Chromatin Heterogeneity and Distribution of Regulatory Elements in the Late-Replicating Intercalary Heterochromatin Domains of Drosophila melanogaster Chromosomes

Abstract

Late-replicating domains (intercalary heterochromatin) in the Drosophila genome display a number of features suggesting their organization is quite unique. Typically, they are quite large and encompass clusters of functionally unrelated tissue-specific genes. They correspond to the topologically associating domains and conserved microsynteny blocks. Our study aims at exploring further details of molecular organization of intercalary heterochromatin and has uncovered surprising heterogeneity of chromatin composition in these regions. Using the 4HMM model developed in our group earlier, intercalary heterochromatin regions were found to host chromatin fragments with a particular epigenetic profile. Aquamarine chromatin fragments (spanning 0.67% of late-replicating regions) are characterized as a class of sequences that appear heterogeneous in terms of their decompactization. These fragments are enriched with enhancer sequences and binding sites for insulator proteins. They likely mark the chromatin state that is related to the binding of cis-regulatory proteins. Malachite chromatin fragments (11% of late-replicating regions) appear to function as universal transitional regions between two contrasting chromatin states. Namely, they invariably delimit intercalary heterochromatin regions from the adjacent active chromatin of interbands. Malachite fragments also flank aquamarine fragments embedded in the repressed chromatin of late-replicating regions. Significant enrichment of insulator proteins CP190, SU(HW), and MOD2.2 was observed in malachite chromatin. Neither aquamarine nor malachite chromatin types appear to correlate with the positions of highly conserved non-coding elements (HCNE) that are typically replete in intercalary heterochromatin. Malachite chromatin found on the flanks of intercalary heterochromatin regions tends to replicate earlier than the malachite chromatin embedded in intercalary heterochromatin. In other words, there exists a gradient of replication progressing from the flanks of intercalary heterochromatin regions center-wise. The peculiar organization and features of replication in large late-replicating regions are discussed as possible factors shaping the evolutionary stability of intercalary heterochromatin.

The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana

“…X -axis denotes the genomic intervals relative to TSS, Y -axis – the ratio of total length of overlap between EBRs and a certain interval to the total length of EBRs. Data labels denote p- values derived from Monte-Carlo permutation test (Khoroshko et al, 2016, see Monte-Carlo Permutation Test for Genome Tracks).…”

“…X -axis denotes genomic intervals relative to TSS, Y -axis – the ratio of total length of overlap between EBR fragments and a certain interval to the total length of EBR fragments. Data labels denote p -values derived from the Monte-Carlo permutation test (Khoroshko et al, 2016; see Materials and Methods). Green/Blue/Red fonts of labels denote enrichment of the observed values respective to the expected ones, the gray font corresponds to depletion.…”

“…To estimate non-randomness of the overlap between various tracks of genome regions – EBRs, the domains of the chromatin states, EBR fragments (see above), the tracks of upstream gene regions (see below) – we used Monte-Carlo permutation test as described in (Khoroshko et al, 2016). We used the ratio of the total overlap length to the total length of the permutated track as a measure of overlap between two tracks.…”

Arp2/3 and Unc45 maintain heterochromatin stability in Drosophila polytene chromosomes

“…Late-replicating regions (i.e., pericentromeric heterochromatin, and silenced genes along chromosome arms called intercalary heterochromatin [32,34,[37][38][39]) remain largely underreplicated in polytene chromosomes. This results in stalling and collapse of forks entering the domain, followed by mutagenic repair [40][41][42].…”

Architecture of promoters of house-keeping genes in polytene chromosome interbands of drosophila melanogaster

“…Используя сведения о локализации белков, характерных для генетически активного хроматина, мы разработали стереотип его классификации по принципу степени компактизации от минимального (aquamarine, соответствует междискам) до максимального (ruby, соответствует чёрным плотным дискам). Ещё два состояния lazurite и malachite в основном соответствуют кодирующим частям генов [2, 4] и краям блоков генов развития [5].…”