Amelia Cervera 🧬Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation.
#Transposons #CompositeTransposons #Enhancers #BivalentHistoneMarks
#Erythropoiesis #Myelopoiesis #Hematopoiesis
PLOS BiologyThe maternal-to-zygotic transition in #zebrafish is activated by TFs that open #chromatin via enhancers lacking H3K4me2. @MTLeeLab &co identify a parallel pathway that is activated by #enhancers that bear H3K4me2, showing that both act in combination @PLOSBiology https://plos.io/3IFqYMc
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes.
#EndogenousRetroviruses #ERVs #MusD #VirusLikeParticles #TopologicallyAssociatingDomains #Enhancers #LimbDevelopment #Apoptosis #Dactylaplasia
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype can be rescued by mutations in the retrotransposon coding sequence.
CellBioNews#Corn's ancient ancestors are calling: #Genomic encyclopedia sheds light on #domestication 9,000 years ago.
#maize #teosinte #MaizeCODE #ENCODE #enhancers
https://phys.org/news/2025-02-corn-ancient-ancestors-genomic-encyclopedia.html
Corn's ancient ancestors are calling: Genomic encyclopedia sheds light on domestication 9,000 years ago
The domestication of maize is one of the greatest examples of humankind's impact on evolution. Early farmers' pre-industrial plant breeding choices turned corn from a nearly inedible crop into the major global food source it is today.
Enhancers associated with unstable RNAs are rare in plants.
Enhancers associated with unstable RNAs are rare in plants | Nature Plants
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (nascent) transcripts across diverse crops and other plants using capped small (cs)RNA sequencing. We discovered that unstable transcripts are rare in plants, unlike in vertebrates, and when present, often originate from promoters. In addition, many ‘distal’ elements in plants initiate tissue-specific stable transcripts and are likely bona fide promoters of as-yet-unannotated genes or non-coding RNAs, cautioning against using reference genome annotations to infer putative enhancer sites. To investigate enhancer function, we integrated data from self-transcribing active regulatory region (STARR) sequencing. We found that annotated promoters and other regions that initiate stable transcripts, but not those marked by unstable or bidirectional unstable transcripts, showed stronger enhancer activity in this assay. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements can encompass diverse structures and mechanisms in eukaryotes, including humans. Unstable transcripts like enhancer RNAs are common in vertebrates. McDonald et al. show that such unstable transcripts are rare in plants and that promoters can function as potent enhancers, suggesting diverse cis-regulatory mechanisms in eukaryotes.
Sally Lowell*Very* exciting progress towards precision treatments for aggressive cancers. Very interesting science behind it too.
Dan BoseThis allows condensate behaviour to respond to different inputs, such as lysine #acetylation in IDRs in other CBP domains. It can help to explain how #transcription factors binding to different regions of CBP differentially regulate CBP activity. #enhancers #generegulation #llps #chromatin #imaging #biochemistry #molecularbiology #CellBiology
preLightsIn order to understand complex gene regulatory landscapes, build them from scratch! 🏗️
Milan Antonovic #MPI_MolGen covers work from Henry Thomas, Songjie Feng & colleagues #BueckerLab. #preprint
#preLight 👉 https://prelights.biologists.com/highlights/enhancer-cooperativity-can-compensate-for-loss-of-activity-over-large-genomic-distances-v2/
How #cells in developing #embryos change the way they use #enhancers to regulate #gene #expression.
How cells in developing embryos change the way they use enhancers to regulate gene expression
If you look at a nerve cell, a muscle cell, or a skin cell under the microscope, they appear strikingly different. However, every cell in our body has the same DNA and has descended from a common ancestorâthe fertilized egg cell. The diversity we observe arises due to differentiationâa process during development where cells mature into their final functional forms.
Researchers define new class of #regulatory element in #DNA.
https://phys.org/news/2023-12-class-regulatory-element-dna.html
Researchers define new class of regulatory element in DNA
Researchers at the MRC Weatherall Institute of Molecular Medicine's Laboratory of Gene Regulation, led by Professor Doug Higgs and Dr. Mira Kassouf, have published a study in the journal Cell, in which they reveal another piece of the puzzle of how the code in our DNA is read.