scholarly journals The Chloroplast Epitranscriptome: Factors, Sites, Regulation, and Detection Methods

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1121
Author(s):  
Nikolay Manavski ◽  
Alexandre Vicente ◽  
Wei Chi ◽  
Jörg Meurer
Keyword(s):  
Gene Expression ◽  
Detection Methods ◽  
Stress Reactions ◽  
Rna Modifications ◽  
Chloroplast Gene Expression ◽  
Wide Range ◽  
Domains Of Life ◽  
A Site ◽  
Post Transcriptional Regulation ◽  
Processing Stability

Modifications in nucleic acids are present in all three domains of life. More than 170 distinct chemical modifications have been reported in cellular RNAs to date. Collectively termed as epitranscriptome, these RNA modifications are often dynamic and involve distinct regulatory proteins that install, remove, and interpret these marks in a site-specific manner. Covalent nucleotide modifications-such as methylations at diverse positions in the bases, polyuridylation, and pseudouridylation and many others impact various events in the lifecycle of an RNA such as folding, localization, processing, stability, ribosome assembly, and translational processes and are thus crucial regulators of the RNA metabolism. In plants, the nuclear/cytoplasmic epitranscriptome plays important roles in a wide range of biological processes, such as organ development, viral infection, and physiological means. Notably, recent transcriptome-wide analyses have also revealed novel dynamic modifications not only in plant nuclear/cytoplasmic RNAs related to photosynthesis but especially in chloroplast mRNAs, suggesting important and hitherto undefined regulatory steps in plastid functions and gene expression. Here we report on the latest findings of known plastid RNA modifications and highlight their relevance for the post-transcriptional regulation of chloroplast gene expression and their role in controlling plant development, stress reactions, and acclimation processes.

RNA Modifications in the Central Nervous System

2020 ◽  
Author(s):  
Dan Ohtan Wang
Keyword(s):  
Gene Expression ◽  
Cell Function ◽  
Gene Expression Regulation ◽  
Spinal Injury ◽  
Regulation Of Gene Expression ◽  
Modified Nucleosides ◽  
Rna Modifications ◽  
The Central Nervous System ◽  
Post Transcriptional Regulation ◽  
The Brain

Epitranscriptomics, a recently emerged field to investigate post-transcriptional regulation of gene expression through enzyme-mediated RNA modifications, is rapidly evolving and integrating with neuroscience. Using a rich repertoire of modified nucleosides and strategically positioning them to the functionally important and evolutionarily conserved regions of the RNA, epitranscriptomics dictates RNA-mediated cell function. The new field is quickly changing our view of the genetic geography in the brain during development and plasticity, impacting major functions from cortical neurogenesis, circadian rhythm, learning and memory, to reward, addiction, stress, stroke, and spinal injury, etc. Thus understanding the molecular components and operational rules of this pathway is becoming a key for us to decipher the genetic code for brain development, function, and disease. What RNA modifications are expressed in the brain? What RNAs carry them and rely on them for function? Are they dynamically regulated? How are they regulated and how do they contribute to gene expression regulation and brain function? This chapter summarizes recent advances that are beginning to answer these questions.

Post-Transcriptional Regulation of Chloroplast Gene Expression in Chlamydomonas

1994 ◽  
pp. 371-379
Author(s):  
Jean-David Rochaix ◽  
Michel Goldschmidt-Clermont ◽  
Caroline Monod ◽  
William Zerges
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Chloroplast Gene ◽  
Chloroplast Gene Expression ◽  
Post Transcriptional Regulation

Transcriptional and Post-Transcriptional Regulation of Chloroplast Gene Expression

1987 ◽  
pp. 135-148 ◽  
Author(s):  
Wilhelm Gruissem ◽  
Xing-Wang Deng ◽  
Helen Jones ◽  
David Stern ◽  
John Tonkyn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Chloroplast Gene ◽  
Chloroplast Gene Expression ◽  
Post Transcriptional Regulation

scholarly journals Organization and expression of organellar genomes

2010 ◽  
Vol 365 (1541) ◽  
pp. 785-797 ◽  
Author(s):  
Adrian C. Barbrook ◽  
Christopher J. Howe ◽  
Davy P. Kurniawan ◽  
Sarah J. Tarr
Keyword(s):  
Gene Expression ◽  
Mitochondrial Gene ◽  
Gene Content ◽  
Rrna Genes ◽  
Control Of Gene Expression ◽  
Photosynthetic Organisms ◽  
Wide Range ◽  
Redox Poise ◽  
Post Transcriptional Regulation ◽  
And Control

