Developmental regulation of transcription initiation: more than just changing the actors

Müller, Ferenc; Zaucker, Andreas; Tora, Làszlò

doi:10.1016/j.gde.2010.06.004

Cited by 79 publications

(65 citation statements)

References 66 publications

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“…Our studies were specifically aimed at tracking components of the core promoter regulatory factors and were instigated by the recent evidence that multisubunit transcription cofactors may play unexpectedly important regulatory roles during differentiation and development (for reviews, see D'Alessio et al 2009;Goodrich and Tjian 2010;Muller et al 2010). Although much has been gleaned regarding the regulatory functions of transcription cofactor complexes employing a combination of in vitro biochemical assays, in vivo RNAi functional assays, and structural analyses (Zhai et al 2005;Marr et al 2006;Liu et al 2009), investigations have only recently been turned to how these key basal factors target specific genes in living cells (Giglia-Mari et al 2009;de Graaf et al 2010).…”

Section: Discussionmentioning

confidence: 99%

Subnuclear segregation of genes and core promoter factors in myogenesis

Yao¹,

Fetter²,

Hu³

et al. 2011

Genes Dev.

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Recent findings implicate alternate core promoter recognition complexes in regulating cellular differentiation. Here we report a spatial segregation of the alternative core factor TAF3, but not canonical TFIID subunits, away from the nuclear periphery, where the key myogenic gene MyoD is preferentially localized in myoblasts. This segregation is correlated with the differential occupancy of TAF3 versus TFIID at the MyoD promoter. Loss of this segregation by modulating either the intranuclear location of the MyoD gene or TAF3 protein leads to altered TAF3 occupancy at the MyoD promoter. Intriguingly, in differentiated myotubes, the MyoD gene is repositioned to the nuclear interior, where TAF3 resides. The specific high-affinity recognition of H3K4Me3 by the TAF3 PHD (plant homeodomain) finger appears to be required for the sequestration of TAF3 to the nuclear interior. We suggest that intranuclear sequestration of core transcription components and their target genes provides an additional mechanism for promoter selectivity during differentiation.

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Section: Discussionmentioning

confidence: 99%

Subnuclear segregation of genes and core promoter factors in myogenesis

Yao¹,

Fetter²,

Hu³

et al. 2011

Genes Dev.

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“…The absence of TAFs was confirmed by multiple, independent experimental approaches including immunoblotting (Figure 1A and Figure 1—figure supplement 3), qRT-PCR (Figure 1B) and ChIP (Figure 4B). Previous studies have reported tissue-specific TAF variants and alterations in TAF expression (reviewed in D'Alessio et al, 2009; Müller et al, 2010), but the composition of hESC TAFs is unprecedented and is likely highly specific, if not unique, to hESCs. For example, we find that mouse ESCs, which bear both similarities and differences to hESCs (Ginis et al, 2004; Wei et al, 2005; Schnerch et al, 2010), express all TFIID TAFs analyzed (Figure 9), consistent with the results of a recent study that focused on the role of TAF3 in mouse ESCs (Liu et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…Consistent with the existence of TAF-independent promoters, more recent studies have found that TAFs are depleted upon terminal differentiation of muscle (Deato and Tjian, 2007; Deato et al, 2008) and liver (D'Alessio et al, 2011). TFIID diversity is also promoted by tissue-specific variants of TAFs as well as TBP derivatives referred to as TBP-related factors (reviewed in D'Alessio et al, 2009; Müller et al, 2010). …”

Section: Introductionmentioning

confidence: 99%

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

Maston

Zhu

Chamberlain

et al. 2012

eLife

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The general transcription factor TFIID comprises the TATA-box-binding protein (TBP) and approximately 14 TBP-associated factors (TAFs). Here we find, unexpectedly, that undifferentiated human embryonic stem cells (hESCs) contain only six TAFs (TAFs 2, 3, 5, 6, 7 and 11), whereas following differentiation all TAFs are expressed. Directed and global chromatin immunoprecipitation analyses reveal an unprecedented promoter occupancy pattern: most active genes are bound by only TAFs 3 and 5 along with TBP, whereas the remaining active genes are bound by TBP and all six hESC TAFs. Consistent with these results, hESCs contain a previously undescribed complex comprising TAFs 2, 6, 7, 11 and TBP. Altering the composition of hESC TAFs, either by depleting TAFs that are present or ectopically expressing TAFs that are absent, results in misregulated expression of pluripotency genes and induction of differentiation. Thus, the selective expression and use of TAFs underlies the ability of hESCs to self-renew.DOI: http://dx.doi.org/10.7554/eLife.00068.001

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“…Both are multisubunit complexes that not only recognize key promoter/PAS sequences, which are strikingly similar (TATAAA vs. AAUAAA), but also contain subunits that bind additional promoter/PAS elements. TFIID exists as tissue-specific and cell type-specific subcomplexes and can also contain distinct isoforms of different subunits (Muller et al 2010). As we shall see, a similar picture of CPSF is beginning to emerge.…”

Section: Cpsf and Aauaaa Recognitionmentioning

confidence: 99%

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

2015

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The key RNA sequence elements and protein factors necessary for 3 ′ processing of polyadenylated mRNA precursors are well known. Recent studies, however, have significantly reshaped current models for the protein-RNA interactions involved in poly(A) site recognition, painting a picture more complex than previously envisioned and also providing new insights into regulation of this important step in gene expression. Here we review the recent advances in this area and provide a perspective for future studies.

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Developmental regulation of transcription initiation: more than just changing the actors

Cited by 79 publications

References 66 publications

Subnuclear segregation of genes and core promoter factors in myogenesis

Subnuclear segregation of genes and core promoter factors in myogenesis

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

The end of the message: multiple protein–RNA interactions define the mRNA polyadenylation site

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