lncRNAs in fertility: redefining the gene expression paradigm?

Tzur, Yonatan B

doi:10.1016/j.tig.2022.05.013

Cited by 8 publications

(7 citation statements)

References 80 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Several others have specifically focused on the testis [19][20][21][22] , including studies in domesticated animals linking fertility robustness to several lncRNAs [23][24][25] . In a study with mice using microarrays, the testis was shown to have the highest number of expressed and specific lncRNAs 22 .…”

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

View full text Add to dashboard Cite

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.

show abstract

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

View full text Add to dashboard Cite

show abstract

“…As a step forward in dissecting the molecular basis of fertility, transcriptomic studies have become a powerful tool to understand how gene expression controls cellular functions and their role in determining specific phenotypes [75,76]. In measuring the genome-wide expression of RNA molecules such as mRNAs, miRNAs, and lncRNAs, the assumption is that differences in dynamically expressed RNAs can partially explain phenotypic variation across animals [76]. Divergence in gene expression may result from differences in the physiological status of the animal at a specific time point and genetic variation in regulatory regions [77].…”

Section: Transcriptomicsmentioning

confidence: 99%

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

Kertz,

Banerjee,

Dyce

et al. 2023

Animals

View full text Add to dashboard Cite

Female fertility is the foundation of the cow–calf industry, impacting both efficiency and profitability. Reproductive failure is the primary reason why beef cows are sold in the U.S. and the cause of an estimated annual gross loss of USD 2.8 billion. In this review, we discuss the status of the genomics, transcriptomics, and systems genomics approaches currently applied to female fertility and the tools available to cow–calf producers to maximize genetic progress. We highlight the opportunities and limitations associated with using genomic and transcriptomic approaches to discover genes and regulatory mechanisms related to beef fertility. Considering the complex nature of fertility, significant advances in precision breeding will rely on holistic, multidisciplinary approaches to further advance our ability to understand, predict, and improve reproductive performance. While these technologies have advanced our knowledge, the next step is to translate research findings from bench to on-farm applications.

show abstract

“…Several studies show the role of lncRNAs in male germ cells, which was summarized in recent reviews [ 6 , 64 , 65 , 66 ]. Here, we introduce functional lncRNAs with a focus on how to screen them in testis.…”

Section: Testicular Lncrnas: Functionalitymentioning

confidence: 99%

LncRNA Functional Screening in Organismal Development

Zhai

Tong

et al. 2023

ncRNA

View full text Add to dashboard Cite

Controversy continues over the functional prevalence of long non-coding RNAs (lncRNAs) despite their being widely investigated in all kinds of cells and organisms. In animals, lncRNAs have aroused general interest from exponentially increasing transcriptomic repertoires reporting their highly tissue-specific and developmentally dynamic expression, and more importantly, from growing experimental evidence supporting their functionality in facilitating organogenesis and individual fitness. In mammalian testes, while a great multitude of lncRNA species are identified, only a minority of them have been shown to be useful, and even fewer have been demonstrated as true requirements for male fertility using knockout models to date. This noticeable gap is attributed to the virtual existence of a large number of junk lncRNAs, the lack of an ideal germline culture system, difficulty in loss-of-function interrogation, and limited screening strategies. Facing these challenges, in this review, we discuss lncRNA functionality in organismal development and especially in mouse testis, with a focus on lncRNAs with functional screening.

show abstract

lncRNAs in fertility: redefining the gene expression paradigm?

Cited by 8 publications

References 80 publications

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

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

Harnessing Genomics and Transcriptomics Approaches to Improve Female Fertility in Beef Cattle—A Review

LncRNA Functional Screening in Organismal Development

Contact Info

Product

Resources

About