Developmental Progression of DNA Puffs in Sciara coprophila: Amplification and Transcription

Wu, Nan; Liang, Chun; DiBartolomeis, Susan M.; Smith, Heidi S.; Gerbi, Susan A.

doi:10.1006/dbio.1993.1287

Cited by 42 publications

(63 citation statements)

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“…Moreover, gene expression in these tissues also likely occurs over a longer developmental window, and this could negate a need for amplification. Another example of developmental gene amplification occurs in the sciarid flies, in which genes encoding cocoon proteins are amplified in the larval salivary glands (Glover et al 1982;Wu et al 1993;Santelli et al 2004) In the case of the eggshell protein genes in the Drosophila follicle cells and the cocoon protein genes in the sciarid flies, it may be that when confronted with the developmental demand to express a limited set of genes at extremely high levels over a brief developmental window, increased copy number of a subset of genes above the overall ploidy of the genome has been selected.…”

Section: Developmental Control Of Differential Replicationmentioning

confidence: 99%

Developmental control of the DNA replication and transcription programs

Nordman¹,

Li²,

Eng³

et al. 2010

Genome Res.

129

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Polyploid or polytene cells, which have more than 2C DNA content, are widespread throughout nature and present in most differentiated Drosophila tissues. These cells also can display differential replication, that is, genomic regions of increased or decreased DNA copy number relative to overall genomic ploidy. How frequently differential replication is used as a developmental strategy remains unclear. Here, we use genome-wide array-based comparative genomic hybridization (aCGH) to profile differential DNA replication in isolated and purified larval fat body and midgut tissues of Drosophila, and we compare them with recent aCGH profiles of the larval salivary gland. We identify sites of euchromatic underreplication that are common to all three tissues and others that are tissue specific. We demonstrate that both common and tissuespecific underreplicated sites are dependent on the Suppressor of Underreplication protein, SUUR. mRNA-seq profiling shows that whereas underreplicated regions are generally transcriptionally silent in the larval midgut and salivary gland, transcriptional silencing and underreplication have been uncoupled in the larval fat body. In addition to revealing the prevalence of differential replication, our results show that transcriptional silencing and underreplication can be mechanistically uncoupled.

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Section: Developmental Control Of Differential Replicationmentioning

confidence: 99%

Developmental control of the DNA replication and transcription programs

Nordman¹,

Li²,

Eng³

et al. 2010

Genome Res.

129

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“…These genomic regions constitute sites of developmentally regulated gene amplification and transcription (Basso et al, 2002;Foulk et al, 2006;Gerbi et al, 1993;Lara et al, 1991;Stocker et al, 1996). The formation of DNA puffs is induced by ecdysone and is concomitant with the transcription of the genes which present the highest levels of amplification within the amplicons (Fontes et al, 1992;Gerbi et al, 1993;Glover et al, 1982;Paçó-Larson et al, 1992;Penalva et al, 1997;Santelli et al, 1991Santelli et al, , 2004Wu et al, 1993;Yokosawa et al, 1999).…”

mentioning

confidence: 99%

Functional and bioinformatics analyses reveal conservation of cis‐regulatory elements between sciaridae and drosophilidae

Lecci

Malta

Flausino

et al. 2008

Genesis

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Summary: The sciarid DNA puff C4 BhC4-1 gene is amplified and transcribed in salivary glands at the end of the larval stage. In transgenic Drosophila, the BhC4-1 promoter drives transcription in prepupal salivary glands and in the ring gland of late embryos. A bioinformatics analysis has identified 162 sequences similar to distinct regions of the BhC4-1 proximal promoter, which are predominantly located either in 5 0 or 3 0 regions or introns in the Drosophila melanogaster genome. A significant number of the identified sequences are found in the regulatory regions of Drosophila genes that are expressed in the salivary gland. Functional assays in Drosophila reveal that the BhC4-1 proximal promoter contains both a 129 bp (2186/258) salivary gland enhancer and a 67 bp

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“…Our model system is the developmentally regulated DNA amplification in DNA puff II/9A in salivary gland chromosomes of the fungus fly Sciara coprophila. DNA puffs are specific loci not only of active transcription but also of up to almost 20-fold DNA amplification in polytene chromosomes of late-larval salivary glands (35). Puff II/9A contains two genes (II/9-1 and II/9-2) which are about 3 kb apart and have 85% sequence similarity with each other (9).…”

mentioning

confidence: 99%

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method.

Liang¹,

Gerbi²

1994

Mol. Cell. Biol.

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The replication origin region for DNA amplification in Sciara coprophila DNA puff IV/9A was analyzed with a novel three-dimensional (3D) gel method. Our 3D gel method involves running a neutral/neutral 2D gel and then cutting out vertical gel slices from the area containing replication intermediates, rotating these slices 90°to form the third dimension, and running an alkaline gel for each of the slices. Therefore, replication intermediates are separated into forks and bubbles and then are resolved into parental and nascent strands. We used this technique to determine the size of forks and bubbles and to confirm the location of the major initiation region previously mapped by 2D gels to a 1-kb region. Furthermore, our 3D gel analyses suggest that only one initiation event in the origin region occurs on a single DNA molecule and that the fork arc in the composite fork-plus-bubble pattern in neutral/neutral 2D gels does not result from broken bubbles.Studies on the mechanism of eukaryotic DNA replication have been largely limited to viral systems in which specific origins of replication are well defined. This reflects the difficulty in identifying and elucidating chromosomal origins of replication. A search for cellular replication origins has been prompted by the development of two-dimensional (2D) gel techniques (5, 21).Neutral/neutral 2D gels developed by Brewer and Fangman (5) separate replication intermediates (forks, bubbles, etc.) derived from a given restriction fragment from each other and from nonreplicating linear DNA. This is achieved by running the first dimension of a low-percentage gel at a low voltage, which resolves DNA primarily by mass, and the second dimension of a higher-percentage gel at a higher voltage so as to separate DNA by shape as well as by mass. Sequential hybridization of the 2D gel blots with probes from different restriction fragments will indicate whether a given fragment contains a replication origin (a bubble arc is seen) or is replicated by a passing fork (a fork arc is seen). A recent modification of this 2D gel method using digestion by a second restriction enzyme before running the second dimension of the gel allows determination of the direction of fork movement (13).The first dimension of neutral/alkaline 2D gels developed by Huberman et al. (21) is the same as that of neutral/neutral 2D gels, but the second dimension is an alkaline gel which separates replication intermediates into nascent and parental strands and resolves them by size. By hybridizing the 2D gel blots with short probes from different areas within a restriction fragment, the direction of fork movement can be deduced from the size distribution of nascent strands detected by each probe. A probe at the end where forks enter the fragment will detect nascent strands of all sizes, while a probe at the other end will detect only very large nascent strands. The map position where fork movement changes from one direction to another is presumed to be the origin of bidirectional replication. probe complementary to a...

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Developmental Progression of DNA Puffs in Sciara coprophila: Amplification and Transcription

Cited by 42 publications

References 0 publications

Developmental control of the DNA replication and transcription programs

Developmental control of the DNA replication and transcription programs

Functional and bioinformatics analyses reveal conservation of cis‐regulatory elements between sciaridae and drosophilidae

Analysis of an origin of DNA amplification in Sciara coprophila by a novel three-dimensional gel method.

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