Efficient and quantitative high-throughput tRNA sequencing

Zheng, Guoliang; Qin, Yidan; Clark, Wesley C.; Dai, Qing; Yi, Chengqi; He, Chuan; Lambowitz, Alan M.; Pan, Tao

doi:10.1038/nmeth.3478

Cited by 462 publications

(644 citation statements)

References 20 publications

Supporting

Mentioning

586

Contrasting

Order By: Relevance

“…Pan and co-workers also developed the DM-tRNA-seq method (Zheng et al 2015). They used AlkB to remove m1A, m3C, and m1G methylations, and a thermostable group II intron reverse transcriptase (TGIRT) to synthesis cDNA from highly structured tRNA.…”

Section: The State Of the Trna Population In The Cellmentioning

confidence: 99%

Protein folding and tRNA biology

2017

View full text Add to dashboard Cite

Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.

show abstract

Section: The State Of the Trna Population In The Cellmentioning

confidence: 99%

Protein folding and tRNA biology

2017

View full text Add to dashboard Cite

show abstract

“…Further structural and function analysis of ARS genes provide evidence that they have an impact on human life and contribute to the regulation and coordination processes in the mitochondria and nuclear genes simultaneously. Besides playing the major canonical role, their non-canonical pathways have a widespread impact; indeed, many researchers consider them as the hotspot of the regulation system [7][8][9][10][11][12][13]21,22]. Different factors are found to be associated with these gene mutations, like abnormal synthesis of enzyme, oxidative stress condition and other intrinsic and extrinsic causes.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, an extensive catalogue of diseases link with the pool of (n)tRNA, (mt)tRNA, ARS and ARS2 genes. The process of analyzing tRNA expression by deep sequencing is a recent favorite [22]. Emergence of deep sequencing to assess the genome-wide tissuespecific tRNA expression level has revealed that the (n) tRNAs and (mt) tRNAs exhibit distinct expression patterns, indicating that tRNAs might potentially be used as biomarkers for cancer.…”

Section: Introductionmentioning

confidence: 99%

tRN-A-RS Acts As Biomarker for Cancer and Other Diseases

Samadder¹,

Mitra²,

Chakraborty³

et al. 2016

J Mol Biomark Diagn

View full text Add to dashboard Cite

“…In 2015, Pan's team described a potential way to quantify modifications, at least in another class of RNA called transfer RNAs 11 . The approach uses a reverse transcriptase that can read through the modifications efficiently, thereby capturing sequences downstream of the first modification it encounters.…”

Section: Moving Beyond Mappingmentioning

confidence: 99%

The RNA code comes into focus

Rae¹

2017

Nature

View full text Add to dashboard Cite

As researchers open up to the reality of RNA modification, an expanded epitranscriptomics toolbox takes shape. THE RNA CODE COMES INTO FOCUSBY K E L LY R A E C H I I n 2004, oncologist Gideon Rechavi at Tel Aviv University in Israel and his colleagues compared all the human genomic DNA sequences then available with their corresponding messenger RNAs -the molecules that carry the information needed to make a protein from a gene. They were looking for signs that one of the nucleotide building blocks in the RNA sequence, called adenosine (A), had changed to another building block called inosine (I). This ' A-to-I editing' can alter a protein's coding sequence, and, in humans, is crucial for keeping the innate immune response in check. "It sounds simple, but in real life it was really complicated," Rechavi recalls. "Several groups had tried it before and failed" because sequencing mistakes and single-nucleotide mutations had made the data noisy. But using a new bioinformatics approach, his team uncovered thousands of sites in the transcriptome -the complete set of mRNAs found in an organism or cell population -and later studies upped the number into the millions 1 . Inosine is something of a special case: researchers can readily detect this chink in the armour by comparing DNA and RNA sequences. But at least one-quarter of our mRNAs harbour chemical tags -decorations to the A, C, G and U nucleotides -that are invisible to today's sequencing technologies. (Similar chemical tags, called epigenetic markers, are also found on DNA.) Researchers aren't sure what these chemical changes in RNA do, but they're trying to find out.A wave of studies over the past five yearsmany of which focus on a specific RNA mark called N 6 -methyladenosine (m 6 A) -have mapped these alterations across transcriptomes and demonstrated their importance to health and disease. But the problem is vast: these marks coat not only mRNA but other RNA transcripts as well, and they cut across TECHNOLOGY FEATURE © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e . A l l r i g h t s r e s e r v e d .

show abstract

Efficient and quantitative high-throughput tRNA sequencing

Cited by 462 publications

References 20 publications

Protein folding and tRNA biology

Protein folding and tRNA biology

tRN-A-RS Acts As Biomarker for Cancer and Other Diseases

The RNA code comes into focus

Contact Info

Product

Resources

About