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Gao NP, Gandrillon O, Páldi A, Herbach U, Gunawan R. Single-cell transcriptional uncertainty landscape of cell differentiation. F1000Res 2023; 12:426. [PMID: 37545651 PMCID: PMC10400935 DOI: 10.12688/f1000research.131861.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/08/2023] Open
Abstract
Background: Single-cell studies have demonstrated the presence of significant cell-to-cell heterogeneity in gene expression. Whether such heterogeneity is only a bystander or has a functional role in the cell differentiation process is still hotly debated. Methods: In this study, we quantified and followed single-cell transcriptional uncertainty - a measure of gene transcriptional stochasticity in single cells - in 10 cell differentiation systems of varying cell lineage progressions, from single to multi-branching trajectories, using the stochastic two-state gene transcription model. Results: By visualizing the transcriptional uncertainty as a landscape over a two-dimensional representation of the single-cell gene expression data, we observed universal features in the cell differentiation trajectories that include: (i) a peak in single-cell uncertainty during transition states, and in systems with bifurcating differentiation trajectories, each branching point represents a state of high transcriptional uncertainty; (ii) a positive correlation of transcriptional uncertainty with transcriptional burst size and frequency; (iii) an increase in RNA velocity preceding the increase in the cell transcriptional uncertainty. Conclusions: Our findings suggest a possible universal mechanism during the cell differentiation process, in which stem cells engage stochastic exploratory dynamics of gene expression at the start of the cell differentiation by increasing gene transcriptional bursts, and disengage such dynamics once cells have decided on a particular terminal cell identity. Notably, the peak of single-cell transcriptional uncertainty signifies the decision-making point in the cell differentiation process.
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Affiliation(s)
- Nan Papili Gao
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Zurich, 8093, Switzerland
| | - Olivier Gandrillon
- Laboratoire de Biologie et Modélisation de la Cellule, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, F69364, France
- Équipe Dracula, Inria Center Lyon, Villeurbanne, F69100, France
| | - András Páldi
- St-Antoine Research Center, Ecole Pratique des Hautes Etudes PSL, Paris, F-75012, France
| | - Ulysse Herbach
- CNRS, Inria, IECL, Université de Lorraine, Nancy, F-54000, France
| | - Rudiyanto Gunawan
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Zurich, 8093, Switzerland
- Department of Chemical and Biological Engineering, University at Buffalo - SUNY, Buffalo, NY, 14260, USA
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Bhandari RK, Haque MM, Skinner MK. Global genome analysis of the downstream binding targets of testis determining factor SRY and SOX9. PLoS One 2012; 7:e43380. [PMID: 22984422 PMCID: PMC3440412 DOI: 10.1371/journal.pone.0043380] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 07/23/2012] [Indexed: 12/04/2022] Open
Abstract
A major event in mammalian male sex determination is the induction of the testis determining factor Sry and its downstream gene Sox9. The current study provides one of the first genome wide analyses of the downstream gene binding targets for SRY and SOX9 to help elucidate the molecular control of Sertoli cell differentiation and testis development. A modified ChIP-Chip analysis using a comparative hybridization was used to identify 71 direct downstream binding targets for SRY and 109 binding targets for SOX9. Interestingly, only 5 gene targets overlapped between SRY and SOX9. In addition to the direct response element binding gene targets, a large number of atypical binding gene targets were identified for both SRY and SOX9. Bioinformatic analysis of the downstream binding targets identified gene networks and cellular pathways potentially involved in the induction of Sertoli cell differentiation and testis development. The specific DNA sequence binding site motifs for both SRY and SOX9 were identified. Observations provide insights into the molecular control of male gonadal sex determination.
