1
|
Duan X, Wang H, Cao Z, Su N, Wang Y, Zheng Y. Deficiency of ValRS-m Causes Male Infertility in Drosophila melanogaster. Int J Mol Sci 2024; 25:7489. [PMID: 39000597 PMCID: PMC11242588 DOI: 10.3390/ijms25137489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Drosophila spermatogenesis involves the renewal of germline stem cells, meiosis of spermatocytes, and morphological transformation of spermatids into mature sperm. We previously demonstrated that Ocnus (ocn) plays an essential role in spermatogenesis. The ValRS-m (Valyl-tRNA synthetase, mitochondrial) gene was down-regulated in ocn RNAi testes. Here, we found that ValRS-m-knockdown induced complete sterility in male flies. The depletion of ValRS-m blocked mitochondrial behavior and ATP synthesis, thus inhibiting the transition from spermatogonia to spermatocytes, and eventually, inducing the accumulation of spermatogonia during spermatogenesis. To understand the intrinsic reason for this, we further conducted transcriptome-sequencing analysis for control and ValRS-m-knockdown testes. The differentially expressed genes (DEGs) between these two groups were selected with a fold change of ≥2 or ≤1/2. Compared with the control group, 4725 genes were down-regulated (dDEGs) and 2985 genes were up-regulated (uDEGs) in the ValRS-m RNAi group. The dDEGs were mainly concentrated in the glycolytic pathway and pyruvate metabolic pathway, and the uDEGs were primarily related to ribosomal biogenesis. A total of 28 DEGs associated with mitochondria and 6 meiosis-related genes were verified to be suppressed when ValRS-m was deficient. Overall, these results suggest that ValRS-m plays a wide and vital role in mitochondrial behavior and spermatogonia differentiation in Drosophila.
Collapse
Affiliation(s)
- Xin Duan
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Haolin Wang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Zhixian Cao
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Na Su
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Yufeng Wang
- School of Life Sciences, Central China Normal University, Wuhan 430079, China; (X.D.); (H.W.); (Z.C.); (Y.W.)
| | - Ya Zheng
- School of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| |
Collapse
|
2
|
Anderson JT, Henikoff S, Ahmad K. Chromosome-specific maturation of the epigenome in the Drosophila male germline. eLife 2023; 12:RP89373. [PMID: 38032818 PMCID: PMC10688970 DOI: 10.7554/elife.89373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.
Collapse
Affiliation(s)
- James T Anderson
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer CenterSeattleUnited States
| |
Collapse
|
3
|
Anderson J, Henikoff S, Ahmad K. Chromosome-specific maturation of the epigenome in the Drosophila male germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529909. [PMID: 37873332 PMCID: PMC10592605 DOI: 10.1101/2023.02.24.529909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Spermatogenesis in the Drosophila male germline proceeds through a unique transcriptional program controlled both by germline-specific transcription factors and by testis-specific versions of core transcriptional machinery. This program includes the activation of genes on the heterochromatic Y chromosome, and reduced transcription from the X chromosome, but how expression from these sex chromosomes is regulated has not been defined. To resolve this, we profiled active chromatin features in the testes from wildtype and meiotic arrest mutants and integrate this with single-cell gene expression data from the Fly Cell Atlas. These data assign the timing of promoter activation for genes with germline-enriched expression throughout spermatogenesis, and general alterations of promoter regulation in germline cells. By profiling both active RNA polymerase II and histone modifications in isolated spermatocytes, we detail widespread patterns associated with regulation of the sex chromosomes. Our results demonstrate that the X chromosome is not enriched for silencing histone modifications, implying that sex chromosome inactivation does not occur in the Drosophila male germline. Instead, a lack of dosage compensation in spermatocytes accounts for the reduced expression from this chromosome. Finally, profiling uncovers dramatic ubiquitinylation of histone H2A and lysine-16 acetylation of histone H4 across the Y chromosome in spermatocytes that may contribute to the activation of this heterochromatic chromosome.
