In Silico Identification of lncRNAs Regulating Sperm Motility in the Turkey (Meleagris gallopavo L.)

Jastrzebski, J; Lipka, Aleksandra; Majewska, Marta; Makowczenko, Karol G; Paukszto, Łukasz; Bukowska, Joanna; Dorocki, Sławomir; Kozłowski, Krzysztof; Słowińska, Mariola

doi:10.3390/ijms23147642

Cited by 5 publications

(1 citation statement)

References 98 publications

(117 reference statements)

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“…More recently, using public microarray data, Joshi et al identified fifteen functionally conserved lncRNAs across multiple studies in humans and mice 25 , which with HISTA, we explore deeply. Broadly, in the testis, lncRNA could A) regulate the expression of protein-coding genes involved in sperm production or function 26 . B) Directly interact with sperm cells or other cells in the testis 27 , potentially binding to receptors on the surface of sperm cells, altering their motility or ability to fertilize an egg or interact with the Sertoli cells or Leydig cells.…”

Section: Vignette 1: Novel Sets Of Lncrna Molecules Identified As Key...mentioning

confidence: 99%

The human infertility single‐cell testis atlas (HISTA): an interactive molecular scRNA‐Seq reference of the human testis

Mahyari,

Vigh‐Conrad,

Daube

et al. 2024

Andrology

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BackgroundSingle‐cell RNA‐seq (scRNA‐Seq) has been widely adopted to study gene expression of the human testis. Several datasets of scRNA‐Seq from human testis have been generated from different groups processed with different informatics pipelines. An integrated atlas of scRNA‐Seq expression constructed from multiple donors, developmental ages, and fertility states would be widely useful for the testis research community.ObjectiveTo describe the generation and use of the human infertility single‐cell testis atlas (HISTA), an interactive web tool for understanding human spermatogenesis through scRNA‐Seq analysis.MethodsWe obtained scRNA‐Seq datasets derived from 12 donors, including healthy adult controls, juveniles, and several infertility cases, and reprocessed these data using methods to remove batch effects. Using Shiny, an open‐source environment for data visualization, we created numerous interactive tools for exploring the data, some of which support simple statistical hypothesis testing. We used the resulting HISTA browser and its underlying data to demonstrate HISTA's value for testis researchers.ResultsA primary application of HISTA is to search by a single gene or a set of genes; thus, we present various analyses that quantify and visualize gene expression across the testis cells and pathology. HISTA also contains machine‐learning‐derived gene modules (“components”) that capture the entire transcriptional landscape of the testis tissue. We show how the use of these components can simplify the highly complex data in HISTA and assist with the interpretation of genes with unknown functions. Finally, we demonstrate the diverse ways HISTA can be used for new data analysis, including hypothesis testing.Discussion and conclusionsHISTA is a research environment that can help scientists organize and understand the high‐dimensional transcriptional landscape of the human testis. HISTA has already contributed to published testis research and can be updated as needed with input from the research community or downloaded and modified for individual needs.

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Section: Vignette 1: Novel Sets Of Lncrna Molecules Identified As Key...mentioning

confidence: 99%

The human infertility single‐cell testis atlas (HISTA): an interactive molecular scRNA‐Seq reference of the human testis

Mahyari,

Vigh‐Conrad,

Daube

et al. 2024

Andrology

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Importance and variability of the paternal component in sow reproductive traits

Cieleń,

Sell-Kubiak

2024

J Appl Genetics

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Reproductive traits are an integral part of the goals of the breeding programs that contribute to the economic success of production. Reproductive phenotypes such as litter size, number of piglets born alive, or litter weight at birth are mainly attributed to females. Thus, the maternal components can be found by default in quantitative genetics’ animal models. Still, paternal contribution to variance components should not be discarded. In this review, we indicate the importance of paternal effects in pig breeding by describing both the biology and genetics of boars’ traits, the use of (non-)genetic service sire effects in quantitative genetic models for traits measured on females, and genes involved in male reproduction. We start by describing the important biological traits of boars that have the most important effect on their reproductive abilities, i.e., sexual maturity, sperm quality, and testes parameters. Then we move to the possible environmental effects that could affect those traits of boars (e.g., feed, temperature). The main part of the review in detail describes the genetics of boars’ reproductive traits (i.e., heritability) and their direct effect on reproductive traits of females (i.e., genetic correlations). We then move to the use of both genetic and non-genetic service sire effects in quantitative models estimated as their percentage in the total variance of traits, which vary depending on the breed from 1 to 4.5% or from 1 to 2%, respectively. Finally, we focus on the description of candidate genes and confirmed mutations affecting male reproduction success: IGF2, Tgm8, ESR1, ZSWIM7, and ELMO1. In conclusion, the observed variance of paternal effects in female reproduction traits might come from various attributes of boars including biological and genetic aspects. Those attributes of boars should not be neglected as they contribute to the success of female reproductive traits.

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