The DOI matches its Crossref record; 220 of the 220 references it cites were found in a registry or an index.
Deciphering the multi-scale, quantitative cis-regulatory code
Open accessAbstract
Uncovering the cis-regulatory code that governs when and how much each gene is transcribed in a given genome and cellular state remains a central goal of biology. Here, we discuss major layers of regulation that influence how transcriptional outputs are encoded by DNA sequence and cellular context. We first discuss how transcription factors bind specific DNA sequences in a dosage-dependent and cooperative manner and then proceed to the cofactors that facilitate transcription factor function and mediate the activity of modular cis-regulatory elements such as enhancers, silencers, and promoters. We then consider the complex and poorly understood interplay of these diverse elements within regulatory landscapes and its relationships with chromatin states and nuclear organization. We propose that a mechanistically informed, quantitative model of transcriptional regulation that integrates these multiple regulatory layers will be the key to ultimately cracking the cis-regulatory code.
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Gene regulatory network inference in the era of single-cell multi-omics
Badia-i-Mompel, P., Wessels, L., Müller-Dott, S., Trimbour, R., Ramirez Flores, R. O., Argelaguet, R., & Saez-Rodriguez, J. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00618-5 · Cited by 469
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Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Liu, H., Zeng, Q., Zhou, J., Bartlett, A., Wang, B.-A., Berube, P., Tian, W., Kenworthy, M., Altshul, J., Nery, J. R., et al. (2023) · Nature · doi:10.1038/s41586-023-06805-y · Cited by 139
Hold out the genome: a roadmap to solving the cis-regulatory code
de Boer, C. G., & Taipale, J. (2024) · Nature · doi:10.1038/s41586-023-06661-w · Cited by 107
GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences
Fishman, V., Kuratov, Y., Shmelev, A., Petrov, M., Penzar, D., Shepelin, D., Chekanov, N., Kardymon, O., & Burtsev, M. (2023) · doi:10.1101/2023.06.12.544594 · Cited by 137
“While the translation of messenger RNA to amino acid sequences employs a widely-accepted genetic code, other forms of encoding, notably the epigenetic code, are more challenging [1].”
Metadata
- Authors
- Kim, S., & Wysocka, J.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2023-02
- Volume
- 83
- Issue
- 3
- Pages
- 373-392
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W4318027593
- Cited by
- 293
- References
- 220
- FWCI
- 21.82
- Type
- journal article
- Language
- en
- Open access
- hybrid
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