Genes Containing Long Introns Occupy Series of Bands and Interbands in Drosophila melanogaster Polytene Chromosomes

Abstract

The Drosophila melanogaster polytene chromosomes are the best model for studying the genome organization during interphase. Despite of the long-term studies available on genetic organization of polytene chromosome bands and interbands, little is known regarding long gene location on chromosomes. To analyze it, we used bioinformatic approaches and characterized genome-wide distribution of introns in gene bodies and in different chromatin states, and using fluorescent in situ hybridization we juxtaposed them with the chromosome structures. Short introns up to 2 kb in length are located in the bodies of housekeeping genes (grey bands or lazurite chromatin). In the group of 70 longest genes in the Drosophila genome, 95% of total gene length accrues to introns. The mapping of the 15 long genes showed that they could occupy extended sections of polytene chromosomes containing band and interband series, with promoters located in the interband fragments (aquamarine chromatin). Introns (malachite and ruby chromatin) in polytene chromosomes form independent bands, which can contain either both introns and exons or intron material only. Thus, a novel type of the gene arrangement in polytene chromosomes was discovered; peculiarities of such genetic organization are discussed.

The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophila melanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication

“…The laza and 4053 probes are located in banded region 79E1-4–79F, which has never been considered heterochromatic. The CkII, Vps and CG17454 probes map to banded region 80AC, which has always been considered heterochromatic because of its late replication [ 7 ]. The CkII fragment localizes to banded region 80A1-2/80B1-2 and thus limits it from the distal end, while a fragment of the CG17454 gene localizes to the bands in region 80C and thus limits region 80AC from the proximal side.…”

“…So, each housekeeping gene lies in part in one chromosomal structure, in part in another. The Ruby and Malachite chromatin states correspond to the black bands containing developmental genes and long introns [ 1 , 6 , 7 , 8 ].…”

Super-resolution microscopy reveals stochastic initiation of replication in Drosophila polytene chromosomes

“…The thickness of polytene chromosome structures cytologically revealed as gray bands varies considerably and ranges from 2 kbp (the minimum band visible by electron microscopy in semithin sections) to tens of kilobase pairs (Vatolina et al 2011;Demakova et al 2020;Khoroshko et al 2020). In the present work, we estimated the size of the 21C6 gray band to be ~60 kbp.…”