Chromatin and DNA sequences in defining promoters for transcription initiation

Müller, Ferenc; Tora, Làszlò

doi:10.1016/j.bbagrm.2013.11.003

Cited by 68 publications

(60 citation statements)

References 156 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recent observations suggest that alternative initiation complexes can replace canonical TFIID [26]. For example, whereas constitutive expression of the MHC class I genes depends on the TFIID complex, γ-interferon-activated transcription bypasses the requirement for canonical TFIID, depending instead on the transcriptional co-activator class II trans-activator (CIITA).…”

Section: The Transcriptional Machinerymentioning

confidence: 99%

Core promoters in transcription: old problem, new insights

Roy

Singer

2015

Trends in Biochemical Sciences

112

106

View full text Add to dashboard Cite

Early studies established that transcription initiates within a ~50 bp DNA segment capable of nucleating the assembly of RNA Polymerase II and associated general transcription factors necessary for transcriptional initiation; this region is called a core promoter. Subsequent analyses identified a series of conserved DNA sequence elements, present in various combinations or not at all, in core promoters. Recent genome-wide analyses have provided further insights into the complexity of core promoter architecture and function. Here we review recent studies that delineate the active role of core promoters in transcriptional regulation of diverse physiological systems.

show abstract

Section: The Transcriptional Machinerymentioning

confidence: 99%

Core promoters in transcription: old problem, new insights

Roy

Singer

2015

Trends in Biochemical Sciences

112

106

View full text Add to dashboard Cite

show abstract

“…TFIID is structurally organized into three lobes with lobe C (Tafs 1, 2, and 7) binding several promoter DNA elements found in higher eukaryotes (e.g., Inr, DPE, MTE) (Cianfrocco and Nogales, 2013; Louder et al, 2016; Theisen et al, 2010; Verrijzer et al, 1995). TFIID also binds transcription activators, acetylated nucleosomes, the universally required coactivator Mediator and probably other components of the basal transcription machinery (Müller and Tora, 2014). These functions allow TFIID to respond to regulatory inputs from both UAS elements and the chromatin state and to act as a platform for assembly of the transcription preinitiation complex (PIC).…”

Section: Introductionmentioning

confidence: 99%

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

et al. 2017

View full text Add to dashboard Cite

SUMMARY Previous studies suggested that expression of most yeast mRNAs is dominated by either transcription factor TFIID or SAGA. We reexamined the role of TFIID by rapid depletion of S. cerevisiae TFIID subunits and measurement of changes in nascent transcription. We find that transcription of nearly all mRNAs is strongly dependent on TFIID function. Degron-dependent depletion of Tafs 1,2,7,11, and 13 showed similar transcription decreases for genes in the Taf1-depleted, Taf1-enriched, TATA-containing and TATA-less gene classes. The magnitude of TFIID-dependence varies with growth conditions, although this variation is similar genome-wide. Many studies have suggested differences in gene regulatory mechanisms between TATA and TATA-less genes and these differences have been attributed in part to differential dependence on SAGA or TFIID. Our work indicates that TFIID participates in expression of nearly all yeast mRNAs and that differences in regulation between these two gene categories is due to other properties.

show abstract

“…Several functional cis -elements have been identified such as the TATA-box and the Inr element, as well as a growing number of additional elements such as DPE, BREu and BREd, DCEs (recently reviewed in [152, 153]). These elements act together as an assembly platform for GTFs and co-activators, leading to formation of the preinitiation complex.…”

Section: Introductionmentioning

confidence: 99%

In the loop: promoter–enhancer interactions and bioinformatics

Mora¹,

Sandve²,

Gabrielsen³

et al. 2015

Brief Bioinform

105

104

View full text Add to dashboard Cite

Enhancer–promoter regulation is a fundamental mechanism underlying differential transcriptional regulation. Spatial chromatin organization brings remote enhancers in contact with target promoters in cis to regulate gene expression. There is considerable evidence for promoter–enhancer interactions (PEIs). In the recent years, genome-wide analyses have identified signatures and mapped novel enhancers; however, being able to precisely identify their target gene(s) requires massive biological and bioinformatics efforts. In this review, we give a short overview of the chromatin landscape and transcriptional regulation. We discuss some key concepts and problems related to chromatin interaction detection technologies, and emerging knowledge from genome-wide chromatin interaction data sets. Then, we critically review different types of bioinformatics analysis methods and tools related to representation and visualization of PEI data, raw data processing and PEI prediction. Lastly, we provide specific examples of how PEIs have been used to elucidate a functional role of non-coding single-nucleotide polymorphisms. The topic is at the forefront of epigenetic research, and by highlighting some future bioinformatics challenges in the field, this review provides a comprehensive background for future PEI studies.

show abstract

Chromatin and DNA sequences in defining promoters for transcription initiation

Cited by 68 publications

References 156 publications

Core promoters in transcription: old problem, new insights

Core promoters in transcription: old problem, new insights

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID

In the loop: promoter–enhancer interactions and bioinformatics

Contact Info

Product

Resources

About