Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment

ABSTRACTBackgroundRNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter-and trans-generational inheritance. In the nematode Caenorhabditis elegans environmental double-stranded RNA provided by feeding can lead to heritable changes in phenotype and gene expression. Notably, transmission efficiency differs between the male and female germline, yet the underlying mechanisms remain elusive.ResultsHere we use high-throughput sequencing of dissected gonads to quantify sex-specific endogenous piRNAs, miRNAs and siRNAs in the C. elegans germline and the somatic gonad. We identify genes with exceptionally high levels of 22G RNAs that are associated with low mRNA expression, a signature compatible with silencing. We further demonstrate that contrary to the hermaphrodite germline, the male germline, but not male soma, is resistant to environmental RNAi triggers provided by feeding. This sex-difference in silencing efficacy is associated with lower levels of gonadal RNAi amplification products. Moreover, this tissue-and sex-specific RNAi resistance is regulated by the germline, since mutant males with a feminized germline are RNAi sensitive.ConclusionThis study provides important sex-and tissue-specific expression data of miRNA, piRNA and siRNA as well as mechanistic insights into sex-differences of gene regulation in response to environmental cues.

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SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans

eLife ◽

10.7554/elife.60681 ◽

2021 ◽

Vol 10 ◽

Author(s):

Charlotte P Choi ◽

Rebecca J Tay ◽

Margaret R Starostik ◽

Suhua Feng ◽

James J Moresco ◽

...

Keyword(s):

Transcription Factor ◽

Ectopic Expression ◽

Sexually Dimorphic ◽

Small Nuclear Rna ◽

Germline Development ◽

C Elegans ◽

Male Germline ◽

Nuclear Rna ◽

Specific Regulation ◽

Male Specific

Piwi-interacting RNAs (piRNAs) play essential roles in silencing repetitive elements to promote fertility in metazoans. Studies in worms, flies, and mammals reveal that piRNAs are expressed in a sex-specific manner. However, the mechanisms underlying this sex-specific regulation are unknown. Here we identify SNPC-1.3, a male germline-enriched variant of a conserved subunit of the small nuclear RNA-activating protein complex, as a male-specific piRNA transcription factor in Caenorhabditis elegans. SNPC-1.3 colocalizes with the core piRNA transcription factor, SNPC-4, in nuclear foci of the male germline. Binding of SNPC-1.3 at male piRNA loci drives spermatogenic piRNA transcription and requires SNPC-4. Loss of snpc-1.3 leads to depletion of male piRNAs and defects in male-dependent fertility. Furthermore, TRA-1, a master regulator of sex determination, binds to the snpc-1.3 promoter and represses its expression during oogenesis. Loss of TRA-1 targeting causes ectopic expression of snpc-1.3 and male piRNAs during oogenesis. Thus, sexually dimorphic regulation of snpc-1.3 expression coordinates male and female piRNA expression during germline development.

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Characterization of germline development and identification of genes associated with germline specification in pineapple

Horticulture Research ◽

10.1038/s41438-021-00669-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Lihua Zhao ◽

Liping Liu ◽

Yanhui Liu ◽

Xianying Dou ◽

Hanyang Cai ◽

...

Keyword(s):

Plant Species ◽

Mother Cell ◽

Expression Patterns ◽

Germline Development ◽

Regulatory Pathways ◽

Male Germline ◽

Agricultural Applications ◽

Related Plant ◽

Female Gametophyte Development ◽

Female Germline

AbstractUnderstanding germline specification in plants could be advantageous for agricultural applications. In recent decades, substantial efforts have been made to understand germline specification in several plant species, including Arabidopsis, rice, and maize. However, our knowledge of germline specification in many agronomically important plant species remains obscure. Here, we characterized the female germline specification and subsequent female gametophyte development in pineapple using callose staining, cytological, and whole-mount immunolocalization analyses. We also determined the male germline specification and gametophyte developmental timeline and observed male meiotic behavior using chromosome spreading assays. Furthermore, we identified 229 genes that are preferentially expressed at the megaspore mother cell (MMC) stage during ovule development and 478 genes that are preferentially expressed at the pollen mother cell (PMC) stage of anther development using comparative transcriptomic analysis. The biological functions, associated regulatory pathways and expression patterns of these genes were also analyzed. Our study provides a convenient cytological reference for exploring pineapple germline development and a molecular basis for the future functional analysis of germline specification in related plant species.

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Nanos promotes epigenetic reprograming of the germline by down-regulation of the THAP transcription factor LIN-15B

eLife ◽

10.7554/elife.30201 ◽

2017 ◽

Vol 6 ◽

Cited By ~ 15

Author(s):

Chih-Yung Sean Lee ◽

Tu Lu ◽

Geraldine Seydoux

Keyword(s):

Transcription Factor ◽

Cell Fate ◽

Transcriptional Activation ◽

Rna Binding ◽

Rna Binding Proteins ◽

Primordial Germ Cells ◽

Germline Development ◽

C Elegans ◽

Maternal Transcripts ◽

Underlying Mechanisms

Nanos RNA-binding proteins are required for germline development in metazoans, but the underlying mechanisms remain poorly understood. We have profiled the transcriptome of primordial germ cells (PGCs) lacking the nanos homologs nos-1 and nos-2 in C. elegans. nos-1nos-2 PGCs fail to silence hundreds of transcripts normally expressed in oocytes. We find that this misregulation is due to both delayed turnover of maternal transcripts and inappropriate transcriptional activation. The latter appears to be an indirect consequence of delayed turnover of the maternally-inherited transcription factor LIN-15B, a synMuvB class transcription factor known to antagonize PRC2 activity. PRC2 is required for chromatin reprogramming in the germline, and the transcriptome of PGCs lacking PRC2 resembles that of nos-1nos-2 PGCs. Loss of maternal LIN-15B restores fertility to nos-1nos-2 mutants. These findings suggest that Nanos promotes germ cell fate by downregulating maternal RNAs and proteins that would otherwise interfere with PRC2-dependent reprogramming of PGC chromatin.

