Ioquat
@loquat.bsky.social
Fascinated by biology. Interested in transposons.
Reposted by Ioquat
For obvious reasons, I've become fascinated with retrotransposons. So we ( @alexwhiteley.bsky.social and I) wrote an article now out in Neuron @cellpress.bsky.social on how we think retrotransposons influence brain function and health! kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
October 20, 2025 at 8:00 PM
For obvious reasons, I've become fascinated with retrotransposons. So we ( @alexwhiteley.bsky.social and I) wrote an article now out in Neuron @cellpress.bsky.social on how we think retrotransposons influence brain function and health! kwnsfk27.r.eu-west-1.awstrack.me/L0/https:%2F...
Reposted by Ioquat
Look at this gorgeous chonk of a baby. Look at his lil face. We are treating his life-threatening ultra-rare genetic condition with super cool science. With a gene editing tool that we stole from bacteria! Just in case you also needed a reminder that humanity can still do some pretty awesome stuff.
A promising genetic treatment tailor-made for a baby born with a rare disorder
For the first time, doctors have created a customized treatment using the revolutionary gene-editing technique known as CRISPR to treat a baby with a rare, life-threatening genetic disorder.
www.npr.org
May 16, 2025 at 3:34 AM
Look at this gorgeous chonk of a baby. Look at his lil face. We are treating his life-threatening ultra-rare genetic condition with super cool science. With a gene editing tool that we stole from bacteria! Just in case you also needed a reminder that humanity can still do some pretty awesome stuff.
Reposted by Ioquat
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Massively parallel jumping assay decodes Alu retrotransposition activity - Nature Communications
Here, the authors develop a high-throughput assay to measure the jumping potential of thousands of transposons in parallel.
www.nature.com
May 9, 2025 at 3:50 AM
Massively parallel jumping assay (MPJA) enables to test the jumping potential of thousands of transposons. Analysis of >160,000 Alu haplotypes identified transposition-asssociated domains. Amazing work by Navneet Matharu, Jingjing Zhao, Martin Kircher and many others.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ioquat
💥🥳 At long last, our latest paper is out!
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS
Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound
of TE-derived sequences repurposed for organismal function. ...
www.pnas.org
April 30, 2025 at 10:45 AM
💥🥳 At long last, our latest paper is out!
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Gag proteins of endogenous retroviruses are required for zebrafish development
www.pnas.org/doi/10.1073/...
Led heroically by Sylvia Chang & @jonowells.bsky.social
A study which has changed the way I think of #transposons! No less! 🧵 1/n
Reposted by Ioquat
Online now! The Berchowitz lab found that two retrotransposon-derived proteins, PNMA1 and PNMA4, support mammalian fertility in both sexes and become increasingly important during aging. (rdcu.be/eiT3z)
doi.org/10.1038/s435...
doi.org/10.1038/s435...
The retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity
Nature Aging - PNMA-family genes are gag-like elements of ancient retrotransposon origin whose roles in mammalian genomes is incompletely understood. Wood et al. found that two...
rdcu.be
April 23, 2025 at 7:51 AM
Online now! The Berchowitz lab found that two retrotransposon-derived proteins, PNMA1 and PNMA4, support mammalian fertility in both sexes and become increasingly important during aging. (rdcu.be/eiT3z)
doi.org/10.1038/s435...
doi.org/10.1038/s435...
Reposted by Ioquat
FYI: New online! Reactivation of retrotransposable elements is associated with environmental stress and ageing
Reactivation of retrotransposable elements is associated with environmental stress and ageing
Nature Reviews Genetics, Published online: 02 April 2025; doi:10.1038/s41576-025-00829-yIn this Review, Della Valle et al. discuss the role of retrotransposable elements (RTEs) in the onset and progression of ageing and ageing-related disease, including evidence that environmental stressors act through RTEs to shift the trajectory towards unhealthy ageing.
www.nature.com
April 23, 2025 at 2:03 PM
FYI: New online! Reactivation of retrotransposable elements is associated with environmental stress and ageing
Reposted by Ioquat
STITCHR enables scarless, CRISPR-guided integration using retrotransposons—elegant in vitro, Cas9-dependent, and promising for non-dividing cells.
