scholarly journals A novel assay identifies transcript elongation roles for the Nup84 complex and RNA processing factors

2011 ◽  
Vol 30 (10) ◽  
pp. 1953-1964 ◽  
Author(s):  
Cristina Tous ◽  
Ana G Rondón ◽  
María García-Rubio ◽  
Cristina González-Aguilera ◽  
Rosa Luna ◽  
...  
Keyword(s):  
Rna Processing ◽  
Transcript Elongation ◽  
Processing Factors

scholarly journals In Arabidopsis thaliana mitochondria 5′ end polymorphisms of nad4L-atp4 and nad3-rps12 transcripts are linked to RNA PROCESSING FACTORs 1 and 8

2021 ◽  
Author(s):  
Sarah Schleicher ◽  
Stefan Binder
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Processing ◽  
Degradation Products ◽  
Underlying Mechanism ◽  
Transcriptional Level ◽  
Pentatricopeptide Repeat ◽  
Repeat Proteins ◽  
P Type ◽  
Pentatricopeptide Repeat Proteins ◽  
Processing Factors

Abstract Key message RNA PROCESSING FACTORs 1 AND 8 (RPF1 and RPF8), both restorer of fertility like pentatricopeptide repeat proteins, are required for processing of dicistronic nad4L-atp4 and nad3-rps12 transcripts in Arabidopsis mitochondria. Abstract In mitochondria of Arabidopsis thaliana (Arabidopsis), the 5′ termini of many RNAs are generated on the post-transcriptional level. This process is still poorly understood in terms of both the underlying mechanism as well as proteins required. Our studies now link the generation of polymorphic 5′ extremities of the dicistronic nad3-rps12 and nad4L-atp4 transcripts to the function of the P-type pentatricopeptide repeat proteins RNA PROCESSING FACTORs 8 (RPF8) and 1 (RPF1). RPF8 is required to generate the nad3-rps12 -141 5′ end in ecotype Van-0 whereas the RPF8 allele in Col has no function in the generation of any 5′ terminus of this transcript. This observation strongly suggests the involvement of an additional factor in the generation of the -229 5′ end of nad3-rps12 transcripts in Col. RPF1, previously found to be necessary for the generation of the -228 5′ end of the major 1538 nucleotide-long nad4 mRNAs, is also important for the formation of nad4L-atp4 transcripts with a 5′ end at position -318 in Col. Many Arabidopsis ecotypes contain inactive RPF1 alleles resulting in the accumulation of various low abundant nad4L-atp4 RNAs which might represent precursor and/or degradation products. Some of these ecotypes accumulate major, but slightly smaller RNA species. The introduction of RPF1 into these lines not only establishes the formation of the major nad4L-atp4 dicistronic mRNA with the -318 5′ terminus, the presence of this gene also suppresses the accumulation of most alternative nad4L-atp4 RNAs. Beside RPF1, several other factors contribute to nad4L-atp4 transcript formation.

Compartmentalization of RNA Processing Factors within Nuclear Speckles

2000 ◽  
Vol 129 (2-3) ◽  
pp. 241-251 ◽  
Author(s):  
Paul J. Mintz ◽  
David L. Spector
Keyword(s):  
Rna Processing ◽  
Nuclear Speckles ◽  
Processing Factors

scholarly journals Pre-Messenger RNA Processing Factors in the Drosophila Genome

2000 ◽  
Vol 150 (2) ◽  
pp. F37-F44 ◽  
Author(s):  
Stephen M. Mount ◽  
Helen K. Salz
Keyword(s):  
Rna Processing ◽  
Messenger Rna ◽  
Drosophila Genome ◽  
Processing Factors

scholarly journals Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation

eLife ◽  
2022 ◽  
Vol 11 ◽  
Author(s):  
Maxim I Maron ◽  
Alyssa D Casill ◽  
Varun Gupta ◽  
Jacob S Roth ◽  
Simone Sidoli ◽  
...  
Keyword(s):  
Arginine Methylation ◽  
Targeted Mutagenesis ◽  
Type I ◽  
Type Ii ◽  
Protein Arginine Methyltransferases ◽  
Polyadenylated Rna ◽  
Transcript Elongation ◽  
Retained Introns ◽  
Method Analysis ◽  
Processing Factors

Protein arginine methyltransferases (PRMTs) are required for the regulation of RNA processing factors. Type I PRMT enzymes catalyze mono- and asymmetric dimethylation; Type II enzymes catalyze mono- and symmetric dimethylation. To understand the specific mechanisms of PRMT activity in splicing regulation, we inhibited Type I and II PRMTs and probed their transcriptomic consequences. Using the newly developed Splicing Kinetics and Transcript Elongation Rates by Sequencing (SKaTER-seq) method, analysis of co-transcriptional splicing demonstrated that PRMT inhibition resulted in altered splicing rates. Surprisingly, co-transcriptional splicing kinetics did not correlate with final changes in splicing of polyadenylated RNA. This was particularly true for retained introns (RI). By using actinomycin D to inhibit ongoing transcription, we determined that PRMTs post-transcriptionally regulate RI. Subsequent proteomic analysis of both PRMT-inhibited chromatin and chromatin-associated polyadenylated RNA identified altered binding of many proteins, including the Type I substrate, CHTOP, and the Type II substrate, SmB. Targeted mutagenesis of all methylarginine sites in SmD3, SmB, and SmD1 recapitulated splicing changes seen with Type II PRMT inhibition, without disrupting snRNP assembly. Similarly, mutagenesis of all methylarginine sites in CHTOP recapitulated the splicing changes seen with Type I PRMT inhibition. Examination of subcellular fractions further revealed that RI were enriched in the nucleoplasm and chromatin. Together, these data demonstrate that, through Sm and CHTOP arginine methylation, PRMTs regulate the post-transcriptional processing of nuclear, detained introns.

scholarly journals Emerging roles of RNA processing factors in regulating long non-coding RNAs

RNA Biology ◽  
2014 ◽  
Vol 11 (7) ◽  
pp. 793-797 ◽  
Author(s):  
Huiming Zhang ◽  
Jian-Kang Zhu
Keyword(s):  
Rna Processing ◽  
Non Coding Rnas ◽  
Processing Factors
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