Pilar G Marchante
@pilargmarch.bsky.social
🧬 Bioinformatics PhD student
🔎 Transposable elements and miRNAs in development and disease
📌 @herassr.bsky.social lab in GENYO (Granada, Spain)
🔎 Transposable elements and miRNAs in development and disease
📌 @herassr.bsky.social lab in GENYO (Granada, Spain)
Reposted by Pilar G Marchante
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
November 15, 2025 at 5:23 PM
Thrilled to share our new review in Current Opinion in Genetics & Development on TE driven innovation in gene regulation🤘. I am honored to be part of this with two major TE aficionados @cedricfeschotte.bsky.social and @trono-lab.bsky.social
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
#TEsky #TEworldwide
authors.elsevier.com/c/1m6MC,LqAZ...
Reposted by Pilar G Marchante
Magnífica charla de @pilargmarch.bsky.social en Genyo contando nuestras investigaciones y futuros trabajos sobre la activación de la ruta del interferón en pacientes con el síndrome 22q11 y su relación con elementos móviles.
November 4, 2025 at 10:22 AM
Magnífica charla de @pilargmarch.bsky.social en Genyo contando nuestras investigaciones y futuros trabajos sobre la activación de la ruta del interferón en pacientes con el síndrome 22q11 y su relación con elementos móviles.
Reposted by Pilar G Marchante
📣 New preprint from the Jakobsson lab!
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
This protocol describes the workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). The protocol illustrates how to design gRNAs to targ...
www.biorxiv.org
October 29, 2025 at 8:24 AM
📣 New preprint from the Jakobsson lab!
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
We describe a detailed protocol to inhibit the expression of transposable elements in human pluripotent stem cells, developed thanks to @asapresearch.parkinsonsroadmap.org funding.
Special shoutout to @anitaada.bsky.social!
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...
Epigenetic lockdown of type I interferon sensing and signalling in human pluripotent cells.
The Human Silencing Hub (HUSH) complex safeguards genome integrity in human somatic cells by repressing transposable elements and regulating type I interferon (IFN-I) induction. In early development, ...
www.biorxiv.org
October 29, 2025 at 6:03 PM
How do pluripotent stem cells resist harmful interferon responses to safeguard development? Through total epigenetic lockdown of ligands, sensors and effectors of IFN-I. In our preprint, James Holt shares his PhD discoveries on the ground state of immune evasion 😊: www.biorxiv.org/cgi/content/...
Reposted by Pilar G Marchante
Reposted by Pilar G Marchante
I would usually write a summary but I will defer to the text this time and just express thanks for the interactions and experiences this work generated. Its been a gateway into a lot of fun science that we are still unpacking...
October 2, 2025 at 2:20 PM
I would usually write a summary but I will defer to the text this time and just express thanks for the interactions and experiences this work generated. Its been a gateway into a lot of fun science that we are still unpacking...
Reposted by Pilar G Marchante
#TEsky Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes doi.org/10.1002/advs...
Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes
By integrating phylogenetic relationships derived from nuclear DNA with population genetic analyses across ten pufferfish species, the genetic differentiation mechanisms underpinning the radiative sp....
doi.org
September 11, 2025 at 1:23 PM
#TEsky Patterns and Processes of Genomic Evolution Inferred From the Ten Smallest Vertebrate Genomes doi.org/10.1002/advs...
Reposted by Pilar G Marchante
New preprint from my lab! We describe how transposable elements are activated in Parkinson’s disease, which is linked to an interferon response. We believe this study significantly advances our understanding of transposons and their role in human brains.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson's disease
Parkinson's disease (PD) is a common age-related neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TE) have been linked to i...
www.biorxiv.org
September 7, 2025 at 7:59 PM
New preprint from my lab! We describe how transposable elements are activated in Parkinson’s disease, which is linked to an interferon response. We believe this study significantly advances our understanding of transposons and their role in human brains.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
New paper from our lab! We found that LINE-1 transposons contribute to early human brain development.
Funded by @asapresearch.parkinsonsroadmap.org
www.cell.com/cell-genomic...
Funded by @asapresearch.parkinsonsroadmap.org
www.cell.com/cell-genomic...
LINE-1 retrotransposons mediate cis-acting transcriptional control in human pluripotent stem cells and regulate early brain development
Adami et al. demonstrate that evolutionarily young L1s are expressed in human pluripotent
stem cells and are dynamically regulated throughout neural differentiation. The study
examines the role of L1s...
www.cell.com
August 23, 2025 at 9:47 AM
New paper from our lab! We found that LINE-1 transposons contribute to early human brain development.
Funded by @asapresearch.parkinsonsroadmap.org
www.cell.com/cell-genomic...
Funded by @asapresearch.parkinsonsroadmap.org
www.cell.com/cell-genomic...
Reposted by Pilar G Marchante
Structural variation in 1,019 diverse humans based on long-read sequencing 🏺🧪
www.nature.com/articles/s41...
More than half of the new genomic variation uncovered in the study was found in those tricky repetitive regions, including in transposons, also known as jumping genes.
www.nature.com/articles/s41...
