Luis G. Palma

Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation This study reveals that composite transposons with bivalent histone marks can serve as RNA-dependent enhancers, controlling key developmental and aging-related gene programs.

Outstanding paper describing how SVAs are regulated,what's their function in gene regulation and its impact in cell fate

Composite transposons with bivalent histone marks function as RNA-dependent enhancers in cell fate regulation | Cell

#TEs #CellFate #HSCs #Aging

www.cell.com/cell/fulltex...

Human whole epigenome modelling for clinical applications with Pleiades www.biorxiv.org/content/10.1... 🧬🖥️🧪

Thanks everyone involved in the work. Special thanks also to our amazing team of collaborators: @mercedesbarrero.bsky.social, Payer lab and Menendez lab

Thrilled to share with you the latest work from my PhD in Bigas lab at @researchmar.bsky.social @carrerasijc.bsky.social published in @bloodjournal.bsky.social

We’ve programmed blood stem cells from PSCs using CRISPRa screen and found a new “bloody” cocktail

#CRISPR #HSCs #StemCells #CellFate

Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness Daniel Álvarez-Villanueva et al. dissect distinct roles of the NF-κB inhibitor IκBα by generating separation-of-function mutants. Their findings reveal that chromatin-bound IκBα, independent of NF-κB ...

Very happy to have our latest work on how IκBα regulates stemness independently from NF-κB. It has been a terrific collaborative work led by Lluís Espinosa and Daniel Alvarez-Villanueva @researchmar.bsky.social

#nfkb #ikb #inflammation #stemcells

www.cell.com/cell-reports...

Bivalent chromatin instructs lineage specification during hematopoiesis Yagi et al. show that, unexpectedly, H3K4 methylation is dispensable for hematopoietic stem cell maintenance but essential for progenitor cell maturation into all blood cell types by opposing H3K27 me...

H3K4 methylation instructs blood specification in vivo

Bivalent chromatin instructs lineage specification during hematopoiesis | Cell

#Hematopoiesis #CellFate #Chromatin

www.cell.com/cell/abstrac...

(1/n) Thread @matteomazzocca.bsky.social @domenicnarducci.bsky.social Simon Grosse-Holz @jessematthias.bsky.social preprint

Q: how does chromatin move?

Using MINFLUX, SPT & SRLCI, we track chromatin dynamics across 7 orders of magnitude in time to provide answers www.biorxiv.org/content/10.1...

Emerging roles for the nucleolus in development and stem cells Summary: This Review explores roles of the nucleolus in mammalian development, with a particular focus on genome organisation and chromatin regulation.

Nice review about alternative roles of nucleolus in genome organization in stem cells

Emerging roles for the nucleolus in development and stem cells | Development

#Review #Heterochromatin #GenomeOrganization #StemCells

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

Lively conversations, shared laughs, and engaging networking during the breaks at #EMBLChromatin 🧬💬🤝

Transposable elements as genome regulators in normal and malignant haematopoiesis - Blood Cancer Journal Blood Cancer Journal - Transposable elements as genome regulators in normal and malignant haematopoiesis

I am excited to share our lab's first review out with in Blood Cancer Journal. We discuss the impact of transposable elements on genome regulation and variation in both normal
haematopoietic processes and haematological cancers. www.nature.com/articles/s41...

Stem cells as role models for reprogramming and repair Stem cells are a promising source for cellular therapies across many diseases and tissues. Their inherent ability to differentiate into other cell types has been the focus of investigation over decade...

Review about principles of stem cell biology and cellular reprogramming approaches and their use for current and future therapeutic purposes

Stem cells as role models for reprogramming and repair | Science

#Review #StemCells #Reprogramming #RegenerativeMedicine

www.science.org/doi/10.1126/...

The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways In vivo screening in mouse embryos provides insights into the functional interplay between chromatin and the nuclear envelope in the establishment of lamina-associated domains, the earliest feature of...

Maternal H3K27me3 inheritance over de novo methylation shapes chromatin architecture

The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways | Cell

#3DGenome #Chromatin #Development

www.cell.com/cell/fulltex...

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb...

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes | Science

#TranscriptionFactors #GeneRegulation #Hematopoiesis

www.science.org/doi/10.1126/...

The HuSH complex silences retrotransposable elements. We identify HuSH2, centered on TASOR2, targeting KRAB-ZNFs and interferon genes, balancing retrotransposon silencing and immune regulation. www.nature.com/articles/s41...

Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin Interaction between the N6-methyladenosine (m6A) methyltransferase METTL3 and METTL14 is critical for METTL3 to deposit m6A on various types of RNAs. …

p300 acetylates METTL3 specifically on H3K27ac chromatin to promote transcription

Spatial control of m6A deposition on enhancer and promoter RNAs through co-acetylation of METTL3 and H3K27 on chromatin | Molecular Cell

#m6a #chromatin #transcription #mettl3

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

The molecular basis of heterochromatin assembly and epigenetic inheritance Heterochromatin plays a fundamental role in gene regulation, genome integrity, and silencing of repetitive DNA elements. Histone modifications are ess…

The molecular basis of heterochromatin assembly and epigenetic inheritance | Molecular Cell

#Heterochromatin #EpigeneticInheritance #Review

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

Predictable Engineering of Signal-Dependent Cis-Regulatory Elements

Our latest: uncovering hierarchical design rules for cis-regulatory elements with a high-throughput screen

CRE activity follows multiplicative modular rules, tuned by spacing & positioning

Enables engineering synthetic CREs for predictable tissue patterning

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

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens Sood et al. used high-throughput screening to identify regulators of gene bursting and find both gene- and cell-type-specific effectors. Acetylation alters burst size in a gene-specific manner but is ...

