A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues

Abstract Background Small nucleolar RNAs (snoRNAs) are mid-size non-coding RNAs required for ribosomal RNA modification, implying a ubiquitous tissue distribution linked to ribosome synthesis. However, increasing numbers of studies identify extra-ribosomal roles of snoRNAs in modulating gene expression, suggesting more complex snoRNA abundance patterns. Therefore, there is a great need for mapping the snoRNome in different human tissues as the blueprint for snoRNA functions. Results We used a low structure bias RNA-Seq approach to accurately quantify snoRNAs and compare them to the entire transcriptome in seven healthy human tissues (breast, ovary, prostate, testis, skeletal muscle, liver, and brain). We identify 475 expressed snoRNAs categorized in two abundance classes that differ significantly in their function, conservation level, and correlation with their host gene: 390 snoRNAs are uniformly expressed and 85 are enriched in the brain or reproductive tissues. Most tissue-enriched snoRNAs are embedded in lncRNAs and display strong correlation of abundance with them, whereas uniformly expressed snoRNAs are mostly embedded in protein-coding host genes and are mainly non- or anticorrelated with them. Fifty-nine percent of the non-correlated or anticorrelated protein-coding host gene/snoRNA pairs feature dual-initiation promoters, compared to only 16% of the correlated non-coding host gene/snoRNA pairs. Conclusions Our results demonstrate that snoRNAs are not a single homogeneous group of housekeeping genes but include highly regulated tissue-enriched RNAs. Indeed, our work indicates that the architecture of snoRNA host genes varies to uncouple the host and snoRNA expressions in order to meet the different snoRNA abundance levels and functional needs of human tissues.

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Biogenesis and Function of Small Non-Coding RNAs Derived from Eukaryotic Ribosomal RNA

10.20944/preprints201810.0596.v1 ◽

2018 ◽

Author(s):

Marine Lambert ◽

Abderrahim Benmoussa ◽

Patrick Provost

Keyword(s):

Ribosomal Rna ◽

Potential Role ◽

A Priori ◽

Biological Significance ◽

Rna Seq ◽

New Class ◽

Scientific Mind ◽

Non Coding Rnas ◽

And Function ◽

Rrna Sequences

The advent of RNA-sequencing (RNA-Seq) technologies has markedly improved our knowledge and expanded the compendium of small non-coding RNAs, most of which derive from the processing of longer RNA precursors. In this review article, we will discuss about the biogenesis and function of small non-coding RNAs derived from eukaryotic ribosomal RNA (rRNA), called rRNA fragments (rRFs), and their potential role(s) as regulator of gene expression. This relatively new class of ncRNAs remained poorly investigated and underappreciated until recently, due mainly to the a priori exclusion of rRNA sequences—because of their overabundance—from RNA-Seq datasets. The situation surrounding rRFs resembles that of microRNAs (miRNAs), which used to be readily discarded from further analyses, for more than five decades, because we could not believe that RNA of such a short length could bear biological significance. As if we had not yet learned our lesson not to restrain our investigative, scientific mind from challenging widely accepted beliefs or dogmas, and from looking for the hidden treasures in the most unexpected places.

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Ribo-Zero Gold Kit: improved RNA-seq results after removal of cytoplasmic and mitochondrial ribosomal RNA

Nature Methods ◽

10.1038/nmeth.f.352 ◽

2011 ◽

Vol 8 (11) ◽

pp. iii-iv ◽

Cited By ~ 9

Author(s):

Vladimir Benes ◽

Jonathon Blake ◽

Ken Doyle

Keyword(s):

Ribosomal Rna ◽

Rna Seq

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Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data

BMC Genomics ◽

10.1186/1471-2164-13-412 ◽

2012 ◽

Vol 13 (1) ◽

pp. 412 ◽

Cited By ~ 23

Author(s):

Peter Tonner ◽

Vinodh Srinivasasainagendra ◽

Shaojie Zhang ◽

Degui Zhi

Keyword(s):

Ribosomal Protein ◽

Human Tissues ◽

Rna Seq

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Novel monoclonal antibodies specific for human cardiac myosin light-chain 1: useful tools for analysis of normal and pathological hearts.

Journal of Histochemistry & Cytochemistry ◽

10.1177/41.1.8417110 ◽

1993 ◽

Vol 41 (1) ◽

pp. 35-42 ◽

Cited By ~ 4

Author(s):

K Fujimoto ◽

H Yasue ◽

K Nakao ◽

H Yamamoto ◽

Y Hitoshi ◽

...

Keyword(s):

Skeletal Muscle ◽

Monoclonal Antibodies ◽

Light Chain ◽

Myosin Light Chain ◽

Normal Adult ◽

Human Tissues ◽

Cardiac Myosin ◽

Adult Type ◽

Adult Human ◽

Slow Type

To investigate the developmental, physiological and pathophysiological roles of human cardiac myosin light-chain 1 (LC1s), we developed two novel monoclonal antibodies (KA1 and KB1) against human cardiac LC1s and examined LC1s in normal and pathological hearts immunohistochemically. KA1 and KB1 were specific only for atrial LC1 (ALC1) and for both ALC1 and ventricular LC1 (VLC1), respectively, in human hearts. Among human tissues tested, including skeletal muscle, vascular smooth muscle, and liver, KA1 did not crossreact with proteins in any other tissues than atria, whereas KB1 crossreacted with the slow-type LC1 of skeletal muscle. Among adult mammalian hearts of several other species including pig, dog, hamster, and rat, KA1 and KB1 crossreacted only with ALC1 and with both ALC1 and VLC1, respectively. ALC1 was strongly and uniformly observed in human fetal atria and ventricles and in normal adult human atria, but sporadically in normal adult human ventricles. In the overloaded ventricle (dilated cardiomyopathy), ALC1 was highly augmented but not uniform. These results suggest that the fetal VLC1 is immunohistochemically identical to the adult type of ALC1 and that ALC1 is expressed homogeneously in human fetal ventricles and sporadically in normal adult ventricles, and is re-expressed heterogeneously and in an increased amount in the overloaded ventricle.

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Comparison of Poly-A+ Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq

Non-Coding RNA ◽

10.3390/ncrna6030032 ◽

2020 ◽

Vol 6 (3) ◽

pp. 32 ◽

Cited By ~ 1

Author(s):

Anna R. Dahlgren ◽

Erica Y. Scott ◽

Tamer Mansour ◽

Erin N. Hales ◽

Pablo J. Ross ◽

...

Keyword(s):

Ribosomal Rna ◽

Preparation Method ◽

Parietal Lobe ◽

Library Preparation ◽

Rna Seq ◽

The Past ◽

Rrna Depletion ◽

Non Coding Rnas ◽

Nucleolar Rna ◽

Library Preparation Method

Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.

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