More than half of the new genomic variation uncovered in the study was found in those tricky repetitive regions, including in transposons, also known as jumping genes.
August 26, 2025 at 3:12 PM
Structural variation in 1,019 diverse humans based on long-read sequencing 🏺🧪
www.nature.com/articles/s41...
More than half of the new genomic variation uncovered in the study was found in those tricky repetitive regions, including in transposons, also known as jumping genes.
www.nature.com/articles/s41...
More than half of the new genomic variation uncovered in the study was found in those tricky repetitive regions, including in transposons, also known as jumping genes.
Reposted by Pilar G Marchante
A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses.
cc/ @pilargmarch.bsky.social @saramaciasrna.bsky.social @herassr.bsky.social
www.biorxiv.org/content/10.1...
cc/ @pilargmarch.bsky.social @saramaciasrna.bsky.social @herassr.bsky.social
www.biorxiv.org/content/10.1...
A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses
Human endogenous retroviruses (HERVs) occupy nearly 8% of the human genome, yet their protein-coding potential remains largely unexplored. Like their exogenous counterparts, HERVs derive from ancestra...
www.biorxiv.org
July 27, 2025 at 9:37 PM
A Comprehensive Annotation of Conserved Protein Domains in Human Endogenous Retroviruses.
cc/ @pilargmarch.bsky.social @saramaciasrna.bsky.social @herassr.bsky.social
www.biorxiv.org/content/10.1...
cc/ @pilargmarch.bsky.social @saramaciasrna.bsky.social @herassr.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
🚨 Another preprint from the lab out today! 🚨
This work led by former trainee Dr. Juan Brado @the-te-guy.bsky.social and new grad student Ms. Eyael Tewelde, to undertstand how upregulation of a single retrotransposon (here, AluJB) impacts cellular phenotypes! A 🧵, 1/9
www.biorxiv.org/content/10.1...
This work led by former trainee Dr. Juan Brado @the-te-guy.bsky.social and new grad student Ms. Eyael Tewelde, to undertstand how upregulation of a single retrotransposon (here, AluJB) impacts cellular phenotypes! A 🧵, 1/9
www.biorxiv.org/content/10.1...
A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways
During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human...
www.biorxiv.org
July 17, 2025 at 5:03 PM
🚨 Another preprint from the lab out today! 🚨
This work led by former trainee Dr. Juan Brado @the-te-guy.bsky.social and new grad student Ms. Eyael Tewelde, to undertstand how upregulation of a single retrotransposon (here, AluJB) impacts cellular phenotypes! A 🧵, 1/9
www.biorxiv.org/content/10.1...
This work led by former trainee Dr. Juan Brado @the-te-guy.bsky.social and new grad student Ms. Eyael Tewelde, to undertstand how upregulation of a single retrotransposon (here, AluJB) impacts cellular phenotypes! A 🧵, 1/9
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Long-read RNA sequencing of transposable elements from single cells using CELLO-seq - Nature Protocols
Single-cell long-read RNA sequencing enables the high-fidelity mapping of single-cell expression data from highly sequence-similar transposable elements to unique genomic loci by correcting errors fro...
doi.org
July 16, 2025 at 4:55 PM
Very happy to share our protocols paper for CELLO-seq. This will make single cell long read RNA-seq more accessible and provides analysis guidelines. We hope this helps the #transposon #TEsky community and folks working on #singleCell isoform and allelic #gene expression. doi.org/10.1038/s415...
Reposted by Pilar G Marchante
🚨 Our new preprint!
In collaboration with @saramaciasrna.bsky.social and @heick.bsky.social labs
🧬 Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 and its implications in 22q11.2 deletion syndrome.
#22q11 #TEsky #RNAsky
In collaboration with @saramaciasrna.bsky.social and @heick.bsky.social labs
🧬 Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 and its implications in 22q11.2 deletion syndrome.
#22q11 #TEsky #RNAsky
Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prevent viral spread while avoiding excessive immune respon...
www.biorxiv.org
June 3, 2025 at 3:09 PM
🚨 Our new preprint!
In collaboration with @saramaciasrna.bsky.social and @heick.bsky.social labs
🧬 Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 and its implications in 22q11.2 deletion syndrome.
#22q11 #TEsky #RNAsky
In collaboration with @saramaciasrna.bsky.social and @heick.bsky.social labs
🧬 Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8 and its implications in 22q11.2 deletion syndrome.
#22q11 #TEsky #RNAsky
Reposted by Pilar G Marchante
In our last preprint we identify endogenous dsRNAs capable of activating the interferon response. Could these be relevant to our understanding of DiGeorge syndrome (22qDS)?
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prevent viral spread while avoiding excessive immune respon...
www.biorxiv.org
June 2, 2025 at 12:55 PM
In our last preprint we identify endogenous dsRNAs capable of activating the interferon response. Could these be relevant to our understanding of DiGeorge syndrome (22qDS)?
