Pedro Rocha

Superstar

🚨Reposts appreciated‼️If I had read this PhD offer five years ago, I wouldn’t have hesitated for a second to apply 😉
Passionate about gene regulation, chromatin, and developmental biology? Just contact @radaiglesiaslab.bsky.social at @ibbtec.bsky.social 🧬✨

#PhD #3DGenome

We recently reported that promoter competition can contribute to the robust insulation of gene regulatory domains (www.nature.com/articles/s41...).
We now offer a 4-years PhD contract to investigate whether the dirsuption of this regulatory mechanism can lead to congenital defects. More details 👇

Our latest paper has just been published in Cell!

doi.org/10.1016/j.ce...

We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.

Young KRAB-zinc finger gene clusters are highly dynamic incubators of ERV-driven genetic heterogeneity in mice - Nature Communications KRAB-zinc finger proteins repress retrotransposons and rapidly evolve in mammals. Here, the authors show that ERV insertions drive the emergence and diversification of new KZFP genes in mice, revealin...

Having a lot of fun at #EMBOMobileGenome 😃
Perfect timing for our paper from the lab of @toddmacfarlan.bsky.social to be out @natcomms.nature.com!!

…and I’m currently on the job market looking for a new scientific home!

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

In vitro approaches to study centriole and cilium function in early mouse embryogenesis Although centrioles and primary cilia play an essential role in early mammalian development, their specific function during the interval between their initial formation and the subsequent arrest of em...

Really excited to see this out in the open: www.life-science-alliance.org/content/9/1/...! @isabellavoelkl.bsky.social explored and compared different in vitro developmental model systems to study ciliogenesis.

Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!

dont know if it’s cheaper but when the labs are not shutdown, we use platinum taq from fisher. very robust even with quickly lysed tails. Not proofreading though

Federal worker here.

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....

Our collab w. V Goel, @nicholas-aboreden.bsky.social , J Jusuf, G Blobel, L Mirny, @irate-physicist.bsky.social out in @natsmb.nature.com www.nature.com/articles/s41...

Was co-submitted with @allanaschooley.bsky.social @jobdekker.bsky.social whose paper should also come out soon

Brief thread 👇

Enhancer-promoter compatibility is mediated by the promoter-proximal region Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

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

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?

Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...

If you’re interested in exploring the relationship between chromatin organization and epigenetic memory using chromatin tracing microscopy, my group is recruiting a talented PhD student 🥳

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...

Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.

In a new preprint, we share some clues about when, how, and why this happens!

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

Loop extrusion provides mechanical robustness to chromatin Chromosomes are complex biopolymers folded into dynamic loops via a loop extrusion process and may experience various mechanical forces in vivo . We develop a force-dependent model of chromatin loop e...

New preprint from the lab !! Loop extrusion may provide mechanical robustness to chromatin. Great work by Hossein Salari. @cnrs.fr @lbmcinlyon.bsky.social
www.biorxiv.org/content/10.1...

Morphogen and juxtacrine signalling dynamically integrate to specify cell fates with single-cell resolution Morphogen gradients guide tissue patterning but do not act in isolation. How they integrate with other signalling modalities, like juxtacrine signalling, and how these integrations influence pattern r...

Interested in morphogens and how they can robustly specifiy different cell types with single-cell resolution?
Check out this preprint combining experiments and modelling by our colleagues and partners in crime @ucl-cdb.bsky.social:
www.biorxiv.org/content/10.1...

🚨Please share! We are hiring a post-doc! 🪱 🐀
Job posting: www.training.nih.gov/jobs/pdf-gb-...
Lab Website: www.niddk.nih.gov/research-fun...
NIH Trainee info: www.training.nih.gov

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇

The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers DNA replication is molecularly asymmetric, due to distinct mechanisms for lagging and leading strand DNA synthesis. Whether chromatin assembly on newly replicated strands is also asymmetric remains un...

Some (+)ve news to lighten another heavy weekend: our latest preprint (c/o Mattiroli + Ramani labs) is up!
www.biorxiv.org/content/10.1...
A tour-de-force by 1st authors Bruna Eckhardt & @palindromephd.bsky.social, focusing on chromatin replication. RTs welcome; tweetorial in 3,2...(1/n)

Computational image analyst (m/f/d) The Max Planck Institute for Molecular Biomedicine in Münster, Germany, has an opening for a

My lab @mpi-muenster.bsky.social is looking for a computational biologist with a passion for imaging and spatial biology. A staff scientist position with long-term perspective! Apply and spread the word 🙏 jobs.mpi-muenster.mpg.de/jobposting/0...

