scholarly journals Differences in small noncoding RNAs profile between bull X and Y sperm

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9822
Author(s):  
Hao Zhou ◽  
Jiajia Liu ◽  
Wei Sun ◽  
Rui Ding ◽  
Xihe Li ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Sex Differences ◽  
Embryonic Development ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Mature Oocyte ◽  
Small Noncoding Rnas ◽  
Nucleosomal Dna ◽  
Nucleosome Binding

The differences in small noncoding RNAs (sncRNAs), including miRNAs, piRNAs, and tRNA-derived fragments (tsRNAs), between X and Y sperm of mammals remain unclear. Here, we employed high-throughput sequencing to systematically compare the sncRNA profiles of X and Y sperm from bulls (n = 3), which may have a wider implication for the whole mammalian class. For the comparison of miRNA profiles, we found that the abundance of bta-miR-652 and bta-miR-378 were significantly higher in X sperm, while nine miRNAs, including bta-miR-204 and bta-miR-3432a, had greater abundance in Y sperm (p < 0.05). qPCR was then used to further validate their abundances. Subsequent functional analysis revealed that their targeted genes in sperm were significantly involved in nucleosome binding and nucleosomal DNA binding. In contrast, their targeted genes in mature oocyte were significantly enriched in 11 catabolic processes, indicating that these differentially abundant miRNAs may trigger a series of catabolic processes for the catabolization of different X and Y sperm components during fertilization. Furthermore, we found that X and Y sperm showed differences in piRNA clusters distributed in the genome as well as piRNA and tsRNA abundance, two tsRNAs (tRNA-Ser-AGA and tRNA-Ser-TGA) had lower abundance in X sperm than Y sperm (p < 0.05). Overall, our work describes the different sncRNA profiles of X and Y sperm in cattle and enhances our understanding of their potential roles in the regulation of sex differences in sperm and early embryonic development.

scholarly journals Non-micro-short RNAs: the new kids on the block

2012 ◽  
Vol 23 (24) ◽  
pp. 4664-4667 ◽  
Author(s):  
Bijan K. Dey ◽  
Adam C. Mueller ◽  
Anindya Dutta
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Mechanisms Of Action ◽  
Biological Processes ◽  
Large Group ◽  
Small Noncoding Rnas ◽  
Short Rnas ◽  
Functional Classes ◽  
Functional Relevance

The advent of ultra–high-throughput sequencing has led to the discovery of a large group of small, noncoding RNAs that are not microRNAs. The functional relevance of microRNAs has been well established over the last decade. In this Perspective, we focus on the non-micro-short RNAs that comprise a variety of functional classes and range from 16–40 nucleotides in size. We will highlight how some of these non-micro-short RNAs were discovered, as well as their biogenesis, potential mechanisms of action, and role in diverse biological processes, development, and disease. Finally, we will describe what must be done to further our understanding of these enigmatic molecules.

scholarly journals Beyond the Ribosome: Extra-translational Functions of tRNA Fragments

2016 ◽  
Vol 11s1 ◽  
pp. BMI.S35904 ◽  
Author(s):  
Kevin W. Diebel ◽  
Kun Zhou ◽  
Aaron B. Clarke ◽  
Lynne T. Bemis
Keyword(s):  
Data Analysis ◽  
High Throughput ◽  
Biological Samples ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Degradation Products ◽  
Noncoding Rnas ◽  
Transfer Rnas ◽  
Sequencing Studies ◽  
Domains Of Life

High-throughput sequencing studies of small RNAs reveal a complex milieu of noncoding RNAs in biological samples. Early data analysis was often limited to microRNAs due to their regulatory nature and potential as biomarkers; however, many more classes of noncoding RNAs are now being recognized. A class of fragments initially excluded from analysis were those derived from transfer RNAs (tRNAs) because they were thought to be degradation products. More recently, critical cellular function has been attributed to tRNA fragments (tRFs), and their conservation across all domains of life has propelled them into an emerging area of scientific study. The biogenesis of tRFs is currently being elucidated, and initial studies show that a diverse array of tRFs are genera ted from all parts of a tRNA molecule. The goal of this review was to present what is currently known about tRFs and their potential as biomarkers for the earlier detection of disease.

scholarly journals Regeneration in the sponge Sycon ciliatum partly mimics postlarval development

Development ◽  
2020 ◽  
Vol 147 (22) ◽  
pp. dev193714
Author(s):  
Anael Soubigou ◽  
Ethan G. Ross ◽  
Yousef Touhami ◽  
Nathan Chrismas ◽  
Vengamanaidu Modepalli
Keyword(s):  
Cell Death ◽  
Embryonic Development ◽  
High Throughput ◽  
Morphological Analysis ◽  
High Throughput Sequencing ◽  
Postembryonic Development ◽  
Developmental Pathways ◽  
Genetic Features ◽  
Dissociated Cells ◽  
Comparative Transcriptomic Analysis

ABSTRACTSomatic cells dissociated from an adult sponge can reorganize and develop into a juvenile-like sponge, a remarkable phenomenon of regeneration. However, the extent to which regeneration recapitulates embryonic developmental pathways has remained enigmatic. We have standardized and established a sponge Sycon ciliatum regeneration protocol from dissociated cells. Morphological analysis demonstrated that dissociated sponge cells follow a series of morphological events resembling postembryonic development. We performed high-throughput sequencing on regenerating samples and compared the data with that from regular postlarval development. Our comparative transcriptomic analysis revealed that sponge regeneration is as equally dynamic as embryogenesis. We found that sponge regeneration is orchestrated by recruiting pathways similar to those utilized in embryonic development. We also demonstrated that sponge regeneration is accompanied by cell death at early stages, revealing the importance of apoptosis in remodelling the primmorphs to initiate re-development. Because sponges are likely to be the first branch of extant multicellular animals, we suggest that this system can be explored to study the genetic features underlying the evolution of multicellularity and regeneration.