Collapse
Affiliation(s)
- James Anderson
- Basic Sciences Division, Fred Hutchinson Cancer Center; Seattle, WA, 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center; Seattle, WA, 98109, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center; Seattle, WA, 98109, USA
| |
Collapse
|
4
|
Raz AA, Vida GS, Stern SR, Mahadevaraju S, Fingerhut JM, Viveiros JM, Pal S, Grey JR, Grace MR, Berry CW, Li H, Janssens J, Saelens W, Shao Z, Hu C, Yamashita YM, Przytycka T, Oliver B, Brill JA, Krause H, Matunis EL, White-Cooper H, DiNardo S, Fuller MT. Emergent dynamics of adult stem cell lineages from single nucleus and single cell RNA-Seq of Drosophila testes. eLife 2023; 12:e82201. [PMID: 36795469 PMCID: PMC9934865 DOI: 10.7554/elife.82201] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
Proper differentiation of sperm from germline stem cells, essential for production of the next generation, requires dramatic changes in gene expression that drive remodeling of almost all cellular components, from chromatin to organelles to cell shape itself. Here, we provide a single nucleus and single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq (snRNA-seq) data from the Fly Cell Atlas (FCA) study. With over 44,000 nuclei and 6000 cells analyzed, the data provide identification of rare cell types, mapping of intermediate steps in differentiation, and the potential to identify new factors impacting fertility or controlling differentiation of germline and supporting somatic cells. We justify assignment of key germline and somatic cell types using combinations of known markers, in situ hybridization, and analysis of extant protein traps. Comparison of single cell and single nucleus datasets proved particularly revealing of dynamic developmental transitions in germline differentiation. To complement the web-based portals for data analysis hosted by the FCA, we provide datasets compatible with commonly used software such as Seurat and Monocle. The foundation provided here will enable communities studying spermatogenesis to interrogate the datasets to identify candidate genes to test for function in vivo.
Collapse
Affiliation(s)
- Amelie A Raz
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Gabriela S Vida
- Department of Cell and Developmental Biology, The Perelman School of Medicine and The Penn Institute for Regenerative MedicinePhiladelphiaUnited States
| | - Sarah R Stern
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
| | - Sharvani Mahadevaraju
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Jaclyn M Fingerhut
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Jennifer M Viveiros
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Soumitra Pal
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Jasmine R Grey
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Mara R Grace
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Cameron W Berry
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
| | - Hongjie Li
- Huffington Center on Aging and Department of Molecular and Human Genetics, Baylor College of MedicineHoustonUnited States
| | - Jasper Janssens
- JVIB Center for Brain & Disease Research, and the Department of Human Genetics, KU LeuvenLeuvenBelgium
| | - Wouter Saelens
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, and Department of Applied Mathematics, Computer Science and Statistics, Ghent UniversityGhentBelgium
| | - Zhantao Shao
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Chun Hu
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Yukiko M Yamashita
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Howard Hughes Medical InstituteCambridgeUnited States
| | - Teresa Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Brian Oliver
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaUnited States
| | - Julie A Brill
- Cell Biology Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
- Institute of Medical Science, University of TorontoTorontoCanada
| | - Henry Krause
- Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Molecular Genetics, University of TorontoTorontoCanada
| | - Erika L Matunis
- Department of Cell Biology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | | | - Stephen DiNardo
- Department of Cell and Developmental Biology, The Perelman School of Medicine and The Penn Institute for Regenerative MedicinePhiladelphiaUnited States
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
| |
Collapse
|
5
|
Ridwan SM, Antel M, Inaba M. Enrichment of Undifferentiated Germline and Somatic Cells from Drosophila Testes. Methods Mol Biol 2023; 2677:127-138. [PMID: 37464239 DOI: 10.1007/978-1-0716-3259-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Drosophila male germline provides a strong model system to understand numerous developmental and cell-biological processes, owing to a well-defined anatomy and cell type markers in combination with various genetic tools available for the Drosophila system. A major weakness of this system has been the difficulty of approaches for obtaining material for biochemical assays, proteomics, and genomic or transcriptomic profiling due to small-size and complex tissues. However, the recent development of techniques has started allowing us the usage of a low amount of material for these analyses and now we can strategize many new experiments. The method for enrichment or isolation of rare populations of cells is still challenging and should meaningfully influence the reliability of the results. Here, we provide our semi-optimized protocol of enrichment of undifferentiated germ cells and somatic cells from non-tumorous Drosophila testis, which we have successfully improved after multiple trials.
