Structure and DNA Binding of the Human Rtf1 Plus3 Domain

Jong, Rob N. de; Truffault, Vincent; Diercks, Tammo; Ab, Eiso; Daniëls, Mark A.; Kaptein, R.; Folkers, Gert E.

doi:10.1016/j.str.2007.10.018

Cited by 48 publications

(75 citation statements)

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“…We conclude that, because of the absence of these interactions, the localization of the HMD is deregulated and its histone modification function appears to be uncoupled from RNA pol II. Most likely, other regions of Paf1C, such as the Rtf1 ORF association/Plus3 domain (44,48), are dominant to the HMD in controlling the localization of Paf1C. Based on our analysis of paf1Δ, ctr9Δ, and cdc73Δ mutants, Rtf1 is the key member of Paf1C with respect to the establishment of H2B K123 ubiquitylation and downstream marks.…”

Section: Discussionmentioning

confidence: 89%

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

Piro

Mayekar

Warner

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Histone modifications regulate transcription by RNA polymerase II and maintain a balance between active and repressed chromatin states. The conserved Paf1 complex (Paf1C) promotes specific histone modifications during transcription elongation, but the mechanisms by which it facilitates these marks are undefined. We previously identified a 90-amino acid region within the Rtf1 subunit of Paf1C that is necessary for Paf1C-dependent histone modifications in Saccharomyces cerevisiae. Here we show that this histone modification domain (HMD), when expressed as the only source of Rtf1, can promote H3 K4 and K79 methylation and H2B K123 ubiquitylation in yeast. The HMD can restore histone modifications in rtf1Δ cells whether or not it is directed to DNA by a fusion to a DNA binding domain. The HMD can facilitate histone modifications independently of other Paf1C subunits and does not bypass the requirement for Rad6-Bre1. The isolated HMD localizes to chromatin, and this interaction requires residues important for histone modification. When expressed outside the context of fulllength Rtf1, the HMD associates with and causes Paf1C-dependent histone modifications to appear at transcriptionally inactive loci, suggesting that its function has become deregulated. Finally, the Rtf1 HMDs from other species can function in yeast. Our findings suggest a direct and conserved role for Paf1C in coupling histone modifications to transcription elongation.transcription-coupled histone modifications | nucleosome I n eukaryotes, transcription occurs within the context of a restrictive, yet dynamic, chromatin environment. The posttranslational modification of histones represents a major mechanism by which cells control the structure of chromatin. Some modifications of histones include acetylation, methylation, and ubiquitylation. These modifications can alter the structural properties of nucleosomes and serve as specific effectors for the recruitment of proteins that further modify the chromatin template and regulate transcription (1).Monoubiquitylation of histone H2B on lysine (K) 123 in Saccharomyces cerevisiae is a conserved modification that is enriched on active genes but plays roles in both transcriptional repression and activation (2-4). Consistent with a repressive role, H2B monoubiquitylation stabilizes nucleosomes at yeast promoters (5), inhibits the association of the RNA polymerase (pol) II kinase Ctk1 with genes in yeast (6), and interferes with the recruitment of the elongation factor TFIIS to genes in human cells (7). In other studies, H2B monoubiquitylation has been shown to stimulate transcription of chromatin templates (8), promote nucleosome reassembly during transcription elongation (9), and inhibit chromatin compaction (10). H2B monoubiquitylation is also a prerequisite for other histone modifications that mark active genes. Ubiquitylation of H2B K123 by the Rad6-Bre1 ubiquitin conjugase-ligase proteins in yeast (11-13) is required for dimethylation and trimethylation of H3 K4 and K79 by the Set1/COMPASS and Dot1 methy...