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Affiliation(s)
- Ramji K. Bhandari
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Md. M. Haque
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
| | - Michael K. Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, Washington, United States of America
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Hendriksen PJ, Drews U, Frankenhuis MT, Veerhuis R, Hengst SM, Wagner U, Braun S, Booman P. Daudi supernatant, unlike other H-Y antigen sources, exerts a sex-reversing effect on embryonic chick gonad differentiation. ANATOMY AND EMBRYOLOGY 1994; 189:317-25. [PMID: 8074322 DOI: 10.1007/bf00190588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In vitro cultures of intact chick gonads (organ cultures) and reaggregation cultures of dispersed gonad cells (roller cultures) were made. Gonads or gonad cells from 7-day-old chick embryos, at the stage when sex-specific differentiation begins, were cultured in the presence of presumed H-Y antigen-containing supernatants, or co-cultured in the presence of H-Y antigen-producing cell lines. The H-Y antigen-producing cells tested were of human, mouse, bovine and chicken origin. During organ culture, addition of supernatant of the human lymphoma cell line Daudi, or co-culture with Daudi cells, stimulated a clear proliferation of the germinal epithelium in male gonads, indicating feminization. A similar effect was obtained by treatment with estradiol. In reaggregation culture, the increase in nuclear size of germ cells was chosen as a parameter for feminization. A significant increase of germ cell nuclear size was observed in gonads cultured in the presence of Daudi supernatant. In both organ cultures and reaggregation cultures, other tested H-Y antigen sources and semi-purified H-Y antigen fractions did not exert significant effects on differentiation of the gonads or on the average area of the germ cell nuclei. These findings suggest that it is not H-Y antigen, but another protein produced by Daudi cells, that might be responsible for the sex-reversing effects.
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Affiliation(s)
- P J Hendriksen
- DLO-Institute for Animal Science and Health (ID-DLO), Research Branch Zeist, The Netherlands
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Lattermann U, Müller U. Immunoprecipitation of a male-specific polypeptide after in vitro translation of testicular poly(A)+ RNA. Hum Genet 1988; 79:305-8. [PMID: 3044974 DOI: 10.1007/bf00282166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Poly(A)+ RNAs from male and female gonads of 20-day-old rats were translated in vitro using rabbit reticulocyte lysates. The resulting polypeptides were incubated with specific anti-male (anti-H-Y) antisera raised in female rats by intrasplenic immunization with syngeneic male skin. Using a second antibody, a male-specific polypeptide of molecular weight approximately 18,000 was immunoprecipitated. This male-specific polypeptide was not cotranslationally modified in vitro and appeared to be identical to serological H-Y antigen.
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Affiliation(s)
- U Lattermann
- Abteilung für Gynäkologie und Geburfshilfe der Rheinisch-Westfälischen Technischen Hochschule, Aachen, Federal Republic of Germany
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Yang TJ. H-Y antigen expression in heterogametic males (XY) and females (ZW): a factor in reproductive strategy? EXPERIENTIA 1986; 42:190-1. [PMID: 3948974 DOI: 10.1007/bf01952462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The cells of heterogametic females with ZW sex chromosomes express H-Y or H-W antigen. A hypothesis is formulated to explain why these animals are capable of 'practicing' amphigonia retardata, i.e., delay in actual fertilization of eggs by retaining viable sperm within the oviduct for a considerable time (several months).
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Abstract
A concise overview of the transplantation biology of the H-Y antigen is presented with particular reference to: its prototypic behavior as a weak transplantation antigen; the facility with which mice of certain inbred strains can be rendered tolerant of H-Y incompatible skin grafts; its capacity to instigate graft-versus-host reactions; its significance in clinical transplantation; and finally, H-2 control of anti-H-Y immune responses. The role of the H-Y antigen in natural transplantation, i.e. pregnancy, is then reviewed. Evidence is presented to support the hypothesis that in certain cases maternal immune responses directed specifically to the H-Y antigen can exert selective pressures on male zygotes, producing deviant sex ratios in certain experimental and clinical situations.
