Conserved Gene Order at the Nuclear Periphery in Drosophila

Ranz, José M.; Díaz-Castillo, Carlos; Petersen, Rita

doi:10.1093/molbev/msr178

Cited by 12 publications

(18 citation statements)

References 26 publications

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“…Thus, organization and protein composition of lazurite chromatin appear consistent with our view of this chromatin type as composed of actively and broadly transcribed sequences many of which are protein-coding [80-83]. Malachite chromatin type is rich in natural transposon insertions [84]. Transposons and expression thereof are known to have a regulatory role in the genome [80-82].…”

Section: Discussionmentioning

confidence: 52%

Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines

Boldyreva¹,

Goncharov²,

Demakova³

et al. 2017

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Background: Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby.Results: Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5’ untranslated regions (5’UTRs) of the genes, is enriched in diverse “open” chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the “closed” chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.

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Section: Discussionmentioning

confidence: 52%

Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines

Boldyreva¹,

Goncharov²,

Demakova³

et al. 2017

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“…The clustering is also reported for peaks of HCNEs (Sahagun and Ranz 2012). One of the possible mechanisms underlying such clustering might be linked with the preferential association of conserved syntenic blocks with nuclear periphery through LAMIN binding (Ranz et al 2012) or extended regions of silent chromatin (Andreyenkova et al 2013). …”

Section: Discussionmentioning

confidence: 99%

“…Regions with the conserved gene order tend to bind LAM and SUUR (Ranz et al 2012). LAM plays an important role in chromosome and nucleus structure (Shevelyov and Nurminsky 2012).…”

Section: Introductionmentioning

confidence: 99%

Underreplicated Regions in Drosophila melanogaster Are Enriched with Fast-Evolving Genes and Highly Conserved Noncoding Sequences

Makunin

Колесникова

Andreyenkova

2014

Genome Biology and Evolution

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Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution.

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“…Furthermore, IH is characterized by low gene density, and IH-resident genes typically have narrow tissue-and stage-specific expression patterns, being particularly active in the male germ line (MacAlpine et al 2004;Belyakin et al 2010). Additionally, in different Drosophila species, the gene order in the latereplicating and SUUR-containing regions is well conserved throughout evolution (Ranz et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin

et al. 2012

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In salivary gland polytene chromosomes of Drosophila melanogaster, the regions of intercalary heterochromatin are characterized by late replication, under-replication, and genetic silencing. Using Gal4/UAS system, we induced transcription of sequences adjacent to transgene insertions in the band 11A6-9. This activation resulted in a loss of "silent" and appearance of "active" epigenetic marks, recruitment of RNA polymerase II, and formation of a puff. The activated region is now early replicating and shows increased level of DNA polytenization. Notably, all these changes are restricted to the area around the inserts, whereas the rest of the band remains inactive and late replicating. Although only a short area near the insertion site is transcribed, it results in an "open" chromatin conformation in a much broader region. We conclude that regions of intercalary heterochromatin do not form stand-alone units of late replication and under-replication. Every part of such regions can be activated and polytenized independently of other parts.

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Conserved Gene Order at the Nuclear Periphery in Drosophila

Cited by 12 publications

References 26 publications

Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines

Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines

Underreplicated Regions in Drosophila melanogaster Are Enriched with Fast-Evolving Genes and Highly Conserved Noncoding Sequences

Induced transcription results in local changes in chromatin structure, replication timing, and DNA polytenization in a site of intercalary heterochromatin

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