Guide for protein fold change and <i>p</i>-value calculation for non-experts in proteomics

Aguilan, Jennifer; Kulej, Katarzyna; Sidoli, Simone

doi:10.1039/d0mo00087f

Cited by 101 publications

(82 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Data were transformed, normalized and statistics were applied as described previously ( Aguilan et al, 2020 ). Briefly, the data were log 2 transformed and normalized by the average of the data distribution.…”

Section: Methodsmentioning

confidence: 99%

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

Maron

Casill

Gupta

et al. 2022

eLife

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Methodsmentioning

confidence: 99%

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

Maron

Casill

Gupta

et al. 2022

eLife

Self Cite

View full text Add to dashboard Cite

show abstract

“…Peptide and protein false discovery rate was set to 1%. Data transformation, normalization and statistical analysis using heteroscedastic t-test was performed as previously described [ 71 ].…”

Section: Methodsmentioning

confidence: 99%

VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms

Fouracre

Chen

et al. 2021

PLoS Genet

Self Cite

View full text Add to dashboard Cite

How organisms control when to transition between different stages of development is a key question in biology. In plants, epigenetic silencing by Polycomb repressive complex 1 (PRC1) and PRC2 plays a crucial role in promoting developmental transitions, including from juvenile-to-adult phases of vegetative growth. PRC1/2 are known to repress the master regulator of vegetative phase change, miR156, leading to the transition to adult growth, but how this process is regulated temporally is unknown. Here we investigate whether transcription factors in the VIVIPAROUS/ABI3-LIKE (VAL) gene family provide the temporal signal for the epigenetic repression of miR156. Exploiting a novel val1 allele, we found that VAL1 and VAL2 redundantly regulate vegetative phase change by controlling the overall level, rather than temporal dynamics, of miR156 expression. Furthermore, we discovered that VAL1 and VAL2 also act independently of miR156 to control this important developmental transition. In combination, our results highlight the complexity of temporal regulation in plants.

show abstract

Section: Star Methodsmentioning

confidence: 99%

VALgenes regulate vegetative phase change via miR156-dependent and independent mechanisms

Fouracre

Chen

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

How organisms control when to transition between different stages of development is a key question in biology. In plants, epigenetic silencing by Polycomb repressive complex 1 (PRC1) and PRC2 plays a crucial role in promoting developmental transitions, including from juvenile-to-adult phases of vegetative growth. It is well established that PRC1/2 repress the master regulator of vegetative phase change, miR156, leading to the transition to adult growth, but how this process in temporally regulated is unknown. Here we investigate whether transcription factors in the VIVIPAROUS/ABI3-LIKE (VAL) gene family provide the temporal signal for the epigenetic repression of miR156. Exploiting a novel val1 allele, we found that VAL1 and VAL2 redundantly regulate vegetative phase change by controlling the overall level, rather than temporal dynamics, of miR156 expression. Furthermore, we discovered that VAL1 and VAL2 also act independently of miR156 to control this important developmental transition.

show abstract

Guide for protein fold change and p-value calculation for non-experts in proteomics

Abstract: Proteomics data can be processed using simple speadsheet formula.

Cited by 101 publications

References 55 publications

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

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

VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms

VALgenes regulate vegetative phase change via miR156-dependent and independent mechanisms

Contact Info

Product

Resources

About