Yang XF
@fly-yang.bsky.social
Single-cell analysis, ectoderm patterning, morphogen gradient, signaling activity
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Integrated Single-cell Analysis Uncovers Regulatory Logic of Cranial Ectoderm Development
Embryonic ectoderm patterning in the cranial region establishes the neural plate, neural crest, sensory placodes, and non-neural ectoderm in coordination with the underlying mesoderm and endoderm. Alt...
www.biorxiv.org
December 19, 2025 at 1:42 AM
Single-cell analysis, ectoderm patterning, morphogen gradient, signaling activity
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Transposable element reactivation on ecDNA rdcu.be/eVm9q
Enhancer activation from transposable elements in extrachromosomal DNA
Nature Cell Biology - Kraft, Murphy, Jones et al. identify extrachromosomal DNA (ecDNA)-interacting elements (EIEs) enriched for transposable elements within ecDNA in colorectal cancer cells. They...
rdcu.be
December 19, 2025 at 1:27 AM
Transposable element reactivation on ecDNA rdcu.be/eVm9q
A shifting of the perspective brings new insights! GENE BODY also contributes! Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 22, 2025 at 1:05 AM
A shifting of the perspective brings new insights! GENE BODY also contributes! Functional maps of a genomic locus reveal confinement of an enhancer by its target gene | Science www.science.org/doi/10.1126/...
Nice work! 👍👍👍 Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development www.biorxiv.org/content/10.1...
Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development
The trophectoderm produced from totipotent blastomeres initiates trophoblast development, while placental deficiencies can cause pregnancy disorders. Yet, a culture system that fully recapitulates the...
www.biorxiv.org
September 1, 2025 at 12:57 AM
Nice work! 👍👍👍 Capturing trophectoderm-like stem cells enables step-wisely remodeling of placental development www.biorxiv.org/content/10.1...
Thrilled to share our most recent work concerning the mechanistic study of developmental enhancers. Cis or trans may be a spatial-temporal choice 😁😁😁
advanced.onlinelibrary.wiley.com/doi/10.1002/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Gastrula‐Premarked Posterior Enhancer Primes Posterior Tissue Development Through Cross‐Talk with TGF‐β Signaling Pathway
A gastrula-premarked enhancer within the first intron of Cdx2 governs posterior embryonic development via both regulating Cdx2 expression in cis and coordinating TGF-β signaling in trans to ensure pr...
advanced.onlinelibrary.wiley.com
June 30, 2025 at 9:31 AM
Thrilled to share our most recent work concerning the mechanistic study of developmental enhancers. Cis or trans may be a spatial-temporal choice 😁😁😁
advanced.onlinelibrary.wiley.com/doi/10.1002/...
advanced.onlinelibrary.wiley.com/doi/10.1002/...
Very nice work! Gastruloids set up the cellular basis for prospective functional celltypes. In-depth molecular survey determining the exact similarity or translational application validating the functionality may be the next steps. | Science www.science.org/doi/full/10....
www.science.org
June 15, 2025 at 8:42 AM
Very nice work! Gastruloids set up the cellular basis for prospective functional celltypes. In-depth molecular survey determining the exact similarity or translational application validating the functionality may be the next steps. | Science www.science.org/doi/full/10....
Heterogeneous intrinsic features for superenhancer, balance between details and landscape.
Quote: ‘The partitioning of sub-units within SEs as constitutively active (PU) or decommissioned (DM) proposes a mechanism by preserving pluripotency as cells prepare for subsequent differentiation.’
Quote: ‘The partitioning of sub-units within SEs as constitutively active (PU) or decommissioned (DM) proposes a mechanism by preserving pluripotency as cells prepare for subsequent differentiation.’
Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency
Nature Communications - Clusters of enhancers, called super-enhancers (SEs), control the expression of cell identity genes. Here, the authors identify two types of enhancer units within SEs in...
rdcu.be
June 5, 2025 at 5:53 AM
Heterogeneous intrinsic features for superenhancer, balance between details and landscape.
Quote: ‘The partitioning of sub-units within SEs as constitutively active (PU) or decommissioned (DM) proposes a mechanism by preserving pluripotency as cells prepare for subsequent differentiation.’
Quote: ‘The partitioning of sub-units within SEs as constitutively active (PU) or decommissioned (DM) proposes a mechanism by preserving pluripotency as cells prepare for subsequent differentiation.’
Thrilled to share our newly published work about how primitive endoderm fate is regulated by a lncRNA gene (Gm26793)-mediated inter-chromosomal interaction.
P.S. Biology is like magic. Keep smart and stay alert to strike the gold. Unknown but crucial things ahead!
P.S. Biology is like magic. Keep smart and stay alert to strike the gold. Unknown but crucial things ahead!
Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal interaction with Cubn to ensure proper stem cell differentiation in vitro and in vivo - Cell Discovery
Cell Discovery - Genomic locus of lncRNA-Gm26793 forms an inter-chromosomal interaction with Cubn to ensure proper stem cell differentiation in vitro and in vivo
www.nature.com
June 4, 2025 at 2:52 AM
Thrilled to share our newly published work about how primitive endoderm fate is regulated by a lncRNA gene (Gm26793)-mediated inter-chromosomal interaction.
P.S. Biology is like magic. Keep smart and stay alert to strike the gold. Unknown but crucial things ahead!
P.S. Biology is like magic. Keep smart and stay alert to strike the gold. Unknown but crucial things ahead!
The offspring from GF mothers were highly susceptible to metabolic syndrome characterized by an exacerbation of obesity and glucose intolerance in association with reduced energy expenditure upon high-fat diet consumption during adulthood.
