A promoter is the region at which transcription of a gene begins. In vertebrates a promoter rarely uses a single start base; it fires from a cluster of neighboring positions, and which position dominates can change between developmental stages. CAGE sequences the first bases of capped RNAs and therefore measures these start positions directly.
This track shows 28,142 consensus promoters, called by combining the CAGE tag clusters of all DANIO-CODE samples into one set that is not tied to a single stage. It is intended as a stage-independent reference set of promoter positions. The per-sample tag clusters that go into it are in the DC CAGE-seq track.
This track is part of the DANIO-CODE collection.
Promoters are drawn as blocks. The score reflects the CAGE expression supporting the promoter.
The DANIO-CODE consortium assembled 1,802 zebrafish developmental genomics datasets, 1,438 of them already published and 366 generated by consortium members, and reprocessed all of them from the raw sequencing reads so that samples from different laboratories and different protocols can be compared with each other. ChIP-seq and ATAC-seq were run through the ENCODE pipelines, CAGE-seq through the FANTOM pipeline, and Hi-C and 4C-seq through the pipelines of the groups that produced them. The pipelines are published at gitlab.com/danio-code, and samples were assigned to developmental stages using ZFIN and ENCODE nomenclature. See Baranasic et al. 2022 for details.
CAGE libraries from all developmental stages were processed with the FANTOM pipeline, tag clusters were called per sample, and the clusters were combined across samples into a consensus set.
At UCSC the tracks were converted from the consortium's public track hub at trackhub2.genereg.net/DANIO-CODE with the script danioCodeHubToRa.py, and the data files were copied from the same server. The data themselves were not modified. The steps are documented in our makeDoc.
The data can be explored interactively in table format with the Table Browser or the Data Integrator and exported from there to spreadsheet or tab-separated tables. From scripts, the data can be accessed through our API, track=dcConsensus_promoters.
For automated download and analysis, the annotations are stored in bigBed files that can be downloaded from our download server. The file is consens.canonical.danRer11.bigBed. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain features within a given range, for example
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer11/danioCode/consens.canonical.danRer11.bigBed \
-chrom=chr1 -start=20000000 -end=20100000 stdout
The original data files, and the sample and protocol metadata behind them, are available from the DANIO-CODE data coordination center at danio-code.zfin.org and from the consortium's track hub at trackhub2.genereg.net/DANIO-CODE.
Thanks to the DANIO-CODE consortium for collecting, reprocessing and publishing these data, and to the laboratories that produced the original datasets.
Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N et al. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis- regulatory elements. Nat Genet. 2022 Jul;54(7):1037-1050. PMID: 35789323; PMC: PMC9279159