human promoters, there are some that are specific to Xenopus, indicative of both similarities and differences between the two species. Some of the known core promoter motifs and the known CRE, Ets, Nrf-1, YY1, and NF-Y promoter motifs are also found in this study. All these positionally enriched...
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Method: P-value-based regulatory motif discovery using positional weight matrices
- Holger Hartmann,
- Eckhart W. Guthöhrlein,
- Matthias Siebert,
- Sebastian Luehr,
- and Johannes Söding
Genome Res. January 2013 23: 181-194; Published in Advance September 18, 2012, doi:10.1101/gr.139881.112
.... But, in contrast to the very specific YY1 (rev) motif, which we find in only 1.2% of EPD core promoter sequences, motif XX6 occurs in 6.6% and is equally well positioned at the TSS. This Initiator element is also similar to the much less informative Initiator motif YYANWYY that was defined based on in...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...) is a common feature of cis -regulatory modules in invertebrate animals, but the occurrence of such homotypic clusters of TFBSs (HCTs) in the human genome has remained largely unknown. To explore whether HCTs are also common in human and other vertebrates, we used known binding motifs for vertebrate TFs...
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Research: Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis
- Paola Cornejo-Páramo,
- Kathrein Roper,
- Sandie M. Degnan,
- Bernard M. Degnan,
- and Emily S. Wong
Genome Res. March 2022 32: 474-487; Published in Advance January 19, 2022, doi:10.1101/gr.275864.121
...was low. Consistent with this, YY1 negatively regulates TP53 and has dual activator and repressor function in other animals (Sui et al. 2004).In summary, we find chromatin-accessible regions harbor specific combinations of TF motifs in a developmental stage-dependent manner. These relationships...
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Research: Sequence features that drive human promoter function and tissue specificity
- Jane M. Landolin,
- David S. Johnson,
- Nathan D. Trinklein,
- Shelly F. Aldred,
- Catherine Medina,
- Hennady Shulha,
- Zhiping Weng,
- and Richard M. Myers
Genome Res. July 2010 20: 890-898; Published in Advance May 25, 2010, doi:10.1101/gr.100370.109
...promoters reveals dual regulatory roles of YY1. Genome Res 17: 798–806. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M. 2005. Systematic discovery of regulatory motifs in human promoters and 39UTRs by comparison of several mammals.Nature 434: 338–345. ZhangX, LuX, Shi Q...
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ARTICLE: A code for transcription initiation in mammalian genomes
- Martin C. Frith,
- Eivind Valen,
- Anders Krogh,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Albin Sandelin
Genome Res. January 2008 18: 1-12; Published in Advance November 21, 2007, doi:10.1101/gr.6831208
..., RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan Abstract Genome-wide detection of transcription start sites (TSSs) has revealed that RNA Polymerase II transcription initiates at millions of positions in mammalian genomes. Most core promoters do not have a single TSS...
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Methods: A transcription factor affinity-based code for mammalian transcription initiation
- Molly Megraw,
- Fernando Pereira,
- Shane T. Jensen,
- Uwe Ohler,
- and Artemis G. Hatzigeorgiou
Genome Res. April 2009 19: 644-656; Published in Advance January 13, 2009, doi:10.1101/gr.085449.108
..., several factors have been suggested to be over-represented at specific regions in the vicinity of TSS, for example, YY1 and CREB ( Xi et al. 2007 ), but none have been previously used to predict TSS location. We observe that within all models, the regions of enrichment for some TFs are broadly defined...
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Resource: The transcription start site landscape of C. elegans
- Taro Leo Saito,
- Shin-ichi Hashimoto,
- Sam Guoping Gu,
- J. Jason Morton,
- Michael Stadler,
- Thomas Blumenthal,
- Andrew Fire,
- and Shinichi Morishita
Genome Res. August 2013 23: 1348-1361; Published in Advance May 1, 2013, doi:10.1101/gr.151571.112
...-elements to be multiply counted, providing some impetus to mine the representative TSS collection preferentially. Candidate promoter regions were analyzed usingMEME (Bailey and Elkan 1994), a widely used program that identifies over-represented sequence motifs within a set of input sequences (see Methods). We used MEME...
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