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

Abstract

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

IRES in distress: translational regulation of the inhibitor of apoptosis proteins XIAP and HIAP2 during cell stress

“…Both the XIAP IRES and the c-myc IRES are bound by hnRNPC1/C2, and this binding affects translation initiation from these IRES elements. 39,52 XIAP IRES activity was found to be very low in SKOV3 cells compared to other cell lines tested (about three-to four-fold lower). 39 Moreover, the low level of XIAP IRES activity in SKOV3 cells was found to correlate with low hnRNPC1/C2 expression in this cell line, and the addition of exogenous hnRNPC1/C2 to SKOV3 cells was shown to increase XIAP IRES activity.…”

“…52,73 Following phorbol-12-myristate-13-acetate (PMA) or TNF-a induction of apoptosis, hnRNPC1/C2 translocates from the nucleus to the cytoplasm in a Rho-associated kinase-(ROCK) dependent manner, and this translocation requires the C-terminal 40-amino-acid residues of hnRNPC1/C2. 73 Thus, the authors suggest that the ROCK signaling pathway is involved in a novel nuclear export of hnRNPC1/C2.…”

Heterogeneous nuclear ribonucleoprotein C1/C2, MeCP1, and SWI/SNF form a chromatin remodeling complex at the β-globin locus control region

“…However, deletion of the LCR DNA sequences severely reduces the transcription of the ␤-like genes, but the DNase hypersensitivity and polymerase II association with promoters of the remaining ␤-globin genes persists (17)(18)(19). Several biochemical studies in cell lines suggest that the MARE sequences of HS2, apart from their involvement in the enhancement of transcription, also take part in the alteration of the chromatin structure of HS2 and a linked promoter (20)(21)(22)(23). These studies suggest the possible association of the LCR with specific chromatin remodeling activities, although such a LCR-specific chromatin remodeling activity has not been isolated.…”

Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription

“…Many correlations between transcription and nucleosome modifications have been found. For example, active ␤-globin loci are enriched in hyperacetylated histones H3 and H4, and H3 dimethylated on lysine 4 (met 2 H3-K4), whereas the silent domain flanking the chicken locus has hypoacetylated histones and H3 dimethylated on K9 (met 2 H3-K9; Litt et al 2001;Bulger et al 2003;Kim and Dean 2003). How histone modifications influence transcription is still debated.…”