Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

Sun, Yu; Wang, Anqi; Song, Chi; Shankar, Goutham; Srivastava, Rajesh K.; Au, Kin Fai; Li, Xin Zhiguo

doi:10.1038/s41467-021-21524-6

Cited by 53 publications

(39 citation statements)

References 97 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Meanwhile, one thing that should be mentioned is that abundant non-coding RNAs exist in mammalian tissues, especially in the brain and testis, and exert important regulatory functions essential for tissues despite not encoding proteins [48][49][50].…”

Section: Discussionmentioning

confidence: 99%

Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals

Qian

Ying

Chen

et al. 2021

Preprint

View full text Add to dashboard Cite

In the evolutionary model of dosage compensation, per-allele expression level of the X chromosome was proposed to have two-fold upregulation, compensating for its dose reduction in males (XY) compared to females (XX). However, the upregulation of X chromosome is still in dispute, and comprehensive evaluations are still lacking. By integrating multi-omics datasets in mammals, we investigated the expression ratios and underlying pattern of X to autosomes (X:AA ratio) and X to orthologs (X:XX ratio) at the transcriptome, translatome, and proteome layers. The results indicated a dynamic spatial-temporal X:AA ratio during development in human and mouse. Meanwhile, by tracing the evolution of orthologous gene expressions in chicken, platypus, and opossum, we found a constant expression ratio between X-linked genes in human and their autosomal orthologs in other species (X:XX ~1) across tissues and developmental stages, demonstrating stable dosage compensation in mammals. We also revealed that different epigenetic regulations could shape the higher tissue- and stage-specificity of X-linked gene expression, and affect X:AA ratios. We conclude that the dynamics of X:AA ratios are attributed to the different gene contents and expression preferences of the X chromosome, instead of the stable dosage compensation.

show abstract

Section: Discussionmentioning

confidence: 99%

Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals

Qian

Ying

Chen

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Similar to that of PacBio, because it does not go through RNA fragmentation, the structure of the noncoding RNA is retained and can avoid computational algorithm error during template assembly. Thus, this method is suitable for detecting structural variations and isoforms (e.g., [188]. Because ONT can process cRNA directly without cDNA synthesis, RNA modification and epigenetic information are also retained, similar to methylation and other modifications [1,182].…”

Section: Oxford Nanopore Technology (Ont)mentioning

confidence: 99%

The role of noncoding RNAs in Parkinson’s disease: biomarkers and associations with pathogenic pathways

et al. 2021

View full text Add to dashboard Cite

The discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments. These ncRNAs have the ability to regulate gene expression and modify metabolic pathways. Thus, they may have important roles as diagnostic biomarkers or therapeutic targets in various diseases, including neurodegenerative disorders, especially Parkinson’s disease. Recently, through diverse sequencing technologies and a wide variety of bioinformatic analytical tools, such as reverse transcriptase quantitative PCR, microarrays, next-generation sequencing and long-read sequencing, numerous ncRNAs have been shown to be associated with neurodegenerative disorders, including Parkinson’s disease. In this review article, we will first introduce the biogenesis of different ncRNAs, including microRNAs, PIWI-interacting RNAs, circular RNAs, long noncoding RNAs, and tRNA-derived fragments. The pros and cons of the detection platforms of ncRNAs and the reproducibility of bioinformatic analytical tools will be discussed in the second part. Finally, the recent discovery of numerous PD-associated ncRNAs and their association with the diagnosis and pathophysiology of PD are reviewed, and microRNAs and long ncRNAs that are transported by exosomes in biofluids are particularly emphasized.

show abstract

“…Nevertheless, evidence of both coding and non-coding spRNAs were proclaimed in different livestock species, including cattle, pigs, and stallion ( Kempisty et al, 2008 ). Notably, full-length mRNA transcripts have also been reported ( Sun et al, 2021 ) that had the potential to be translated de novo under certain circumstances ( Miller and Ostermeier, 2006 ).…”

Section: Introductionmentioning

confidence: 99%

Significance and Relevance of Spermatozoal RNAs to Male Fertility in Livestock

et al. 2021

View full text Add to dashboard Cite

Livestock production contributes to a significant part of the economy in developing countries. Although artificial insemination techniques brought substantial improvements in reproductive efficiency, male infertility remains a leading challenge in livestock. Current strategies for the diagnosis of male infertility largely depend on the evaluation of semen parameters and fail to diagnose idiopathic infertility in most cases. Recent evidences show that spermatozoa contains a suit of RNA population whose profile differs between fertile and infertile males. Studies have also demonstrated the crucial roles of spermatozoal RNA (spRNA) in spermatogenesis, fertilization, and early embryonic development. Thus, the spRNA profile may serve as unique molecular signatures of fertile sperm and may play pivotal roles in the diagnosis and treatment of male fertility. This manuscript provides an update on various spRNA populations, including protein-coding and non-coding RNAs, in livestock species and their potential role in semen quality, particularly sperm motility, freezability, and fertility. The contribution of seminal plasma to the spRNA population is also discussed. Furthermore, we discussed the significance of rare non-coding RNAs (ncRNAs) such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs) in spermatogenic events.

show abstract

Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

Cited by 53 publications

References 97 publications

Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals

Dynamic Spatial-Temporal Expression Ratio of X Chromosome to Autosomes but Stable Dosage Compensation in Mammals

The role of noncoding RNAs in Parkinson’s disease: biomarkers and associations with pathogenic pathways

Significance and Relevance of Spermatozoal RNAs to Male Fertility in Livestock

Contact Info

Product

Resources

About