Maternal gut microbiota in pregnancy influences offspring metabolic phenotype in mice
The mother’s gut microbiota during pregnancy tunes energy homeostasis and sympathetic nervous system development in offspring.
www.science.org
May 30, 2025 at 5:31 AM
The offspring from GF mothers were highly susceptible to metabolic syndrome characterized by an exacerbation of obesity and glucose intolerance in association with reduced energy expenditure upon high-fat diet consumption during adulthood.
Reposted by Yang XF
May 19, 2025 at 6:06 PM
Very impressive work! 👍👍👍 Remaining questions: How do initial cell states (naive vs. primed) exhibit differential responsiveness to the same signal stimuli? How does certain additional extrinsic signals (Nodal signaling here) eliminate the differences? Signaling principles and cell fate choice
Deciphering signaling mechanisms and developmental dynamics in extraembryonic mesoderm specification from hESCs - Nature Communications
Extraembryonic mesoderm (ExM) is crucial but its formation is unclear. Here, authors develop efficient systems to specify ExM from hESCs and dissect the signaling mechanisms, specification dynamics, a...
www.nature.com
May 26, 2025 at 1:53 AM
Very impressive work! 👍👍👍 Remaining questions: How do initial cell states (naive vs. primed) exhibit differential responsiveness to the same signal stimuli? How does certain additional extrinsic signals (Nodal signaling here) eliminate the differences? Signaling principles and cell fate choice
Just see a post about the Great Lady- Ms Lu on the day of China Female football team win the Asian champion. Salute to the history
May 25, 2025 at 4:17 AM
Just see a post about the Great Lady- Ms Lu on the day of China Female football team win the Asian champion. Salute to the history
The off target effects is never a random phenomenon and also not be specific for epigenetic editing at age-associated CpGs for the bystander effect. Worth further studies!
Epigenetic editing at individual age-associated CpGs affects the genome-wide epigenetic aging landscape - Nature Aging
Using CRISPR-guided editing, Liesenfelder et al. modify DNA methylation at epigenetic clock sites, which evokes genome-wide age-associated epigenetic modifications. Their findings suggest age-associat...
www.nature.com
May 23, 2025 at 5:27 AM
The off target effects is never a random phenomenon and also not be specific for epigenetic editing at age-associated CpGs for the bystander effect. Worth further studies!
DNA replication time sequencing. Pluripotency factors play a role in the firing efficiency of mESCs. What about the cell differentiation process? 2025.01.07.631761v1
Pluripotency factors enhance the firing efficiency of late DNA replication origins in mouse embryonic stem cells
DNA replication initiates at genomic loci known as origins, which fire according to a spatiotemporal program, still not yet well-defined in mammals. Here, we investigated whether pluripotent mouse emb...
www.biorxiv.org
May 20, 2025 at 5:31 AM
DNA replication time sequencing. Pluripotency factors play a role in the firing efficiency of mESCs. What about the cell differentiation process? 2025.01.07.631761v1
Really smart design of leveraging polyA-tailed transposome to unify the molecular approach for spatial epigenome, transcriptome and cell lineages👍 www.pnas.org/doi/10.1073/...
Unified molecular approach for spatial epigenome, transcriptome, and cell lineages | PNAS
Spatial epigenomics and multiomics can provide fine-grained insights into cellular
states but their widespread adoption is limited by the requireme...
www.pnas.org
May 20, 2025 at 5:20 AM
Really smart design of leveraging polyA-tailed transposome to unify the molecular approach for spatial epigenome, transcriptome and cell lineages👍 www.pnas.org/doi/10.1073/...
Human-specific LTR5Hs regulation of a primate-specific gene is essential for blastoid formation. Definitive study!!! www.biorxiv.org/content/10.1...
A human-specific regulatory mechanism revealed in a preimplantation model
Stem cell-based human embryo models offer a unique opportunity for functional studies of the human-specific features of development. Here, we genetically and epigenetically manipulate human blastoids,...
www.biorxiv.org
May 15, 2025 at 5:07 AM
Human-specific LTR5Hs regulation of a primate-specific gene is essential for blastoid formation. Definitive study!!! www.biorxiv.org/content/10.1...
Does marsupial puppy completely inherent parental's epigenetic memory? What's the specific roles of DNAme during embryo development? www.nature.com/articles/s41...
May 15, 2025 at 2:04 AM
Does marsupial puppy completely inherent parental's epigenetic memory? What's the specific roles of DNAme during embryo development? www.nature.com/articles/s41...
Nice work! Neuronal FAM171A2 mediates α-synuclein fibril uptake and drives Parkinson’s disease | Science www.science.org/doi/10.1126/...
Neuronal FAM171A2 mediates α-synuclein fibril uptake and drives Parkinson’s disease
Neuronal accumulation and spread of pathological α-synuclein (α-syn) fibrils are key events in Parkinson's disease (PD) pathophysiology. However, the neuronal mechanisms underlying the uptake of α-syn...
www.science.org
February 21, 2025 at 3:01 AM
Nice work! Neuronal FAM171A2 mediates α-synuclein fibril uptake and drives Parkinson’s disease | Science www.science.org/doi/10.1126/...
Reposted by Yang XF
Exploiting the SunTag system to study the developmental regulation of mRNA translation https://www.biorxiv.org/content/10.1101/2025.02.09.637317v1
February 10, 2025 at 2:31 AM
Exploiting the SunTag system to study the developmental regulation of mRNA translation https://www.biorxiv.org/content/10.1101/2025.02.09.637317v1
Reposted by Yang XF
Spatially regulated mRNA decay sharpens expression patterns in the Drosophila embryo https://www.biorxiv.org/content/10.1101/2025.02.08.637258v1
February 10, 2025 at 2:31 AM
Spatially regulated mRNA decay sharpens expression patterns in the Drosophila embryo https://www.biorxiv.org/content/10.1101/2025.02.08.637258v1