But:
– Needs fusion proteins 🧬
– Delivery not yet in vivo 🚫
– Still early for therapeutic use ⏳
Cool tech, but not plug-and-play just yet.
But:
– Needs fusion proteins 🧬
– Delivery not yet in vivo 🚫
– Still early for therapeutic use ⏳
Cool tech, but not plug-and-play just yet.
So excited to share our new paper out today in @nature.com. We repurposed R2 retrotransposons to create STITCHR, a tool that can make virtually any kind of edit in mammalian genomes including the scarless multi-kilobase scale insertions 🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reprogramming site-specific retrotransposon activity to new DNA sites - Nature
A study of retrotransposon activity repurposes a retroelement called R2Tocc to create a programmable system called STITCHR that enables diverse genome edits including efficient, scarless large pa...
www.nature.com
April 10, 2025 at 6:30 PM
STITCHR enables scarless, CRISPR-guided integration using retrotransposons—elegant in vitro, Cas9-dependent, and promising for non-dividing cells.
But:
– Needs fusion proteins 🧬
– Delivery not yet in vivo 🚫
– Still early for therapeutic use ⏳
Cool tech, but not plug-and-play just yet.
But:
– Needs fusion proteins 🧬
– Delivery not yet in vivo 🚫
– Still early for therapeutic use ⏳
Cool tech, but not plug-and-play just yet.
Reposted by Ioquat
Why NIH/NIGMS funding of basic research matters with our latest work now out in @cp-cellreports.bsky.social sky.social. We solved a >30-year-old mystery of what transcription factor drives the Flamenco piRNA cluster required for female Drosophila fertility. /1
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Traffic Jam activates the Flamenco piRNA cluster locus and the Piwi pathway to ensure transposon silencing and Drosophila fertility
Rivera et al. discover Drosophila Flamenco piRNA cluster enhancers bound and activated
by the Traffic Jam transcription factor. Traffic Jam also binds many follicle cell
genes including activating mul...
www.cell.com
April 11, 2025 at 4:38 PM
Why NIH/NIGMS funding of basic research matters with our latest work now out in @cp-cellreports.bsky.social sky.social. We solved a >30-year-old mystery of what transcription factor drives the Flamenco piRNA cluster required for female Drosophila fertility. /1
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Ioquat
Human-specific transposable elements shaped the evolution of craniofacial development through regulation of neural crest migration https://www.biorxiv.org/content/10.1101/2025.04.04.647334v1
April 6, 2025 at 8:30 AM
Human-specific transposable elements shaped the evolution of craniofacial development through regulation of neural crest migration https://www.biorxiv.org/content/10.1101/2025.04.04.647334v1
Reposted by Ioquat
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
March 17, 2025 at 11:56 AM
1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯
Our new study reveals how retrotransposons invade the germline directly from somatic cells.
www.biorxiv.org/content/10.1...
A short thread 🧵👇
Reposted by Ioquat
THIS IS INCREDIBLE! Cohen Children’s Medical Center has confirmed that it has successfully ELIMINATED sickle cell disease from Sebastien Beauzile, using the groundbreaking genetic treatment Lyfgenia. He has made HISTORY by becoming the FIRST in New York to be CURED of sickle cell anemia! 🧪🧵⬇️
March 15, 2025 at 4:00 PM
THIS IS INCREDIBLE! Cohen Children’s Medical Center has confirmed that it has successfully ELIMINATED sickle cell disease from Sebastien Beauzile, using the groundbreaking genetic treatment Lyfgenia. He has made HISTORY by becoming the FIRST in New York to be CURED of sickle cell anemia! 🧪🧵⬇️
Reposted by Ioquat
I am thrilled to share our story online at @cellpress.bsky.social . Big thanks to all authors: Zhiping, Bill, @lubanlab.bsky.social, Keith & bluesky-less!
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇
March 9, 2025 at 2:35 AM
I am thrilled to share our story online at @cellpress.bsky.social . Big thanks to all authors: Zhiping, Bill, @lubanlab.bsky.social, Keith & bluesky-less!
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇
authors.elsevier.com/c/1kjdaL7PXu...