In our latest preprinted work, Yajie and Kostas combine computational analysis with precision KO of single variant U1 snRNA genes in human iPSCs to find pronounced deregulation of both gene expression and splicing that seem to affect the cell cycle and the differentiation potency of stem cells. 1/n

Epigenetic relay: Polycomb-directed DNA methylation in mammalian development In mammals, repression of germline-specific gene expression is essential for preserving somatic cell identity and preventing disease. Germline gene silencing is often dependent on the presence of prom...

Very excited to share an excellent review from @teresa-urli.bsky.social, published one week before her PhD defense! We did a deep dive into the fascinating biology of the variant Polycomb complex, PRC1.6 (1/5) journals.plos.org/plosgenetics...

Figure 1 - Live imaging of endogenously tagged YAP-miRFP670, mScarlet-I-SOX2 and CDX2-eGFP during the first fate decision in preimplantation embryos. (A) A developmental timeline of trophectoderm (TE) and inner cell mass (ICM) specification. The first cell differentiation event, between the TE (green) and ICM (purple), initiates at the 16-cell stage, establishing distinct inner, ICM, and outer, TE, cell populations in the 32-cell stage embryo. Embryos in this study are imaged until the 32-cell stage. Days post-fertilization are denoted by embryonic day. (B) Sox2 and Cdx2 expression is regulated by YAP. In ICM cells, YAP is phosphorylated and retained in the cytoplasm, facilitating Sox2 expression. In TE cells, YAP is predominantly localized to the nucleus where it activates expression of Cdx2. (C) Time-lapse images of a representative embryo expressing YAP-miRFP670, mScarlet-I-SOX2 and H2B-miRFP670 from the 8-cell through the late 32-cell stage. A z-stack was acquired every 15 min for YAP and H2B channels, and every 30 min for the SOX2 channel. Maximum intensity projections (MIPs) are shown. Unit of time is hours. Scale bar: 10 µm. (D) Time-lapse images of a representative embryo expressing YAP-miRFP670, CDX2-eGFP and H2B-miRFP670 from the 8-cell stage through the late 32-cell stage. Scale bar: 10 µm.

Mathematical modelling of the first fate decision

This Research Highlight showcases the work from Maria Avdeeva, Madeleine Chalifoux, Bradley Joyce, Stanislav Y. Shvartsman, Eszter Posfai @eposfai.bsky.social :

journals.biologists.com/dev/article/...

Job add showing the lab logo and the following text: WHAT WE OFFER Fully-funded fellowships up to five years Opportunity to start your own research program or lead ongoing projects. Large, diverse and extraordinary scientific network at the NIH/Bethesda campus. Working at NIH offers the possibility of living in a diverse, liberal and vibrant city: Washington DC Or in a calm residential area with great schools and good affordable housing: Bethesda and Rockville. WHO YOU ARE You share our enthusiasm for epigenetics, gene regulation, nuclear organization and mouse development. You have PhD-experience in one or more of the following: mouse development, mouse genetics, epigenetics, or computational biology.

🚨🚨🚨 Please repost
We are looking for postdocs to join our lab at NIH.
Apply:
www.nichd.nih.gov/research/atNICHD/Investigators/rocha/apply
Learn more about training at NIH :
www.training.nih.gov/research-tra...

📢 New in @ImmunityCP: We have mapped the transcription factor “routes” that program two dendritic cell subsets opening paths for personalized #cancer #immunotherapy. Read it here: doi.org/10.1016/j.im...
Here is a summary of what we discovered 🧵:
Illustration by @azuravesta.bsky.social

Liver-specific loss of Atg9a perturbs lipid metabolism and hepatocyte integrity The autophagy-related protein ATG9A is integral to cellular autophagy and lipid mobilization, yet its importance in mammalian physiology remains underexplored. Using a liver-specific conditional At...

Excited to share the first paper from the lab! 🥳 The ATG9 and lipid droplets saga continues! Open source!

I'm really happy to announce that my two main postdoctoral works have been published in the same issue of Developmental Cell! First, the final form of the mouse cortical organoid protocol (tinyurl.com/bddfmx8n), which I recently presented at Development presents (tinyurl.com/36udcpme) and…

Enhancer remodeling by OTX2 directs specification and patterning of mammalian definitive endoderm Correct patterning of emerging tissues in the developing embryo is essential for the formation of functional organ systems. Using genetic tools for controlled protein depletion, Ee et al. identify the...

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...

We chose to forget that.