scholarly journals The RNA Atlas, a single nucleotide resolution map of the human transcriptome

2019 ◽  
Author(s):  
Lucia Lorenzi ◽  
Hua-Sheng Chiu ◽  
Francisco Avila Cobos ◽  
Stephen Gross ◽  
Pieter-Jan Volders ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Human Transcriptome ◽  
Abundance Estimates ◽  
Rna Biology ◽  
Functional Regulation ◽  
Non Coding Rnas ◽  
Nucleotide Resolution ◽  
And Function ◽  
Polyadenylated Rnas ◽  
Single Nucleotide Resolution

AbstractThe human transcriptome consists of various RNA biotypes including multiple types of non-coding RNAs (ncRNAs). Current ncRNA compendia remain incomplete partially because they are almost exclusively derived from the interrogation of small- and polyadenylated RNAs. Here, we present a more comprehensive atlas of the human transcriptome that is derived from matching polyA-, total-, and small-RNA profiles of a heterogeneous collection of nearly 300 human tissues and cell lines. We report on thousands of novel RNA species across all major RNA biotypes, including a hitherto poorly-cataloged class of non-polyadenylated single-exon long non-coding RNAs. In addition, we exploit intron abundance estimates from total RNA-sequencing to test and verify functional regulation by novel non-coding RNAs. Our study represents a substantial expansion of the current catalogue of human ncRNAs and their regulatory interactions. All data, analyses, and results are available in the R2 web portal and serve as a basis to further explore RNA biology and function.

scholarly journals Nucleotide resolution profiling of m3C RNA modification by HAC-seq

2020 ◽  
Author(s):  
Jia Cui ◽  
Qi Liu ◽  
Erdem Sendinc ◽  
Yang Shi ◽  
Richard I Gregory
Keyword(s):  
Rna Modification ◽  
Rna Modifications ◽  
Mcf7 Cells ◽  
Single Nucleotide ◽  
Novel Method ◽  
Specific Mapping ◽  
Nucleotide Resolution ◽  
And Function ◽  
Trna Isoacceptors ◽  
Single Nucleotide Resolution

Abstract Cellular RNAs are subject to a myriad of different chemical modifications that play important roles in controlling RNA expression and function. Dysregulation of certain RNA modifications, the so-called ‘epitranscriptome’, contributes to human disease. One limitation in studying the functional, physiological, and pathological roles of the epitranscriptome is the availability of methods for the precise mapping of individual RNA modifications throughout the transcriptome. 3-Methylcytidine (m3C) modification of certain tRNAs is well established and was also recently detected in mRNA. However, methods for the specific mapping of m3C throughout the transcriptome are lacking. Here, we developed a m3C-specific technique, Hydrazine-Aniline Cleavage sequencing (HAC-seq), to profile the m3C methylome at single-nucleotide resolution. We applied HAC-seq to analyze ribosomal RNA (rRNA)-depleted total RNAs in human cells. We found that tRNAs are the predominant m3C-modified RNA species, with 17 m3C modification sites on 11 cytoplasmic and 2 mitochondrial tRNA isoacceptors in MCF7 cells. We found no evidence for m3C-modification of mRNA or other non-coding RNAs at comparable levels to tRNAs in these cells. HAC-seq provides a novel method for the unbiased, transcriptome-wide identification of m3C RNA modification at single-nucleotide resolution, and could be widely applied to reveal the m3C methylome in different cells and tissues.

scholarly journals Conserved Methyltransferase Spb1 Targets mRNAs for Regulated Modification with 2′-O-Methyl Ribose

2018 ◽  
Author(s):  
Kristen M. Bartoli ◽  
Cassandra Schaening ◽  
Thomas M. Carlile ◽  
Wendy V. Gilbert
Keyword(s):  
List Type ◽  
Single Nucleotide ◽  
Target Mrnas ◽  
Mrna Targets ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution ◽  
Specific Mrna

SUMMARYNon-coding RNAs contain dozens of chemically distinct modifications, of which only a few have been identified in mRNAs. The recent discovery that certain tRNA modifying enzymes also target mRNAs suggests the potential for many additional mRNA modifications. Here, we show that conserved tRNA 2′-O-methyltransferases Trm3, 7,13 and 44, and rRNA 2′-O-methyltransferase Spb1, interact with specific mRNA sites in yeast by crosslinking immunoprecipitation and sequencing (CLIP-seq). We developed sequencing of methylation at two prime hydroxyls (MeTH-seq) for transcriptome-wide mapping of 2′-O-methyl ribose (Nm) with single-nucleotide resolution, and discover thousands of potential Nm sites in mRNAs. Genetic analysis identified hundreds of mRNA targets for the Spb1 methyltransferase, which can target both mRNA and non-coding RNA for environmentally regulated modification. Our work identifies Nm as a prevalent mRNA modification that is likely to be conserved and provides methods to investigate its distribution and regulation.HIGHLIGHTSMeTH-seq identifies 2′-O-methylribose genome-wide at single-nucleotide resolutionFive conserved methyltransferases interact with yeast mRNASpb1 is a major mRNA 2′-O-methyltransferase, and targets most ribosomal protein mRNAsSPB1 expression is required to maintain normal levels of Spb1 target mRNAs

scholarly journals Chemical probing of the homopurine·homopyrimidine tract in supercoiled DNA at single-nucleotide resolution

FEBS Letters ◽  
1988 ◽  
Vol 234 (2) ◽  
pp. 295-299 ◽  
Author(s):  
M. Vojtíšková ◽  
S. Mirkin ◽  
V. Lyamichev ◽  
O. Voloshin ◽  
M. Frank-Kamenetskii ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Supercoiled Dna ◽  
Chemical Probing ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Nanoscale ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 538-547 ◽  
Author(s):  
Hyungbeen Lee ◽  
Sang Won Lee ◽  
Gyudo Lee ◽  
Wonseok Lee ◽  
Kihwan Nam ◽  
...  
Keyword(s):  
Kelvin Probe Force Microscopy ◽  
Powerful Method ◽  
Kelvin Probe ◽  
Single Nucleotide ◽  
Force Microscopy ◽  
Surface Potentials ◽  
Dna Mismatches ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (χ0 to χ5) using Kelvin probe force microscopy (KPFM).

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