ArticleNucleic acids research2017
A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
- UnlockingNAR genomics and bioinformatics · 2026Article
- Massively parallel reporter assay reveals promoter-, position-, and strand-specific effects in transcription start sites.bioRxiv : the preprint server for biology · 2025Article
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Strategies for dissecting the complexity of neurodevelopmental disorders.Trends in genetics : TIG · 2024Review
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- Towards a comprehensive regulatory map of Mammalian Genomes.Research square · 2023Article
- Review
- Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation.Nucleic acids research · 2023Article
- The effects of mutations on gene expression and alternative splicing.Proceedings. Biological sciences · 2023Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- Massively Parallel Reporter Assays for High-Throughput In Vivo Analysis of Cis-Regulatory Elements.Journal of cardiovascular development and disease · 2023Review
- Systematic assays and resources for the functional annotation of non-coding variants.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2022Article
- Multiplexed functional genomic assays to decipher the noncoding genome.Human molecular genetics · 2022Article
- Focus on your locus with a massively parallel reporter assay.Journal of neurodevelopmental disorders · 2022Review
- Computational and experimental methods for classifying variants of unknown clinical significance.Cold Spring Harbor molecular case studies · 2022Article
- Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks.Nucleic acids research · 2021Article
- Mutational sources ofeLife · 2021Article
- MPRAdecoder: Processing of the Raw MPRA Data WithFrontiers in genetics · 2021Article
- Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts.Biological psychiatry · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Recent large-scale genomics efforts to characterize the cis-regulatory sequences that orchestrate genome-wide expression patterns have produced impressive catalogues of putative regulatory elements. Most of these sequences have not been functionally tested, and our limited understanding of the non-coding genome prevents us from predicting which sequences are bona fide cis-regulatory elements. Recently, massively parallel reporter assays (MPRAs) have been deployed to measure the activity of putative cis-regulatory sequences in several biological contexts, each with specific advantages and distinct limitations. We developed LV-MPRA, a novel lentiviral-based, massively parallel reporter gene assay, to study the function of genome-integrated regulatory elements in any mammalian cell type; thus, making it possible to apply MPRAs in more biologically relevant contexts. We measured the activity of 2,600 sequences in U87 glioblastoma cells and human neural progenitor cells (hNPCs) and explored how regulatory activity is encoded in DNA sequence. We demonstrate that LV-MPRA can be applied to estimate the effects of local DNA sequence and regional chromatin on regulatory activity. Our data reveal that primary DNA sequence features, such as GC content and dinucleotide composition, accurately distinguish sequences with high activity from sequences with low activity in a full chromosomal context, and may also function in combination with different transcription factor binding sites to determine cell type specificity. We conclude that LV-MPRA will be an important tool for identifying cis-regulatory elements and stimulating new understanding about how the non-coding genome encodes information.
Indexed as
Identifiers
What OpenQuestion holds
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.