+Transcription begins when RNA polymerase II starts making an RNA at a +transcription start site (TSS). A gene or a regulatory element does not use a +single start site: polymerase initiates across a spread of nearby bases, on both +strands, and which bases get used is set largely by the local DNA sequence and by +the chromatin state around it. Knowing where transcription starts, and how +sharply, matters for reading a promoter, for telling a promoter from an enhancer, +and for deciding which of a gene's annotated transcripts is actually made in a +given cell. +
+ ++Transcription start site is the common term and the one used here, but it names +a position where transcription initiation is the event. Initiation is the more +accurate word: polymerase does not start at one fixed point but initiates over a +window of bases, at rates that differ base by base, so what these tracks report +is the distribution of initiation across a region rather than a single site. +
+ ++No single assay settles where a TSS is. Run-on methods catch the nascent RNA at +the moment it is made, cap-based methods read the protected 5' end of a finished +transcript, long reads follow a transcript from one end to the other, and +sequence models predict initiation without an experiment at all. Each sees a +different slice of the same event, and they disagree in informative ways. This +collection gathers those lines of evidence in one place so they can be compared +at a locus. +
+ ++Tracks currently in the collection: +
+ ++Each track has its own description page covering what it measures or predicts, +how it was made, and how to download it. On T2T-CHM13 only the ProCapNet +predictions are available, since the PRO-cap experiments and the contribution +scores were produced against GRCh38. More TSS evidence tracks will be added here +over time. +
+ ++Tracks are grouped by the evidence they carry, with measurements before +predictions. Signal tracks that distinguish the two strands draw the plus strand +upward and the minus strand downward, so a divergent promoter reads as a pair of +peaks straddling the element. +
+ ++Each track listed above has its own description page with details on methods, +file locations and how to download and intersect the data. +
+ ++PRO-cap data was generated as part of ENCODE by Sagar Shah and the Yu and Lis +labs at Cornell University. ProCapNet was developed by Kelly Cochran in the +Kundaje lab at Stanford University, and the genome-wide predictions and +contribution scores were generated in collaboration with the GENCODE consortium. +
+ ++Cochran K, Yin M, Mantripragada A, Schreiber J, Marinov GK, Shah SR, Yu H, Lis JT, Kundaje A. + +Dissecting the cis-regulatory syntax of transcription initiation with deep learning. +bioRxiv. 2024 Nov 21;. +PMID: 38853896; PMC: PMC11160661 +
+ + + ++Kwak H, Fuda NJ, Core LJ, Lis JT. + +Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. +Science. 2013 Feb 22;339(6122):950-3. +PMID: 23430654; PMC: PMC3974810 +
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