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Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes

ABSTRACT: High-throughput sequencing was used to determine the RNA profiles of the designated genotypes to identify genes with significant expression changes upon deletion of the male germline gene Phf7 in the fruit fly testis.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE98966 | GEO | 2017/09/01

SECONDARY ACCESSION(S): PRJNA387081

REPOSITORIES: GEO

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PHF7 Modulates BRDT Stability and Histone-to-Protamine Exchange during Spermiogenesis

Project description:Spermatogenesis is a complex process of sperm generation, including mitosis, meiosis, and spermiogenesis. During spermiogenesis, histones in post-meiotic spermatids are removed from chromatin and replaced by protamines. Although histone-to-protamine exchange is important for sperm nuclear condensation, the underlying regulatory mechanism is still poorly understood. Here, we identify PHD finger protein 7 (PHF7) as an E3 ubiquitin ligase for histone H3K14 in post-meiotic spermatids. Generation of Phf7-deficient mice and Phf7 C160A knockin mice with impaired E3 ubiquitin ligase activity reveals defects in histone-to-protamine exchange caused by dysregulation of histone removal factor Bromodomain, testis-specific (BRDT) in early condensing spermatids. Surprisingly, E3 ubiquitin ligase activity of PHF7 on histone ubiquitination leads to stabilization of BRDT by attenuating ubiquitination of BRDT. Collectively, our findings identify PHF7 as a critical factor for sperm chromatin condensation and contribute to mechanistic understanding of fundamental phenomenon of histone-to-protamine exchange and potential for drug development for the male reproduction system.

2020-07-28 | GSE136752 | GEO

Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes, and H3K4me2 and H3K4me3 profiles in the undifferentiated male germline

Project description:Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes, and H3K4me2 and H3K4me3 profiles in the undifferentiated male germline

| PRJNA386931 | ENA

Germline masculinization by Phf7 in D. melanogaster requires its evolutionarily novel C-terminus and the HP1-family protein HP1D3csd

Project description:This study is designed to investigate genes regulated by Phf7 in the embryonic germline of D. melanogaster

2021-02-24 | GSE167380 | GEO

PHF7 Links H3K4 Methylation to H2A Ubiquitination During Spermiongenesis [RNA-seq]

Project description:Histone ubiquitination has been suggested to serve as a “tag” for nucleosome removal during histone-to-protamine exchange that is essential for chromatin packaging in round spermatids. Here, we screen for putative E3 ligase and identify that the PHF7, containing both RING finger and PHD domains, is critical for H2A ubiquitination and histone removal. Mechanistically, its PHD domain as a histone code reader can specifically bind H3K4me3/me2 and its RING domain as a histone writer can ubiquinate H2A. PHF7 deficiency results in male infertility in mice by generating Phf7 knockout mice using CRISPR-Cas9 technology. Futhermore, we find impaired histone-to-protamine exchange leads to reduced chromatin compaction in Phf7 knockout sperm. Immunostaining and western blot further confirme abnormal retention of core histones and reduced levels of protamine PRM1 and PRM2 in Phf7 knockout sperm. In order to exclude the possibility that Phf7 regulate the expession of protamine, we sorte the round spermatids from WT and Phf7 knockout females for RNA-seq. The transcriptomes in round spermatids are very similar between WT and Phf7 knockout mice. There are few differentially expressed genes in the two groups and the expression of protamine is also unchanged even if PHF7 deficiency. Therefore we find PHF7 has no effects on gene regulation in histone-to-protamine exchange.

2019-07-05 | GSE119701 | GEO

PHF7 Links H3K4 Methylation to H2A Ubiquitination During Spermiongenesis

Project description:Histone ubiquitination has been suggested to serve as a “tag” for nucleosome removal during histone-to-protamine exchange that is essential for chromatin packaging in round spermatids. Here, we screen for putative E3 ligase and identify that the PHF7, containing both RING finger and PHD domains, is critical for H2A ubiquitination and histone removal. Mechanistically, its PHD domain as a histone code reader can specifically bind H3K4me3/me2 and its RING domain as a histone writer can ubiquinate H2A. So we want to use ChIP-seq to see whether all PHF7-binding peaks overlapped with those of H3K4me3. We report the application of ChIP-seq for high-throughput profiling of histone modifications in spermatids. By obtaining over 240M of sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps and PHF7 binding position of late spermatids. We find binding peaks of PHF7, H3K4me3 and ub-H2A were mainly enriched at gene-regulatory elements (-5kb to +5kb from transcriptional start site), including promoter and enhancers, indicative of important roles in gene regulations. More than 96% (n=15419) of all PHF7-binding peaks overlapped with those of H3K4me3, supporting a specific binding of PHF7 to H3k4me3. Moreover, the common binding sites between PHF7 and H3K4me3 were associated with ub-H2A. Taken together, these results demonstrate that PHF7 ubiquitinate H2A through binding with H3K4me3.

