Lightnews — Scholar-powered news

Reposted by Rob Beagrie

Jase Gehring @skyjase.bsky.social · 18d

don't release preprints without a Methods section
don't release preprints with a Supplementary Materials section
don't release preprints without data
don't release preprints without code

use preprint servers to share your science, not advertisements

6 16 65

Reposted by Rob Beagrie

Johannes Stein @jmstein.bsky.social · Aug 13

(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen!

Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org!
doi.org/10.1073/pnas...
👇🧵

2 21 65

Reposted by Rob Beagrie

Bluma Lesch @ambystoma22.bsky.social · Aug 20

New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...

H3K4me3 amplifies transcription at intergenic active regulatory elements

A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields

genesdev.cshlp.org

3 33 83

Rob Beagrie @rbeagrie.bsky.social · Aug 1

Most people I know are doing PE150 because it almost always ends up cheaper if you’re outsourcing. But I’d be interested to know how much fragment size affect mappability. Presumably the larger the fragment the better the chances of at least one end having a unique alignment?

1 2

Reposted by Rob Beagrie

Guillaume Andrey @guandrey.bsky.social · Jul 9

Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...

Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications

Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...

www.nature.com

3 36 74

Reposted by Rob Beagrie

Evgeny Kvon @evgenykvon.bsky.social · Jul 2

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Range extender mediates long-distance enhancer activity - Nature

The REX element is associated with long-range enhancer–promoter interactions.

www.nature.com

10 90 190

Reposted by Rob Beagrie

Maxim Greenberg @maxvcg.bsky.social · Jun 6

This is the type of transgender mouse research that would get its money stripped away in the US... (jk jk) www.nature.com/articles/s41...

Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature

Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.

www.nature.com

1 5 25

Reposted by Rob Beagrie

Molecular Systems Biology @molsystbiol.org · May 15

Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....

1 11 21

Reposted by Rob Beagrie

franmartinezgr.bsky.social @franmartinezgr.bsky.social · Apr 16

Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease #RareDisease #Genetics genomemedicine.biomedcentral.com/articles/10....

5 7

Reposted by Rob Beagrie

Jordan Meier @doc-jlmeier.bsky.social · Mar 30

My favorite science is the kind that makes you says, "Man, I wish I thought of that!" This is such a paper.

Mass action turns an eraser into a pen. HDACs are metabolite-dependent histone acyltransferases.

@dremilygoldberg.bsky.social @gburslem.bsky.social

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

Reversible histone deacetylase activity catalyzes lysine acylation - Nature Chemical Biology

Tsusaka et al. discover that histone deacetylases, which are well known to remove protein modifications, such as lysine acetylation and β-hydroxybutyrylation, can also reverse their chemical activity ...

www.nature.com

2 16 78

Reposted by Rob Beagrie

Jeff Spence @jeffspence.github.io · Mar 28

A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.

While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)

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

Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations

Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...

www.biorxiv.org

6 22 59

Rob Beagrie @rbeagrie.bsky.social · Mar 27

Delighted to have been able to help out with this project - congratulations Ali and the rest of the @drakesmith-lab.bsky.social - such a fascinating #genetics and #GeneRegulation story 🧪

drakesmith-lab.bsky.social @drakesmith-lab.bsky.social · Mar 24

Wonderful to see this out, a big effort led by Alexandra Preston and fun for the lab to do something new (and very very old); plus it’s only slightly iron-related! 😳😱😀 www.nature.com/articles/s41...

Ancient genomic linkage of α-globin and Nprl3 couples metabolism with erythropoiesis - Nature Communications

Nprl3 controls erythroblast metabolism and is upregulated by α -globin enhancers sited within its introns. This arrangement couples metabolic and developmental control during erythropoiesis and may ex...

www.nature.com

5

Reposted by Rob Beagrie

Connor Rogerson @doctorconnor.bsky.social · Mar 26

This is going to be such a disaster. Cis-women will be outed as trans for genetics they had no idea about. What then?

Sky News @news.sky.com · Mar 25

World Athletics to introduce mandatory sex testing for female competitions

World Athletics will introduce mandatory testing for anyone entering female competitions to verify their biological sex, insisting they are necessary to protect women's sport.

news.sky.com

1 1 3

Reposted by Rob Beagrie

Yvette Cendes @whereisyvette.bsky.social · Mar 16

Pet peeve: I hate how often ppl claim “all the researchers will just move to Europe/Canada!” You vastly under-estimate how little money there is there vs the USA- and unless that changes ASAP this loss is just going to decimate global science, full stop. 🧪🔭

70 630 2.9K

Reposted by Rob Beagrie

Michael Erard @michaelerard.bsky.social · Mar 15

I wrote up some thoughts on the idea of recruiting embattled American scientists to Europe. My main point: it would work best to keep the talent pipeline going, but not to salvage individual careers, especially mature ones. The barriers are many.

michaelerard.com/blog/a-few-t...

