...Laura J. Harrison; Daniel Bose ABSTRACT Enhancers confer precise spatiotemporal patterns of gene expression in response to developmental and environmental stimuli. Over the last decade, the transcription of enhancer RNAs (eRNAs) – nascent RNAs transcribed from active enhancers – has emerged...

... their target genes through higher-order chromatin structures. However, how such architectures and variations in CREs contribute to transcriptional evolvability remains elusive. We use Hoxd genes as a paradigm for the emergence of regulatory innovations, as many relevant enhancers are located in a regulatory...

...Tomás Pachano; Endika Haro; Alvaro Rada-Iglesias ABSTRACT Enhancers control the establishment of spatiotemporal gene expression patterns throughout development. Over the past decade, the development of new technologies has improved our capacity to link enhancers with their target genes based...

... of accumulating data supporting the important role of non-promoter regulatory elements in developmentally programmed gene regulation, we propose that the major influence of global DNA methylation is in fact on the many surrounding enhancers and silencers ( Fig. 1 ) ( Lee et al., 2015 ; Zhang et al., 2013...

... for photoreceptor and bipolar cell formation. How these retinal progenitor cells initially activate Otx2 expression is unclear. To address this, we investigated the cis -regulatory network that controls Otx2 expression in mice. We identified a minimal enhancer element, DHS-4D, that drove expression in newly formed...

...Ivelisse Cajigas; Abhijit Chakraborty; Madison Lynam; Kelsey R. Swyter; Monique Bastidas; Linden Collens; Hao Luo; Ferhat Ay; Jhumku D. Kohtz ABSTRACT The Evf2 long non-coding RNA directs Dlx5/6 ultraconserved enhancer( UCE )-intrachromosomal interactions, regulating genes across a 27 Mb region...

...John D. Thompson; Jianhong Ou; Nutishia Lee; Kwangdeok Shin; Valentina Cigliola; Lingyun Song; Gregory E. Crawford; Junsu Kang; Kenneth D. Poss ABSTRACT To identify candidate tissue regeneration enhancer elements (TREEs) important for zebrafish fin regeneration, we performed ATAC-seq from bulk...

...Noah B. Goodson; Michael A. Kaufman; Ko U. Park; Joseph A. Brzezinski, IV ABSTRACT The transcription factor OTX2 is required for photoreceptor and bipolar cell formation in the retina. It directly activates the transcription factors Prdm1 and Vsx2 through cell type-specific enhancers. PRDM1...

...Iain Williamson; Lauren Kane; Paul S. Devenney; Ilya M. Flyamer; Eve Anderson; Fiona Kilanowski; Robert E. Hill; Wendy A. Bickmore; Laura A. Lettice ABSTRACT Topologically associating domains (TADs) have been proposed to both guide and constrain enhancer activity. Shh is located within a TAD known...

... the cis -regulatory sequences that control dsx expression in the foreleg, which contains multiple types of sex-specific sensory organs. We find that separate modular enhancers are responsible for dsx expression in each sexually dimorphic organ. Expression of dsx in the sex comb is co-regulated by two...

...Guillaume Andrey; Stefan Mundlos The precise expression of genes in time and space during embryogenesis is largely influenced by communication between enhancers and promoters, which is propagated and governed by the physical proximity of these elements in the nucleus. Here, we review how chromatin...

... demethylases cooperate in promoting mouse embryonic stem cell (ESC) identity. However, little is known about their importance at the exit of ESC pluripotency. Here, we reveal that Jmjd2c facilitates this process by stabilising the assembly of mediator-cohesin complexes at lineage-specific enhancers...

... understood. Here, we show that the chromatin remodeling factor Brg1 is required for enhancer activation in mesoderm induction. In an embryonic stem cell-based directed differentiation assay, the absence of Brg1 results in a failure of cardiomyocyte differentiation and broad deregulation of lineage-specific...

...Eve Anderson; Paul S. Devenney; Robert E. Hill; Laura A. Lettice Coordinated gene expression controlled by long-distance enhancers is orchestrated by DNA regulatory sequences involving transcription factors and layers of control mechanisms. The Shh gene and well-established regulators...

... that generally involves transcriptional regulation mediated by multiple separate enhancers, each with its own arrangement of transcription factor (TF)-binding sites and associated activities. Here, by contrast, we show that the expression of the Drosophila Nidogen ( Ndg ) gene at different embryonic stages...

...Michele Markstein; Robert Zinzen; Peter Markstein; Ka-Ping Yee; Albert Erives; Angela Stathopoulos; Michael Levine Bioinformatics methods have identified enhancers that mediate restricted expression in the Drosophila embryo. However, only a small fraction of the predicted enhancers actually work...

... gene with particular focus on r3 and r5 in wild type and Krox-20 −/− mutant embryos. There was a clear loss of expression in r3, which indicated that Hoxa-2 was downstream of Krox-20 . Using transgenic analysis with E. coli lacZ reporter genes we have identified and mapped an r3/r5 enhancer in the 5...