Structural features of 3C6/C7 interband chromatin organization in Drosophila melanogaster polytene chromosomes

Structural and Functional Dissection of the 5′ Region of the Notch Gene in Drosophila melanogaster

“…(7) Borders of the bands in the region, as defined by the 4HMM. (8) DNA fragments capable (white) and not capable (black) of forming an interband in a new genetic environment [38,45]. (9) Deletions of DNA segments from the 5 -regulatory part of the Notch gene causing (black) and not causing (white) the collapse of the endogenous interband 3C6/C7 (current investigation).…”

“…ModEncode data analysis [44] revealed a significant local decrease in nucleosome density in Drosophila cell cultures in the 5 region of the Notch gene. In this region, pronounced binding peaks of a number of insulator proteins (CP190, CTCF, and CHROMATOR (Chriz)) are detected, with the tops of the peaks in all these cases coinciding with the position of the DNA fragment capable of forming an interband [28,38], (Figure 8). In this context, it should be mentioned that a significant fraction of insulator proteins have been demonstrated to map to the boundaries of topologically associated domains, and these boundaries are cytologically related to the polytene chromosome interbands [31,45].…”

“…We previously showed [38,47] that three DNA fragments (1504 bp, 914 dp, and 276 bp) from 5 nontranscribed region of the Notch gene, being transferred in a new genetic environment (region 84F, 3R chromosome) give rise to a novel interband. After removing 246 bp from the 1504-bp DNA fragment the formation of a new interband does not occur.…”

“…Deletion d2 removes 126 bp that fully include a 47-bp tandem repeat that was shown to be functionally important [17]. Deletion d3 removes a fragment of 255 bp, which is necessary for the interband formation in salivary gland polytene chromosomes de novo in the ectopic environment [38]. Deletion d1, in addition to the d2 sequence, removes 146 bp distal to the gene start.…”

In situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila

“…The topological effects observed upon boundary deletion are remarkably consistent with cytological data from the Notch mutant facet-strawberry (fa swb ) where deletion of ã 0.9-kb region spanning the 5′ region of Notch results in loss of an interband and fusion of the 3C7 band containing Notch with the upstream band 26 . Also, reporter assays in transgenic flies and cytological evidence support an autonomous role for the 5′ intergenic region of Notch as a chromatin insulator as the ectopic insertion of this sequence is sufficient and necessary to split a band into two, forming an interband in polytene chromosomes 45,46 . In the case of the intragenic enhancer boundary, deletion of a~2-kb region results in a dramatic increase of ectopic interactions between Notch domains and loss of a~1-Mb domain downstream of Notch (Fig.…”