Collapse
Affiliation(s)
- Sharif M Ridwan
- Department of Cell Biology, University of Connecticut Health, Farmington, CT, USA
| | - Matthew Antel
- Department of Cell Biology, University of Connecticut Health, Farmington, CT, USA
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health, Farmington, CT, USA.
| |
Collapse
|
6
|
Yang D, Xiao F, Li J, Wang S, Fan X, Ni Q, Li Y, Zhang M, Yan T, Yang M, He Z. Age-related ceRNA networks in adult Drosophila ageing. Front Genet 2023; 14:1096902. [PMID: 36926584 PMCID: PMC10012872 DOI: 10.3389/fgene.2023.1096902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/10/2023] [Indexed: 03/06/2023] Open
Abstract
As Drosophila is an extensively used genetic model system, understanding of its regulatory networks has great significance in revealing the genetic mechanisms of ageing and human diseases. Competing endogenous RNA (ceRNA)-mediated regulation is an important mechanism by which circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs) regulate ageing and age-related diseases. However, extensive analyses of the multiomics (circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA) characteristics of adult Drosophila during ageing have not been reported. Here, differentially expressed circRNAs and microRNAs (miRNAs) between 7 and 42-day-old flies were screened and identified. Then, the differentially expressed mRNAs, circRNAs, miRNAs, and lncRNAs between the 7- and 42-day old flies were analysed to identify age-related circRNA/miRNA/mRNA and lncRNA/miRNA/mRNA networks in ageing Drosophila. Several key ceRNA networks were identified, such as the dme_circ_0009500/dme_miR-289-5p/CG31064, dme_circ_0009500/dme_miR-289-5p/frizzled, dme_circ_0009500/dme_miR-985-3p/Abl, and XLOC_027736/dme_miR-985-3p/Abl XLOC_189909/dme_miR-985-3p/Abl networks. Furthermore, real-time quantitative PCR (qPCR) was used to verify the expression level of those genes. Those results suggest that the discovery of these ceRNA networks in ageing adult Drosophila provide new information for research on human ageing and age-related diseases.
Collapse
Affiliation(s)
- Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feng Xiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiamei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Siqi Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qingyong Ni
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
7
|
Rubin T, Macaisne N, Vallés AM, Guilleman C, Gaugué I, Dal Toe L, Huynh JR. Premeiotic pairing of homologous chromosomes during Drosophila male meiosis. Proc Natl Acad Sci U S A 2022; 119:e2207660119. [PMID: 36375065 PMCID: PMC9704699 DOI: 10.1073/pnas.2207660119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 10/07/2022] [Indexed: 11/15/2022] Open
Abstract
In the early stages of meiosis, maternal and paternal chromosomes pair with their homologous partner and recombine to ensure exchange of genetic information and proper segregation. These events can vary drastically between species and between males and females of the same species. In Drosophila, in contrast to females, males do not form synaptonemal complexes (SCs), do not recombine, and have no crossing over; yet, males are able to segregate their chromosomes properly. Here, we investigated the early steps of homolog pairing in Drosophila males. We found that homolog centromeres are not paired in germline stem cells (GSCs) and become paired in the mitotic region before meiotic entry, similarly to females. Surprisingly, male germline cells express SC proteins, which localize to centromeres and promote pairing. We further found that the SUN/KASH (LINC) complex and microtubules are required for homolog pairing as in females. Chromosome movements in males, however, are much slower than in females and we demonstrate that this slow dynamic is compensated in males by having longer cell cycles. In agreement, slowing down cell cycles was sufficient to rescue pairing-defective mutants in female meiosis. Our results demonstrate that although meiosis differs significantly between males and females, sex-specific cell cycle kinetics integrate similar molecular mechanisms to achieve proper centromere pairing.
Collapse
Affiliation(s)
- Thomas Rubin
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | | | - Ana Maria Vallés
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Clara Guilleman
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Isabelle Gaugué
- Department of Genetics and Developmental Biology, CNRS UMR 3215, INSERM U934, Institut Curie, 75005 Paris, France
| | - Laurine Dal Toe
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| | - Jean-René Huynh
- Center for Interdisciplinary Research in Biology, CNRS UMR 7241, INSERM U1050, Collège de France and Paris Sciences & Lettres Research University, 75231 Paris Cedex 05, France
| |
Collapse
|
8
|
Dosage Compensation in Drosophila: Its Canonical and Non-Canonical Mechanisms. Int J Mol Sci 2022; 23:ijms231810976. [PMID: 36142884 PMCID: PMC9506574 DOI: 10.3390/ijms231810976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Dosage compensation equalizes gene expression in a single male X chromosome with that in the pairs of autosomes and female X chromosomes. In the fruit fly Drosophila, canonical dosage compensation is implemented by the male-specific lethal (MSL) complex functioning in all male somatic cells. This complex contains acetyl transferase males absent on the first (MOF), which performs H4K16 hyperacetylation specifically in the male X chromosome, thus facilitating transcription of the X-linked genes. However, accumulating evidence points to an existence of additional, non-canonical dosage compensation mechanisms operating in somatic and germline cells. In this review, we discuss current advances in the understanding of both canonical and non-canonical mechanisms of dosage compensation in Drosophila.
Collapse
|
9
|
Lee S, Chen YC, Gillen AE, Taliaferro JM, Deplancke B, Li H, Lai EC. Diverse cell-specific patterns of alternative polyadenylation in Drosophila. Nat Commun 2022; 13:5372. [PMID: 36100597 PMCID: PMC9470587 DOI: 10.1038/s41467-022-32305-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022] Open
Abstract
Most genes in higher eukaryotes express isoforms with distinct 3' untranslated regions (3' UTRs), generated by alternative polyadenylation (APA). Since 3' UTRs are predominant locations of post-transcriptional regulation, APA can render such programs conditional, and can also alter protein sequences via alternative last exon (ALE) isoforms. We previously used 3'-sequencing from diverse Drosophila samples to define multiple tissue-specific APA landscapes. Here, we exploit comprehensive single nucleus RNA-sequencing data (Fly Cell Atlas) to elucidate cell-type expression of 3' UTRs across >250 adult Drosophila cell types. We reveal the cellular bases of multiple tissue-specific APA/ALE programs, such as 3' UTR lengthening in differentiated neurons and 3' UTR shortening in spermatocytes and spermatids. We trace dynamic 3' UTR patterns across cell lineages, including in the male germline, and discover new APA patterns in the intestinal stem cell lineage. Finally, we correlate expression of RNA binding proteins (RBPs), miRNAs and global levels of cleavage and polyadenylation (CPA) factors in several cell types that exhibit characteristic APA landscapes, yielding candidate regulators of transcriptome complexity. These analyses provide a comprehensive foundation for future investigations of mechanisms and biological impacts of alternative 3' isoforms across the major cell types of this widely-studied model organism.
Collapse
Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY, 10065, USA
| | - Yen-Chung Chen
- Department of Biology, New York University, New York, NY, 10013, USA
| | | | - Austin E Gillen
- Division of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Rocky Mountain Regional VA Medical Center, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Matthew Taliaferro
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bio-engineering & Global Health Institute, School of Life Sciences, EPFL, CH-1015, Lausanne, Switzerland
| | - Hongjie Li
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY, 10065, USA.
| |
Collapse
|
10
|
Su J, Zhang Y, Su H, Wang C, Wang D, Yang Y, Li X, Qi W, Li H, Li X, Song Y, Cao G. Dosage Compensation of the X Chromosome during Sheep Testis Development Revealed by Single-Cell RNA Sequencing. Animals (Basel) 2022; 12:ani12172169. [PMID: 36077890 PMCID: PMC9454834 DOI: 10.3390/ani12172169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Male and female mammals carry the same complement of autosomes but differ with respect to their sex chromosomes: females carry XX chromosomes and males carry XY chromosomes. The evolutionary loss of genes from the Y chromosome led to a disparity in the dosage of X chromosomes versus autosomal genes, with males becoming monosomic for X-linked gene products. An imbalance in gene expression may have detrimental consequences. In males, X-linked genes need to be upregulated to levels equal to those of females, which is called dosage compensation. The existence of dosage compensation in germ cells is controversial. In testis, dosage compensation is thought to cease during meiosis. Some studies showed that the X chromosome is inactivated during meiosis and premature transcriptional inactivation of the X and Y chromosome during mid-spermatogenesis is essential for fertility. However, some studies failed to find support for male germline X inactivation. Using single-cell RNA seq data, in this study, we presented a comprehensive transcriptional map of sheep testes at different developmental stages and found that germ cell types in sheep testes show X-chromosome expression similar to that in the autosomes. The dosage compensation of germ cells at different stages was analyzed. MSL complex members are expressed in female flies and orthologs exist in many species, where dosage compensation mechanisms are absent or fundamentally different. This suggests that the MSL complex members also function outside of the dosage compensation machinery. Studies have shown that MSL complex can regulate mammalian X inactivation and activation. Abstract Dosage compensation is a mechanism first proposed by Susumu Ohno, whereby X inactivation balances X gene output between males (XY) and females (XX), while X upregulation balances X genes with autosomal gene output. These mechanisms have been actively studied in Drosophila and mice, but research regarding them lags behind in domestic species. It is unclear how the X chromosome is regulated in the sheep male germline. To address this, using single-cell RNA sequencing, we analyzed testes in three important developmental stages of sheep. We observed that the total RNA per cell from X and autosomes peaked in SSCs and spermatogonia and was then reduced in early spermatocytes. Furthermore, we counted the detected reads per gene in each cell type for X and autosomes. In cells experiencing dose compensation, close proximity to MSL (male-specific lethal), which is regulated the active X chromosome and was observed. Our results suggest that there is no dose compensation in the pre-meiotic germ cells of sheep testes and, in addition, MSL1 and MSL2 are expressed in early germ cells and involved in regulating mammalian X-chromosome inactivation and activation.
Collapse
Affiliation(s)
- Jie Su
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
- Department of Psychosomatic Medicine, Inner Mongolia Medical University, Hohhot 010030, China
| | - Yue Zhang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Hong Su
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Caiyun Wang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Daqing Wang
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Yanyan Yang
- Inner Mongolia Academy of Agriculture & Animal Husbandry Sciences, Hohhot 010000, China
| | - Xiunan Li
- Inner Mongolia Academy of Agriculture & Animal Husbandry Sciences, Hohhot 010000, China
| | - Wangmei Qi
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Haijun Li
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
| | - Xihe Li
- Inner Mongolia Saikexing Institutes of Breeding and Reproductive Biotechnologies in Domestic Animal, Hohhot 011517, China
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University, Hohhot 010021, China
| | - Yongli Song
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Science, Inner Mongolia University, Hohhot 010021, China
- Correspondence: (Y.S.); (G.C.); Tel.: +86-133-6601-7565 (Y.S.); +86-138-4812-0488 (G.C.)
| | - Guifang Cao
- Inner Mongolia Key Laboratory of Basic Veterinary Science, Inner Mongolia Agriculture University, Hohhot 010018, China
- Correspondence: (Y.S.); (G.C.); Tel.: +86-133-6601-7565 (Y.S.); +86-138-4812-0488 (G.C.)
| |
Collapse
|
11
|
Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O'Connor-Giles KM, Furlong EEM, Shendure J. The continuum of Drosophila embryonic development at single-cell resolution. Science 2022; 377:eabn5800. [PMID: 35926038 PMCID: PMC9371440 DOI: 10.1126/science.abn5800] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning the entirety of embryogenesis. Leveraging developmental asynchronicity within embryo collections, we applied deep neural networks to infer the age of each nucleus, resulting in continuous, multimodal views of molecular and cellular transitions in absolute time. We identify cell lineages; infer their developmental relationships; and link dynamic changes in enhancer usage, transcription factor (TF) expression, and the accessibility of TFs' cognate motifs. With these data, the dynamics of enhancer usage and gene expression can be explored within and across lineages at the scale of minutes, including for precise transitions like zygotic genome activation.
Collapse
Affiliation(s)
- Diego Calderon
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ronnie Blecher-Gonen
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - James Kentro
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Beth Martin
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alessandro Dulja
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
| | - Erica Larschan
- Molecular Biology, Cell Biology, and Biochemistry Graduate Program, Brown University, Providence, RI 02912, USA
| | - Kate M O'Connor-Giles
- Department of Neuroscience and Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.,Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
12
|
Carro MDLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol 2022; 151:245-279. [PMID: 36681472 DOI: 10.1016/bs.ctdb.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Meiosis is characterized by highly regulated transitions in gene expression that require diverse mechanisms of gene regulation. For example, in male mammals, transcription undergoes a global shut-down in early prophase I of meiosis, followed by increasing transcriptional activity into pachynema. Later, as spermiogenesis proceeds, the histones bound to DNA are replaced with transition proteins, which are themselves replaced with protamines, resulting in a highly condensed nucleus with repressed transcriptional activity. In addition, two specialized gene silencing events take place during prophase I: meiotic silencing of unsynapsed chromatin (MSUC), and the sex chromatin specific mechanism, meiotic sex chromosome inactivation (MSCI). Notably, conserved roles for the RNA binding protein (RBP) machinery that functions with small non-coding RNAs have been described as participating in these meiosis-specific mechanisms, suggesting that RNA-mediated gene regulation is critical for fertility in many species. Here, we review roles of small RNAs and their associated RBPs in meiosis-related processes such as centromere function, silencing of unpaired chromatin and meiotic recombination. We will discuss the emerging evidence of non-canonical functions of these components in meiosis.
Collapse
Affiliation(s)
- María de Las Mercedes Carro
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States
| | - Andrew Grimson
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, United States.
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States.
| |
Collapse
|
13
|
Ranjan R, Snedeker J, Wooten M, Chu C, Bracero S, Mouton T, Chen X. Differential condensation of sister chromatids acts with Cdc6 to ensure asynchronous S-phase entry in Drosophila male germline stem cell lineage. Dev Cell 2022; 57:1102-1118.e7. [PMID: 35483360 PMCID: PMC9134767 DOI: 10.1016/j.devcel.2022.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/16/2022] [Accepted: 04/05/2022] [Indexed: 01/06/2023]
Abstract
During Drosophila melanogaster male germline stem cell (GSC) asymmetric division, preexisting old versus newly synthesized histones H3 and H4 are asymmetrically inherited. However, the biological outcomes of this phenomenon have remained unclear. Here, we tracked old and new histones throughout the GSC cell cycle through the use of high spatial and temporal resolution microscopy. We found unique features that differ between old and new histone-enriched sister chromatids, including differences in nucleosome density, chromosomal condensation, and H3 Ser10 phosphorylation. These distinct chromosomal features lead to their differential association with Cdc6, a pre-replication complex component, and subsequent asynchronous DNA replication initiation in the resulting daughter cells. Disruption of asymmetric histone inheritance abolishes differential Cdc6 association and asynchronous S-phase entry, demonstrating that histone asymmetry acts upstream of these critical cell-cycle progression events. Furthermore, disruption of these GSC-specific chromatin features leads to GSC defects, indicating a connection between histone inheritance, cell-cycle progression, and cell fate determination.
Collapse
Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Carolina Chu
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sabrina Bracero
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taylar Mouton
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|
14
|
Mitotic drive in asymmetric epigenetic inheritance. Biochem Soc Trans 2022; 50:675-688. [PMID: 35437581 PMCID: PMC9162470 DOI: 10.1042/bst20200267] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 01/14/2023]
Abstract
Asymmetric cell division (ACD) produces two daughter cells with distinct cell fates. This division mode is widely used during development and by adult stem cells during tissue homeostasis and regeneration, which can be regulated by both extrinsic cues such as signaling molecules and intrinsic factors such as epigenetic information. While the DNA replication process ensures that the sequences of sister chromatids are identical, how epigenetic information is re-distributed during ACD has remained largely unclear in multicellular organisms. Studies of Drosophila male germline stem cells (GSCs) have revealed that sister chromatids incorporate pre-existing and newly synthesized histones differentially and segregate asymmetrically during ACD. To understand the underlying molecular mechanisms of this phenomenon, two key questions must be answered: first, how and when asymmetric histone information is established; and second, how epigenetically distinct sister chromatids are distinguished and segregated. Here, we discuss recent advances which help our understanding of this interesting and important cell division mode.
Collapse
|
15
|
Martinez P, Ballarin L, Ereskovsky AV, Gazave E, Hobmayer B, Manni L, Rottinger E, Sprecher SG, Tiozzo S, Varela-Coelho A, Rinkevich B. Articulating the "stem cell niche" paradigm through the lens of non-model aquatic invertebrates. BMC Biol 2022; 20:23. [PMID: 35057814 PMCID: PMC8781081 DOI: 10.1186/s12915-022-01230-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Stem cells (SCs) in vertebrates typically reside in "stem cell niches" (SCNs), morphologically restricted tissue microenvironments that are important for SC survival and proliferation. SCNs are broadly defined by properties including physical location, but in contrast to vertebrates and other "model" organisms, aquatic invertebrate SCs do not have clearly documented niche outlines or properties. Life strategies such as regeneration or asexual reproduction may have conditioned the niche architectural variability in aquatic or marine animal groups. By both establishing the invertebrates SCNs as independent types, yet allowing inclusiveness among them, the comparative analysis will allow the future functional characterization of SCNs.
