Cracking the epitranscriptome

Schwartz, Schraga

doi:10.1261/rna.054502.115

Cited by 76 publications

(60 citation statements)

References 67 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…RNA modifications that previously went undetected are now known to play major roles in governing gene expression in both prokaryotic and eukaryotic organisms (Deana et al, 2008; Schwartz, 2016). For instance, recent studies have shown that adenosine methylation can stimulate translation and accelerate mRNA degradation in human cells (Wang et al, 2014; Wang et al, 2015; Meyer et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

A Novel RNA Phosphorylation State Enables 5′ End-Dependent Degradation in Escherichia coli

et al. 2017

View full text Add to dashboard Cite

SUMMARY RNA modifications that once escaped detection are now thought to be pivotal for governing RNA lifetimes in both prokaryotes and eukaryotes. For example, converting the 5′-terminal triphosphate of bacterial transcripts to a monophosphate triggers 5′-end-dependent degradation by RNase E. However, the existence of diphosphorylated RNA in bacteria has never been reported, and no biological role for such a modification has ever been proposed. By using a novel assay, we show here for representative Escherichia coli mRNAs that ~35–50% of each transcript is diphosphorylated. The remainder is primarily monophosphorylated, with surprisingly little triphosphorylated RNA evident. Furthermore, diphosphorylated RNA is the preferred substrate of the RNA pyrophosphohydrolase RppH, whose biological function was previously assumed to be pyrophosphate removal from triphosphorylated transcripts. We conclude that triphosphate-to-monophosphate conversion to induce 5′-end-dependent RNA degradation is a two-step process in E. coli involving γ-phosphate removal by an unidentified enzyme to enable subsequent β-phosphate removal by RppH.

show abstract

Section: Discussionmentioning

confidence: 99%

A Novel RNA Phosphorylation State Enables 5′ End-Dependent Degradation in Escherichia coli

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Transcriptome-wide maps have also been obtained for N 1 -methyladenosine (m 1 A) (Dominissini et al 2016), N 6 ,2 ′ -O-dimethyladenosine (m 6 Am) (Linder et al 2015;Mauer et al 2016), 5-methylcytosine (m 5 C) and pseudouridine (Y), revealing their involvement in biological processes such as stress responses (Carlile et al 2014), protein synthesis quality control (Tuorto et al 2012;Hussain et al 2013;Blanco et al 2014), and mRNA stability (Mauer et al 2016), among others. There are several excellent reviews on these few relatively well-characterized RNA modifications (Klungland and Dahl 2014;Li and Mason 2014;Frye et al 2016;Gilbert et al 2016;Li et al 2016;Schwartz 2016;Zhao et al 2016).…”

Section: Introductionmentioning

confidence: 99%

The RNA modification landscape in human disease

Jonkhout

Tran

Smith

et al. 2017

RNA

494

420

View full text Add to dashboard Cite

RNA modifications have been historically considered as fine-tuning chemo-structural features of infrastructural RNAs, such as rRNAs, tRNAs, and snoRNAs. This view has changed dramatically in recent years, to a large extent as a result of systematic efforts to map and quantify various RNA modifications in a transcriptome-wide manner, revealing that RNA modifications are reversible, dynamically regulated, far more widespread than originally thought, and involved in major biological processes, including cell differentiation, sex determination, and stress responses. Here we summarize the state of knowledge and provide a catalog of RNA modifications and their links to neurological disorders, cancers, and other diseases. With the advent of direct RNA-sequencing technologies, we expect that this catalog will help prioritize those RNA modifications for transcriptome-wide maps.

show abstract

“…RNA can harbor nearly distinct 100 chemical modifications after its synthesis (44). Since their initial discovery more than 60 years ago, the vast majority of research on the modification of RNAs has focused on highly abundant RNA species, such as rRNAs, tRNAs, and snRNAs.…”

Section: Epigenetic Modificationsmentioning

confidence: 99%

“…Since their initial discovery more than 60 years ago, the vast majority of research on the modification of RNAs has focused on highly abundant RNA species, such as rRNAs, tRNAs, and snRNAs. However, the lack of sensitive methods has long hampered the characterization of RNA modifications of minimally expressed mRNAs (44). The possibility of the use of next-generation sequencing approaches has now increased the interest in RNA modifications of coding mRNAs and in their functions in normal and pathological situations.…”

Section: Epigenetic Modificationsmentioning

confidence: 99%

Chromatin and Epigenetics at the Forefront: Finding Clues among Peaks

Aranda

Shi

Croce

2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

The symposium brought together some of the most outstanding scientists studying how chromatin structure and epigenetic mechanisms regulate gene function in both development and disease. Junior scientists had the opportunity to interact with experienced researchers by presenting their work and discussing ideas and novel hypotheses. In order to foster interaction and networking, the scientific agenda was balanced with an extended social agenda. This meeting review describes several of the most provocative and exciting talks from the symposium, revealing how fast this research field is evolving and the profound impact it will have on human health. The Canadian town of Whistler, famous as the largest ski resort in North America, held some of the sport events of the XXI Winter Olympics and Paralympic Games during 2010. This year, the so-called Athletes' Village hosted scientists who attended and participated in the Keystone Symposium on Chromatin and Epigenetics, which turned Whistler into a scientists' village for 5 days. The meeting's 320 participants included a large proportion of young scientists, with nearly 50% at the predoctoral or postdoctoral stage of their careers. Moreover, while a large proportion of participants (70%) had academic affiliations, the industrial sector was also well represented (with 12% of total affiliations), revealing the increasing interest of the sector in the epigenetics field.The most relevant topics covered by this meeting are summarized in Fig. 1 with the relative levels of usage of keywords related to the chromatin and epigenetic research fields. Although cancer was the cellular dysfunction that occupied the greatest proportion of the meeting's interest, the impact of epigenetic research has extended to other functions, such as cellular differentiation and pluripotency, aging, and cellular memory. The ten-eleven translocation (Tet) enzymes were the most-studied protein family, although methyltransferases (MTs), in particular, the Polycomb group (PcG) of protein complexes, the mixed lineage leukemia (MLL) proteins, and the DNA methyltransferases (DNMTs), were in close proximity. DNA methylation seems still to be the most-studied epigenetic modification, although research findings concerning novel functions related to RNA modification were presented during the meeting. Recent advances in chromosome conformation capturing technologies (3C and 4C), together with clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 genome editing, provided new exciting insight into the functionality of regulatory elements, such as promoters and enhancers. Finally, novel methods for molecular analysis of chromatin were presented which will probably soon be part of the preferred techniques in the epigenetics research field, together with chromatin immunoprecipitation (ChIP) and massive parallel sequencing of the transcriptome (RNA-seq).In this review, we highlight several of the most relevant findings presented during the meeting concerning the most discussed topics related to (i) the f...

show abstract

Cracking the epitranscriptome

Cited by 76 publications

References 67 publications

A Novel RNA Phosphorylation State Enables 5′ End-Dependent Degradation in Escherichia coli

A Novel RNA Phosphorylation State Enables 5′ End-Dependent Degradation in Escherichia coli

The RNA modification landscape in human disease

Chromatin and Epigenetics at the Forefront: Finding Clues among Peaks

Contact Info

Product

Resources

About