Characterization of H3K9me3- and H4K20me3-associated circulating nucleosomal DNA by high-throughput sequencing in colorectal cancer

Tumor Biology ◽  
2012 ◽  
Vol 34 (1) ◽  
pp. 329-336 ◽  
Author(s):  
Ugur Gezer ◽  
Duran Üstek ◽  
Ebru E. Yörüker ◽  
Aris Cakiris ◽  
Neslihan Abaci ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Nucleosomal Dna

scholarly journals Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

mSystems ◽  
2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Kotaro Chihara ◽  
Thorsten Bischler ◽  
Lars Barquist ◽  
Vivian A. Monzon ◽  
Naohiro Noda ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
Cross Linking ◽  
Rna Seq ◽  
Content Type ◽  
Total Rna ◽  
Small Noncoding Rnas ◽  
Rna Chaperones

ABSTRACT Bacterial small noncoding RNAs (sRNAs) play posttranscriptional regulatory roles in cellular responses to changing environmental cues and in adaptation to harsh conditions. Generally, the RNA-binding protein Hfq helps sRNAs associate with target mRNAs to modulate their translation and to modify global RNA pools depending on physiological state. Here, a combination of in vivo UV cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq) and total RNA-seq showed that Hfq interacts with different regions of the Pseudomonas aeruginosa transcriptome under planktonic versus biofilm conditions. In the present approach, P. aeruginosa Hfq preferentially interacted with repeats of the AAN triplet motif at mRNA 5′ untranslated regions (UTRs) and sRNAs and U-rich sequences at rho-independent terminators. Further transcriptome analysis suggested that the association of sRNAs with Hfq is primarily a function of their expression levels, strongly supporting the notion that the pool of Hfq-associated RNAs is equilibrated by RNA concentration-driven cycling on and off Hfq. Overall, our combinatorial CLIP-seq and total RNA-seq approach highlights conditional sRNA associations with Hfq as a novel aspect of posttranscriptional regulation in P. aeruginosa. IMPORTANCE The Gram-negative bacterium P. aeruginosa is ubiquitously distributed in diverse environments and can cause severe biofilm-related infections in at-risk individuals. Although the presence of a large number of putative sRNAs and widely conserved RNA chaperones in this bacterium implies the importance of posttranscriptional regulatory networks for environmental fluctuations, limited information is available regarding the global role of RNA chaperones such as Hfq in the P. aeruginosa transcriptome, especially under different environmental conditions. Here, we characterize Hfq-dependent differences in gene expression and biological processes in two physiological states: the planktonic and biofilm forms. A combinatorial comparative CLIP-seq and total RNA-seq approach uncovered condition-dependent association of RNAs with Hfq in vivo and expands the potential direct regulatory targets of Hfq in the P. aeruginosa transcriptome.

scholarly journals CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Heming Wang ◽  
Rong Huang ◽  
Ling Li ◽  
Junjin Zhu ◽  
Zhihong Li ◽  
...  
Keyword(s):  
Stem Cell ◽  
High Throughput Sequencing ◽  
Noncoding Rnas ◽  
High Sensitivity ◽  
Small Noncoding Rnas ◽  
Adapter Ligation ◽  
Small Ncrnas ◽  
Mouse Tissues ◽  
Polynucleotide Kinase ◽  
Complex Landscape

AbstractHigh-throughput sequencing reveals the complex landscape of small noncoding RNAs (sRNAs). However, it is limited by requiring 5′-monophosphate and 3′-hydroxyl in RNAs for adapter ligation and hindered by methylated nucleosides that interfere with reverse transcription. Here we develop Cap-Clip acid pyrophosphatase (Cap-Clip), T4 polynucleotide kinase (PNK) and AlkB/AlkB(D135S)-facilitated small ncRNA sequencing (CPA-seq) to detect and quantify sRNAs with terminus multiplicities and nucleoside methylations. CPA-seq identified a large number of previously undetected sRNAs. Comparison of sRNAs with or without AlkB/AlkB(D135S) treatment reveals nucleoside methylations on sRNAs. Using CPA-seq, we profiled the sRNA transcriptomes (sRNomes) of nine mouse tissues and reported the extensive tissue-specific differences of sRNAs. We also observed the transition of sRNomes during hepatic reprogramming. Knockdown of mesenchymal stem cell-enriched U1-5′ snsRNA promoted hepatic reprogramming. CPA-seq is a powerful tool with high sensitivity and specificity for profiling sRNAs with methylated nucleosides and diverse termini.

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