2019-07-05 | GSE112912 | GEO

Widespread Expression of piRNA-like Molecules in Somatic Tissues

Project description:Piwi-interacting RNA (piRNA) are small RNA abundant in the germline across animal species. In fruit flies and mice, piRNA were implicated in maintenance of genomic integrity by transposable elements silencing. Outside of the germline, piRNA have only been found in Drosophila ovarian follicle cells. Previous studies further reported the presence of multiple piRNA-like small RNA (pilRNA) in fly heads and a small number of pilRNA in mouse tissues and human NK cells. Here, by analyzing high-throughput small RNA sequencing data in more than 130 fruit fly, mouse and rhesus macaque samples, we show widespread presence of pilRNA displaying all known characteristics of piRNA in multiple somatic tissues of these three species. In mouse pancreas and macaque epididymis, pilRNA abundance was compatible with piRNA abundance in the germline. Using in situ hybridizations, we further demonstrate pilRNA co-localization with mRNA expression of Piwi-family genes in all macaque tissues. These findings indicate that piRNA-like molecules might play important roles outside of the germline. Small RNA expression profiles were examined in five rhesus macaque tissues (testis, epididymis, prostate, seminal vesicles, cortex) and one mouse tissue (epididymis).

2011-06-01 | E-GEOD-27369 | biostudies-arrayexpress

Transcriptome analysis of bam- vs. Phf7-,bam- mutant testes, and H3K4me2 and H3K4me3 profiles in the undifferentiated male germline

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-09-01 | GSE98968 | GEO

Comparison of gene expression in control bam-Gal4 and control undriven tbrd-2RNAi Drosophila testes with tbrd-2 knockdown testes

Project description:Gene expression is tightly linked to histone acetylation on lysine residues that can be recognized by bromodomains. The testis-specific bromodomain protein tBRD-2 is essential for male fertility, interacts with tBRD-1 and might act as a co-factor of testis-specifc TAFs. Here, we perform microarray analyses and demonstrate that tBRD-2 selectively controls gene expression in male germ cells.

2017-03-23 | GSE81019 | GEO

The histone reader PHF7 cooperates with the SWI/SNF complex at cardiac super-enhancers to promote direct cardiac reprogramming

Project description:Direct cardiac reprogramming of fibroblasts to cardiomyocytes presents an attractive therapeutic strategy to restore cardiac function following injury. Cardiac reprogramming was initially achieved through the overexpression of the transcription factors Gata4, Mef2c, and Tbx5 (GMT), and later, Hand2 (GHMT) and Akt1 (AGHMT) were found to further enhance this process. Yet, staunch epigenetic barriers severely limit the ability of these cocktails to reprogram adult fibroblasts. We undertook a screen of mammalian gene regulatory factors to discover novel regulators of cardiac reprogramming in adult fibroblasts and identified the histone reader PHF7 as the most potent activating factor. Mechanistically, PHF7 localizes to cardiac super-enhancers in fibroblasts, and through cooperation with the SWI/SNF complex, increases chromatin accessibility and transcription factor binding at these sites. Importantly, PHF7 is the first epigenetic factor found to achieve efficient reprogramming in the absence of Gata4. Here, we highlight the underexplored necessity of cardiac epigenetic modifiers, such as PHF7, in harnessing chromatin remodeling complexes to overcome critical barriers to direct cardiac reprogramming.

2021-02-26 | GSE151328 | GEO

Emergent dynamics of adult stem cell lineages from single cell RNA-Seq of Drosophila testes

Project description:Here we provide a single cell RNA-seq resource covering all of spermatogenesis in Drosophila starting from in-depth analysis of adult testis single nucleus RNA-seq . 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 (Li et al., 2022). With over 44,000 nuclei and 6,000 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.

2023-01-10 | GSE220615 | GEO

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