Tamer Ali

Long noncoding RNA-dependent control of Myc transcriptional bursting Li et al. show that the chromatin-associated long noncoding RNA Pvt1 is a negative regulator of Myc transcription by increasing local RNA concentration and limiting bursting from the Myc promoter. This mechanism serves to restrain Myc levels and restrict its proliferative and oncogenic activities.

Long noncoding RNA-dependent control of Myc transcriptional bursting

Happy to share our latest publication, in which we show that the arrangement of nucleosomes around CTCF sites contributes to higher-order organisation of chromatin into TADs: www.embopress.org/doi/full/10....

Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

awesome new work by my @gladstoneinst.bsky.social and @ucsanfrancisco.bsky.social colleagues incl @vram142.bsky.social on how chromatin remodelers affect mesoscale chromatin organization www.science.org/doi/10.1126/...

Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap Nature Protocols, Published online: 30 September 2025; doi:10.1038/s41596-025-01248-3This protocol for imaging-based highly multiplexed in situ profiling of the spatial transcriptome uses three methods: antibody-based protein comapping with STARmap PLUS, ribosome-bound mRNA mapping with RIBOmap and spatiotemporal transcriptome mapping with TEMPOmap.

New Article! Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap

Megabase-scale human genome rearrangement with programmable bridge recombinases Bridge recombinases are naturally occurring RNA-guided DNA recombinases that we previously demonstrated can programmably insert, excise, and invert DNA in vitro and in Escherichia coli. In this study,...

No loxP. No fixed sites. Bridge recombinases work like CRISPR—powered only by bRNA.

www.science.org/doi/10.1126/...

Joint profiling of chromatin accessibility and CRISPR edits via double-stranded DNA deaminases Nature Methods - Targeted deaminase-accessible chromatin sequencing (TDAC-seq) measures chromatin accessibility across long chromatin fibers at targeted loci using double-stranded DNA cytidine...

Joint profiling of chromatin accessibility and CRISPR edits via double-stranded DNA deaminases
www.nature.com/articles/s4...

A rapid, simple, and economical method for the isolation of ribosomes and translational machinery for structural and functional studies - Nature Communications Here, the authors present a method to rapidly isolate actively translating ribosomes in a time- and cost-effective manner using poly-lysine. The method is compatible with a wide variety of cell and ti...

We are looking for a new postdoctoral fellow interested in the further development of our RAPPL technology and studies of translational complexes. Preference will be given to candidates with either structural biology or ribosome profiling backgrounds.

www.nature.com/articles/s41...

ShortStop: a machine learning framework for microprotein discovery - BMC Methods The human genome contains over 3 million small open reading frames (smORFs, ≤ 150 codons). Ribosome profiling and proteogenomics transformed our understanding of these sequences by showing that t...

New at BMC Methods: ShortStop: a machine learning framework for microprotein discovery
bmcmethods.biomedcentral.com/articles/10....

Extrachromosomal DNA biogenesis is dependent on DNA looping and religation by YY1-Lig3-PARylation complex Qin et al. show that Lig3 PARylation promotes ecDNA formation, requiring YY1-mediated DNA looping. The Lig3-YY1 complex establishes a PARylation-dependent acidic microenvironment, inducing unstable Z-DNA transition states, which are religated by Lig3, ultimately mediating the biogenesis of ecDNA.

Online Now: Extrachromosomal DNA biogenesis is dependent on DNA looping and religation by YY1-Lig3-PARylation complex Online now:

This highly innovative in-vivo cell-tracking tool uses nanobody-based PET imaging to track unmodified transplanted cells in immunocompetent mice and avoids bulky antibodies or genetic engineering.
buff.ly/W2layjv

This is why Israel refuses to allow the international press access to Gaza.
Because images like this make it impossible to deny that this is genocide.

Temporal and spatial omics technologies for 4D profiling Nature Methods - This Perspective explores advances and future directions in spatiotemporal omics methods for four-dimensional profiling.

Nature Method: Temporal and spatial omics technologies for 4D profiling
www.nature.com/articles/s4...

