DNA loops: structural and functional properties of scaffold‐attached regions

Roberge, Michel; Gasser, Susan M.

doi:10.1111/j.1365-2958.1992.tb01485.x

Cited by 71 publications

(38 citation statements)

References 44 publications

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“…(i) it has been demonstrated by several authors that SAR functions are conserved across species boundaries (reviewed in 58,59). One example concerns a 1.3 kb SAR fragment of a tobacco gene which behaves like mammalian SAR elements by in vitro and in vivo criteria (27).…”

Section: Discussionmentioning

confidence: 99%

“…Other SAR elements cover several kilobases, they mark regions of decreasing accessibility to DNase I and are therefore candidates for the borders of chromatin domains (13,24,(57)(58)(59). Plant SARs have been identified downstream of the pea plastocyanin gene (40), downstream of the soybean heat shock gene (60) and upstream as well as downstream of the light-inducible potato ST-LS1 gene (Bode, unpublished).…”

Section: Discussionmentioning

confidence: 99%

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A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

et al. 1994

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Integration of foreign genes into plant genomes by the Agrobacterlum T-DNA transfer system has been considered to occur at random. It has been speculated that the chromosomal structure of the integration site might affect the expression pattern of the introduced genes. To gain insight into the molecular structure of T-DNA integration sites and its possible impact on gene expression, we have examined plant DNA sequences In the vicinity of T-DNA borders. Analysis of a transgenic petunia plant containing a chloramphenicol acetyltransferase (CAT) gene regulated by the hemoglobin promoter (PAR) from Parasponia andersonii revealed a scaffold attachment region (SAR) close to one T-DNA end. In addition to having strong binding affinities for both animal and plant nuclear scaffolds this petunia SAR element is as active in mammalian cells as the authentic elements from mammalian sources.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

et al. 1994

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“…Chromatin is anchored to the nuclear matrix by matrix/scaffold attachment regions (M/SARs), thereby organizing genomic DNA into topologically distinct loop domains that are important in replication and transcription (45). M/SARs are often closely associated with transcriptional promoters and enhancers of several genes and have been shown to generate long-range chromatin accessibility (24).…”

Section: Vol 81 2007 Chromatin Context Of Hiv-1 Integration In T Cementioning

confidence: 99%

“…The host genome is assembled into a compact but heterogeneous higher-order chromatin structure (52). Studies of in vitro integrations using naked template DNA have indicated a preference for certain sequences (7,10,27,45); however, the body of evidence also suggests that the primary sequence per se may not be the only requirement (39,41,49,51). Because of the heterogeneity of the chromatin, the site of integration of HIV into the genome could have dramatic effects on its transcriptional activation (26).…”

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confidence: 99%

SATB1-Binding Sequences and Alu -Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites

Kumar

Mehta

Purbey

et al. 2007

J Virol

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Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of Alu-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo. Alu repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both Alu-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the Alu-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.

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“…These elements have been proposed to be important for maintaining proper supercoiling between two convergently oriented, active transcription units (8,29). DNA gyrase, IHF, and DNA polymerase I interact specifically with BIME DNA, suggesting a role for RIB elements in chromosomal folding and the potential formation of topological boundaries in the chromosome (5,8,14,18,19,39,44,54). Because of the palindromic nature of the REP sequences and their ability to form stable stem-loop structures, some of these elements have been shown to be important for transcription termination (17,20).…”

mentioning

confidence: 99%

The RIB element in the goaG-pspF intergenic region of Escherichia coli

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1997

J Bacteriol

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The sequence (2,700 bp) between the aldH and pspF genes of Escherichia coli was determined. The pspF gene encodes a 54 transcriptional activator of the phage shock protein (psp) operon (pspA to pspE). Downstream of the pspF transcribed region are two open reading frames (ORFs), ordL and goaG, convergently oriented with respect to pspF. These two ORFs, together with the adjacent aldH gene, may constitute a novel operon (aldHordL-goaG). The goaG-pspF intergenic region contains a complex extragenic mosaic element, RIB. The structure of this RIB element, which belongs to the BIME-1 family, is Y(REP1) > 16 < Z 1 (REP2), where Y and Z 1 are palindromic units and the central 16 bases contain an L motif with an ihf consensus sequence. DNA fragments containing the L motif of the psp RIB element effectively bind integration host factor (IHF), while the Y palindromic unit (REP1) of the same RIB element binds DNA gyrase weakly. Computer prediction of the pspF mRNA secondary structure suggested that the transcribed stem-loop structures formed by the 3-flanking region of the pspF transcript containing the RIB element can stabilize and protect pspF mRNA. Analysis of pspF steadystate mRNA levels showed that transcripts with an intact RIB element are much more abundant than those truncated at the 3 end by deletion of either the entire RIB element or a single Z 1 sequence (REP2). Thus, the pspF 3-flanking region containing the RIB element has an important role in the stabilization of the pspF transcript.PspF is the constitutively transcribed and constitutively active 54 transcriptional activator of the phage shock protein (psp) operon (pspA to pspE) of Escherichia coli, and its transcription is driven by one major (P1) and two minor (P2 and P3) 70 promoters (27). Analysis of pspF transcription under noninducing and inducing conditions showed a low level of pspF mRNA in both (27). The DNA sequence downstream of the pspF gene contains an extragenic mosaic element, RIB (reiterative ihf BIME [bacterial interspersed mosaic element]) (27). This RIB consists of REP1 and REP2 sequences, oriented head to head and flanking a 16-bp-long DNA sequence that carries a putative binding site for integration host factor (IHF) (27). REPs are repetitive extragenic palindromes and have also been named PU (palindromic unit) sequences. A database search found over 150 sequences in E. coli and three in Shigella species that are highly homologous to all or part of the RIB element 3Ј of pspF (27). Most such RIB elements are found in intercistronic regions or in the 3Ј regions of transcriptional units (13). These elements have been proposed to be important for maintaining proper supercoiling between two convergently oriented, active transcription units (8,29). DNA gyrase, IHF, and DNA polymerase I interact specifically with BIME DNA, suggesting a role for RIB elements in chromosomal folding and the potential formation of topological boundaries in the chromosome (5,8,14,18,19,39,44,54). Because of the palindromic nature of the REP sequences and their abilit...

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DNA loops: structural and functional properties of scaffold‐attached regions

Cited by 71 publications

References 44 publications

A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

A plant scaffold attached region detected close to a T-DNA integration site is active in mammalian cells

SATB1-Binding Sequences and Alu -Like Motifs Define a Unique Chromatin Context in the Vicinity of Human Immunodeficiency Virus Type 1 Integration Sites

The RIB element in the goaG-pspF intergenic region of Escherichia coli

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