Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID

Antonova, Simona; Boeren, Jeffrey; Timmers, H. Th. Marc; Snel, Berend

doi:10.1101/gad.300475.117

Cited by 31 publications

(28 citation statements)

References 72 publications

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“…A more complete comparison of the human and yeast TFIID structures awaits further progress in resolving disordered regions within the complex. Analysis of TFIID sequences throughout evolution shows that yeast TFIID is somewhat of an outlier based on the fact that no chromatin "reader" domains (e.g., PHD or bromodomains) are represented (Antonova et al 2019). However, yeast genomes possess auxiliary bromodomain-containing proteins that associate with TFIID and may replicate specific chromatin-targeting functions (Rhee and Pugh 2012).…”

Section: Tfiidmentioning

confidence: 99%

Structure and mechanism of the RNA polymerase II transcription machinery

2020

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RNA polymerase II (Pol II) transcribes all protein-coding genes and many noncoding RNAs in eukaryotic genomes. Although Pol II is a complex, 12-subunit enzyme, it lacks the ability to initiate transcription and cannot consistently transcribe through long DNA sequences. To execute these essential functions, an array of proteins and protein complexes interact with Pol II to regulate its activity. In this review, we detail the structure and mechanism of over a dozen factors that govern Pol II initiation (e.g., TFIID, TFIIH, and Mediator), pausing, and elongation (e.g., DSIF, NELF, PAF, and P-TEFb). The structural basis for Pol II transcription regulation has advanced rapidly in the past decade, largely due to technological innovations in cryoelectron microscopy. Here, we summarize a wealth of structural and functional data that have enabled a deeper understanding of Pol II transcription mechanisms; we also highlight mechanistic questions that remain unanswered or controversial.

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Section: Tfiidmentioning

confidence: 99%

Structure and mechanism of the RNA polymerase II transcription machinery

2020

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“…From previous work [1][2][3][4] we collected a set of 125 manually curated OGs at LECA level ( Table 3). The comparison to manually curated OGs aligns our evaluation with other evaluation strategies, such as Quest For Orthologs, while the comparison of the inferred OGs to one another gives us a view of how similar the OGs are to each other.…”

Section: Ogs Inferred By Different Methods Show Imperfect Overlap Inmentioning

confidence: 99%

“…Independent gene loss is not random [5]. In fact, there are countless observations that cooccurring (or co-lossed) proteins tend to interact [1][2][3][4]39]. This creates an additional opportunity for evaluating orthology methods, namely how well different methods can predict co-occurrence of interacting proteins.…”

Section: Co-occurrence Of Interacting Proteins Is Predicted Similarlymentioning

confidence: 99%

“…Gaining insight into the evolution of eukaryotic pathways and protein complexes is often obtained by careful and intensive manual efforts of inferring orthologous groups (OGs), often using phylogenetic profiles [1][2][3][4]. The reconstructions of the evolution of these pathways is changing our view of eukaryotic genome evolution.…”

Section: Introductionmentioning

confidence: 99%

“…The reconstructions of the evolution of these pathways is changing our view of eukaryotic genome evolution. With the increase of genomic data, specifically of divergent eukaryotes, the pervasiveness of gene loss became a clear pattern for genetic variation [5][6][7] that has been observed in many eukaryotic functional pathways, protein complexes and metabolic pathways [1][2][3][4]8,9]. From these manual reconstructions it is becoming more apparent that the loss of parts of these complexes or pathways between the Last Eukaryotic Common Ancestor (LECA) and extant species is mostly non-random, as whole (sub)complexes are often co-lost or, at least, co-absent.…”

Section: Introductionmentioning

confidence: 99%

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Comparing orthology methods and their performance by recapitulating patterns of eukaryotic genome evolution