Michael Erard

would it work to recruit American scientists to Europe?

michaelerard.com

2 7

Reposted by Rob Beagrie

Nicky Whiffin @nickywhiffin.bsky.social · Mar 2

A few weeks ago, I had an incredibly emotional call with James Coney, a writer for the Sunday Times whose son Charlie was in the @genomicsengland.bsky.social 100k project and was recently diagnosed with ReNU syndrome. This beautiful article tells their story ❤️ www.thetimes.com/article/0bcc...

My son Charlie — and the breakthrough that changed our lives

James Coney and his wife, Sarah, struggled not knowing why their 12-year-old was born with a severe learning disability. In their darkest moments, they blamed themselves. Then, out of the blue, came a...

www.thetimes.com

5 41 110

Reposted by Rob Beagrie

Pedro Rocha @pedroprocha.bsky.social · Feb 26

Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development.

Loss of a single CTCF motif is sufficient to cause embryonic lethality.

www.sciencedirect.com/science/arti...

Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…

www.sciencedirect.com

8 40 130

Reposted by Rob Beagrie

STITCHES Medicine - the Best of Medical Research @medicine.stitches.today · Feb 21

Prenatal DNA screening successfully predicts preeclampsia risk early in pregnancy, identifying tissue dysfunction months before onset.

by Adil M, Kolarova TR (...) Shree R et 15 al. in Nat Med #MedSky

📖 read the article:

Preeclampsia risk prediction from prenatal cell-free DNA screening - Nature Medicine

Using 1,854 routinely collected clinical samples from early in pregnancy, with validation in an external cohort, low-coverage cfDNA sequence data identified distinctive features among those who developed preeclampsia.

www.nature.com

5 19

Reposted by Rob Beagrie

Sarah Marzi @sj-marzi.bsky.social · Feb 12

📢 Our lab is looking for a bioinformatics postdoc. We have lots of exciting projects to work on, including single cell (epi-)genomics, microglia xenotransplantations and nanopore long reads splicing analysis. Look out for the official advert next week and get in touch in the meantime 🧬🧠

The Marzi Lab in epigenetics band t-shirts

2 17 27

Reposted by Rob Beagrie

Hannah Long @hannahlong.bsky.social · Feb 9

Reminder of an exciting conference 'Hidden Cell, Dark Genome', Edinburgh 3-4th April 2025!

Sessions:
• Regulatory functions of the dark genome
• Uncharted proteins and RNA complexity
• Cellular diversity
• Atomic structures at the cellular scale

Early bird and registration deadline: 28th February!

1 13 22

Reposted by Rob Beagrie

Science Magazine @science.org · Feb 11

When asked to draw a scientist, school-age kids in the United States are increasingly sketching women, according to a study from 2018.

Read more on #WomenInScienceDay: https://scim.ag/4hOUuvx

SCIENCESHOTS What does a scientist look like? Children are drawing women more than ever before

10 180 720

Reposted by Rob Beagrie

WHO @who.int · Feb 11

Today is International Day of Women & Girls in Science.

Marie Curie, the first woman to win a Nobel Prize. Her contributions have left an indelible mark on the world of science & health & continue to inspire generations of scientists & innovators. 🔬 #WomenInScience #WomenInSTEM

Nothing in life is to be feared, it is only to be understood. Marie Curie, Physicist and chemist.

57 1.9K 4.8K

Rob Beagrie @rbeagrie.bsky.social · Feb 10

Anyone else worried about what might happen if funding gets pulled for the Gene Expression Omnibus? Is everything mirrored at EBI or only some of it? #genomics #bioinformatics

2

Reposted by Rob Beagrie

Dan Jagger @auditorynerves.bsky.social · Feb 7

Prenatal stress effects on the placenta.

Maternal stress is a critical factor in the long-term health of offspring. A recent study (below) profiled the effects of prenatal stress on DNA methylation + gene expression in rat placenta & fetal brain.
🧪🧠🐀 #neuroskyence
www.nature.com/articles/s41...

Prenatal stress effects on the placenta - Nature Neuroscience

Nature Neuroscience - Prenatal stress effects on the placenta

www.nature.com

3 17 110

Reposted by Rob Beagrie

Robin Andersson @randersson.bsky.social · Feb 6

Job alert!

We are hiring a postdoc or PhD student focusing on
* developing computational methods to resolve gene regulation in single cells
* investigating the mechanisms and cell-type specific effects of genetic variants

PhD student: bsky.app/profile/jobr...

Postdoc: bsky.app/profile/jobr...

jobRxiv @jobrxiv.org · Feb 6

PhD student – Computational modeling of gene regulation in single cells #ScienceJobs #AcademicSky jobrxiv.org/job/univ...

PhD student - Computational modeling of gene regulation in single cells

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org

7 12