Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution

scientific article

Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1098/RSTB.2013.0022
P8608Fatcat IDrelease_2rveo44w7nfkjejshed4onat2a
P932PMC publication ID3826496
P698PubMed publication ID24218635

P2093author name stringM. A. Nobrega
N. J. Sakabe
P2860cites workIdentification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectQ21061203
Translating the Histone CodeQ22065840
Species-specific transcription in mice carrying human chromosome 21Q22065859
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor bindingQ22065896
On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODEQ22066047
Is junk DNA bunk? A critique of ENCODEQ22066273
An integrated encyclopedia of DNA elements in the human genomeQ22122150
Sequencing and comparison of yeast species to identify genes and regulatory elementsQ22122502
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Core transcriptional regulatory circuitry in human embryonic stem cellsQ24322016
Foxp3 occupancy and regulation of key target genes during T-cell stimulationQ24623384
Histone H3K27ac separates active from poised enhancers and predicts developmental stateQ24628758
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genomeQ28131828
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactylyQ28184095
Histone modifications at human enhancers reflect global cell-type-specific gene expressionQ28238467
Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysisQ28265897
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE projectQ28301622
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila speciesQ28473313
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cellsQ28593119
TimeTree: a public knowledge-base of divergence times among organismsQ29547188
A unique chromatin signature uncovers early developmental enhancers in humansQ29614327
The evolution of gene expression levels in mammalian organsQ29617170
Multivalent engagement of chromatin modifications by linked binding modulesQ29617236
Identification of functional elements and regulatory circuits by Drosophila modENCODEQ29617551
Cell cycle genes are the evolutionarily conserved targets of the E2F4 transcription factor.Q33303668
The evolution of combinatorial gene regulation in fungiQ33321398
Long-range control of gene expression: emerging mechanisms and disruption in diseaseQ33938801
Phenotypic robustness conferred by apparently redundant transcriptional enhancersQ34017526
Heritable individual-specific and allele-specific chromatin signatures in humansQ34087197
Variation in transcription factor binding among humansQ34105133
Comparative Epigenomic Analysis of Murine and Human AdipogenesisQ34179692
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and functionQ34253862
The C-value paradox, junk DNA and ENCODEQ34310617
Can ENCODE tell us how much junk DNA we carry in our genome?Q34522918
Divergence of transcription factor binding sites across related yeast speciesQ34661726
Gene expression differences among primates are associated with changes in a histone epigenetic modificationQ34760532
Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.Q35384578
Evolutionary conservation of histone modifications in mammalsQ36032955
An encyclopedia of mouse DNA elements (Mouse ENCODE).Q36377972
Genome-wide analysis of protein-DNA interactionsQ36488186
DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in DrosophilaQ36504410
A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limbQ36919931
Conservation of core gene expression in vertebrate tissuesQ37209981
Backup in gene regulatory networks explains differences between binding and knockout results.Q37262265
Transcription factor substitution during the evolution of fungal ribosome regulationQ37337000
Transcriptional rewiring of fungal galactose-metabolism circuitryQ37347160
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiationQ37449132
Conserved expression without conserved regulatory sequence: the more things change, the more they stay the sameQ37677317
Genome‐wide maps of transcription regulatory elementsQ37788028
Transcription factor binding variation in the evolution of gene regulationQ37791728
Shadow enhancers as a source of evolutionary noveltyQ38287743
Genetic analysis of variation in transcription factor binding in yeastQ38345613
Switching the mechanism of mating type switching: a domesticated transposase supplants a domesticated homing endonucleaseQ41790568
Tissue-specific transcriptional regulation has diverged significantly between human and mouseQ41833705
Dramatic changes in transcription factor binding over evolutionary timeQ42683249
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.Q43141233
Transposable elements have rewired the core regulatory network of human embryonic stem cellsQ45103037
The ENCODE project: missteps overshadowing a successQ45180939
Evolution of alternative transcriptional circuits with identical logicQ46060628
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila speciesQ51872521
The evolutionary landscape of alternative splicing in vertebrate speciesQ56894874
P433issue1632
P407language of work or nameEnglishQ1860
P921main subjectgenomicsQ222046
P304page(s)20130022
P577publication date2013-12-19
P1433published inPhilosophical Transactions of the Royal Society BQ2153239
P1476titleBeyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution
P478volume368

Reverse relations

cites work (P2860)
Q38161887Deep conservation of cis-regulatory elements in metazoans
Q39013266Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
Q42909090Evolution of transcriptional enhancers and animal diversity.
Q42689540Expression of regulatory genes in the embryonic brain of a lizard and implications for understanding pallial organization and evolution.
Q42284429Human evolution: the non-coding revolution
Q35104777Partially redundant enhancers cooperatively maintain Mammalian pomc expression above a critical functional threshold
Q35700793Populational landscape of INDELs affecting transcription factor-binding sites in humans
Q42249894Spatial distribution of predicted transcription factor binding sites in Drosophila ChIP peaks
Q41329937Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity

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