ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2013
Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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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
12 citing papers in PubMed, 14 citations in OpenAlex.
- Transcriptome and regulatory maps of decidua-derived stromal cells inform gene discovery in preterm birth.Science advances · 2020Article
- Advancing human health in the decade ahead: pregnancy as a key window for discovery: A Burroughs Wellcome Fund Pregnancy Think Tank.American journal of obstetrics and gynecology · 2020Article
- GR and LSD1/KDM1A-Targeted Gene Activation Requires Selective H3K4me2 Demethylation at Enhancers.Cell reports · 2019Article
- Expression of regulatory genes in the embryonic brain of a lizard and implications for understanding pallial organization and evolution.The Journal of comparative neurology · 2018Article
- Human evolution: the non-coding revolution.BMC biology · 2017Review
- Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.eLife · 2017Article
- Review
- Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks.Mechanisms of development · 2016Article
- Populational landscape of INDELs affecting transcription factor-binding sites in humans.BMC genomics · 2015Article
- Partially redundant enhancers cooperatively maintain Mammalian pomc expression above a critical functional threshold.PLoS genetics · 2015Article
- Evolution of transcriptional enhancers and animal diversity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Article
- Deep conservation of cis-regulatory elements in metazoans.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The complex expression patterns observed for many genes are often regulated by distal transcription enhancers. Changes in the nucleotide sequences of enhancers may therefore lead to changes in gene expression, representing a central mechanism by which organisms evolve. With the development of the experimental technique of chromatin immunoprecipitation (ChIP), in which discrete regions of the genome bound by specific proteins can be identified, it is now possible to identify transcription factor binding events (putative cis-regulatory elements) in entire genomes. Comparing protein-DNA binding maps allows us, for the first time, to attempt to identify regulatory differences and infer global patterns of change in gene expression across species. Here, we review studies that used genome-wide ChIP to study the evolution of enhancers. The trend is one of high divergence of cis-regulatory elements between species, possibly compensated by extensive creation and loss of regulatory elements and rewiring of their target genes. We speculate on the meaning of the differences observed and discuss that although ChIP experiments identify the biochemical event of protein-DNA interaction, it cannot determine whether the event results in a biological function, and therefore more studies are required to establish the effect of divergence of binding events on species-specific gene expression.
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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.