Carlos Alfonso
@carlosalfonsog.bsky.social
RNA biologist. @embl.org
Reposted by Carlos Alfonso
Engineering chromatin to encode transcriptional immune memory in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.09.10.750729v1
September 14, 2026 at 2:02 PM
Engineering chromatin to encode transcriptional immune memory in Arabidopsis https://www.biorxiv.org/content/10.64898/2026.09.10.750729v1
Reposted by Carlos Alfonso
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
A noncontiguous code for RNA-guided DNA recognition at the origin of CRISPR-Cas
CRISPR-Cas provides RNA-mediated adaptive immunity, but how its first RNA-guided effector arose is unclear. In this study, we report the discovery of Viral Interference Programmable Repeat (VIPR) syst...
www.science.org
September 19, 2026 at 1:12 AM
Out now in Science: Two papers from our lab reveal VIPR, an RNA-guided DNA-targeting system in bacteriophages, providing clues to the origins of CRISPR
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Congrats to Peter Yoon, @kenjmloi.bsky.social @terryzzy.bsky.social, T.Docter & team
Reposted by Carlos Alfonso
Out now in @science.org
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues
Cell-state diversity drives tissue adaptability, repair, and disease resilience, but capturing this complexity is a challenge. Current approaches rely on transcriptional profiling and overlook organel...
www.science.org
September 18, 2026 at 10:37 AM
Out now in @science.org
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
Multi-organelle signatures map cell-state diversity and metabolic adaptation in tissues | Science www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely unknown. By using live imaging, we reveal that the ...
www.science.org
September 11, 2026 at 5:11 PM
I am rather delighted by this paper. So here’s a thread to tell you why, and why it matters. /1
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
☕ @gabrijelad.bsky.social & co report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the nuclear speckle periphery and undergo synchronous splicing at mitosis, thus contributing to their temporal regulation.
bit.ly/4xpanzZ
bit.ly/4xpanzZ
The periphery of nuclear speckles defines a spatially and temporally regulated compartment of long-lived intron-retained RNAs that resolves during mitosis - Nature Cell Biology
Biayna, Baranovskii and colleagues report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the periphery of nuclear speckles and undergo synchronou...
bit.ly
September 16, 2026 at 12:41 PM
☕ @gabrijelad.bsky.social & co report that intron-retained RNAs derived from cell cycle- and genome maintenance-related genes are pooled at the nuclear speckle periphery and undergo synchronous splicing at mitosis, thus contributing to their temporal regulation.
bit.ly/4xpanzZ
bit.ly/4xpanzZ
Reposted by Carlos Alfonso
Online Now: Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2 Online now:
Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2
Contreras-Pérez et al. address the puzzling role of cohesin on transcription by focusing on the mitotic exit, when cohesin firstly contact chromatin. Combining in vivo labeling, cell-cycle synchronization, and acute protein depletion, authors demonstrate the preservation of cohesin across mitosis and its fundamental role on transcription reactivation of tissue-related genes.
dlvr.it
September 16, 2026 at 7:14 PM
Online Now: Cohesin preservation across mitosis contributes to restart transcription via Cdk9-mediated activation of RNAPol2 Online now:
Reposted by Carlos Alfonso
Finally a more intuitaive way to learn pLDDT/pAE? 😎
sokrypton.github.io/protein_figh...
(Character idea from @hannes-stark.bsky.social & Alex Waldherr)
sokrypton.github.io/protein_figh...
(Character idea from @hannes-stark.bsky.social & Alex Waldherr)
September 14, 2026 at 1:47 PM
Finally a more intuitaive way to learn pLDDT/pAE? 😎
sokrypton.github.io/protein_figh...
(Character idea from @hannes-stark.bsky.social & Alex Waldherr)
sokrypton.github.io/protein_figh...
(Character idea from @hannes-stark.bsky.social & Alex Waldherr)
Reposted by Carlos Alfonso
Although your hair is much softer than steel, razors typically only last for a handful of shaves.
Previously, researchers attributed this to the sharp edge gradually wearing down after each use. But a 2020 study reveals a different process.
Learn more: https://scim.ag/3TvggxK #ScienceMagArchives
Previously, researchers attributed this to the sharp edge gradually wearing down after each use. But a 2020 study reveals a different process.
Learn more: https://scim.ag/3TvggxK #ScienceMagArchives
September 15, 2026 at 4:30 PM
Although your hair is much softer than steel, razors typically only last for a handful of shaves.
Previously, researchers attributed this to the sharp edge gradually wearing down after each use. But a 2020 study reveals a different process.
Learn more: https://scim.ag/3TvggxK #ScienceMagArchives
Previously, researchers attributed this to the sharp edge gradually wearing down after each use. But a 2020 study reveals a different process.
Learn more: https://scim.ag/3TvggxK #ScienceMagArchives
Reposted by Carlos Alfonso
Nature research paper: Predicting genome-wide functional constraints with GPN-Star
go.nature.com/4r3oObw
go.nature.com/4r3oObw
Predicting genome-wide functional constraints with GPN-Star - Nature
GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species.
go.nature.com
September 14, 2026 at 9:16 AM
Nature research paper: Predicting genome-wide functional constraints with GPN-Star
go.nature.com/4r3oObw
go.nature.com/4r3oObw
Reposted by Carlos Alfonso
your starter pack for Single Molecule Genomics!
Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
September 14, 2026 at 12:33 PM
your starter pack for Single Molecule Genomics!
Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
Why you should do it (or not) - How you should do it. Collective effort with @vram142.bsky.social @stirlingchurchman.bsky.social @naltemose.bsky.social A Stergachis M Stadler W Greenleaf @embl.org rdcu.be/PmzSEV529GRa
Reposted by Carlos Alfonso
New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices
PRC2–RNA interactions through the lens of bioinformatics pipeline choices
Nature Reviews Molecular Cell Biology, Published online: 11 September 2026; doi:10.1038/s41580-026-01028-1Four recent studies that have differently assessed PRC2–RNA interactions reveal key technical pitfalls underlying research in the field.
dlvr.it
September 11, 2026 at 12:38 PM
New Online! PRC2–RNA interactions through the lens of bioinformatics pipeline choices
Fantastic work!
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social
A few highlights below... 🧵👇
A few highlights below... 🧵👇
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
www.science.org
September 11, 2026 at 12:22 PM
Fantastic work!
Reposted by Carlos Alfonso
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social
A few highlights below... 🧵👇
A few highlights below... 🧵👇
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...
www.science.org
September 10, 2026 at 10:05 PM
🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social
A few highlights below... 🧵👇
A few highlights below... 🧵👇
Reposted by Carlos Alfonso
EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields.
The abstract deadline is the end of this week, so don’t miss out!
www.embl.org/about/info/c...
The abstract deadline is the end of this week, so don’t miss out!
www.embl.org/about/info/c...
September 10, 2026 at 9:03 AM
EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields.
The abstract deadline is the end of this week, so don’t miss out!
www.embl.org/about/info/c...
The abstract deadline is the end of this week, so don’t miss out!
www.embl.org/about/info/c...
Reposted by Carlos Alfonso
It was great working with students Kun and Ryan and
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
www.nature.com
September 8, 2026 at 10:06 AM
It was great working with students Kun and Ryan and
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...
September 7, 2026 at 9:38 AM
Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...
Reposted by Carlos Alfonso
Reposted by Carlos Alfonso
Dynamic control of cell state transitions during tissue morphogenesis
Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis
link.springer.com/article/10.1...
Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis
link.springer.com/article/10.1...
September 7, 2026 at 10:49 AM
Dynamic control of cell state transitions during tissue morphogenesis
Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis
link.springer.com/article/10.1...
Elias Barriga et al @eliasbarrigalab.bsky.social review how gene expression, chromatin modifications & microenvironmental biophysical factors contribute to robust coordination of morphogenesis
link.springer.com/article/10.1...
Reposted by Carlos Alfonso
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
September 3, 2026 at 8:09 PM
1/ out in @science.org! We found a new asymmetry in large-scale chromosome structure: sister chromatids are shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! A close collaboration w/ @gerlichlab.bsky.social , led by @flaviacorsi.bsky.social www.science.org/doi/10.1126/...
Reposted by Carlos Alfonso
☕Have you read this?
This Perspective highlights the use of current #proteomics technologies to understand reproductive #aging, improve #oocyte quality, and refine the outcomes of assisted reproductive technology (ART).
👉Read here: rdcu.be/BgbMZ6KYkesa
www.nature.com/articles/s41...
This Perspective highlights the use of current #proteomics technologies to understand reproductive #aging, improve #oocyte quality, and refine the outcomes of assisted reproductive technology (ART).
👉Read here: rdcu.be/BgbMZ6KYkesa
www.nature.com/articles/s41...
Proteomics-based insights into mammalian oocyte and early embryo development - Nature Cell Biology
This Perspective highlights the use of current proteomics technologies in defining stage-specific reprogramming events to understand reproductive ageing, improve oocyte quality, and refine the outcome...
www.nature.com
September 4, 2026 at 10:16 AM
☕Have you read this?
This Perspective highlights the use of current #proteomics technologies to understand reproductive #aging, improve #oocyte quality, and refine the outcomes of assisted reproductive technology (ART).
👉Read here: rdcu.be/BgbMZ6KYkesa
www.nature.com/articles/s41...
This Perspective highlights the use of current #proteomics technologies to understand reproductive #aging, improve #oocyte quality, and refine the outcomes of assisted reproductive technology (ART).
👉Read here: rdcu.be/BgbMZ6KYkesa
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Spatial chromatin architecture and accessibility co-profiling of mammalian tissues - Nature Methods
Spatial-ATAC-Hi-C enables the profiling of both chromatin accessibility and organization in a spatially resolved manner, as demonstrated on mouse brain and human glioblastoma and astrocytoma samples.
www.nature.com
September 3, 2026 at 8:41 PM
Spatial-ATAC-Hi-C enables profiling chromatin accessibility and spatial organization, as shown in mouse and human brain samples.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Carlos Alfonso
Reposted by Carlos Alfonso
Really fascinating talk today at #EMBLTranscript from Bienko lab! THE INTROSOMES!
Today’s session recurring question: do regulatory functions emerge from the act of transcription, or from the RNA product itself?
www.biorxiv.org/content/10.1...
Today’s session recurring question: do regulatory functions emerge from the act of transcription, or from the RNA product itself?
www.biorxiv.org/content/10.1...
Chromatin-associated intronic RNAs from long genes form introsomes that shape nuclear architecture in neuronal cells
Cell differentiation towards neurons is accompanied by widespread changes in three-dimensional (3D) genome organization and gene expression. Chromatin-associated RNAs have been proposed to be importan...
www.biorxiv.org
August 27, 2026 at 1:31 PM
Really fascinating talk today at #EMBLTranscript from Bienko lab! THE INTROSOMES!
Today’s session recurring question: do regulatory functions emerge from the act of transcription, or from the RNA product itself?
www.biorxiv.org/content/10.1...
Today’s session recurring question: do regulatory functions emerge from the act of transcription, or from the RNA product itself?
www.biorxiv.org/content/10.1...