Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models.

Marina Naval-Sánchez, Delphine Potier, Gert Hulselmans, Valerie Christiaens, Stein Aerts

Open access · bronzeAbstract read

In one paragraph

Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it

0cells of the map it votes in

7citing papers in PubMed

0.9field-weighted citation impact, top 25% of its field

1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed, 11 citations in OpenAlex.

Benchmarking of ATAC Sequencing Data From BGI's Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions.Frontiers in molecular biosciences · 2022
Article
The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019
Article
Comparing 3D Genome Organization in Multiple Species Using Phylo-HMRF.Cell systems · 2019
Article
Continuous-Trait Probabilistic Model for Comparing Multi-species Functional Genomic Data.Cell systems · 2018
Article
Positional specificity of different transcription factor classes within enhancers.Proceedings of the National Academy of Sciences of the United States of America · 2018
Article
Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.Genetics · 2017
Article
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model.BioMed research international · 2017
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors at 1 institution in 1 country.

Marina Naval-SánchezLaboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium.

Delphine PotierLaboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium.

Gert HulselmansLaboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium.

Valerie ChristiaensLaboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium.

Stein AertsLaboratory of Computational Biology, Department of Human Genetics, University of Leuven, Leuven, Belgium stein.aerts@med.kuleuven.be.

KU Leuven · BE

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Scoring the impact of noncoding variation on the function of cis-regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here, we examine the use of the Ornstein-Uhlenbeck (OU) model to infer selection at the level of predicted cis-regulatory modules (CRMs), and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-Seq and STARR-Seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence.

Indexed as

Regulatory Elements, TranscriptionalAnimalsBase SequenceChromatinCompound Eye, ArthropodConserved SequenceDNA-Binding ProteinsDrosophila melanogasterDrosophila ProteinsGene Expression Regulation, DevelopmentalGenes, InsectGenetic SpeciationMarkov ChainsModels, GeneticPhylogenyProtein BindingChromatinDNA-Binding ProteinsDrosophila Proteinsgrh protein, DrosophilaTranscription Factorscis-regulatory evolutionDrosophila specieseye developmentFAIRE-SeqOrnstein–Uhlenbeck

Identifiers

PMID25944915

DOI10.1093/molbev/msv107

PMCPMC4540964

OpenAlexW2153953387

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

Registered trials

None linked

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.