Ophir Shalem

Link to the original preprint below, hope to be able to share a heavily revised version very soon!
doi.org/10.1101/2024...

As we are sending back the revised version of our pooled prime editing gene tagging paper, I am happy to share a website for design of prime tagging libraries, including some images, all generated from a single pooled transduction and in situ sequencing.
primetagging.org

Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...

Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...

Congratulation @shiraweingarten.bsky.social! Beautiful work!

Excited to to see our collaboration with @gburslem.bsky.social published today! This is part of our ongoing long term goal of achieving scalable non-disruptive and direct imaging and perturbation of the endogenous proteome

Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses Sansbury and Serebrenik et al. use pooled gene tagging with in situ sequencing and high-throughput image analysis to generate a cell pool with endogenous HaloTag fusions. Hydrophobic targeting is then...

Check out our paper, now extensively revised and published in @cp-molcell.bsky.social! This has been a real tour de force led by Stephanie Sansbury and @ysereb.bsky.social and we are very excited about the findings and future potential of this approach
www.cell.com/molecular-ce...

NimbusImage

Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!

Documentation here!
docs.nimbusimage.com

Class I histone deacetylases catalyze lysine lactylation Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM ...

Two new preprints online today!

One with @dremilygoldberg.bsky.social on lysine lactylation
www.biorxiv.org/content/10.1...

Another with @taabaman.bsky.social on new peptide tools to study caspases www.biorxiv.org/content/10.1...

We have a postdoc position available for a very cool collaborative project! Synthetic chemistry expertise is a must!
Unfortunately due to the funding source, this position is only available to US citizens or permanent residents.

chemistryjobs.acs.org/job/postdoct...

Pooled optical screening bootcamp!

Huge congratulations to former lab postdoc @ysereb.bsky.social for starting his own independent lab! Make sure to follow him for exciting future science and check out his lab if you are looking for opportunities in the NJ/NY area!

Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain Harke et al. use sequential DNA-FISH to achieve single-allele resolution of the Sonic hedgehog (Shh) regulatory domain in the mouse forebrain. They show that multiple allelic configurations occur inde...

Our study with @ericjoyce.bsky.social led by Jailynn Harke is out. We show that allelic configurations at the Shh locus are predominately compact in the mouse forebrain, and that long range E-P interactions rely on transcription dependent and independent mechanisms. www.cell.com/molecular-ce...

Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics | Children’s Hospital of Philadelphia Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics in Philadelphia, Pennsylvania, United States. null at Children’s Hospital of Philadelphia

Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics

careers.chop.edu/us/en/event/...

Conserved autism-associated genes tune social feeding behavior in C. elegans - Nature Communications C. elegans aggregate in large clumps during feeding. Here, the authors find conserved autism-associated genes mediate distinct molecular and circuit signaling components that tune C. elegans feed...

New paper ALERT!! Mara Cowen, PhD discovered and defined how conserved autism-associated genes modify a 'social' behavior in C. elegans!! So proud of her work in the lab!
www.nature.com/articles/s41...

Fascinating work from Jongens and @erikaholzbaur.bsky.social labs showing that FMRP granules mark mitochondrial fission sites in axons and dendrites and serve as sites of local translation!

t.co/wXqtte3pqp

Activity-based selection for enhanced base editor mutational scanning Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease...

Happy Friday! New preprint to discuss, led by @ekaplan.bsky.social, entitled "Activity-based selection for enhanced base editor mutational scanning"

www.biorxiv.org/content/10.1...

A thread...

Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanis...

Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy

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

I would guess quite a bit, WPRE is used to stabilize long non terminated transcripts. It is used in lentivirus vectors to compensate for the fact that you cannot use polII termination sequences between the LTRs as this would terminate transcription during lenti production.

Given that lack of nuclear localization can have a profound impact on editing and gene perturbation efficiency, we suggest further investigation across both cultured and in-vivo postmitotic cell models.

Addition of a neuronal specific NLS (2X MeCP2) was able to rescue neuronal nuclear localization, expression level and improve activity when sgRNAs were delivered 2 weeks after differentiation

Other CRISPR enzymes we tested (nCas9 and Zim3) where also found mostly in the cytoplasm of neurons, but were not unstable in neurons

We found two neuronal specific issues: cytoplasmic mislocalization of CRISPR enzymes after differentiation and the destabilization of the KRAB domain outside the nucleus, which was specific to dCas9-KRAB (using the KOX1 domain).

This work was spearheaded by Gregory Cajka, brilliant graduate student in the lab, and Matthew Liu, extremely talented undergrad and post-bac research tech.

CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB-specific degradation The use of CRISPR-associated enzymes in iPSC-derived neurons for precise gene targeting and high-throughput gene perturbation screens offers great potential but presents unique challenges compared to ...

Happy to share our new paper where we explore why dCas9-KRAB protein levels drop so drastically after neuronal differentiation in WTC11 and KOL2.1J iPSC lines.

www.biorxiv.org/content/10.1...