Analyzing the Genome-Wide Distribution of Histone Marks by CUT&amp;Tag in Drosophila Embryos

Zenk, Fides; Cardamone, Francesco; Morales, Daiana de Lima; Atinbayeva, Nazerke; Zhan, Yinxiu; Iovino, Nicola

doi:10.1007/978-1-0716-3143-0_1

Cited by 3 publications

(1 citation statement)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Per experiment, 1 Million cells were used and incubated with 2 µg YAP antibodies (Abcam ab52771, Santa Cruz sc-101199). All following steps were performed as described 43,44 , except that the Tn5 incubation and cutting was performed at a NaCl concentration of 150 mM. To control unspecific cutting we performed the experiment without antibody (Tn5 only) and with a generic anti-rabbit antibody.…”

Section: Experimental Methodsmentioning

confidence: 99%

Morphodynamics of human early brain organoid development

Jain,

Gut,

Sanchis-Calleja

et al. 2023

Preprint

View full text Add to dashboard Cite

Brain organoids enable the mechanistic study of human brain development, and provide opportunities to explore self-organization in unconstrained developmental systems. Here, we establish long-term, live light sheet microscopy on unguided brain organoids generated from fluorescently labeled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviors, and subcellular features over weeks of organoid development. We provide a novel dual-channel, multi-mosaic and multi-protein labeling strategy combined with a computational demultiplexing approach to enable simultaneous quantification of distinct subcellular features during organoid development. We track Actin, Tubulin, plasma membrane, nucleus, and nuclear envelope dynamics, and quantify cell morphometric and alignment changes during tissue state transitions including neuroepithelial induction, maturation, lumenization, and brain regionalization. Based on imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix (ECM) pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrixinduced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signaling pathways, including spatially restricted induction of the Wnt Ligand Secretion Mediator (WLS) that marks the earliest emergence of nontelencephalic brain regions. Altogether, our work provides a new inroad into studying human brain morphodynamics, and supports a view that matrix-linked mechanosensing dynamics play a central role during brain regionalization.

show abstract

Section: Experimental Methodsmentioning

confidence: 99%

Morphodynamics of human early brain organoid development

Jain,

Gut,

Sanchis-Calleja

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Maternally expressed FERTILIZATION-INDEPENDENT ENDOSPERM1 regulates seed dormancy and aleurone development in rice

Cheng,

Zhang,

et al. 2024

The Plant Cell

View full text Add to dashboard Cite

Seed dormancy, an essential trait for plant adaptation, is determined by the embryo itself and the surrounding tissues. Here, we found that rice (Oryza sativa) FERTILIZATION INDEPENDENT ENDOSPERM1 (OsFIE1) regulates endosperm-imposed dormancy and the dorsal aleurone thickness in a manner dependent on the parent of origin. Maternally expressed OsFIE1 suppresses gibberellin (GA) biosynthesis in the endosperm by depositing trimethylation of lysine 27 on histone H3 (H3K27me3) marks on GA biosynthesis-related genes, thus inhibiting germination and aleurone differentiation. Knockout of rice GA 20-oxidase1 (OsGA20ox1) alleviated the phenotypic defects in osfie1. The aleurone-positive determinant Crinkly 4 (OsCR4) is another target of the OsFIE1-containing Polycomb repressive complex 2 (PRC2). We found that OsFIE1 plays an important role in genomic imprinting in the endosperm of germinating seeds, particularly for paternally expressed genes associated with H3K27me3. The increased aleurone thickness of osfie1 substantially improved grain nutritional quality, indicating that the osfie1 gene may be utilized for breeding nutrient-enriched rice. The findings provide insights into the essential roles of PRC2-mediated H3K27me3 methylation in the acquisition of seed dormancy and endosperm cell differentiation in rice.

show abstract

Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

Tsissios,

Leleu,

et al. 2024

Preprint

View full text Add to dashboard Cite

Why mammals cannot regenerate limbs, unlike amphibians, presents a longstanding puzzle in biology. We show that exposingex vivoamputated embryonic mouse limbs to subatmospheric oxygen environment, or stabilizing oxygen-sensitive HIF1A enables not only rapid wound healing, but alters cellular mechanics, and reshapes the histone landscape to prime regenerative fates. Conversely, regenerativeXenopustadpole limbs display low oxygen-sensing capacity, robust wound healing, a regenerative histone landscape, and glycolytic programs even under high oxygen. This reduced oxygen-sensing capacity, in stark contrast to mammals, associates with decreased HIF1A-regulating gene expressions. Our findings thus uncover species-specific oxygen sensing as a unifying mechanism for limb regeneration initiation across vertebrates, reveal how aquatic subatmospheric habitats may enhance regenerative capabilities, and identify targetable barriers to unlock latent limb regenerative programs in adult mammals.

show abstract

Analyzing the Genome-Wide Distribution of Histone Marks by CUT&Tag in Drosophila Embryos

Cited by 3 publications

References 10 publications

Morphodynamics of human early brain organoid development

Morphodynamics of human early brain organoid development

Maternally expressed FERTILIZATION-INDEPENDENT ENDOSPERM1 regulates seed dormancy and aleurone development in rice

Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration

Contact Info

Product

Resources

About