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Section: Discussionmentioning

confidence: 89%

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

Piro

Mayekar

Warner

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…The PLUS3 domain is thought to play a role in nucleic acid binding through 3 conserved positive amino acids (19). There are 5 proteins in Arabidopsis with the PLUS3 domain (Fig.…”

Section: Tzp Is a Large Nuclear-localized Protein Encoded By A Singlmentioning

confidence: 99%

“…Three of these also have a SWIB domain, two have either a CCCH or a C3H3C4 zinc finger, and VERNALIZATION INDEPENDENT 5 (VIP5) contains only the PLUS3 domain (20). VIP5 is a homolog of the yeast RTF1 protein, which is part of the yeast Paf1 complex that regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal Ser-2 phosphorylation, and RNA 3Ј end processing (19). The SWIB domain-containing proteins are part of the SWI/SNF chromatin-remodeling complex (21).…”

Section: Tzp Is a Large Nuclear-localized Protein Encoded By A Singlmentioning

confidence: 99%

A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana

Loudet

Michael

Burger

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Growth in plants is modulated by a complex interplay between internal signals and external cues. Although traditional mutagenesis has been a successful approach for the identification of growth regulatory genes, it is likely that many genes involved in growth control remain to be discovered. In this study, we used the phenotypic variation between Bay-0 and Shahdara, two natural strains (accessions) of Arabidopsis thaliana, to map quantitative trait loci (QTL) affecting light-and temperature-regulated growth of the embryonic stem (hypocotyl). Using heterogeneous inbred families (HIFs), the gene underlying one QTL, LIGHT5, was identified as a tandem zinc knuckle/PLU3 domain encoding gene (At5g43630; TZP), which carries a premature stop codon in Bay-0. Hypocotyl growth assays in monochromatic light and microarray analysis demonstrate that TZP controls blue light associated growth in a time-of-day fashion by regulating genes involved in growth, such as peroxidase and cell wall synthesis genes. TZP expression is phased by the circadian clock and light/dark cycles to the beginning of the day, the time of maximal growth in A. thaliana in short-day conditions. Based on its domain structure and localization in the nucleus, we propose that TZP acts downstream of the circadian clock and photoreceptor signaling pathways to directly control genes responsible for growth. The identification of TZP thus provides new insight into how daily synchronization of growth pathways plays a critical role in growth regulation.blue light ͉ circadian ͉ fine-mapping ͉ quantitative T he embryonic stem or hypocotyl is an excellent model for studying both internal and external factors controlling growth in plants (1). Genetic screens in common laboratory accessions have yielded direct molecular insight into how light-and hormonedependent signaling pathways interact with the circadian clock to regulate the final length of the hypocotyl (1). The power of the hypocotyl assay is its simplicity, as well as its obvious meaningfulness. When germinating seeds are exposed to low levels of light, such as those caused by a covering layer of debris, the hypocotyl has to grow for a while. Only after the surface has been broken by the tip of the hypocotyls can the embryonic leaves, the cotyledons, unfold. Conversely, if a seed has fallen on open ground, there is no need for the hypocotyls to be particularly long. Because of the ease and reproducibility with which hypocotyl length can be measured in thousands of individuals, it has also been a powerful model in mapping genes with more subtle effects on light and hormone regulated growth, by using methods of quantitative genetics (2). Multiple light signaling genes controlling hypocotyl length have been characterized in quantitative trait locus (QTL) studies (3-6).In this study, we use the hypocotyl assay to identify QTL controlling growth in 2 light and 2 temperature conditions. We identified a recessive large effect QTL on chromosome five controlling 40% of the growth variation segregating in Recombinant Inb...

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“…Deletion of either of these subunits reduces the levels of Paf1C that immunoprecipitate with RNA pol II or localize to transcribed genes (10,13). Mutational studies have identified the Plus-3 domain of Rtf1 as being required for Paf1C occupancy on active genes (16), and interestingly, biochemical experiments have revealed binding of the Rtf1 Plus-3 domain to DNA substrates that mimic the transcription bubble (40).…”

mentioning

confidence: 99%

Cdc73 Subunit of Paf1 Complex Contains C-terminal Ras-like Domain That Promotes Association of Paf1 Complex with Chromatin

Amrich

Davis

Rogal

et al. 2012

Journal of Biological Chemistry

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Structure and DNA Binding of the Human Rtf1 Plus3 Domain

Cited by 48 publications

References 50 publications

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

Small region of Rtf1 protein can substitute for complete Paf1 complex in facilitating global histone H2B ubiquitylation in yeast

A zinc knuckle protein that negatively controls morning-specific growth in Arabidopsis thaliana

Cdc73 Subunit of Paf1 Complex Contains C-terminal Ras-like Domain That Promotes Association of Paf1 Complex with Chromatin

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