PsbS: 57-bp Δ at -90 bp → 33× expression (vs 3xENH: 12×)
SBPase: motif #insertions → 16× (deletions ineffective)
Core #promoter gold zone: -400 to -500 bp from TSS
Gene-specific regulatory logic - no universal rules
Minimal non-transgenic edits > foreign #enhancers
Epigenetics Update - Species-specific chromatin architecture and neurogenesis mediated by a human enhancer bit.ly/3PhxTig
Debra L. Silver (Duke University) in Cell Stem Cell
#Epigenetics #Chromatin #Enhancers
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Perfect for cancer, immunology, and aging research; epigenometech.com
Really pleased to share the *final* version of @katiegelder.bsky.social's super work, profiling the functional roles of #IDRs in CBP. Published today 🎉
🔗https://doi.org/10.1016/j.celrep.2026.117109
#IDRs #condensates #transcription #CBP #generegulation #enhancers (1/7)
We specifically repurposed this type of analysis to quantify gene regulation, based on the fact that #enhancers and their target genes may cluster within the 3D nuclear space and display similar #epigenetic properties. (10/n)
No AI slop; just 1950's maths. 🤘🏽😎 #oldschool
10/n METALoci repurposed this type of analysis to quantify gene regulation, based on the fact that #enhancers and their target genes may cluster within the 3D nuclear space and display similar #epigenetic properties
Come and talk 3D #genome, #epigenetics, #enhancers and #G4s at #FOG2026 at London ExCeL today and tomorrow! festivalofgenomics.com/london/poste... and some fresh stuff in there too!
RESEARCH COMMUNICATION: H3K4me3 amplifies transcription at intergenic active regulatory elements
By Yu et. al and Bluma Lesch
➡️ https://genesdev.cshlp.org/content/39/21-22/1290.full
Bluma Lesch
@haomingyu.bsky.social
#transcription #epigenetics #histones #histonePTMs #methylation #enhancers
Such a cool story- great to see it finally out in the wild #enhancers #geneRegulation
Euchromatin hopping explains how some enhancers seem to initiate the formation of active regulatory landscapes, and why some/many enhancer deletions don't affect transcription quantity; there are driver and passenger enhancers.
#chromatin #enhancers #generegulation
Just read this paper by @tesarlab.bsky.social lab and collaborators on the role of SOX6 in oligodendrocytes and found it highly insightful and stimulating. www.cell.com/cell/fulltex... #development #transcription #enhancers
Excited to share our new study in @cp-devcell.bsky.social dissecting how the brain-associated transcription factor OTX2 drives anteriorization of the mammalian gut by enhancer remodeling using stem cell-based models. #development #enhancers #patterning #stemcells
www.cell.com/developmenta...
Parallel paths to enhancer activation during the maternal-to-zygotic transition in zebrafish. Two distinct classes of enhancers emerge as the embryo transitions from maternal to zygotic control. H3K4me1-marked enhancers (red) are established through NPS pioneer factor activity and arise in hypermethylated regions. In contrast, H3K4me2-marked enhancers (blue) originate from mostly hypomethylated regions and become active independently of NPS. These enhancers are also associated with H2A.Z incorporation. Together, they represent parallel regulatory trajectories converging on zygotic genome activation (ZGA). Developmental stages and time in hours post-fertilization (hpf) are indicated above and below.
During #development, maternally derived factors activate the embryo's genome. @vaquerizaslab.bsky.social explores a @plosbiology.org study that identifies H3K4me2-marked #enhancers in #zebrafish that function independently & mirror the gamete state 🧪 Paper: plos.io/3IFqYMc Primer: plos.io/44sbKTw
Parallel paths to enhancer activation during the maternal-to-zygotic transition in zebrafish. Two distinct classes of enhancers emerge as the embryo transitions from maternal to zygotic control. H3K4me1-marked enhancers (red) are established through NPS pioneer factor activity and arise in hypermethylated regions. In contrast, H3K4me2-marked enhancers (blue) originate from mostly hypomethylated regions and become active independently of NPS. These enhancers are also associated with H2A.Z incorporation. Together, they represent parallel regulatory trajectories converging on zygotic genome activation (ZGA). Developmental stages and time in hours post-fertilization (hpf) are indicated above and below.
During #development, maternally derived factors activate the embryo's genome. @vaquerizaslab.bsky.social explores a @plosbiology.org study that identifies H3K4me2-marked #enhancers in #zebrafish that function independently & mirror the gamete state 🧪 Paper: plos.io/3IFqYMc Primer: plos.io/44sbKTw
Parallel paths to enhancer activation during the maternal-to-zygotic transition in zebrafish. Two distinct classes of enhancers emerge as the embryo transitions from maternal to zygotic control. H3K4me1-marked enhancers (red) are established through NPS pioneer factor activity and arise in hypermethylated regions. In contrast, H3K4me2-marked enhancers (blue) originate from mostly hypomethylated regions and become active independently of NPS. These enhancers are also associated with H2A.Z incorporation. Together, they represent parallel regulatory trajectories converging on zygotic genome activation (ZGA). Developmental stages and time in hours post-fertilization (hpf) are indicated above and below.