Protist mitochondrial genomes show a very wide range of gene content, ranging from three genes for respiratory chain components in Apicomplexa and dinoflagellates to nearly 100 genes in Reclinomonas americana . In many organisms the rRNA genes are fragmented, although still functional. Some protist mitochondria encode a full set of tRNAs, while others rely on imported molecules. There is similarly a wide variation in mitochondrial genome organization, even among closely related groups. Mitochondrial gene expression and control are generally poorly characterized. Transcription probably relies on a ‘viral-type’ RNA polymerase, although a ‘bacterial-type’ enzyme may be involved in some cases. Transcripts are heavily edited in many lineages. The chloroplast genome generally shows less variation in gene content and organization, although greatly reduced genomes are found in dinoflagellate algae and non-photosynthetic organisms. Genes in the former are located on small plasmids in contrast to the larger molecules found elsewhere. Control of gene expression in chloroplasts involves transcriptional and post-transcriptional regulation. Redox poise and the ATP/ADP ratio are likely to be important determinants. Some protists have an additional extranuclear genome, the nucleomorph, which is a remnant nucleus. Nucleomorphs of two separate lineages have a number of features in common.

scholarly journals Programmable RNA recognition using a CRISPR-associated Argonaute

2017 ◽  
Author(s):  
Audrone Lapinaite ◽  
Jennifer A. Doudna ◽  
Jamie H. D. Cate
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Complex Mixture ◽  
Seed Region ◽  
Single Nucleotide ◽  
Guide Rna ◽  
Argonaute Proteins ◽  
Wide Range ◽  
Domains Of Life

ABSTRACTArgonaute proteins (Agos) are present in all domains of life. While the physiological function of eukaryotic Agos in regulating gene expression is well documented, the biological roles of many of their prokaryotic counterparts remain enigmatic. In some bacteria, Agos are associated with CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) loci and use non-canonical 5’-hydroxyled guide RNAs (gRNAs) for nucleic acid targeting. Here we show that using 5-bromo-2′-deoxyuridine (BrdU) as the 5’ nucleotide of gRNAs stabilizes in vitro reconstituted CRISPR-associated Marinitoga piezophila Argonaute-gRNA complexes (MpAgo RNPs) and significantly improves their specificity and affinity for RNA targets. Using reconstituted MpAgo RNPs with 5’-BrdU modified gRNAs, we mapped the seed region of the gRNA, and identified the nucleotides of the gRNA that play the most significant role in targeting specificity. We also show that these MpAgo RNPs can be programmed to distinguish between substrates that differ by a single nucleotide, using permutations at the 6th and 7th positions in the gRNA. Using these specificity features, we employed MpAgo RNPs to detect specific Adenosine to Inosine edited RNAs in a complex mixture. These findings broaden our mechanistic understanding of the interactions of Argonautes with guide and substrate RNAs, and demonstrate that MpAgo RNPs with 5’-BrdU modified gRNAs can be used as a highly-specific RNA-targeting platform to probe RNA biology.SIGNIFICANCEArgonaute proteins are present in bacteria, archaea and eukaryotes. They play an important role in a wide range of biological processes, from transcriptional and translational gene expression regulation to defense against viruses and silencing of mobile genetic elements. Here we present mechanistic insights into the interactions of the CRISPR-associated Marinitoga piezophila Argonaute (MpAgo) with its guide RNA (gRNA) and RNA substrates. By modifying the 5’-nucleotide of the gRNA, we demonstrate that MpAgo-gRNA complexes (RNPs) are easily programmable, have high affinity to fully complementary RNA substrates, and can discriminate by over 300 fold between substrates that differ by only a single nucleotide. These MpAgo RNPs should be useful for probing endogenous RNAs in living cells.

Sign in / Sign up

Export Citation Format

Share Document