A major role for the TATA box in recruitment of chromatin modifying complexes to a globin gene promoter

Dean

2012

Molecules and Cells

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Although linearly distant along mouse chromosome 7 and human chromosome 11, the mammalian β-globin gene is located in close proximity to the upstream locus control region enhancer when it is actively transcribed in the nuclear chromatin environment of erythroid cells. This organization is thought to generate a chromatin loop between the LCR, a powerful enhancer, and active globin genes by extruding intervening regions containing inactive genes. Loop formation in the β-globin locus requires erythroid specific transcriptional activators, co-factors and insulator-related factors. Chromatin structural features such as histone modifications and DNase I hypersensitive site formation as well as nuclear localization are all involved in loop formation in the locus through diverse mechanisms. Current models envision the formation of the loop as a necessary step in globin gene transcription activation, but this has not been definitively established and many questions remain about what is necessary to achieve globin gene transcription activation.

Section: Introductionsupporting

confidence: 82%

Chromatin Loop Formation in the β-Globin Locus and Its Role in Globin Gene Transcription

Dean

2012

Molecules and Cells

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“…We previously observed nucleosome mobilization and histone hyperacetylation at the promoter of the transcriptionally active ε-globin gene linked with the 374-bp core HS2 enhancer on stably maintained minichromosomes in K562 cells (16,17). To investigate the chromatin anatomy of a more complete enhancer-gene locus, we created minichromosomes linking ε-globin to a longer 1.46-kb KpnI-to-BglII LCR HS2 enhancer fragment (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…One possibility is that the complexes migrate by tracking (53) across the intervening chromatin, as has been proposed to underlie widespread acetylation in the globin locus (12). Alternatively, an LCR enhancer and promoter may exist in proximity in vivo by looping (31), as suggested by recent work in which distant enhancers and promoters are occupied simultaneously by the HAT CBP (19,35,48,49) and the SWI/SNF components BRG1 (19) and BAF 155 (17). The work of Hatzis and Talianidis (19) elegantly illustrates that these models may not be mutually exclusive, as CBP and BRG1 maintain enhancer association as they progress through intervening sequences to the promoter.…”

mentioning

confidence: 99%

A Human Globin Enhancer Causes both Discrete and Widespread Alterations in Chromatin Structure

Molecular and Cellular Biology

Dean

2003

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Gene activation requires alteration of chromatin structure to facilitate active transcription complex formation at a gene promoter. Nucleosome remodeling complexes and histone modifying complexes each play unique and interdependent roles in bringing about these changes. The role of distant enhancers in these structural alterations is not well understood. We studied nucleosome remodeling and covalent histone modification mediated by the ␤-globin locus control region HS2 enhancer at nucleosome-level resolution throughout a 5.5-kb globin gene model locus in vivo in K562 cells. We compared the transcriptionally active locus to one in which HS2 was inactivated by mutations in the core NF-E2 sites. In contrast to inactive templates, nucleosomes were mobilized in discrete areas of the active locus, including the HS2 core and the proximal promoter. Large differences in restriction enzyme accessibility between the active and inactive templates were limited to the regions of nucleosome mobilization, which subsumed the DNase I hypersensitive sites. In contrast to this discrete pattern, histone H3 and H4 acetylation and H3 K4 methylation were elevated across the entire active locus, accompanied by depletion of linker histone H1. The coding region of the gene differed from the regulatory regions, demonstrating both nucleosome mobilization and histone hyperacetylation, but lacked differences in restriction enzyme accessibility between transcriptionally active and inactive genes. Thus, although the histone modification pattern we observe is consistent with the spreading of histone modifying activity from the distant enhancer, the pattern of nucleosome mobilization is more compatible with direct contact between an enhancer and promoter.During gene activation, ATP-dependent nucleosome remodeling complexes and complexes that covalently modify histones, such as acetyl transferases (HATs) and methyl transferases, alter the repressive nucleosomal structure of chromatin and provide a permissive environment for transcription. Remodeling by ATP-dependent complexes such as yeast SWI/ SNF and ISWI results in a positional change (mobilization or sliding) and/or a conformational (structural) change in nucleosomes in vitro (54). Histone acetylation modifies lysine residues in the N-terminal tails of the core histones H3 and H4, decreasing the stability of histone-DNA interactions and loosening the compaction of nucleosomal arrays (7). The structural effects of histone methylation are less clear and can be associated with activation (H3 K4 methylation) or repression (H3

“…The formation of loops in minichromosomes would not be impeded, since 2.5 kb of native sequence separate the enhancer and promoter (38). The TATA box may be important for such interactions in the model locus (14). Looping interactions in chromosomes between the LCR HSs and the ␤-globin gene are not compromised by deletion of the promoter of the gene, arguing against this possibility (37).…”

Section: Discussionmentioning

confidence: 99%

β-Globin Intergenic Transcription and Histone Acetylation Dependent on an Enhancer

Molecular and Cellular Biology

Zhao

Ifrim

et al. 2007

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Histone acetyltransferases are associated with the elongating RNA polymerase II (Pol II) complex, supporting the idea that histone acetylation and transcription are intertwined mechanistically in gene coding sequences. Here, we studied the establishment and function of histone acetylation and transcription in noncoding sequences by using a model locus linking the ␤-globin HS2 enhancer and the embryonic -globin gene in chromatin. An intact HS2 enhancer that recruits RNA Pol II is required for intergenic transcription and histone H3 acetylation and K4 methylation between the enhancer and target gene. RNA Pol II recruitment to the target gene TATA box is not required for the intergenic transcription or intergenic histone modifications, strongly implying that they are properties conferred by the enhancer. However, Pol II recruitment at HS2, intergenic transcription, and intergenic histone modification are not sufficient for transcription or modification of the target gene: these changes require initiation at the TATA box of the gene. The results suggest that intergenic and genic transcription complexes are independent and possibly differ from one another.