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Cell Non-autonomous Function of daf-18/PTEN in the Somatic Gonad Coordinates Somatic Gonad and Germline Development in C. elegans Dauer Larvae

Current Biology ◽

10.1016/j.cub.2019.01.076 ◽

2019 ◽

Vol 29 (6) ◽

pp. 1064-1072.e8 ◽

Cited By ~ 7

Author(s):

Claudia C. Tenen ◽

Iva Greenwald

Keyword(s):

Germline Development ◽

C Elegans ◽

Autonomous Function ◽

Somatic Gonad ◽

Dauer Larvae

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An interview with Swathi Arur

Development ◽

10.1242/dev.199366 ◽

2021 ◽

Vol 148 (2) ◽

pp. dev199366

Author(s):

Alex Eve

Keyword(s):

American Association ◽

Associate Professor ◽

Cancer Center ◽

Germline Development ◽

Faculty Mentor ◽

C Elegans ◽

Distinguished Research ◽

Md Anderson ◽

Female Germline ◽

Research Faculty

Swathi Arur is an Associate Professor for the Department of Genetics at the MD Anderson Cancer Center, USA, where she uses multidisciplinary approaches to understand female germline development and fertility. She has received numerous accolades, including the MD Anderson Distinguished Research Faculty Mentor Award in 2017. In 2020, she was elected to the American Association for the Advancement of Science (AAAS). Swathi joined the team at Development as an Academic Editor in 2020, and we met with her over Zoom to hear more about her life, her career and her love for C. elegans.

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Epigenetic processes in the male germline

Reproduction Fertility and Development ◽

10.1071/rd14167 ◽

2015 ◽

Vol 27 (5) ◽

pp. 725 ◽

Cited By ~ 21

Author(s):

Alan M. O'Doherty ◽

Paul A. McGettigan

Keyword(s):

Dna Methylation ◽

High Throughput Sequencing ◽

De Novo ◽

Dna Packaging ◽

Sperm Chromatin ◽

Germline Development ◽

Paternal Genome ◽

Male Germline ◽

Non Coding Rnas ◽

Epigenetic Processes

Sperm undergo some of the most extensive chromatin modifications seen in mammalian biology. During male germline development, paternal DNA methylation marks are erased and established on a global scale through waves of demethylation and de novo methylation. As spermatogenesis progresses, the majority of the histones are removed and replaced by protamines, enabling a tighter packaging of the DNA and transcriptional shutdown. Following fertilisation, the paternal genome is rapidly reactivated, actively demethylated, the protamines are replaced with histones and the embryonic genome is activated. The development of new assays, made possible by high-throughput sequencing technology, has resulted in the revisiting of what was considered settled science regarding the state of DNA packaging in mammalian spermatozoa. Researchers have discovered that not all histones are replaced by protamines and, in certain experiments, various species of RNA have been detected in what was previously considered transcriptionally quiescent spermatozoa. Most controversially, several groups have suggested that environmental modifications of the epigenetic state of spermatozoa may operate as a non-DNA-based form of inheritance, a process known as ‘transgenerational epigenetic inheritance’. Other developments in the field include the increased focus on the involvement of short RNAs, such as microRNAs, long non-coding RNAs and piwi-interacting RNAs. There has also been an accumulation of evidence illustrating associations between defects in sperm DNA packaging and disease and fertility. In this paper we review the literature, recent findings and areas of controversy associated with epigenetic processes in the male germline, focusing on DNA methylation dynamics, non-coding RNAs, the biology of sperm chromatin packaging and transgenerational inheritance.

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stand still, a Drosophila Gene Involved in the Female Germline for Proper Survival, Sex Determination and Differentiation

Genetics ◽

10.1093/genetics/145.4.975 ◽

1997 ◽

Vol 145 (4) ◽

pp. 975-987

Author(s):

Giuseppa Pennetta ◽

Daniel Pauli

Keyword(s):

Sex Determination ◽

Germ Cells ◽

Loss Of Function ◽

Germline Development ◽

Survival Sex ◽

Male Germline ◽

New Gene ◽

Mutant Phenotypes ◽

Female Germline ◽

Novel Protein

We identified a new gene, stand still (stil), required in the female germline for proper survival, sex determination and differentiation. Three strong loss-of-function alleles were isolated. The strongest phenotype exhibited by ovaries dissected from adult females is the complete absence of germ cells. In other ovaries, the few surviving germ cells frequently show a morphology typical of primary spermatocytes. stil is not required either for fly viability or for male germline development. The gene was cloned and found to encode a novel protein. stil is strongly expressed in the female germ cells. Using P[stil +] transgenes, we show that stil and a closely localized gene are involved in the modification of the ovarian phenotypes of the dominant alleles of ovo caused by heterozygosity of region 49 A-D. The similarity of the mutant phenotypes of stil to that of otu and ovo suggests that the three genes function in a common or in parallel pathways necessary in the female germline for its survival, sex determination and differentiation.

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