How to tame a genome invader? It takes wild koalas 🐨🐨 to learn it.
#Retrovirus #koala #piRNA
More below 👇
Reposted by Ioquat
Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?
March 5, 2025 at 4:02 PM
Happy to share our manuscript on the in situ visualization of the copia retrotransposon in its final form today published in @cellcellpress.bsky.social www.cell.com/cell/fulltex.... What’s new?
Reposted by Ioquat
It's been a while because I've felt distracted lately with...*gestures at everything* but, I've gone and updated TE Hub @tehub.bsky.social with new tools, databases and TE lineages tehub.org #TEsky
TE Hub
tehub.org
February 23, 2025 at 7:28 PM
It's been a while because I've felt distracted lately with...*gestures at everything* but, I've gone and updated TE Hub @tehub.bsky.social with new tools, databases and TE lineages tehub.org #TEsky
Reposted by Ioquat
Review: Diversity and consequences of structural variation in the human genome https://www.nature.com/articles/s41576-024-00808-9 (read free: https://rdcu.be/d64zN) 🧬🖥️🧪
January 21, 2025 at 10:22 PM
Review: Diversity and consequences of structural variation in the human genome https://www.nature.com/articles/s41576-024-00808-9 (read free: https://rdcu.be/d64zN) 🧬🖥️🧪
Reposted by Ioquat
Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵
A short thread to highlight some of our findings 🧵
January 20, 2025 at 8:29 PM
Very excited to share our paper on Gene and Transposable Element expression in mammalian preimplantation development, online today! www.cell.com/cell/fulltex...
A short thread to highlight some of our findings 🧵
A short thread to highlight some of our findings 🧵
Reposted by Ioquat
🚨 New pre-print from Team Jakobsson! LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development.
This work was led by @anitaada.bsky.social, @raquelgarza.bsky.social and @jakobssonlab.bsky.social from the Jakobsson Lab.
www.biorxiv.org/content/10.1...
This work was led by @anitaada.bsky.social, @raquelgarza.bsky.social and @jakobssonlab.bsky.social from the Jakobsson Lab.
www.biorxiv.org/content/10.1...
LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development
Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human development...
www.biorxiv.org
January 18, 2025 at 9:41 AM
🚨 New pre-print from Team Jakobsson! LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development.
This work was led by @anitaada.bsky.social, @raquelgarza.bsky.social and @jakobssonlab.bsky.social from the Jakobsson Lab.
www.biorxiv.org/content/10.1...
This work was led by @anitaada.bsky.social, @raquelgarza.bsky.social and @jakobssonlab.bsky.social from the Jakobsson Lab.
www.biorxiv.org/content/10.1...
Reposted by Ioquat
What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients
It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...
www.biorxiv.org
January 15, 2025 at 11:12 AM
What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Ioquat
Massively parallel characterization of transcriptional regulatory elements
www.nature.com/articles/s41...
@vagar.bsky.social @jshendure.bsky.social @nadavahituv.bsky.social
www.nature.com/articles/s41...
@vagar.bsky.social @jshendure.bsky.social @nadavahituv.bsky.social
Massively parallel characterization of transcriptional regulatory elements - Nature
Lentivirus-based reporter assays for 680,000 regulatory sequences from three cell lines coupled to machine-learning models lead to insights into the grammar of cis-regulatory elements.
www.nature.com
January 15, 2025 at 11:16 PM
Massively parallel characterization of transcriptional regulatory elements
www.nature.com/articles/s41...
@vagar.bsky.social @jshendure.bsky.social @nadavahituv.bsky.social
www.nature.com/articles/s41...
