Elongation factor 1 is a component of the Arabidopsis RNA polymerase II elongation complex and associates with a subset of transcribed genes

Abstract

Summary Elongation factors modulate the efficiency of mRNA synthesis by RNA polymerase II (RNAPII) in the context of chromatin, thus contributing to implement proper gene expression programmes. The zinc‐finger protein elongation factor 1 (ELF1) is a conserved transcript elongation factor (TEF), whose molecular function so far has not been studied in plants. Using biochemical approaches, we examined the interaction of Arabidopsis ELF1 with DNA and histones in vitro and with the RNAPII elongation complex in vivo. In addition, cytological assays demonstrated the nuclear localisation of the protein, and by means of double‐mutant analyses, interplay with genes encoding other elongation factors was explored. The genome‐wide distribution of ELF1 was addressed by chromatin immunoprecipitation. ELF1 isolated from Arabidopsis cells robustly copurified with RNAPII and various other elongation factors including SPT4‐SPT5, SPT6, IWS1, FACT and PAF1C. Analysis of a CRISPR‐Cas9‐mediated gene editing mutant of ELF1 revealed distinct genetic interactions with mutants deficient in other elongation factors. Moreover, ELF1 associated with genomic regions actively transcribed by RNAPII. However, ELF1 occupied only c. 33% of the RNAPII transcribed loci with preference for inducible rather than constitutively expressed genes. Collectively, these results establish that Arabidopsis ELF1 shares several characteristic attributes with RNAPII TEFs.

Arabidopsis mRNA export factor MOS11: molecular interactions and role in abiotic stress responses

“…The T‐DNA insertion lines were obtained from the Nottingham Arabidopsis Stock Centre (https://arabidopsis.info/) and were previously reported mos11‐2 (Germain et al ., 2010), aly1‐1 , aly2‐1 , aly3‐1 and aly4‐1 (Pfaff et al ., 2018). Double and triple mutants were generated by genetic crossing as previously described (Lolas et al ., 2010; Markusch et al ., 2023). Agrobacterium ‐mediated plant transformation, selection of primary transformants, characterisation of transgenic lines and PCR‐based genotyping of plants using primers specific for DNA insertions and target genes (Supporting Information Table S1) as well as propagation and examination for consistent phenotype were performed as previously described (Antosz et al ., 2020; Michl‐Holzinger et al ., 2022).…”

Transcript elongation by RNA polymerase II in plants: factors, regulation and impact on gene expression

“…In addition, chromatin remodelling complexes, NAP1 histone chaperones and several histone-modifying enzymes including Elongator were found to associate with the TEC (Antosz et al, 2017). Recently, the TEF ELF1 was identified as another component of the Arabidopsis TEC, although it appears to associate only with a subpopulation of elongating RNAPII molecules (Markusch et al, 2023).…”

“…In addition, chromatin remodelling complexes, NAP1 histone chaperones and several histone‐modifying enzymes including Elongator were found to associate with the TEC (Antosz et al., 2017). Recently, the TEF ELF1 was identified as another component of the Arabidopsis TEC, although it appears to associate only with a subpopulation of elongating RNAPII molecules (Markusch et al., 2023). During the past few years, advances in cryo‐electron microscopy in combination with X‐ray crystallography enabled enormous progress resolving the three‐dimensional structure of the RNAPII‐TEC of yeast and mammals.…”

“…Recombinant ELF1 interacted in vitro with DNA, histones and nucleosomes. ELF1 is a nuclear protein, and AP‐MS analyses demonstrated that it co‐purified with RNAPII and various TEFs including SPT4‐SPT5, SPT6L, IWS1, PAF1C and FACT (Markusch et al., 2023). Plants lacking ELF1 basically have wild‐type appearance, which is in agreement with the yeast elf1Δ mutation that caused no significant growth defect (Prather et al., 2005).…”

“…Characteristic of TEFs, ELF1 associated with genomic regions occupied by elongating RNAPII, as evident from the coverage of the RNAPII‐S2P chromatin immunoprecipitation signal. However, ELF1 occupied only one‐third of the RNAPII transcribed loci with preference for inducible rather than constitutively expressed genes (Markusch et al., 2023). Taken together, these results indicate that Arabidopsis ELF1 represents a functional plant orthologue of ELF1/ELOF1 of other organisms.…”