HSF recruitment and loss at mostDrosophila heat shock loci is coordinated and depends on proximal promoter sequences

Shopland, Lindsay S.; Lis, John T.

doi:10.1007/bf02509497

Cited by 41 publications

(12 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We used well-characterized ChIP-grade HSF antiserum [23], [35] which specifically recognizes one HSF-RNAi sensitive Western blot band from whole S2 cell extract (Figure 1A) [35] and generates the expected global HSF-binding pattern observed by indirect immunofluorescence (IF) polytene staining [19], [36], [37]. Despite the specificity observed in these assays, we set out to directly assess specificity in genome-wide ChIP by identifying any HSF-non-specific DNA pull-down.…”

Section: Resultsmentioning

confidence: 99%

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

2010

Self Cite

View full text Add to dashboard Cite

Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but target DNA elements are not sufficient to specify TF binding in vivo. In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones, which package DNA into nucleosomes. We used the ChIP-seq assay to examine the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization. HSF binds to 464 sites after heat shock, the vast majority of which contain HSF Sequence-binding Elements (HSEs). HSF-bound sequence motifs represent only a small fraction of the total HSEs present in the genome. ModENCODE ChIP-chip datasets, generated during non-heat shock conditions, were used to show that inducibly bound HSE motifs are associated with histone acetylation, H3K4 trimethylation, RNA Polymerase II, and coactivators, compared to HSE motifs that remain HSF-free. Furthermore, directly changing the chromatin landscape, from an inactive to an active state, permits inducible HSF binding. There is a strong correlation of bound HSEs to active chromatin marks present prior to induced HSF binding, indicating that an HSE's residence in “active” chromatin is a primary determinant of whether HSF can bind following heat shock.

show abstract

Section: Resultsmentioning

confidence: 99%

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

2010

Self Cite

View full text Add to dashboard Cite

show abstract

“…Such tandemly arrayed sequences are known to be relatively stable in bacteria (18) and can persist for many generations in transgenic fly lines (9,19). A hammerhead ribozyme sequence (20) is incorporated at the 3Ј end of each unit, to allow self-cleavage of the long multimeric pre-iaRNA transcript to yield the mature pentavalent iaRNA.…”

Section: Resultsmentioning

confidence: 99%

RNA aptamers as effective protein antagonists in a multicellular organism

Shi

Hoffman

Lis

1999

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

Self Cite

118

View full text Add to dashboard Cite

RNA aptamers selected against proteins can be used to modulate specific protein function. Expression of such reagents in cells and whole organisms could provide a means of dissecting and controlling molecular mechanisms in vivo. We demonstrate that Drosophila B52 protein can be specifically inhibited in vitro and in vivo by a multivalent RNA aptamer. This inhibitory aptamer RNA binds B52 avidly and inhibits B52-stimulated pre-mRNA splicing. It can be expressed in cultured cells and whole animals in a stable form that accumulates up to 10% of total mRNA. It binds B52 in vivo and suppresses all phenotypes caused by B52 overexpression. The strategies presented here should prove general in design and expression of functional and therapeutic RNAs.Multiprotein assemblies drive a variety of highly regulated biological processes. To better understand and control such processes, novel reagents are needed to modulate functions of specific proteins in cells and whole organisms. An ideal reagent would, (i) like an antibody, be made to order specifically for a particular protein, (ii) like a small organic molecule, be able to rapidly target a specific protein domain within cells, and (iii) like a conditional allele, be able to exert its effect in whole organisms, but (iv) also be targetable to specific tissues, cells, or stages of development.Although many strategies exist for inactivating genes or gene products, use of RNA aptamers (1) presents several compelling advantages. Extremely rare RNAs that have high affinity for specific proteins can be selected in vitro (SELEX) (2, 3). Genetically controlled induction of such high affinity RNA aptamers could provide a means of rapidly inactivating a specific domain of a protein and thereby assessing its primary function and mechanism of action in vivo. Alternatively, continuous expression of specific RNA aptamers after stable gene transfer could achieve a long-term alteration in the activity of a target protein. In yeast, the constitutive expression of an aptamer against RNA polymerase II caused cell growth defects under conditions in which the RNA polymerase level was artificially reduced (4). Although this study demonstrated the potential of RNA aptamers as inhibitors of protein function in vivo, several advances are needed to apply this approach to multicellular organisms.Previously, we selected and characterized RNA aptamers to B52, a regulator of RNA splicing in Drosophila melanogaster. B52, also known as SRp55, is a member of the Drosophila SR protein family, a group of nuclear proteins that are essential for pre-mRNA splicing and influence splice site choice (5, 6). B52 contains two RNA recognition motifs in its N-terminal half and a domain rich in serine-arginine dipeptide repeats in its C-terminal half (7). RNA aptamers that bind B52 with high affinity (K d ϭ 20-50 nM) and specificity were selected from a large pool of RNAs (8). The B52 binding sites (BBS) on members of this nonclonally derived family of RNA aptamers not only have a ''conserved'' consensus sequen...

show abstract

“…Drosophila polytene chromosomes from the Bg61-4.1 fly line were stained by using indirect immunofluorescence as described (15). dTAF250 was detected by using anti-dTAF250 (mouse monoclonal), and dTRF2 was detected by using the polyclonal rabbit antibody described above, and then with an affinity-purified secondary antibody (donkey anti-rabbit or anti-mouse IgG conjugated with FITC and Texas red, respectively.)…”

Section: Methodsmentioning

confidence: 99%

TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family

Rabenstein

Zhou²,

Lis³

et al. 1999

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

Self Cite

163

184

View full text Add to dashboard Cite

The TATA box-binding protein (TBP) is an essential component of the RNA polymerase II transcription apparatus in eukaryotic cells. Until recently, it was thought that the general transcriptional machinery was largely invariant and relied on a single TBP, whereas a large and diverse collection of activators and repressors were primarily responsible for imparting specificity to transcription initiation. However, it now appears that the ''basal'' transcriptional machinery also contributes to specificity via tissue-specific versions of TBP-associated factors as well as a tissue-specific TBP-related factor (TRF1) responsible for gene selectivity in Drosophila. Here we report the cloning of a TBP-related factor (TRF2) that is found in humans, Drosophila, Caenorhabditis elegans, and other metazoans. Like TRF1 and TBP, TRF2 binds transcription factor IIA (TFIIA) and TFIIB and appears to be part of a larger protein complex. TRF2's primary amino acid structure suggests divergence in the putative DNA binding domain, and not surprisingly, it fails to bind to DNA containing canonical TATA boxes. Most importantly, TRF2 is associated with loci on Drosophila chromosomes distinct from either TBP or TRF1, so it may have different promoter specificity and regulate a select subset of genes. These findings suggest that metazoans have evolved multiple TBPs to accommodate the vast increase in genes and expression patterns during development and cellular differentiation.

show abstract

HSF recruitment and loss at mostDrosophila heat shock loci is coordinated and depends on proximal promoter sequences

Cited by 41 publications

References 57 publications

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

RNA aptamers as effective protein antagonists in a multicellular organism

TATA box-binding protein (TBP)-related factor 2 (TRF2), a third member of the TBP family

Contact Info

Product

Resources

About