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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
...binding factors can give rise to long-range interactions via bridging-induced clustering. We propose that long-range interactions between cis-regulatory elements are driven by at least three distinct processes: cohesin-mediated loop extrusion, polycomb contacts, and clustering of active regions.The large...
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Method: A universal framework for detecting cis-regulatory diversity in DNA regions
- Anushua Biswas and
- Leelavati Narlikar
Genome Res. September 2021 31: 1646-1662; Published in Advance July 19, 2021, doi:10.1101/gr.274563.120
...different modules. These methods have been used to predict complexes forming along the chromatin and colocalization of TFs. However, they explicitly require regulatory information in terms of other high-throughput experiments for each region, which act as features for clustering. They do not incorporate...
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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
...has been extensively studied and used for predicting novel regulatory elements and their function, grouping of binding sites for the same transcription factor (TF) into homotypic clusters of TFBSs (HCTs) has been studied and observed almost exclusively in invertebrates, especially inDrosophila...
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Research: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators
- David van Dijk,
- Eilon Sharon,
- Maya Lotan-Pompan,
- Adina Weinberger,
- Eran Segal,
- and Lucas B. Carey
Genome Res. January 2017 27: 87-94; Published in Advance December 13, 2016, doi:10.1101/gr.212316.116
...for understanding the wiring of these large regulatory networks, they are not informative about how the quantitative relationship between TF and target gene expression is encoded in the DNA. It is still not well understood how promoter architecture determines how each target of a TF will respond to changes...
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Method: Genome-wide identification of conserved regulatory function in diverged sequences
- Leila Taher,
- David M. McGaughey,
- Samantha Maragh,
- Ivy Aneas,
- Seneca L. Bessling,
- Webb Miller,
- Marcelo A. Nobrega,
- Andrew S. McCallion,
- and Ivan Ovcharenko
Genome Res. July 2011 21: 1139-1149; Published in Advance May 31, 2011, doi:10.1101/gr.119016.110
...; Schmidt et al. 2010; Xie et al. 2010). In these elements, which we term ‘‘covert’’ elements, the regulatory encryption is conserved, but embedded within a divergent sequence background. Individual instances of covert regulatory elements have been previously reported in Drosophila (Dermitzakis et al. 2003...
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Method: Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
- J. Omar Yáñez-Cuna,
- Huy Q. Dinh,
- Evgeny Z. Kvon,
- Daria Shlyueva,
- and Alexander Stark
Genome Res. October 2012 22: 2018-2030; Published in Advance April 25, 2012, doi:10.1101/gr.132811.111
...predict context-specific binding and that the predictions work across different Drosophila species suggests that characteristic motif combinations are shared between sites, revealing context-specific motif codes ( cis -regulatory signatures), which appear to be conserved during evolution. Taken together...
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Research: Enhancers display constrained sequence flexibility and context-specific modulation of motif function
- Franziska Reiter,
- Bernardo P. de Almeida,
- and Alexander Stark
Genome Res. March 2023 33: 346-358; Published in Advance March 20, 2023, doi:10.1101/gr.277246.122
...the activity of TF motifs, remains poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in Drosophila melanogaster S2 cells: we (1) replace important TF motifs by all possible 65,536 eight-nucleotide-long sequences and (2) paste eight important TF motif types into 763...
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Research: Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding
- Guillaume Andrey,
- Robert Schöpflin,
- Ivana Jerković,
- Verena Heinrich,
- Daniel M. Ibrahim,
- Christina Paliou,
- Myriam Hochradel,
- Bernd Timmermann,
- Stefan Haas,
- Martin Vingron,
- and Stefan Mundlos
Genome Res. February 2017 27: 223-233; Published in Advance December 6, 2016, doi:10.1101/gr.213066.116
...and preferentially in a homotypic fashion: Active promoters contact more often active chromatin sites than expected by the -wide distribution of chromatin states, and vice versa, repressed promoters contact repressed chromatin sites more often, in line with the findings reported for the HoxD cluster (Noordermeer et...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...in enhancers or active TSSs, maintained borders are located in euchromatin and lost borders in euchromatin islands in heterochromatin.Compared to maintained and new borders, lost TAD borders are also enriched in clusters of noncoding regulatory elements that display extreme levels of sequence conservation...
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Method: Global mapping of RNA homodimers in living cells
- Marta M. Gabryelska,
- Andrew P. Badrock,
- Jian You Lau,
- Raymond T. O'Keefe,
- Yanick J. Crow,
- and Grzegorz Kudla
Genome Res. May 2022 32: 956-967; Published in Advance March 24, 2022, doi:10.1101/gr.275900.121
...expression by miRNA and siRNAs. Intramolecular and intermolecular interactions are interdependent, and according to the competing endogenous RNA (ceRNA) hypothesis (Salmena et al. 2011; Gardiner et al. 2015), intermolecular RNA interactions have the potential to rewire regulatory networks and expand...
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