The selection and function of cell type-specific enhancers
The human body contains several hundred cell types, all of which share the same genome.
In metazoans, much of the regulatory code that drives cell type-specific gene expression is …
In metazoans, much of the regulatory code that drives cell type-specific gene expression is …
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Promoters are crucial for gene regulation. They vary greatly in terms of associated regulatory
elements, sequence motifs, the choice of transcription start sites and other features. Several …
elements, sequence motifs, the choice of transcription start sites and other features. Several …
The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons
To connect human biology to fish biomedical models, we sequenced the genome of spotted
gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome …
gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome …
Deep conservation of the enhancer regulatory code in animals
INTRODUCTION In animals, gene regulatory networks specify cell identity in space and
time. Transcription of genes in these networks is modulated by a class of cis-regulatory …
time. Transcription of genes in these networks is modulated by a class of cis-regulatory …
Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells
Divergent lncRNAs that are transcribed in the opposite direction to nearby protein-coding
genes comprise a significant proportion (∼ 20%) of total lncRNAs in mammalian genomes …
genes comprise a significant proportion (∼ 20%) of total lncRNAs in mammalian genomes …
[HTML][HTML] Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription
Recent studies suggest a hierarchical model in which lineage-determining factors act in a
collaborative manner to select and prime cell-specific enhancers, thereby enabling signal …
collaborative manner to select and prime cell-specific enhancers, thereby enabling signal …
Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales
BC Faircloth, JE McCormack, NG Crawford… - Systematic …, 2012 - academic.oup.com
Although massively parallel sequencing has facilitated large-scale DNA sequencing,
comparisons among distantly related species rely upon small portions of the genome that …
comparisons among distantly related species rely upon small portions of the genome that …
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
A Siepel, G Bejerano, JS Pedersen… - Genome …, 2005 - genome.cshlp.org
We have conducted a comprehensive search for conserved elements in vertebrate
genomes, using genome-wide multiple alignments of five vertebrate species (human …
genomes, using genome-wide multiple alignments of five vertebrate species (human …
[HTML][HTML] A bivalent chromatin structure marks key developmental genes in embryonic stem cells
The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster
within regions enriched for genes encoding developmentally important transcription factors …
within regions enriched for genes encoding developmentally important transcription factors …
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand … - nature, 2007 - nature.com
We report the generation and analysis of functional data from multiple, diverse experiments
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …
performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE …