scholarly journals On the origin and evolution of Drosophila new genes during spermatogenesis

2021 ◽  
Author(s):  
Qianwei Su ◽  
Huangyi He ◽  
Qi Zhou
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Origin And Evolution ◽  
Functional Studies ◽  
New Genes ◽  
Male Germline ◽  
New Gene ◽  
Direct Cell ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Origin of functional new genes is a basic biological process that has a significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testis, and avoid the X chromosome presumably because meitoic sex chromosome inactivation (MSCI). Here we analyse the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared to their parental copies, probably due to more intensive sperm competition or sexual conflict. Our results dissect the complex factors including the age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testis, and identify new gene cases that show divergent expression pattern from their progenitors for future functional studies.

scholarly journals On the Origin and Evolution of Drosophila New Genes during Spermatogenesis

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1796
Author(s):  
Qianwei Su ◽  
Huangyi He ◽  
Qi Zhou
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Expression Patterns ◽  
Cell Level ◽  
Origin And Evolution ◽  
Functional Studies ◽  
New Genes ◽  
Meiotic Sex Chromosome Inactivation ◽  
New Gene ◽  
Cell Transcriptome

The origin of functional new genes is a basic biological process that has significant contribution to organismal diversity. Previous studies in both Drosophila and mammals showed that new genes tend to be expressed in testes and avoid the X chromosome, presumably because of meiotic sex chromosome inactivation (MSCI). Here, we analyze the published single-cell transcriptome data of Drosophila adult testis and find an enrichment of male germline mitotic genes, but an underrepresentation of meiotic genes on the X chromosome. This can be attributed to an excess of autosomal meiotic genes that were derived from their X-linked mitotic progenitors, which provides direct cell-level evidence for MSCI in Drosophila. We reveal that new genes, particularly those produced by retrotransposition, tend to exhibit an expression shift toward late spermatogenesis compared with their parental copies, probably due to the more intensive sperm competition or sexual conflict. Our results dissect the complex factors including age, the origination mechanisms and the chromosomal locations that influence the new gene origination and evolution in testes, and identify new gene cases that show divergent cell-level expression patterns from their progenitors for future functional studies.

scholarly journals Targeting Subsets of Mammalian Neurons

2020 ◽  
Vol 15 ◽  
pp. 263310552090853
Author(s):  
Boris V. Zemelman
Keyword(s):  
In Vivo Imaging ◽  
Inhibitory Neuron ◽  
Human Perception ◽  
Cell Populations ◽  
Inhibitory Interneurons ◽  
Transcriptome Data ◽  
Functional Studies ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Functional dissection of mammalian neuronal circuits depends on accurate targeting of constituent cell classes. Transgenic mice offer precise and predictable access to genetically defined cell populations, but there is the pressing need to target neuronal assemblies in species less amenable to genomic manipulations, such as the primate, which is an important animal model for human perception, cognition, and action. We have developed several virus-based methods for accessing all forebrain inhibitory interneurons as well as the major excitatory and inhibitory neuron subclasses. These methods rely on the wealth of emerging single-cell transcriptome data and harness gene expression variations to refine neuron targeting. Our approach enables nuanced functional studies, including in vivo imaging and manipulation, of the diverse cell populations of the mammalian neocortex, and it represents a timely blueprint for transgenics-independent interrogation of functionally significant cell classes.

scholarly journals Repeated Evolution of Testis-Specific New Genes: The Case of Telomere-Capping Genes in Drosophila

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Raphaëlle Dubruille ◽  
Gabriel A. B. Marais ◽  
Benjamin Loppin
Keyword(s):  
Gene Family ◽  
Specific Expression ◽  
Functional Studies ◽  
Evolutionary Forces ◽  
New Genes ◽  
Male Gametes ◽  
Duplication Events ◽  
New Gene ◽  
Telomere Capping ◽  
Specific Expression Pattern

Comparative genome analysis has allowed the identification of various mechanisms involved in gene birth. However, understanding the evolutionary forces driving new gene origination still represents a major challenge. In particular, an intriguing and not yet fully understood trend has emerged from the study of new genes: many of them show a testis-specific expression pattern, which has remained poorly understood. Here we review the case of such a new gene, which involves a telomere-capping gene family in Drosophila. hiphop and its testis-specific paralog K81 are critical for the protection of chromosome ends in somatic cells and male gametes, respectively. Two independent functional studies recently proposed that these genes evolved under a reproductive-subfunctionalization regime. The 2011 release of new Drosophila genome sequences from the melanogaster group of species allowed us to deepen our phylogenetic analysis of the hiphop/K81 family. This work reveals an unsuspected dynamic of gene birth and death within the group, with recurrent duplication events through retroposition mechanisms. Finally, we discuss the plausibility of different evolutionary scenarios that could explain the diversification of this gene family.

scholarly journals Pooled CRISPR screening with single-cell transcriptome read-out

2016 ◽  
Author(s):  
Paul Datlinger ◽  
Christian Schmidl ◽  
André F Rendeiro ◽  
Peter Traxler ◽  
Johanna Klughammer ◽  
...  
Keyword(s):  
Single Cell ◽  
Selectable Marker ◽  
Single Cells ◽  
Transcriptome Profiling ◽  
Genetic Screens ◽  
Biological Mechanisms ◽  
Guide Rna ◽  
New Gene ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

AbstractCRISPR-based genetic screens have revolutionized the search for new gene functions and biological mechanisms. However, widely used pooled screens are limited to simple read-outs of cell proliferation or the production of a selectable marker protein. Arrayed screens allow for more complex molecular read-outs such as transcriptome profiling, but they provide much lower throughput. Here we demonstrate CRISPR genome editing together with single-cell RNA sequencing as a new screening paradigm that combines key advantages of pooled and arrayed screens. This approach allowed us to link guide-RNA expression to the associated transcriptome responses in thousands of single cells using a straightforward and broadly applicable screening workflow.

Single-cell profiling identifies myeloid cell subsets with distinct fates during neuroinflammation

Science ◽  
2019 ◽  
Vol 363 (6425) ◽  
pp. eaat7554 ◽  
Author(s):  
Marta Joana Costa Jordão ◽  
Roman Sankowski ◽  
Stefanie M. Brendecke ◽  
Sagar ◽  
Giuseppe Locatelli ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Myeloid Cell ◽  
Innate Immune ◽  
Functional Studies ◽  
Cell Diversity ◽  
Single Cell Profiling ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

The innate immune cell compartment is highly diverse in the healthy central nervous system (CNS), including parenchymal and non-parenchymal macrophages. However, this complexity is increased in inflammatory settings by the recruitment of circulating myeloid cells. It is unclear which disease-specific myeloid subsets exist and what their transcriptional profiles and dynamics during CNS pathology are. Combining deep single-cell transcriptome analysis, fate mapping, in vivo imaging, clonal analysis, and transgenic mouse lines, we comprehensively characterized unappreciated myeloid subsets in several CNS compartments during neuroinflammation. During inflammation, CNS macrophage subsets undergo self-renewal, and random proliferation shifts toward clonal expansion. Last, functional studies demonstrated that endogenous CNS tissue macrophages are redundant for antigen presentation. Our results highlight myeloid cell diversity and provide insights into the brain’s innate immune system.

scholarly journals Bisection of the X chromosome disrupts the initiation of chromosome silencing during meiosis in Caenorhabditis elegans

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yisrael Rappaport ◽  
Hanna Achache ◽  
Roni Falk ◽  
Omer Murik ◽  
Oren Ram ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Rna Polymerase Ii ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Transcription Analysis ◽  
X Chromosomes ◽  
Unique Character ◽  
Active Transcription ◽  
Heterogametic Sex

AbstractDuring meiosis, gene expression is silenced in aberrantly unsynapsed chromatin and in heterogametic sex chromosomes. Initiation of sex chromosome silencing is disrupted in meiocytes with sex chromosome-autosome translocations. To determine whether this is due to aberrant synapsis or loss of continuity of sex chromosomes, we engineered Caenorhabditis elegans nematodes with non-translocated, bisected X chromosomes. In early meiocytes of mutant males and hermaphrodites, X segments are enriched with euchromatin assembly markers and active RNA polymerase II staining, indicating active transcription. Analysis of RNA-seq data showed that genes from the X chromosome are upregulated in gonads of mutant worms. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, our data indicate that unsynapsed X segments are transcribed. Therefore, our results suggest that sex chromosome chromatin has a unique character that facilitates its meiotic expression when its continuity is lost, regardless of whether or not it is synapsed.

scholarly journals Single cell transcriptome atlas of mouse mammary epithelial cells across development

2021 ◽  
Vol 23 (1) ◽  
Author(s):  
Bhupinder Pal ◽  
Yunshun Chen ◽  
Michael J. G. Milevskiy ◽  
François Vaillant ◽  
Lexie Prokopuk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Single Cell ◽  
Developmental Stages ◽  
Mammary Epithelial Cells ◽  
Expression Profiles ◽  
Single Cells ◽  
Chromatin Accessibility ◽  
Mammary Epithelial ◽  
Cell Transcriptome ◽  
Single Cell Transcriptome

Abstract Background Heterogeneity within the mouse mammary epithelium and potential lineage relationships have been recently explored by single-cell RNA profiling. To further understand how cellular diversity changes during mammary ontogeny, we profiled single cells from nine different developmental stages spanning late embryogenesis, early postnatal, prepuberty, adult, mid-pregnancy, late-pregnancy, and post-involution, as well as the transcriptomes of micro-dissected terminal end buds (TEBs) and subtending ducts during puberty. Methods The single cell transcriptomes of 132,599 mammary epithelial cells from 9 different developmental stages were determined on the 10x Genomics Chromium platform, and integrative analyses were performed to compare specific time points. Results The mammary rudiment at E18.5 closely aligned with the basal lineage, while prepubertal epithelial cells exhibited lineage segregation but to a less differentiated state than their adult counterparts. Comparison of micro-dissected TEBs versus ducts showed that luminal cells within TEBs harbored intermediate expression profiles. Ductal basal cells exhibited increased chromatin accessibility of luminal genes compared to their TEB counterparts suggesting that lineage-specific chromatin is established within the subtending ducts during puberty. An integrative analysis of five stages spanning the pregnancy cycle revealed distinct stage-specific profiles and the presence of cycling basal, mixed-lineage, and 'late' alveolar intermediates in pregnancy. Moreover, a number of intermediates were uncovered along the basal-luminal progenitor cell axis, suggesting a continuum of alveolar-restricted progenitor states. Conclusions This extended single cell transcriptome atlas of mouse mammary epithelial cells provides the most complete coverage for mammary epithelial cells during morphogenesis to date. Together with chromatin accessibility analysis of TEB structures, it represents a valuable framework for understanding developmental decisions within the mouse mammary gland.

scholarly journals Deficit of Mitonuclear Genes on the Human X Chromosome Predates Sex Chromosome Formation

2015 ◽  
Vol 7 (2) ◽  
pp. 636-641 ◽  
Author(s):  
Rebecca Dean ◽  
Fabian Zimmer ◽  
Judith E. Mank
Keyword(s):  
X Chromosome ◽  
Sex Chromosome ◽  
Chromosome Formation
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