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
🔴 A new preprint up on @biorxiv-molbio.bsky.social about the control of retrotransposon-driven activation of the interferon response by the double-stranded
RNA binding protein DGCR8.
www.biorxiv.org/content/10.1...
RNA binding protein DGCR8.
www.biorxiv.org/content/10.1...
Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prevent viral spread while avoiding excessive immune respon...
www.biorxiv.org
June 2, 2025 at 10:58 AM
🔴 A new preprint up on @biorxiv-molbio.bsky.social about the control of retrotransposon-driven activation of the interferon response by the double-stranded
RNA binding protein DGCR8.
www.biorxiv.org/content/10.1...
RNA binding protein DGCR8.
www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
I am thrilled to share our preprint where we take advantage of the unique opportunities offered by human blastoids to uncover a human-specific mechanism potentially playing a role in preimplantation 🧵. www.biorxiv.org/content/10.1...
May 12, 2025 at 8:25 PM
I am thrilled to share our preprint where we take advantage of the unique opportunities offered by human blastoids to uncover a human-specific mechanism potentially playing a role in preimplantation 🧵. www.biorxiv.org/content/10.1...
Reposted by Pilar G Marchante
💥🥳 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 Pilar G Marchante
Our latest paper is out in NAR! 🥳
In collaboration with @saramaciasrna.bsky.social, we show DGCR8 haploinsufficiency disrupts pluripotency in hESC by affecting primate-specific miRNAs and TEs. Our findings highlight a co-evolved miRNA-TE network in primates.
Read:
academic.oup.com/nar/article-...
In collaboration with @saramaciasrna.bsky.social, we show DGCR8 haploinsufficiency disrupts pluripotency in hESC by affecting primate-specific miRNAs and TEs. Our findings highlight a co-evolved miRNA-TE network in primates.
Read:
academic.oup.com/nar/article-...
DGCR8 haploinsufficiency leads to primate-specific RNA dysregulation and pluripotency defects
Abstract. The 22q11.2 deletion syndrome (22qDS) is a human disorder where the majority of clinical manifestations originate during embryonic development. 2
academic.oup.com
March 27, 2025 at 10:13 AM
Our latest paper is out in NAR! 🥳
In collaboration with @saramaciasrna.bsky.social, we show DGCR8 haploinsufficiency disrupts pluripotency in hESC by affecting primate-specific miRNAs and TEs. Our findings highlight a co-evolved miRNA-TE network in primates.
Read:
academic.oup.com/nar/article-...
In collaboration with @saramaciasrna.bsky.social, we show DGCR8 haploinsufficiency disrupts pluripotency in hESC by affecting primate-specific miRNAs and TEs. Our findings highlight a co-evolved miRNA-TE network in primates.
Read:
academic.oup.com/nar/article-...
Reposted by Pilar G Marchante
NCBI websites are patchy at present, but now feel far less secure for long-term storage than they used to.
For sequencing datasets consider using ArrayExpress:
www.ebi.ac.uk/biostudies/a...
Many, if not all, GEO datasets are on there.
For sequencing datasets consider using ArrayExpress:
www.ebi.ac.uk/biostudies/a...
Many, if not all, GEO datasets are on there.
BioStudies < The European Bioinformatics Institute < EMBL-EBI
BioStudies – one package for all the data supporting a study
www.ebi.ac.uk
March 2, 2025 at 9:32 AM
NCBI websites are patchy at present, but now feel far less secure for long-term storage than they used to.
For sequencing datasets consider using ArrayExpress:
www.ebi.ac.uk/biostudies/a...
Many, if not all, GEO datasets are on there.
For sequencing datasets consider using ArrayExpress:
www.ebi.ac.uk/biostudies/a...
Many, if not all, GEO datasets are on there.
Reposted by Pilar G Marchante
A new study in @cellpress.bsky.social Immunity from the lab of Dr. Benjamin Greenbaum provides insights into how #PancreaticCancer cells accommodate active retrotransposons without triggering the innate immune response. #oncsky #medsky
Cancer cells restrict immunogenicity of retrotransposon expression via distinct mechanisms
Overexpression of transposable elements is a common feature of cancer. Sun, You, et al.
show that, in pancreatic ductal adenocarcinoma, tumor cells adapt through different
mechanisms to mitigate a spe...
www.cell.com
December 2, 2024 at 2:20 PM
Reposted by Pilar G Marchante
Tracking transposable element (TE) activity in genomics data can be a pain, but there are solutions! Our lab built TEtranscripts -- which we've updated to work for small RNAs (TEsmall), bulk RNA at the locus level (TElocal), and in single-cell data (TEsingle). Check it out!
www.mghlab.org/software
www.mghlab.org/software
November 18, 2024 at 11:14 PM
Tracking transposable element (TE) activity in genomics data can be a pain, but there are solutions! Our lab built TEtranscripts -- which we've updated to work for small RNAs (TEsmall), bulk RNA at the locus level (TElocal), and in single-cell data (TEsingle). Check it out!
www.mghlab.org/software
www.mghlab.org/software