Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors

Pfab, Alexander; Antosz, Wojciech; Holzinger, Philipp; Bruckmann, Astrid; Griesenbeck, Joachim; Grasser, Klaus D.

doi:10.1007/978-1-4939-7125-1_8

Cited by 5 publications

(5 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nuclei were isolated from aerial parts of 7 days after stratification (DAS) plants as previously described ( Pfab et al., 2017 ) and analyzed by fluorescence microscopy and immunoblotting as previously described ( Antosz et al., 2017 ; Pfab et al., 2018 ). RNA was extracted from frozen nuclei using the TRIzol method (Invitrogen).…”

Section: Methodsmentioning

confidence: 99%

“…Amplification with cDNA as a template was performed using the Kapa SYBR FAST system (ThermoFisher Scientific) and gene-specific primers (Table S1) with a Mastercycler ep realplex 2 (Eppendorf) as previously described (Antosz et al, 2017). The qPCR measurements were analyzed using the DDCt method implemented with the 'pcr' package (Ahmed and Kim, 2018).…”

Section: Rt-qpcr Analysesmentioning

confidence: 99%

“…Accordingly, most of the subunits based on the mutants were termed early flowering (elf) and/or vernalization independence (vip): PAF1 (At-ELF7), CTR9 (At-ELF8, At-VIP6), LEO1 (At-VIP4), RTF1 (At-VIP5), WDR61/SKI8 (At-VIP3) and CDC73 (At-CDC73, At-PHP) (He et al, 2004;Oh et al, 2004;Park et al, 2010). Coimmunoprecipitation and affinity-purification in combination with mass spectrometry analyses revealed that in common with mammals, Arabidopsis PAF1C consists of these six subunits (Oh et al, 2004;Antosz et al, 2017). Arabidopsis mutants deficient in PAF1C subunits VIP3, VIP4, VIP5, VIP6/ELF8 and ELF7 exhibit marked early flowering phenotypes that are commonly associated by reduced expression of the floral repressor FLC (and paralogs) (Zhang and van Nocker, 2002;Zhang et al, 2003;He et al, 2004;Oh et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming

et al. 2022

Self Cite

View full text Add to dashboard Cite

Transcript elongation by RNA polymerase II (RNAPII) is dynamic and highly regulated, thereby contributing to the implementation of gene expression programs during plant development or in response to environmental cues. The heterohexameric polymerase-associated factor 1 complex (PAF1C) stabilizes the RNAPII elongation complex promoting efficient transcript synthesis. In addition, PAF1C links transcriptional elongation with various post-translational histone modifications at transcribed loci. We have exposed Arabidopsis mutants deficient in the PAF1C subunits ELF7 or CDC73 to elevated NaCl concentrations to provoke a transcriptional response. The growth of elf7 plants was reduced relative to that of wildtype under these challenging conditions, whereas cdc73 plants exhibited rather enhanced tolerance. Profiling of the transcriptional changes upon NaCl exposure revealed that cdc73 responded similar to wildtype. Relative to wildtype and cdc73, the transcriptional response of elf7 plants was severely reduced in accord with their greater susceptibility to NaCl. The data also imply that CDC73 is more relevant for the transcription of longer genes. Despite the fact that both ELF7 and CDC73 are part of PAF1C the strikingly different transcriptional response of the mutants upon NaCl exposure suggests that the subunits have (partially) specific functions.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Rt-qpcr Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming

et al. 2022

Self Cite

View full text Add to dashboard Cite

show abstract

“…The Co-IP experiments were performed as described in (Pfab et al, 2017) with minor modifications. 2 grams of 14-day-old seedlings were used for a Co-IP.…”

Section: Methodsmentioning

confidence: 99%

Cotranscriptional demethylation induces global loss of H3K4me2 from active genes inArabidopsis

Kakutani

Mori

Oya

et al. 2023

Preprint

View full text Add to dashboard Cite

Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is disrupted in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 in plants as chromatin memory for transcriptionally repressive states, which ensures robust gene control.

show abstract

“…The Co‐IP experiments were performed as described in Pfab et al (2017) with minor modifications. Two grams of 14‐day‐old seedlings were used for a Co‐IP.…”

Section: Methodsmentioning

confidence: 99%

Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis

Mori,

Oya,

Takahashi

et al. 2023

The EMBO Journal

View full text Add to dashboard Cite

Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono‐, di‐, and tri‐methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE‐SPECIFIC DEMETHYLASE 1‐LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3‐mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C‐terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is significantly attenuated in the ldl3 mutant, demonstrating the genome‐wide impacts of the transcription‐driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 demethylation in plants as chromatin records of transcriptional activity, which ensures robust gene control.

show abstract

Analysis of In Vivo Chromatin and Protein Interactions of Arabidopsis Transcript Elongation Factors

Cited by 5 publications

References 17 publications

Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming

Distinct role of subunits of the Arabidopsis RNA polymerase II elongation factor PAF1C in transcriptional reprogramming

Cotranscriptional demethylation induces global loss of H3K4me2 from active genes inArabidopsis

Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis

Contact Info

Product

Resources

About