A meta-analysis reveals complex regulatory properties at Taf14-repressed genes

Abstract

BackgroundRegulation of gene transcription in response to stress is central to a cell’s ability to cope with environmental challenges. Taf14 is a YEATS domain protein in S.cerevisiae that physically associates with several transcriptionally relevant multisubunit complexes including the general transcription factors TFIID and TFIIF and the chromatin-modifying complexes SWI/SNF, INO80, RSC and NuA3. TAF14 deletion strains are sensitive to a variety of stresses suggesting that it plays a role in the transcriptional stress response.ResultsIn this report we survey published genome-wide transcriptome and occupancy data to define regulatory properties associated with Taf14-dependent genes. Our transcriptome analysis reveals that stress related, TATA-containing and SAGA-dependent genes were much more affected by TAF14 deletion than were TFIID-dependent genes. Comparison of Taf14 and multiple transcription factor occupancy at promoters genome-wide identified a group of proteins whose occupancy correlates with that of Taf14 and whose proximity to Taf14 suggests functional interactions. We show that Taf14-repressed genes tend to be extensively regulated, positively by SAGA complex and the stress dependent activators, Msn2/4 and negatively by a wide number of repressors that act upon promoter chromatin and TBP.ConclusionsTaken together our analyses suggest a novel role for Taf14 in repression and derepression of stress induced genes, most probably as part of a regulatory network which includes Cyc8-Tup1, Srb10 and histone modifying enzymes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3544-6) contains supplementary material, which is available to authorized users.

Elucidating the regulatory mechanism of Swi1 prion in global transcription and stress responses

“…6 ). This is consistent with earlier observations that Snf2, Snf5 and Taf14 are involved in the stress alleviation 64 , 65 . Other than this, diverse responses of swi1∆ and [ SWI + ] cells to a variety of chemical stresses highlights the complexity of ESR mediated by the Swi1 prion and its null mutant.…”

RNA Sequencing Reveals Specific Transcriptomic Signatures Distinguishing Effects of the [SWI+] Prion and SWI1 Deletion in Yeast Saccharomyces cerevisiae

“…Indeed, the Snf2 catalytic subunit of SWI/SNF was shown to be recruited to response of the genes under osmotic stress by means of the Cyc8-Tup1 regulatory network [75], and this recruitment is positively affected by kinases of the PKA family [76]. In addition, the sets of genes misregulated by deletions of SWI2 and TAF14 that encode the transcriptional regulator involved in the stress alleviation overlap significantly [77]. However, it does not explain why most of the response types are positively modulated in the swi1 Δ cells, while the oxidative stress response is repressed.…”

BcTaf14 regulates growth and development, virulence, and stress responses in the phytopathogenic fungus Botrytis cinerea

“…Yeast cells devoid of Taf14 have defects in actin organization, morphology, and cytoskeleton formation and show increased sensitivity to temperature, osmotic stress, and DNA‐damaging agents (Henry et al, 1994; Nemet et al, 2017; Welch et al, 1993). Structural analysis revealed that the acylated H3K9 peptide is sandwiched in an aromatic cage formed by two aromatic residues, phenylalanine at position 62 (F62) and tryptophan at position 81 (W81), and mutation of W81 can disrupt the interaction between the YEATS domain and the H3K9ac peptide (Shanle et al, 2015).…”