Further evidence that the #gastruloid system models the natural embryo from this spatiotemporal map of mouse #gastrulation
www.cell.com/cell-reports...
important as it provides a context for the, some times surprising, findings that the model is providing.

Starvation in Gaza is destroying communities – and will leave generational scars Health and societal ramifications of extreme hunger will reverberate long after the war is over

www.theguardian.com/world/2025/j...

Not even a single rape case. You people never stop fake narrative. Just want to justify your terror.

Everyone who fights to free his land is a hero and his act is courageous.

Go check you twitter tweets after the courageous attack on October 7th.
You said “we have the write to defend ourselves”. Since then I unfollowed your account. This not a lie. Please. Go check it out.

You were supporting this horror initially.

In vivo prime editing rescues alternating hemiplegia of childhood in mice Prime editing and base editing in mouse models and human cells effectively correct mutations in a gene that causes a childhood neurodevelopmental disorder called alternating hemiplegia of childhood. In vivo prime editing in the brain results in significant improvements in neurological symptoms and lifespan, highlighting a potential one-time gene therapy approach for the disorder.

Now online! In vivo prime editing rescues alternating hemiplegia of childhood in mice

In vivo prime editing rescues alternating hemiplegia of childhood in mice Prime editing and base editing in mouse models and human cells effectively correct mutations in a gene that causes a childhood neurodevelopmental disorder called alternating hemiplegia of childhood. I...

One-shot prime genome editing ("CRISPR 3.0") of the brain in vivo corrected AHC, a rare genetic disorder, in the mouse model. Another big step forward in the genome editing field.
www.cell.com/cell/fulltex...

GitHub - vierstralab/hotspot3: A chromatin accessibility peak caller with an adaptive background model A chromatin accessibility peak caller with an adaptive background model - vierstralab/hotspot3

We have created a new DNase I- & ATAC-seq peak caller that uses an adaptive background model that controls for copy number variation & aneuploidy. It performs a per-nucleotide test (+FDR correction) and is very fast. Please try it out and give us feedback!

github.com/vierstralab/...

New online! Non-retroviral RNA viruses in eukaryotic genomes

Structural variants in the 3D genome as drivers of disease - Nature Reviews Genetics Disruption of the 3D genome caused by structural variation contributes to developmental disorders and cancer. The authors review the causes and molecular and clinical consequences of position effects ...

🚀 Thrilled to share our new review on how structural variants reshape 3D genome architecture and cause disease! 🧬🔀
Out now in Nature Reviews Genetics: www.nature.com/articles/s41...
#3D-Genome #StructuralVariants #uksh

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging @cellcellpress.bsky.social @lgmartelotto.bsky.social @hoheyn.bsky.social
www.cell.com/cell/fulltex...

Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain In Drosophila, tethering elements are DNA regulatory regions that facilitate long-range interactions between enhancers and promoters as well as between the promoters of distant paralogous genes. Hu et al. demonstrate that the Vostok protein binds to these elements in the larval brain and is essential for the correct expression of associated genes.

Vostok: A looping factor for the organization of the regulatory genome in the Drosophila brain

Collaborative science is just so much fun! From our brilliant collaboration with Liz Robertson from @dunnschool.bsky.social; embryology, single cell omics and computational biology deliver new insights into the intricacies of blood and endothelial development. www.sciencedirect.com/science/arti...

Molecular basis of positional memory in limb regeneration - Nature A molecular analysis of axolotl limb regeneration has identified a positive genetic circuit that maintains posterior cell identity and can be used to reprogramme anterior cells into posterior cells.

Nature research paper: Molecular basis of positional memory in limb regeneration

https://go.nature.com/44OtQj3

Here we study the origin of the cardiac cell lineages in the mouse embryo. Separate but coordinated lineages independently specified at gastrulation generate the myocardium and endocardium. Credits: Miquel Sendra & coll: Jorge Dominguez, K. McDole and L. Guinard
authors.elsevier.com/sd/article/S...

1/10 Today in @science.org in collaboration with
the Liu group we report the development of a laboratory-evolved CRISPR-associated transposase (evoCAST) that supports therapeutically relevant levels of RNA-programmable gene insertion in human cells. drive.google.com/file/d/1I-Ub...