PXD072017-1

PXD072017 is an original dataset announced via ProteomeXchange.

Title	Dynamic regulatory grammar of human promoters uncovered by MPRA-trained deep learning
Description	One of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. Promoters play a key role in gene regulation, yet their regulatory logic remains incompletely understood. Here, we present PARM, a cell-type specific deep learning model trained on specially designed massively parallel reporter assays that query human promoter sequences. PARM is computationally light-weight and reliably predicts autonomous promoter activity across the genome from DNA sequence alone, in multiple cell types. PARM can also design purely synthetic strong promoters. We leveraged PARM to systematically identify transcription factor (TF) binding sites that likely to contribute to the activity of each natural human promoter, and to detect the rewiring of these regulatory interactions upon various stimuli to the cells. We also uncovered and experimentally confirmed striking positional preferences of TFs that differ between activating and repressive regulatory functions, as well as a complex grammar of motif-motif interactions. Our approach provides a foundation towards a deeper understanding of the dynamic regulation of human promoters by TFs.
HostingRepository	PRIDE
AnnounceDate	2026-01-14
AnnouncementXML	Submission_2026-01-14_03:54:37.991.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Miguel Hernandez Quiles
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-12-15 12:59:48	ID requested
⏵ 1	2026-01-14 03:54:38	announced

Dataset with its publication pending

submitter keyword: synthetic biology, massively parallel reporter assay, convolutional neural network, promoter,Gene regulation, transcription factor, deep learning in genomics., genetics

Prof. Dr. Michiel Vermeulen
contact affiliation	3 Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
contact email	mi.vermeulen@nki.nl
lab head
Miguel Hernandez Quiles
contact affiliation	Netherlands Cancer Institute
contact email	m.hernandez@nki.nl
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/01/PXD072017

PRIDE project URI

• PRIDE
  1. PXD072017
     1. Label: PRIDE project
     2. Name: Dynamic regulatory grammar of human promoters uncovered by MPRA-trained deep learning