Collapse
Affiliation(s)
- P Martinez
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - L Ballarin
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35100, Padova, Italy
| | - A V Ereskovsky
- Aix Marseille University, Avignon Université, CNRS, IRD, IMBE, Marseille, France
- St. Petersburg State University, Biological Faculty, Universitetskaya emb. 7/9, St. Petersburg, 199034, Russia
- N. K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Street 26, Moscow, 119334, Russia
| | - E Gazave
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - B Hobmayer
- Department of Zoology and Center of Molecular Biosciences, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - L Manni
- Department of Biology, University of Padova, Via U. Bassi 58/B, 35100, Padova, Italy
| | - E Rottinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN), Nice, France
- Université Côte d'Azur, Federative Research Institute - Marine Resources (IFR MARRES), Nice, France
| | - S G Sprecher
- Department of Biology, University of Fribourg, Chemin du Musee 10, 1700, Fribourg, Switzerland
| | - S Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer (LBDV), Paris, France
| | - A Varela-Coelho
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Av. da República, 2780-157, Oeiras, Portugal
| | - B Rinkevich
- Israel Oceanography and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 8030, 31080, Haifa, Israel.
| |
Collapse
|
16
|
Ilyin AA, Kononkova AD, Golova AV, Shloma VV, Olenkina O, Nenasheva V, Abramov Y, Kotov AA, Maksimov D, Laktionov P, Pindyurin A, Galitsyna A, Ulianov S, Khrameeva E, Gelfand M, Belyakin S, Razin S, Shevelyov Y. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3203-3225. [PMID: 35166842 PMCID: PMC8989536 DOI: 10.1093/nar/gkac109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.
Collapse
Affiliation(s)
| | | | | | | | | | - Valentina V Nenasheva
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Yuri A Abramov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Alexei A Kotov
- Institute of Molecular Genetics of National Research Centre “Kurchatov Institute”, Moscow 123182, Russia
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Petr P Laktionov
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Ekaterina E Khrameeva
- Correspondence may also be addressed to Ekaterina Khrameeva. Tel: +7 495 2801481; Fax: +7 495 2801481;
| | - Mikhail S Gelfand
- Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Stepan N Belyakin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow119334, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yuri Y Shevelyov
- To whom correspondence should be addressed. Tel: +7 499 1960809; Fax: +7 499 1960221;
| |
Collapse
|
17
|
Gadre P, Nitsure N, Mazumdar D, Gupta S, Ray K. The rates of stem cell division determine the cell cycle lengths of its lineage. iScience 2021; 24:103232. [PMID: 34746698 PMCID: PMC8555441 DOI: 10.1016/j.isci.2021.103232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 09/10/2021] [Accepted: 10/01/2021] [Indexed: 01/10/2023] Open
Abstract
Adult stem cells and their transit-amplifying progeny alter their proliferation rates to maintain tissue homeostasis. To test how the division rates of stem cells and transit-amplifying progeny affect tissue growth and differentiation, we developed a computation strategy that estimates the average cell-cycle lengths (lifespans) of germline stem cells and their progeny from fixed-tissue demography in the Drosophila testis. Analysis of the wild-type data using this method indicated that during the germline transit-amplification, the cellular lifespans extend by nearly 1.3-fold after the first division and shrink by about 2-folds after the second division. Cell-autonomous perturbations of the stem cell lifespan accordingly altered the lifespans of successive transit-amplifying stages. Remarkably, almost 2-fold alterations in the lifespans of stem cells and their immediate daughters did not affect the subsequent differentiation. The results indicate that the early germline division rates can adjust the following division rates and the onset of differentiation. Prediction of cellular lifespan from the demography of transit-amplifying cells Lifespans of spermatogonial cells change anomalously during transit-amplification Anomalous lifespan extension during transit-amplification precedes the onset of Bam Lifespan changes of early TA stages readjust that of the subsequent stages
Collapse
Affiliation(s)
- Purna Gadre
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Nitin Nitsure
- School of Mathematics, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| | - Debasmita Mazumdar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.,Biology Department, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India
| | - Samir Gupta
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India.,Department of Molecular and Life Sciences, University Zurich, 80006 Zürich, Switzerland
| | - Krishanu Ray
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, Maharashtra 400005, India
| |
Collapse
|
18
|
Li YR, Lai HW, Huang HH, Chen HC, Fugmann SD, Yang SY. Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation. Genome Res 2021; 31:1011-1023. [PMID: 33858841 PMCID: PMC8168578 DOI: 10.1101/gr.271148.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 04/07/2021] [Indexed: 01/29/2023]
Abstract
Germ cells in Drosophila melanogaster are specified maternally shortly after fertilization and are transcriptionally quiescent until their zygotic genome is activated to sustain further development. To understand the molecular basis of this process, we analyzed the progressing transcriptomes of early male and female germ cells at the single-cell level between germline specification and coalescence with somatic gonadal cells. Our data comprehensively cover zygotic activation in the germline genome, and analyses on genes that exhibit germline-restricted expression reveal that polymerase pausing and differential RNA stability are important mechanisms that establish gene expression differences between the germline and soma. In addition, we observe an immediate bifurcation between the male and female germ cells as zygotic transcription begins. The main difference between the two sexes is an elevation in X Chromosome expression in females relative to males, signifying incomplete dosage compensation, with a few select genes exhibiting even higher expression increases. These indicate that the male program is the default mode in the germline that is driven to female development with a second X Chromosome.