During #development, maternally derived factors activate the embryo's genome. @vaquerizaslab.bsky.social explores a @plosbiology.org study that identifies H3K4me2-marked #enhancers in #zebrafish that function independently & mirror the gamete state 🧪 Paper: plos.io/3IFqYMc Primer: plos.io/44sbKTw
Parallel enhancer activation pathways during the maternal-to-zygotic transition. Enhancers that lack evidence for gamete activity are hypermethylated, rely on NPS-pioneering, and are marked with H3K4me1 but not H3K4me2 in the embryo. Enhancers that have evidence for gamete activity are hypomethylated, recruit H2A.Z-containing placeholder nucleosomes rather than relying on NPS pioneering, and are marked with H3K4me2.
The maternal-to-zygotic transition in #zebrafish is activated by TFs that open #chromatin via enhancers lacking H3K4me2. @mtleelab.bsky.social &co identify a parallel pathway that is activated by #enhancers that bear H3K4me2, showing that both act in combination @plosbiology.org 🧪 plos.io/3IFqYMc
Parallel enhancer activation pathways during the maternal-to-zygotic transition. Enhancers that lack evidence for gamete activity are hypermethylated, rely on NPS-pioneering, and are marked with H3K4me1 but not H3K4me2 in the embryo. Enhancers that have evidence for gamete activity are hypomethylated, recruit H2A.Z-containing placeholder nucleosomes rather than relying on NPS pioneering, and are marked with H3K4me2.
The maternal-to-zygotic transition in #zebrafish is activated by TFs that open #chromatin via enhancers lacking H3K4me2. @mtleelab.bsky.social &co identify a parallel pathway that is activated by #enhancers that bear H3K4me2, showing that both act in combination @plosbiology.org 🧪 plos.io/3IFqYMc
Parallel enhancer activation pathways during the maternal-to-zygotic transition. Enhancers that lack evidence for gamete activity are hypermethylated, rely on NPS-pioneering, and are marked with H3K4me1 but not H3K4me2 in the embryo. Enhancers that have evidence for gamete activity are hypomethylated, recruit H2A.Z-containing placeholder nucleosomes rather than relying on NPS pioneering, and are marked with H3K4me2.
The maternal-to-zygotic transition in #zebrafish is activated by TFs that open #chromatin via enhancers lacking H3K4me2. @mtleelab.bsky.social &co identify a parallel pathway that is activated by #enhancers that bear H3K4me2, showing that both act in combination @plosbiology.org 🧪 plos.io/3IFqYMc
2/3
In collaboration with @radaiglesiaslab.bsky.social, we applied and expanded POSTRE, a bioinformatics tool that rapidly classifies structural variants in the pituitary, distinguishing pathogenic duplications from benign ones in diagnostic settings.
#SVs #GPR101 #enhancers #TADs #TADopathies
The multilayered actions of #enhancers and associating regulatory DNAs, such as facilitators and Range Extenders, dynamically modulate the clustering of transcription machineries to flexibly control the dynamics of #geneexpression during development
www.sciencedirect.com/science/arti...
Sad to not be there this time, but say hi 👋 to the awesome @nicola-carruthers.bsky.social who's presenting her work! #enhancers #chromatin #EMBOenhanceropathies 🇩🇰
How does (local #DNA) structure affect (3D #genome) structure? Can mutating G4s abolish #enhancers key for #blood function?
In the second part of our explorations of #G4s in gene regulation, we show how abolishing G-quadruplex structures in the genome disrupts enhancers. 1/9
doi.org/10.1186/s130...
Fresh, right out of the oven 🔥 ...
New Preprint Alert 🧬
I am excited to share our latest work, now available on bioRxiv:
Thanks to an amazing team and collaborators who made this work possible!
#Epigenetics #FunctionalGenomics #Enhancers #CRISPR #iPSC #bioRxiv #Preprint #GeneRegulation
Last week to apply! #PhD #Chromatin #StemCells #ProteinStructure #Enhancers #Transcription #LineageCommitment
Epigenetics Update - Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex bit.ly/4jlPqiC
Trygve E. Bakken (Allen Institute for Brain Science)
#Epigenetics #Chromatin #Enhancers
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Gain deeper insights into gene regulation; epigenometech.com
Fantastic talk from @nicola-carruthers.bsky.social at today's @mcb-sheffield.bsky.social postdoc talk series! #CBP #RNAs #enhancers and everything in between- smashed it! 👏
3. G4s and Z-DNA are enriched at #promoters and #enhancers, as well as at origins of replication.
4. #Repetitive sequences carry more non-B DNA motifs than non-repetitive sequences.
Just out on bioRxiv!
Our latest study uncovers a widespread class of dual-function elements: Exonic Enhancers (EEs) — coding sequences that also act as cis-regulatory enhancers.
Check it out 👉 www.biorxiv.org/content/10.1...
#Genomics #GeneRegulation #Enhancers #ExonEnhancers
/ rant on:
Abbreviating cis-regulatory elements as *CRE* is a terrible abbreviation in a field that uses *Cre* recombinase as major lineage trace tool. 🐭🐟🧬
/ rant off
#devbio #MakeMoreTransgenics #Crelox #enhancers
Epigenetics Review - Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies go.nature.com/4bnycyZ
#Epigenetics #Enhancers #Reviews
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Empower your research with high-res epigenetic insights at epigenome.us
Do you have an exciting story about #enhancers or #enhanceropathies?. Then submit your abstract to the @embo.org workshop on "Enhancer mechanics and Enhanceropathies" in Denmark before is too late: the deadline for abstract submissions is in two weeks (March 17th)!
meetings.embo.org/event/25-enh...
