Evolution of the repertoire of nuclear receptor binding sites in genomes

Cotnoir-White, David; Laperrière, David; Mader, Sylvie

doi:10.1016/j.mce.2010.10.021

Cited by 59 publications

(53 citation statements)

References 121 publications

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“…In contrast, biochemical studies suggest that only a single motif spacing, or at most two to three spacings, are compatible with direct cooperativity through TF dimerization (Grove et al 2009;Cotnoir-White et al 2011;Slattery et al 2011). Moreover, even when TFs are seen to dimerize at a few different possible spacings, one spacing typically dominates in terms of binding affinity.…”

Section: Discussionmentioning

confidence: 98%

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

et al. 2013

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The binding of transcription factors (TFs) to their specific motifs in genomic regulatory regions is commonly studied in isolation. However, in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers and to infer the precise nature of these interactions. So far, only a small number of such dimeric complexes are known. Here, we present an algorithm for predicting cell-type-specific TF-TF dimerization on DNA on a large scale, using DNase I hypersensitivity data from 78 human cell lines. We represented the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type-specific DNase I hypersensitive sites. Based on~1.4 billion tests for motif complex enrichment, we predicted 603 highly significant celltype-specific TF dimers, the vast majority of which are novel. Our predictions included 76% (19/25) of the known dimeric complexes and showed significant overlap with an experimental database of protein-protein interactions. They were also independently supported by evolutionary conservation, as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Overall, our results indicate that chromatin openness profiles are highly predictive of cell-type-specific TF-TF interactions. Moreover, cooperative TF dimerization seems to be a widespread phenomenon, with multiple TF complexes predicted in most cell types.

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Section: Discussionmentioning

confidence: 98%

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

et al. 2013

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“…This relation with transposable elements seems to be true with regard to steroid receptors in particular (77). Alu SINEs alone are known to form the substrate for response elements for progesterone, glucocorticoids, and vitamin D (78,79).…”

Section: Transposons: Controlling Elements After All?mentioning

confidence: 88%

Stress and the dynamic genome: Steroids, epigenetics, and the transposome

Hunter

Gagnidze

McEwen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

117

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Stress plays a substantial role in shaping behavior and brain function, often with lasting effects. How these lasting effects occur in the context of a fixed postmitotic neuronal genome has been an enduring question for the field. Synaptic plasticity and neurogenesis have provided some of the answers to this question, and more recently epigenetic mechanisms have come to the fore. The exploration of epigenetic mechanisms recently led us to discover that a single acute stress can regulate the expression of retrotransposons in the rat hippocampus via an epigenetic mechanism. We propose that this response may represent a genomic stress response aimed at maintaining genomic and transcriptional stability in vulnerable brain regions such as the hippocampus. This finding and those of other researchers have made clear that retrotransposons and the genomic plasticity they permit play a significant role in brain function during stress and disease. These observations also raise the possibility that the transposome might have adaptive functions at the level of both evolution and the individual organism.hippocampus | retrotransposon | histone marks | brain | genomic stress response

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“…12,13) atRA functions as the activating ligand for retinoic acid receptors (RARs), and atRA-RAR complexes regulate the expression of over 500 target genes as a transcription factor. 11,[13][14][15][16] RARs are a member of the nuclear receptor superfamily, 17,18) and consist of three isotypes: α, β, and γ. In response to atRA signaling, RARs occupy characteristic retinoic acid response elements (RAREs) located in the promoter regions of target genes.…”

Section: Tal2mentioning

confidence: 99%

Transcriptional Regulation of <i>Tal2</i> Gene by All-<i>trans</i> Retinoic Acid (atRA) in P19 Cells

Kobayashi

Suzuki

Morikawa

et al. 2015

Biological & Pharmaceutical Bulletin

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TAL2 is a transcription factor required in the normal development of mouse brain. In a previous study, we demonstrated that the expression of Tal2 gene is induced by the complex of all-trans retinoic acid (atRA) and retinoic acid receptor α (RARα) in mouse embryonal carcinoma P19 cells. atRA is also known to be important in inducing P19 cells to differentiate into the neural lineage. Therefore, we believe that the function of TAL2 in neural differentiation may be clarified by utilizing P19 cells. As the atRA-RARα complex induced the expression of Tal2, we focused on the regulatory region that is involved in its transcription. The atRA-RARα complex occupies a characteristic retinoic acid response element (RARE) located in the promoter of target genes. Therefore, we searched for RARE on the mouse Tal2 and found that a RARE-like element was located in the intron. We also found that a TATA-box-like element was located in the 5′-region of Tal2. Involvement between transcriptional activity and the TATA-box-like element was confirmed in the luciferase assay, and TATA-box binding protein was bound to this element upstream of Tal2 in P19 cells. atRA signaling activated the transcription through the RARE-like element, and RARα was bound to this element on Tal2 in P19 cells. In addition, the interaction between these elements on Tal2 was shown in the chromatin immunoprecipitation assay. These results suggest that the transcription of Tal2 is coordinately mediated by two distal regulatory elements.Key words Tal2 gene; retinoic acid receptor α (RARα); TATA-box binding protein (TBP); retinoic acid response element (RARE); TATA-box TAL2 1,2) is a transcription factor required for the normal development of mouse brain. The expression of Tal2 gene is observed in the diencephalon, mesencephalon, and metencephalon of the developing mouse brain.3) Tal2-null mutant mice are viable at birth and initially appear normal. However, they develop signs of runting and die between 13 and 32 d after birth. 4) Therefore, Tal2 is thought to play a pivotal role in development of the brain.We found that Tal2 expression is altered in P19 cells after addition of all-trans retinoic acid (atRA) and suspension culture for cell aggregation. Moreover, we showed that its expression is induced by atRA.5) P19 cells are a line of pluripotent embryonal carcinoma and appear to differentiate into derivatives of three germ layers-endoderm, mesoderm, or ectoderm-depending on the inducers and culture conditions, using the same mechanisms as normal embryonic cells. atRA treatment and cell aggregation have an important role in the induction of neural differentiation in P19 cells.6-8) Because these cells have been used as a model in studies of neural differentiation, we believe that the function of Tal2 in development may be clarified by utilizing P19 cells.atRA, which is a metabolic product of vitamin A, is one of the most important morphogens, and is a signal molecule involved in neural differentiation. [9][10][11] atRA is also known to be capable of inducing embr...

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Evolution of the repertoire of nuclear receptor binding sites in genomes

Cited by 59 publications

References 121 publications

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Stress and the dynamic genome: Steroids, epigenetics, and the transposome

Transcriptional Regulation of <i>Tal2</i> Gene by All-<i>trans</i> Retinoic Acid (atRA) in P19 Cells

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