ArticleNucleic acids research2015
Global identification of the genetic networks and cis-regulatory elements of the cold response in zebrafish.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 1 of them a synthesis that pooled it.
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Who cites it
22 citing papers in PubMed, 1 synthesis or guideline pooled it, 88 citations in OpenAlex.
- Pooled it
- Developmental and tissue expression breadth define distinct but overlapping classes of housekeeping genes.PLoS computational biology · 2026Article
- Integrative epigenomic and transcriptomic profiling reveals organ-specific and coordinated cold stress responses in the brain and gill of Nile tilapia.Stress biology · 2026Article
- Chromatin dynamics and transcriptional regulation of heat stress in an ectothermic fish.Proceedings. Biological sciences · 2025Article
- Metabolomic-based analysis reveals bile acid-mediated ovarian failure induced by low temperature in zebrafish.Zoological research · 2024Article
- Article
- Mitophagy: A Bridge Linking HMGB1 and Parkinson's Disease Using Adult Zebrafish as a Model Organism.Brain sciences · 2023Article
- Transcriptomic Networks Reveal the Tissue-Specific Cold Shock Responses in Japanese Flounder (Biology · 2023Article
- Article
- Understanding the Function and Mechanism of Zebrafish Tmem39b in Regulating Cold Resistance.International journal of molecular sciences · 2022Article
- Prediction and Experimental Validation of a New Salinity-Responsive Cis-Regulatory Element (CRE) in a Tilapia Cell Line.Life (Basel, Switzerland) · 2022Article
- Mild cold stress specifically disturbs clustering movement of DFCs and sequential organ left-right patterning in zebrafish.Frontiers in cell and developmental biology · 2022Article
- Alternative splicing of medaka bcl6aa and its repression by Prdm1a and Prdm1b.Fish physiology and biochemistry · 2021Article
- Characterization of Biological Pathways Regulating Acute Cold Resistance of Zebrafish.International journal of molecular sciences · 2021Article
- Identification and characterization of miRNAs involved in cold acclimation of zebrafish ZF4 cells.PloS one · 2020Article
- Transcriptome analyses provide the first insight into the molecular basis of cold tolerance in Larimichthys polyactis.Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology · 2020Article
- Deficiency in the membrane protein Tmbim3a/Grinaa initiates cold-induced ER stress and cell death by activating an intrinsic apoptotic pathway in zebrafish.The Journal of biological chemistry · 2019Article
- Article
- Temporally distinct transcriptional regulation of myocyte dedifferentiation and Myofiber growth during muscle regeneration.BMC genomics · 2017Article
- Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai-Tibetan Plateau.G3 (Bethesda, Md.) · 2017Article
Corrections and comments
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. However, the cis- and trans-factors governing cold responses are not well characterized. We profiled transcriptional changes in eight zebrafish tissues exposed to mildly and severely cold temperatures using RNA-Seq. A total of 1943 differentially expressed genes (DEGs) were identified, from which 34 clusters representing distinct tissue and temperature response expression patterns were derived using the k-means fuzzy clustering algorithm. The promoter regions of the clustered DEGs that demonstrated strong co-regulation were analysed for enriched cis-regulatory elements with a motif discovery program, DREME. Seventeen motifs, ten known and seven novel, were identified, which covered 23% of the DEGs. Two motifs predicted to be the binding sites for the transcription factors Bcl6 and Jun, respectively, were chosen for experimental verification, and they demonstrated the expected cold-induced and cold-repressed patterns of gene regulation. Protein interaction modeling of the network components followed by experimental validation suggested that Jun physically interacts with Bcl6 and might be a hub factor that orchestrates the cold response in zebrafish. Thus, the methodology used and the regulatory networks uncovered in this study provide a foundation for exploring the mechanisms of cold adaptation in teleosts.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.