Deutekom

Snel

Dam

2020

Preprint

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Insights into the evolution of ancestral complexes and pathways are generally achieved through careful and time-intensive manual analysis often using phylogenetic profiles of the constituent proteins. This manual analysis limits the possibility of including more protein-complex components, repeating the analyses for updated genome sets, or expanding the analyses to larger scales. Automated orthology inference should allow such large scale analyses, but substantial differences between orthologous groups generated by different approaches are observed.We evaluate orthology methods for their ability to recapitulate a number of observations that have been made with regards to genome evolution in eukaryotes. Specifically, we investigate phylogenetic profile similarity (co-occurrence of complexes), the Last Eukaryotic Common Ancestor's gene content, pervasiveness of gene loss, and the overlap with manually determined orthologous groups. Moreover, we compare the inferred orthologies to each other.We find that most orthology methods reconstruct a large Last Eukaryotic Common Ancestor, with substantial gene loss, and can predict interacting proteins reasonably well when applying phylogenetic co-occurrence. At the same time derived orthologous groups show imperfect overlap with manually curated orthologous groups. There is no strong indication of which orthology method performs better than another on individual or all of these aspects. Counterintuitively, despite the orthology methods behaving similarly regarding large scale evaluation, the obtained orthologous groups differ vastly from one another. Availability and implementationThe data and code underlying this article are available in github and/or upon reasonable request to the corresponding author: https://github.com/ESDeutekom/ComparingOrthologies. Summary •We compared multiple orthology inference methods by looking at how well they perform in recapitulating multiple observations made in eukaryotic genome evolution.• Co-occurrence of proteins is predicted fairly well by most methods and all show similar behaviour when looking at loss numbers and dynamics.• All the methods show imperfect overlap when compared to manually curated orthologous groups and when compared to orthologous groups of the other methods. •Differences are compared between methods by looking at how the inferred orthologies represent a high-quality set of manually curated orthologous groups. •We conclude that all methods behave similar when describing general patterns in eukaryotic genome evolution. However, there are large differences within the orthologies themselves, arising from how a method can differentiate between distant homology, recent duplications, or classifying orthologous groups.

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Participation of the TBP‐associated factors (TAFs) in cell differentiation

Luna‐Arias,

Castro‐Muñozledo

2023

Journal Cellular Physiology

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The understanding of the mechanisms that regulate gene expression to establish differentiation programs and determine cell lineages, is one of the major challenges in Developmental Biology. Besides the participation of tissue‐specific transcription factors and epigenetic processes, the role of general transcription factors has been ignored. Only in recent years, there have been scarce studies that address this issue. Here, we review the studies on the biological activity of some TATA‐box binding protein (TBP)‐associated factors (TAFs) during the proliferation of stem/progenitor cells and their involvement in cell differentiation. Particularly, the accumulated evidence suggests that TAF4, TAF4b, TAF7L, TAF8, TAF9, and TAF10, among others, participate in nervous system development, adipogenesis, myogenesis, and epidermal differentiation; while TAF1, TAF7, TAF15 may be involved in the regulation of stem cell proliferative abilities and cell cycle progression. On the other hand, evidence suggests that TBP variants such as TBPL1 and TBPL2 might be regulating some developmental processes such as germ cell maturation and differentiation, myogenesis, or ventral specification during development. Our analysis shows that it is necessary to study in greater depth the biological function of these factors and its participation in the assembly of specific transcription complexes that contribute to the differential gene expression that gives rise to the great diversity of cell types existing in an organism. The understanding of TAFs' regulation might lead to the development of new therapies for patients which suffer from mutations, alterations, and dysregulation of these essential elements of the transcriptional machinery.

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Epigenetics and transcription regulation during eukaryotic diversification: the saga of TFIID

Cited by 31 publications

References 72 publications

Structure and mechanism of the RNA polymerase II transcription machinery

Structure and mechanism of the RNA polymerase II transcription machinery

Comparing orthology methods and their performance by recapitulating patterns of eukaryotic genome evolution

Participation of the TBP‐associated factors (TAFs) in cell differentiation

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