51
|
Chetverina D, Savitskaya E, Maksimenko O, Melnikova L, Zaytseva O, Parshikov A, Galkin AV, Georgiev P. Red flag on the white reporter: a versatile insulator abuts the white gene in Drosophila and is omnipresent in mini-white constructs. Nucleic Acids Res 2007; 36:929-37. [PMID: 18086699 PMCID: PMC2241909 DOI: 10.1093/nar/gkm992] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Much of the research on insulators in Drosophila has been done with transgenic constructs using the white gene (mini-white) as reporter. Hereby we report that the sequence between the white and CG32795 genes in Drosophila melanogaster contains an insulator of a novel kind. Its functional core is within a 368 bp segment almost contiguous to the white 3′UTR, hence we name it as Wari (white-abutting resident insulator). Though Wari contains no binding sites for known insulator proteins and does not require Su(Hw) or Mod(mdg4) for its activity, it can equally well interact with another copy of Wari and with unrelated Su(Hw)-dependent insulators, gypsy or 1A2. In its natural downstream position, Wari reinforces enhancer blocking by any of the three insulators placed between the enhancer and the promoter; again, Wari–Wari, Wari–gypsy or 1A2–Wari pairing results in mutual neutralization (insulator bypass) when they precede the promoter. The distressing issue is that this element hides in all mini-white constructs employed worldwide to study various insulators and other regulatory elements as well as long-range genomic interactions, and its versatile effects could have seriously influenced the results and conclusions of many works.
Collapse
Affiliation(s)
- Darya Chetverina
- Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, University of Oslo, Centre for Medical Studies in Russia, Moscow 199334, Russia
| | | | | | | | | | | | | | | |
Collapse
|
52
|
A stage-specific factor confers Fab-7 boundary activity during early embryogenesis in Drosophila. Mol Cell Biol 2007; 28:1047-60. [PMID: 18039839 DOI: 10.1128/mcb.01622-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Fab-7 boundary is required to ensure that the iab-6 and iab-7 cis-regulatory domains in the Drosophila Bithorax complex can function autonomously. Though Fab-7 functions as a boundary from early embryogenesis through to the adult stage, this constitutive boundary activity depends on subelements whose activity is developmentally restricted. In the studies reported here, we have identified a factor, called early boundary activity (Elba), that confers Fab-7 boundary activity during early embryogenesis. The Elba factor binds to a recognition sequence within a Fab-7 subelement that has enhancer-blocking activity during early embryogenesis, but not during mid-embryogenesis or in the adult. We found that the Elba factor is present in early embryos but largely disappears during mid-embryogenesis. We show that mutations in the Elba recognition sequence that eliminate Elba binding in nuclear extracts disrupt the early boundary activity of the Fab-7 subelement. Conversely, we find that early boundary activity can be reconstituted by multimerizing the Elba recognition site.
Collapse
|
53
|
Mohan M, Bartkuhn M, Herold M, Philippen A, Heinl N, Bardenhagen I, Leers J, White RAH, Renkawitz-Pohl R, Saumweber H, Renkawitz R. The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning. EMBO J 2007; 26:4203-14. [PMID: 17805343 PMCID: PMC2230845 DOI: 10.1038/sj.emboj.7601851] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 08/15/2007] [Indexed: 01/08/2023] Open
Abstract
Insulator sequences guide the function of distantly located enhancer elements to the appropriate target genes by blocking inappropriate interactions. In Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates. Here we find that the structurally related factors dCTCF and Su(Hw) have distinct binding targets. In contrast, the Su(Hw) interacting factor CP190 largely overlapped with dCTCF binding sites and interacts with dCTCF. Binding of dCTCF to targets requires CP190 in many cases, whereas others are independent of CP190. Analysis of the bithorax complex revealed that six of the borders between the parasegment specific regulatory domains are bound by dCTCF and by CP190 in vivo. dCTCF null mutations affect expression of Abdominal-B, cause pharate lethality and a homeotic phenotype. A short pulse of dCTCF expression during larval development rescues the dCTCF loss of function phenotype. Overall, we demonstrate the importance of dCTCF in fly development and in the regulation of abdominal segmentation.
Collapse
Affiliation(s)
- Man Mohan
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Martin Herold
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Angela Philippen
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Nina Heinl
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Imke Bardenhagen
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Joerg Leers
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
| | - Robert A H White
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Renate Renkawitz-Pohl
- Philipps-Universität Marburg, Fachbereich Biologie, Entwicklungsbiologie, Marburg, Germany
| | - Harald Saumweber
- Cytogenetics Division, Institute of Biology, Humboldt University, Berlin, Germany
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring, Giessen, Germany
- Institute for Genetics, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58-62, Giessen 35392, Germany. Tel.: +49 641 99 35460; Fax: +49 641 99 35469; E-mail:
| |
Collapse
|
54
|
Dorman ER, Bushey AM, Corces VG. The role of insulator elements in large-scale chromatin structure in interphase. Semin Cell Dev Biol 2007; 18:682-90. [PMID: 17919949 DOI: 10.1016/j.semcdb.2007.08.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 08/22/2007] [Indexed: 11/19/2022]
Abstract
Insulator elements can be classified as enhancer-blocking or barrier insulators depending on whether they interfere with enhancer-promoter interactions or act as barriers against the spreading of heterochromatin. The former class may exert its function at least in part by attaching the chromatin fiber to a nuclear substrate such as the nuclear matrix, resulting in the formation of chromatin loops. The latter class functions by recruiting histone-modifying enzymes, although some barrier insulators have also been shown to create chromatin loops. These loops may correspond to functional nuclear domains containing clusters of co-expressed genes. Thus, insulators may determine specific patterns of nuclear organization that are important in establishing specific programs of gene expression during cell differentiation and development.
Collapse
Affiliation(s)
- Elizabeth R Dorman
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
| | | | | |
Collapse
|
55
|
Kurshakova M, Maksimenko O, Golovnin A, Pulina M, Georgieva S, Georgiev P, Krasnov A. Evolutionarily conserved E(y)2/Sus1 protein is essential for the barrier activity of Su(Hw)-dependent insulators in Drosophila. Mol Cell 2007; 27:332-338. [PMID: 17643381 DOI: 10.1016/j.molcel.2007.05.035] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 04/12/2007] [Accepted: 05/25/2007] [Indexed: 11/28/2022]
Abstract
Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers for spreading of repressive chromatin. The Su(Hw) protein is responsible for activity of the best-studied Drosophila insulators. Here we demonstrate that an evolutionarily conserved protein, E(y)2/Sus1, is recruited to the Su(Hw) insulators via binding to the zinc-finger domain of Su(Hw). Partial inactivation of E(y)2 in a weak mutation, e(y)2(u1), impairs only the barrier, but not the enhancer-blocking, activity of the Su(Hw) insulators. Whereas neither su(Hw)(-) nor e(y)2(u1) affects fly viability, their combination proves lethal, testifying to functional interaction between Su(Hw) and E(y)2 in vivo. Apparently, different domains of Su(Hw) recruit proteins responsible for enhancer-blocking and for the barrier activity.
Collapse
Affiliation(s)
- Maria Kurshakova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Oksana Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anton Golovnin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; University of Oslo, Centre for Medical Studies in Russia, Moscow 119334, Russia
| | - Maria Pulina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Sofia Georgieva
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; University of Oslo, Centre for Medical Studies in Russia, Moscow 119334, Russia; Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
| | - Pavel Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia.
| | - Aleksey Krasnov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; University of Oslo, Centre for Medical Studies in Russia, Moscow 119334, Russia.
| |
Collapse
|