Changes in promoter histone acetylation and gene bursting are uncoupled

Identification of molecular determinants of gene-specific bursting patterns by high-throughput imaging screens | Molecular Cell

#GeneRegulation #Transcription

www.cell.com/molecular-ce...

Transposon–host arms race: a saga of genome evolution Once considered ‘junk DNA,’ transposons or transposable elements (TEs) are now recognized as key drivers of genome evolution, contributing to genetic diversity, gene regulation, and species diversific...

Transposon–host arms race: a saga of genome evolution | Trends in Genetics

#review #transposon #HUSH #KRAB

www.cell.com/trends/genet...

Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability Losing parental histones during DNA replication fork passage challenges differentiation competence and cell viability.

𝐇𝐨𝐰 𝐝𝐨 𝐜𝐞𝐥𝐥𝐬 𝐫𝐞𝐦𝐞𝐦𝐛𝐞𝐫 𝐰𝐡𝐨 𝐭𝐡𝐞𝐲 𝐚𝐫𝐞 𝐚𝐟𝐭𝐞𝐫 𝐃𝐍𝐀 𝐫𝐞𝐩𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧? Our new study “Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability” is out in 𝘚𝘤𝘪𝘦𝘯𝘤𝘦 𝘈𝘥𝘷𝘢𝘯𝘤𝘦𝘴. Led by @lleonie.bsky.social @biranalva.bsky.social 🧵 More below👇

RNA polymerase II coordinates histone deacetylation at active promoters Transcription initiation limits histone acetylation and H2AZ incorporation at promoters.

Histone modifications occur independently of transcription

RNA polymerase II coordinates histone deacetylation at active promoters | Science Advances

#chromatin #transcription #generegulation

www.science.org/doi/10.1126/...

Sequencing technologies to measure translation in single cells - Nature Reviews Molecular Cell Biology Recent sequencing-based methods, including novel ribosome profiling, ribosome affinity purification and spatial translation methods, have enabled the measurement of translation at single-cell resoluti...

Sequencing technologies to measure translation in single cells | Nature Reviews Molecular Cell Biology

#Review #Sequencing #Translation #SingleCell

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

Uncovering the whole genome silencers of human cells via Ss-STARR-seq - Nature Communications Silencers play a critical role in gene transcription regulation. Here, the authors developed the Ss-STARR-seq technique to identify tens of thousands of silencers in human cells. These silencers posse...

Uncovering the whole genome silencers of human cells via Ss-STARR-seq | Nature Communications

#Chromatin #GeneRegulation #Enhancers

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

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation Beyond its role as RNA m6A writer, METTL3-METTL14 can mediate 5mC deposition on DNA by recruiting the DNA methyltransferase DNMT1 to chromatin. The two marks co-orchestrate the expression of key genes...

www.cell.com/action/showP...

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation Beyond its role as RNA m6A writer, METTL3-METTL14 can mediate 5mC deposition on DNA by recruiting the DNA methyltransferase DNMT1 to chromatin. The two marks co-orchestrate the expression of key genes...

Linking RNA modifications to DNMT1 function on gene bodies

Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation | Cell

#Epigenetics #DNAme #Development #DNMT1 #RNA

www.cell.com/cell/abstrac...

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.

Promoters have strong orientation-bias, but not the enhancers

Massively parallel characterization of transcriptional regulatory elements | Nature

#transcription #generegulation #chromatin

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

Resolution of a human super-enhancer by targeted genome randomisation Human gene expression is controlled from distance via enhancers, which can form longer "super-enhancer"-regions of intense regulatory activity. Whether super-enhancers constitute a separate regulatory...

Resolution of a human super-enhancer by targeted genome randomisation | BioRxiv

#generegulation #enhancer #chromatin #preprint

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

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture Chromatin organization plays a crucial role in gene regulation [[1][1], [2][2], [3][3]], but disentangling the contributions of various epigenetic components to gene-scale chromatin structure remains ...

In vitro synthesis of up to 96 nucleosomes. Amazing platform to study chromatin folding!!

Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture | BioRxiv

#chromatin #nucleosome #3Dchromatin #preprint

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

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia Gambi et al. highlight the critical role of 3D chromatin hubs for T cell leukemia progression. By integrating multi-omics data and employing CRISPR screening techniques, the researchers identify key regulatory elements controlling oncogenes expression and disease markers. The findings offer new insights into tumor heterogeneity, patient stratification, and potential therapeutic targets.

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia | Molecular Cell

#Chromatin #3DGenome #Leukemia

www.cell.com/molecular-ce...

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF ZNF143 has been implicated in gene activation and chromatin looping. Magnitov et al. show that ZNF143 has no general looping factor activity and explain why this function has been misattributed. Instead, ZNF143 regulates transcription of nuclear-encoded mitochondrial genes, ensuring energy homeostasis, proliferation, and differentiation potential of stem cells.

ZFN143 doesn’t affect 3D chromatin, but rather mitochondrial gene expression

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF | Molecular Cell

#TrancriptionFactors #Chromatin #Mitochondria

www.cell.com/molecular-ce...