Mitch Guttman

Molecular biologist interested in non-coding RNAs, nuclear organization, and gene regulation. Professor at Caltech

[Mitch Guttman @mitchguttman]

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in @NatureGenet describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.

https://t.co/0aINMj2MTu

[Nature Reviews Molecular Cell Biology @NatRevMCB]

New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices https://t.co/3ZF3yG0uun

[Yodai Takei @yodai_takei]

Happy to share the published version of our work on chromatin recording with LagTag! https://t.co/F0oEJ2K984

[Igor Ulitsky @IgorUlitsky]

One of the (well, >1) problems in the lncRNA field is that some of the lncRNAs are not real genes, i.e., do not represent a standalone locus that produces independent transcripts. Some cases are more 🤔 than others, e.g. lncDACH that Matt Bennet from @bakergroupcvs dove into 🧵

[Cai Lab @LongCai_Lab]

Quality of the data matters! at least for predicting glioma progression from a patient's initial biopsy before any progression has occurred. Excited to share our new pre-print, authored by Michal Polonsky, Jonathan Fox, Yunrui Lu and Sheel Shah. (1/7)

https://t.co/sXX4NyxPJW

[Jian Ma @jmuiuc]

Very excited to share our @ScienceMagazine paper on single-cell #3D #genome reorganization in #Alzheimer's disease.
We jointly measured gene expression and 3D genome architecture in individual human brain cells using #GAGEseq, then integrated these data w/ chromatin accessibility and spatial transcriptomics. We uncovered increased #compartment #mingling and distance-dependent rewiring of gene regulatory contacts in AD.
We also developed #Hicformer, a transformer-based model that integrates DNA sequence with 3D genome features to predict cell type-specific gene expression and prioritize candidate regulatory elements.
Huge kudos to co-first authors @zocean636 and @xinyuelu1999; and many thanks to Zhijun Duan @UW, Hansruedi Mathys @PittTweet, & David Bennett @rushalzheimers for the wonderful collaboration, as well as to all our co-authors. @CarnegieMellon @SCSatCMU @CMUCompBio #AlzheimersDisease #3DGenome #SingleCell #AI

https://t.co/G3yPdRMeym

[Yodai Takei @yodai_takei]

We are inviting applications for a Postdoctoral Fellow/Scientist I (Cell Engineering) to join our growing team at Biohub NY's Lab of Synthetic Spatial Omics and work together! @biohub

Please help spread the word🙏
https://t.co/cyBnLQ9fq5

[Jesse Engreitz @jengreitz]

An encyclopedia of enhancer-gene regulatory interactions — online today! https://t.co/LN4hCxDQ3M

Now with an improved model, expanded maps across 1400+ biosamples, larger validation CRISPR datasets, and guidance on applying the model

1/

[Jason Tan @yxjtan]

Does every enhancer work with every promoter?

With @jengreitz and @WJGreenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field.

A tour 🧵👇
https://t.co/iFzqPqKzhN

[Christine Mayr @Mayr_Christine]

Finally out in @Cellcellpress!
Proteins with long intrinsically disordered regions (IDRs) are prone to misfolding during protein synthesis.
This is prevented by mRNA 3′UTRs that act as mRNA-based IDR chaperones.
https://t.co/Pa4bWYhOMe

[Cai Lab @LongCai_Lab]

Thrilled to share our @CellCellPress paper with Shosei Yoshida & Ben Simons, led by @ChakraArun:
1) spatial geometry can resolve temporal dynamics
2) Sertoli cells run an intrinsic cycle coupled to germline, suggesting oscillator coupling as a principle of tissue organization

[Arun Chakravorty @ChakraArun]

Our paper is finally out in Cell! Years of work on one of biology's most beautiful tissue clocks, and finding an intrinsic oscillator that helps organize tissue dynamics. From my PhD work at @LongCai_Lab, with Shosei Yoshida and Ben Simons!
🧵(1/10)
https://t.co/fRFxG3rbo2

[Shinichi Nakagawa @smoltblue]

昨今御伽話みたいな論文が多い中、こういうしっかりとした仕事は本当に貴重

[Yongsheng Shi @YongshengShi]

🔥 A new study from our lab, led by star student @LVSoles, reveals splicing and 3′ processing aren't just coordinated — they're actively competing. Disrupting splicing (via U1, U2, U2AF, SF3b) unleashes thousands of intronic polyadenylation sites and triggers widespread premature transcription termination. 🧬 #RNAbiology #Transcription

The competition between splicing and 3′ processing shapes the human transcriptome
https://t.co/cJCbeYyH2V

[Igor Ulitsky @IgorUlitsky]

Now out in @NatureBiotech ! Do lncRNAs commonly bind 1000s of genomic sites? Maybe they do, but the dozens of studies that report genomic binding maps of lncRNAs are deeply flawed, with probes binding suprious DNA sites rather than RNA-bound ones. https://t.co/01NroM67dK

[Cell @CellCellPress]

Now online! D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response https://t.co/6hFxxuTWPo

[Igor Ulitsky @IgorUlitsky]

🆕 review with @jp_unfried out in @NatureSMB 🧐. Direct roles of lncRNAs in transcriptional activation. What do we understand about how lncRNAs lure Pol2 and set the stage for RNA production, and what do we still miss? https://t.co/iYJQ7Rbb9d

[Vijay Sankaran @bloodgenes]

🚨 Excited to share a new paper in Cell! Human genetics led us to HOTSCRAMBL, a HOXA-locus lncRNA that regulates 🩸#stemcell self-renewal and HOXA9 splicing, with implications for AML.

Amazing work by @lvchosen1 with @silvirouskin, @Armstrong_dfci, and many more!

https://t.co/Kralk3tmzg

[IdoAmitLab @IdoAmitLab]

Beautiful work @garber_manuel and co. Immunology is magical!
https://t.co/GmFx8aeiAz

[William J. Greenleaf @WJGreenleaf]

Our Human Multiomic Development Atlas paper is out in Nature today! A heart-felt "thank you" to all co-authors for their tireless work on this complex yet exciting project! Congrats all! https://t.co/iUiZz00KOt

[Jian Ma @jmuiuc]

We are sharing SkillFoundry, a framework for converting heterogeneous scientific resources into validated #agent #skills. In addition to benchmark improvements, we show utility on genomics workflows. Still early, but very encouraging. https://t.co/98YD27iHwj