Constitutive heterochromatin: a surprising variety of expressed sequences

Dimitri, Patrizio; Caizzi, Ruggiero; Giordano, Elena; Accardo, Maria Carmela; Lattanzi, Giovanna; Biamonti, Giuseppe

doi:10.1007/s00412-009-0211-y

Cited by 53 publications

(65 citation statements)

References 126 publications

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“…Similar to any set of euchromatic genes, heterochromatic genes encode an extensive array of proteins with a wide variety of molecular functions, as has been established by a number of genetic and molecular studies (Biggs et al 1994;Warner et al 1998;Rollins et al 1999;Schulze et al 2005;Yasuhara et al 2005;Hallson et al 2008). This conclusion is also clearly supported by the recent annotation of heterochromatin sequence (Hoskins et al 2007;Dimitri et al 2009;Tweedie et al 2009). Additionally, the expression profiles of heterochromatic genes are not especially restricted; heterochromatic genes are often expressed Six novel essential loci were uncovered while the molecular identity of two previously reported essential loci, l(2)41Ab and uex, was discovered.…”

Section: Genesupporting

confidence: 74%

“…A schematic map of the heterochromatic segment of the right arm of mitotic chromosome 2 is shown in Figure 1 (modified from figure 1 of Dimitri et al 2009). In the current work, we focus on the region of 2Rh extending from CG42595 to Nipped-B in cytological bands h45-h46.…”

Section: Resultsmentioning

confidence: 99%

“…In the current work, we focus on the region of 2Rh extending from CG42595 to Nipped-B in cytological bands h45-h46. Our initial objective was to resolve the issue of the genetic identity of l(2)41Ae, which was mapped to h46 (Dimitri 1991;Coulthard et al 2003;Dimitri et al 2009). However, we also planned to characterize as many of the other essential loci in the region as possible.…”

Section: Resultsmentioning

confidence: 99%

“…It should be emphasized that early mapping studies placed l(2)41Ab proximal to the rl gene (for review see Coulthard et al 2003), but based on the recent annotation of heterochromatin (Hoskins et al 2007) and the more recent evidence from Dimitri et al (2009), l(2)41Ab should be located distal to rl. Indeed, CG41265 is located distal to rl (see Figure 1).…”

Section: Genementioning

confidence: 99%

“…Putative homologs were determined using BLASTp available at http:/ /blast.ncbi.nlm.nih.gov. throughout development and in different tissues (for examples, see Biggs et al 1994;Marygold et al 2005;Schulze et al 2005;Dimitri et al 2009). …”

Section: Genementioning

confidence: 99%

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Essential Loci in Centromeric Heterochromatin of Drosophila melanogaster. I: The Right Arm of Chromosome 2

et al. 2010

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With the most recent releases of the Drosophila melanogaster genome sequences, much of the previously absent heterochromatic sequences have now been annotated. We undertook an extensive genetic analysis of existing lethal mutations, as well as molecular mapping and sequence analysis (using a candidate gene approach) to identify as many essential genes as possible in the centromeric heterochromatin on the right arm of the second chromosome (2Rh) of D. melanogaster. We also utilized available RNA interference lines to knock down the expression of genes in 2Rh as another approach to identifying essential genes. In total, we verified the existence of eight novel essential loci in 2Rh: CG17665, CG17683, CG17684, CG17883, CG40127, CG41265, CG42595, and Atf6. Two of these essential loci, CG41265 and CG42595, are synonymous with the previously characterized loci l(2)41Ab and unextended, respectively. The genetic and molecular analysis of the previously reported locus, l(2)41Ae, revealed that this is not a single locus, but rather it is a large region of 2Rh that extends from unextended (CG42595) to CG17665 and includes four of the novel loci uncovered here.

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Section: Genesupporting

confidence: 74%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Genementioning

confidence: 99%

Section: Genementioning

confidence: 99%

See 3 more Smart Citations

Essential Loci in Centromeric Heterochromatin of Drosophila melanogaster. I: The Right Arm of Chromosome 2

et al. 2010

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Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (BACs) to Mitotic Heterochromatin of Drosophila

Accardo

Dimitri

2010

Methods in Molecular Biology

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The organization of eukaryotic chromosomes into euchromatin and heterochromatin represents an enigmatic aspect of genome evolution. Constitutive heterochromatin is a basic, yet still poorly understood component of eukaryotic genomes and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Drosophila melanogaster polytene chromosomes do not seem to be particularly useful to map heterochromatin sequences because the typical features of heterochromatin, organized as it is into a chromocenter, limit cytogenetic analysis. In contrast, constitutive heterochromatin has been well-defined at the cytological level in mitotic chromosomes of neuroblasts and has been subdivided into several bands with differential staining properties. Fluorescence in situ hybridization (FISH) using Bacterial Artificial Chromosomes (BAC) probes that carry large genomic portions defined by sequence annotation has yielded a "revolution" in the field of cytogenetics because it has allowed the mapping of multiple genes at once, thus rendering constitutive heterochromatin amenable to easy and fast cytogenetics analyses. Indeed, BAC-based FISH approaches on Drosophila mitotic chromosomes have made it possible to correlate genomic sequences to their cytogenetic location, aiming to build an integrated map of the pericentric heterochromatin. This chapter presents our standard protocols for BAC-based FISH, aimed at mapping large chromosomal regions of mitotic heterochromatin in Drosophila melanogaster.

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Naturally Occurring Minichromosome Platforms in Chromosome Engineering: An Overview

Raimondi

2011

Methods in Molecular Biology

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Artificially modified chromosome vectors are non-integrating gene delivery platforms that can shuttle very large DNA fragments in various recipient cells: theoretically, no size limit exists for the chromosome segments that an engineered minichromosome can accommodate. Therefore, genetically manipulated chromosomes might be potentially ideal vector systems, especially when the complexity of higher eukaryotic genes is concerned. This review focuses on those chromosome vectors generated using spontaneously occurring small markers as starting material. The definition and manipulation of the centromere domain is one of the main obstacles in chromosome engineering: naturally occurring minichromosomes, due to their inherent small size, were helpful in defining some aspects of centromere function. In addition, several distinctive features of small marker chromosomes, like their appearance as supernumerary elements in otherwise normal karyotypes, have been successfully exploited to use them as gene delivery vectors. The key technologies employed for minichromosome engineering are: size reduction, gene targeting, and vector delivery in various recipient cells. In spite of the significant advances that have been recently achieved in all these fields, several unsolved problems limit the potential of artificially modified chromosomes. Still, these vector systems have been exploited in a number of applications where the investigation of the controlled expression of large DNA segments is needed. A typical example is the analysis of genes whose expression strictly depends on the chromosomal environment in which they are positioned, where engineered chromosomes can be envisaged as epigenetically regulated expression systems. A novel and exciting advance concerns the use of engineered minichromosomes to study the organization and dynamics of local chromatin structures.

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Constitutive heterochromatin: a surprising variety of expressed sequences

Cited by 53 publications

References 126 publications

Essential Loci in Centromeric Heterochromatin of Drosophila melanogaster. I: The Right Arm of Chromosome 2

Essential Loci in Centromeric Heterochromatin of Drosophila melanogaster. I: The Right Arm of Chromosome 2

Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (BACs) to Mitotic Heterochromatin of Drosophila

Naturally Occurring Minichromosome Platforms in Chromosome Engineering: An Overview

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