Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

Liu, Xiao; Long, Fuhui; Peng, Hanchuan; Aerni, Sarah J.; Jiang, Min; Sánchez-Blanco, Adolfo; Murray, John I.; Preston, Elicia; Mericle, Barbara; Batzoglou, Serafim; Myers, Eugene W.; Kim, Stuart K.

doi:10.1016/j.cell.2009.08.044

Cited by 135 publications

(164 citation statements)

References 30 publications

Supporting

Mentioning

159

Contrasting

Order By: Relevance

“…6E). Gene expression in C. elegans L1 larval cells, which may represent an intermediate state in this process, still show variation that reflects embryonic cell lineage (25).…”

Section: (B)mentioning

confidence: 99%

Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation

Skora

Spradling

2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Stem and embryonic cells facilitate programming toward multiple daughter cell fates, whereas differentiated cells resist reprogramming and oncogenic transformation. How alterations in the chromatin-based machinery of epigenetic inheritance contribute to these differences remains poorly known. We observed random, heritable changes in GAL4/UAS transgene programming during Drosophila ovarian follicle stem cell differentiation and used them to measure the stage-specific epigenetic stability of gene programming. The frequency of GAL4/UAS reprogramming declines more than 100-fold over the nine divisions comprising this stem cell lineage. Stabilization acts in cis, suggesting that it is chromatin-based, and correlates with increased S phase length. Our results suggest that stem/early progenitor cells cannot accurately transmit nongenetic information to their progeny; full epigenetic competence is acquired only gradually during early differentiation. Modulating epigenetic inheritance may be a critical process controlling transitions between the pleuripotent and differentiated states.epigenetic inheritance | pleuripotency | cell lineage | reprogramming

show abstract

“…6E). Gene expression in C. elegans L1 larval cells, which may represent an intermediate state in this process, still show variation that reflects embryonic cell lineage (25).…”

Section: (B)mentioning

confidence: 99%

Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation

Skora

Spradling

2010

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Other promoters are less than 2 kb, mostly because their upstream intergenic regions are short. It has been demonstrated that 2 kb upstream of a worm gene accurately drives gene expression in most cases (19,20). Therefore, the majority of our reporters should largely recapitulate endogenous gene expression.…”

Section: Systematic Prediction Of Lateral Neuroblast Regulators In Cmentioning

confidence: 99%

“…Therefore, the majority of our reporters should largely recapitulate endogenous gene expression. We profiled their expression in trunk ectoderm of newly hatched L1 larvae at the resolution of single cells using an imaging analysis pipeline (19) (Fig. 5).…”

Section: Systematic Prediction Of Lateral Neuroblast Regulators In Cmentioning

confidence: 99%

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Zhao

Horie

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

The lateral neural plate border (NPB), the neural part of the vertebrate neural border, is composed of central nervous system (CNS) progenitors and peripheral nervous system (PNS) progenitors. In invertebrates, PNS progenitors are also juxtaposed to the lateral boundary of the CNS. Whether there are conserved molecular mechanisms determining vertebrate and invertebrate lateral neural borders remains unclear. Using single-cell-resolution gene-expression profiling and genetic analysis, we present evidence that orthologs of the NPB specification module specify the invertebrate lateral neural border, which is composed of CNS and PNS progenitors. First, like in vertebrates, the conserved neuroectoderm lateral border specifier Msx/vab-15 specifies lateral neuroblasts in Caenorhabditis elegans. Second, orthologs of the vertebrate NPB specification module (Msx/vab-15, Pax3/7/pax-3, and Zic/ref-2) are significantly enriched in worm lateral neuroblasts. In addition, like in other bilaterians, the expression domain of Msx/vab-15 is more lateral than those of Pax3/7/pax-3 and Zic/ref-2 in C. elegans. Third, we show that Msx/vab-15 regulates the development of mechanosensory neurons derived from lateral neural progenitors in multiple invertebrate species, including C. elegans, Drosophila melanogaster, and Ciona intestinalis. We also identify a novel lateral neural border specifier, ZNF703/tlp-1, which functions synergistically with Msx/vab-15 in both C. elegans and Xenopus laevis. These data suggest a common origin of the molecular mechanism specifying lateral neural borders across bilaterians.C. elegans | neural plate border | neural border | Msx/vab-15 | ZNF703/tlp-1 T he vertebrate neural border is a transient embryonic domain located between the neural plate and nonneurogenic ectoderm from late gastrulation to early neurulation. The neural border is composed of the lateral neural plate border (NPB) and preplacode ectoderm (PPE) subdomains (1, 2). The NPB and PPE give rise to the neural crest and placode, respectively, both of which undergo epithelial-to-mesenchymal transition/delamination, migrate in prototypical paths, and give rise to the peripheral nervous system (PNS) and many other cell types (3, 4). However, the NPB and PPE also have many different features (5). For example, the PPE is confined to the anterior half of embryos and does not contribute to the central nervous system (CNS), whereas the NPB is the lateral border of the whole neural plate and consists not only of progenitors for the PNS but also those for the CNS in the dorsal neural tube. The juxtaposed localization of the CNS neuroectoderm and PNS progenitors also occurs in the trunk of invertebrate embryos such as nematodes, arthropods, annelids, and urochordates (6-9), reminiscent of vertebrate NPB. In Caenorhabditis elegans, lateral neuroblasts (P, Q, and V5 cells) are located between the embryonic CNS and skin from the birth of these cells (10). In addition, worm lateral neuroblasts possess several key cellular and developmental features of vertebra...

show abstract

“…The nematode Coenorhabditis elegans, having the most ancient evolutionary emergence among the considered animal models, has a largely invariant cell lineage and stereotyped development which greatly facilitates comparisons between different individuals (Murray et al, 2008;Liu et al, 2009;Long et al, 2009).…”

Section: Animal Modelsmentioning

confidence: 99%

“…Carson et al (2005) discovered gene expression possibly related to Parkinson disease. Liu et al (2009) showed in C. elegans that different gene regulatory pathways can correlate with identical cell fates. However, cell fate modules with specific molecular signatures repeatedly occurred along the cell lineage, revealing bifurcations toward cell differentiation.…”

Section: Biological Insightsmentioning

confidence: 99%

Assembling models of embryo development: Image analysis and the construction of digital atlases

Castro-González

Ledesma-Carbayo

Peyriéras

et al. 2012

Birth Defects Research Pt C

View full text Add to dashboard Cite

Digital atlases of animal development provide a quantitative description of morphogenesis, opening the path toward processes modeling. Prototype atlases offer a data integration framework where to gather information from cohorts of individuals with phenotypic variability. Relevant information for further theoretical reconstruction includes measurements in time and space for cell behaviors and gene expression. The latter as well as data integration in a prototypic model, rely on image processing strategies. Developing the tools to integrate and analyze biological multidimensional data are highly relevant for assessing chemical toxicity or performing drugs preclinical testing. This article surveys some of the most prominent efforts to assemble these prototypes, categorizes them according to salient criteria and discusses the key questions in the field and the future challenges toward the reconstruction of multiscale dynamics in model organisms.

show abstract

Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans

Cited by 135 publications

References 30 publications

Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation

Epigenetic stability increases extensively during Drosophila follicle stem cell differentiation

Conserved gene regulatory module specifies lateral neural borders across bilaterians

Assembling models of embryo development: Image analysis and the construction of digital atlases

Contact Info

Product

Resources

About