@vagar.bsky.social @jshendure.bsky.social @nadavahituv.bsky.social
Reposted by Ioquat
I ❤️ Diversity-Generating Retroelements! DGRs are abundant in prokaryotes and have been domesticated to create protein diversity via reverse transcription. This new structural study reveals a unique way of priming RT via precise positioning of the RNA around the enzyme.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
RNA control of reverse transcription in a diversity-generating retroelement - Nature
This study presents cryogenic electron microscopy structural analysis of a diversity-generating retroelement (DGR) reverse transcription system from Bordetella bacteriophage, with results indicating t...
www.nature.com
January 8, 2025 at 8:10 PM
I ❤️ Diversity-Generating Retroelements! DGRs are abundant in prokaryotes and have been domesticated to create protein diversity via reverse transcription. This new structural study reveals a unique way of priming RT via precise positioning of the RNA around the enzyme.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ioquat
Been looking forward to sharing this for a long time! Great collaboration with folks from across the world in which we identified a SVA_E insertion missed by standard clinical testing in individuals with Canavan disease, an early onset neurodegenerative disease.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
A Diagnostic Blind Spot: Deep intronic SVA_E Insertion identified as the most Common Pathogenic Variant Associated with Canavan Disease
Canavan disease (CD) is a neurodegenerative disorder caused by biallelic disease-causing variants in the ASPA gene. Here, we utilized long-read sequencing (LRS) to investigate eight individuals clinic...
www.medrxiv.org
December 23, 2024 at 2:49 AM
Been looking forward to sharing this for a long time! Great collaboration with folks from across the world in which we identified a SVA_E insertion missed by standard clinical testing in individuals with Canavan disease, an early onset neurodegenerative disease.
www.medrxiv.org/content/10.1...
www.medrxiv.org/content/10.1...
Reposted by Ioquat
We're thrilled to introduce LexicMap v0.5.0🎉
It's more accurate and slightly faster!
LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes!
We'll provide an index for ATB on AWS later.
github.com/shenwei356/L...
It's more accurate and slightly faster!
LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes!
We'll provide an index for ATB on AWS later.
github.com/shenwei356/L...
December 19, 2024 at 9:32 AM
We're thrilled to introduce LexicMap v0.5.0🎉
It's more accurate and slightly faster!
LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes!
We'll provide an index for ATB on AWS later.
github.com/shenwei356/L...
It's more accurate and slightly faster!
LexicMap has helped some scientists align genes and plasmids in AllTheBacteria and GenBank, each has > 2 million prokaryotic genomes!
We'll provide an index for ATB on AWS later.
github.com/shenwei356/L...
Reposted by Ioquat
The NIH funded R&D for 354 of the 356 drugs approved by the FDA from 2010-2019: jamanetwork.com/journals/jam...
In FY2022, NIH research funding generated $96.84 billion in economic activity—2.64 of economic activity for every $1 of funding (www.researchamerica.org/2023-oped-us...)
Impressive!
In FY2022, NIH research funding generated $96.84 billion in economic activity—2.64 of economic activity for every $1 of funding (www.researchamerica.org/2023-oped-us...)
Impressive!
December 17, 2024 at 12:05 AM
The NIH funded R&D for 354 of the 356 drugs approved by the FDA from 2010-2019: jamanetwork.com/journals/jam...
In FY2022, NIH research funding generated $96.84 billion in economic activity—2.64 of economic activity for every $1 of funding (www.researchamerica.org/2023-oped-us...)
Impressive!
In FY2022, NIH research funding generated $96.84 billion in economic activity—2.64 of economic activity for every $1 of funding (www.researchamerica.org/2023-oped-us...)
Impressive!
Reposted by Ioquat
I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪
Regulation of human interferon signaling by transposon exonization
Transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2.
www.cell.com
December 12, 2024 at 6:57 PM
I’m excited to share our latest study led by @giuliapasquesi.bsky.social out today in @cellpress.bsky.social , uncovering a new way transposons have been repurposed for human interferon signaling! Read on for a thread on cryptic splice variants, decoy receptors, and viruses (1/N) 👇🧵 #TESky 🧪
Reposted by Ioquat
Breaking news: In a major advance, the FDA on Friday approved two gene therapies that target sickle cell disease, one of which is the first commercially available treatment in the United States based on gene editing technology
FDA approves two sickle cell therapies, including the first CRISPR medicine
The therapies offer hope for a long-overlooked genetic illness that can cause excruciating pain and cut decades off people’s lives.
www.washingtonpost.com
December 8, 2023 at 4:57 PM
Breaking news: In a major advance, the FDA on Friday approved two gene therapies that target sickle cell disease, one of which is the first commercially available treatment in the United States based on gene editing technology