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Wachtel SS, Koo GC, Breg WR, Genel M. H-Y antigen in X,i(Xq) gonadal dysgenesis: evidence of X-linked genes in testicular differentiation. Hum Genet 1980; 56:183-7. [PMID: 7450775 DOI: 10.1007/bf00295692] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Three years ago, we detected H-Y antigen in the white blood cells of a phenotypic female with several of the stigmata of Turner's syndrome, and the mosaic karyotype: 45,X/46,X,i(Xq). We surmised at the time that the isochromosome, i(Xq), may have contained occult Y-Chromosome-derived material. We have now confirmed the presence of H-Y in this patient and we have obtained evidence for the presence of H-Y in four of five other similar patients, all of whom are notable for carrying at least a single cell line with the karyotype 46,Xi(Xq). Although we cannot categorically exclude the presence of Y-chromosomal genes in the cells of these patients, there is no cytogenetic evidence of structural rearrangement involving the Y in any of the cases. Expression of H-Y structural genes are X-situated, or alternatively that they are autosomal and X-regulated. It would follow that the H-Y+ cellular phenotype per se is not a valid marker for the Y-chromosome, and that H-Y genes that have been mapped to the pericentric region of the Y may be regulatory.
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Abstract
Anti-H-Y antiserum, raised in highly inbred rats, is absorbed by gonadal cells of various species of fish. This cross-reactivity proved to be restricted to the male sex in the cyprinodont species Lebistes and Xiphophorus, known to have the XX/XY mechanism of sex determination. In members of the more primitive fish orders Isospondyli and Ostariophysi, cross-reactivity was shown to occur as well, but the amount of antiserum absorbed was very similar in both sexes. An antigen cross-reacting with mammalian anti-H-Y antiserum is assumed to exist in fish similar to that found in higher vertebrates. If this is true, this antigen may have been shared originally by both sexes. However, during evolution, its expression has become restricted to the heterogametic sex.
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Abstract
H-Y antigen, presumably the product of mammalian testis-determining genes, has been detected in three species of teleost fish, Xiphophorus maculatus. Haplochromis burtoni, and Oryzias latipes, and in hybrids of the genus Tilapia. In X. maculatus H-Y was most readily detected in YY males, suggesting that a genetic determinant of H-Y antigen expression may exist on the teleost Y-chromosome. Although H-Y was detected in males and not in feamles in each of the species that we studied, male heterogamety has not been firmly established for H. burtoni. Thus despite the extreme phlyogenetic conservation of H-Y genes and their association with the Y-chromosome, it remains open to question whether H-Y will always be found in the heterogametic sex, and whether serologically defined H-Y antigen plays any part in the differentiation of the teleost gonad.
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Nagai Y, Ciccarese S, Ohno S. The identification of human H-Y antigen and testicular transformation induced by its interaction with the receptor site of bovine fetal ovarian cells. Differentiation 1979; 13:155-64. [PMID: 94287 DOI: 10.1111/j.1432-0436.1979.tb01578.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
beta 2m(-), HLA (-) Daudi human male Burkitt lymphoma cells excreted a group of protein subunits that shared three distinctive characteristics; their conspicuously longer half-lives compared to more hydrophilic Daudi excreted proteins, their tendency to form progressively larger polymers by means of interchain disulfide bridges, and the extreme hydrophobicity of these polymers. The plasma membrane of extragonadal somatic cells absorbed 1.2 to 2.8% of these hydrophobic proteins. The unoccupied H-Y receptor sites residing on the plasma membrane of bovine fetal ovarian cells, on the other hand, selectively absorbed polymers of 18,000 mol. wt. subunits, and this antigen-receptor interaction, if allowed to continue for five days, induced the formation of tunica albuginea and seminiferous tubules in bovine XX embryonic indifferent gonads. In this manner, human H-Y antigen excreted by Daudi cells has functionally been identified as a series of polymers derived from 18,000 mol. wt. subunits. While, the H-Y antigenic determinants were retained even by the largest polymeric form that became irreversibly water insoluble, the receptor binding activity was shown only by 36.8% of the available polymeric forms of 18,000 mol. wt. subunits, at the most. Nevertheless, once bound to the receptor site, these polymers were rapidly reduced to the monomeric form on the plasma membrane of bovine fetal ovarian cells. Accordingly, the 18,000 mol. wt. monomer might actually represent the functional form of H-Y antigen.
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