Collapse
Affiliation(s)
- Yi-Ru Li
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsiao Wen Lai
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsiao Han Huang
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Hsing-Chun Chen
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan
| | - Sebastian D Fugmann
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Department of Nephrology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan
| | - Shu Yuan Yang
- Department and College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan 333 Taiwan.,Department of Gynecology, Linkou Chang Gung Memorial Hospital, Kweishan, Taoyuan 333 Taiwan
| |
Collapse
|
19
|
Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos. Sci Rep 2021; 11:4890. [PMID: 33649478 PMCID: PMC7921590 DOI: 10.1038/s41598-021-84402-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Dosage compensation is a mechanism that equalizes sex chromosome gene expression between the sexes. In Drosophila, individuals with two X chromosomes (XX) become female, whereas males have one X chromosome (XY). In males, dosage compensation of the X chromosome in the soma is achieved by five proteins and two non-coding RNAs, which assemble into the male-specific lethal (MSL) complex to upregulate X-linked genes twofold. By contrast, it remains unclear whether dosage compensation occurs in the germline. To address this issue, we performed transcriptome analysis of male and female primordial germ cells (PGCs). We found that the expression levels of X-linked genes were approximately twofold higher in female PGCs than in male PGCs. Acetylation of lysine residue 16 on histone H4 (H4K16ac), which is catalyzed by the MSL complex, was undetectable in these cells. In male PGCs, hyperactivation of X-linked genes and H4K16ac were induced by overexpression of the essential components of the MSL complex, which were expressed at very low levels in PGCs. Together, these findings indicate that failure of MSL complex formation results in the absence of X-chromosome dosage compensation in male PGCs.
Collapse
|
20
|
Ma B, Trieu TJ, Cheng J, Zhou S, Tang Q, Xie J, Liu JL, Zhao K, Habib SJ, Chen X. Differential Histone Distribution Patterns in Induced Asymmetrically Dividing Mouse Embryonic Stem Cells. Cell Rep 2020; 32:108003. [PMID: 32783931 PMCID: PMC7962874 DOI: 10.1016/j.celrep.2020.108003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 11/03/2019] [Accepted: 07/15/2020] [Indexed: 12/14/2022] Open
Abstract
Wnt3a-coated beads can induce asymmetric divisions of mouse embryonic stem cells (mESCs), resulting in one self-renewed mESC and one differentiating epiblast stem cell. This provides an opportunity for studying histone inheritance pattern at a single-cell resolution in cell culture. Here, we report that mESCs with Wnt3a-bead induction display nonoverlapping preexisting (old) versus newly synthesized (new) histone H3 patterns, but mESCs without Wnt3a beads have largely overlapping patterns. Furthermore, H4K20me2/3, an old histone-enriched modification, displays a higher instance of asymmetric distribution on chromatin fibers from Wnt3a-induced mESCs than those from non-induced mESCs. These locally distinct distributions between old and new histones have both cellular specificity in Wnt3a-induced mESCs and molecular specificity for histones H3 and H4. Given that post-translational modifications at H3 and H4 carry the major histone modifications, our findings provide a mammalian cell culture system to study histone inheritance for maintaining stem cell fate and for resetting it during differentiation.
Collapse
Affiliation(s)
- Binbin Ma
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Research Center for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China; Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tung-Jui Trieu
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Ji Cheng
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA
| | - Shuang Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qingsong Tang
- Systems Biology Center, Division of Intramural Research, NHLBI, NIH, Bethesda, MD, USA
| | - Jing Xie
- Research Center for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Keji Zhao
- Systems Biology Center, Division of Intramural Research, NHLBI, NIH, Bethesda, MD, USA
| | - Shukry J Habib
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| |
Collapse
|