DNA and Histone Modifications Identify a Putative Controlling Element (CE) on the X Chromosome of Sciara coprophila
Posukh O.V. Shloma V.V. Skrypnik P.A. Maksimov D.A. Antoshina P.A. Kalashnikova D.A. Nurislamov A. Lukyanchikova V.A. Torgunakov N. Battulin N.R. Fishman V.S. Vyatkin Y.V. Smelova A.A. Romanov S.E. Laktionov P.P. Valishayev D. Belyakin S.N. Singh P.B.
August 2025Multidisciplinary Digital Publishing Institute (MDPI)
Cells
2025#14Issue 16
The term chromosomal imprinting was introduced to denote the parent-of-origin-dependent behavior of chromosomes in the fungus gnat originally named Sciara coprophila (current taxonomic name is Bradysia coprophila). Such behavior is observed in Sciara coprophila embryos, where paternal X chromosomes (Xp) are specifically eliminated during the 7th–8th cleavage divisions. Elimination is regulated by a controlling element (CE) that has been mapped to heterochromomere II (H2) within the sub-telomeric short arm of polytene X chromosomes. Here, using a combination of a new Sciara genome assembly, along with ChIP-Seq and MeDIP analyses, we show that a 1.2 Mb region within the CE locus has a repressive epigenetic signature that is characterised by enrichments of H3K9me3, H4K20me3 and 5′-methyl cytosine (5meC). These data provide evidence for a model where the H3K9me3/HP1/H4K20me3 pathway operates to assemble a heterochromatin-like complex at the CE that renders it silent on Xp chromosomes that are not eliminated. In this regard, our findings support the idea that the H3K9me3/HP1/H4K20me3 pathway represents the most evolutionarily conserved mechanism linked to chromosomal imprinting in animals.
DNA methylation , genomic imprinting , H3K9me3 , H4K20me3 , heterochromatin-like complexes , HP1
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Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, Pirogov Str. 2, Novosibirsk, 630090, Russian Federation
Institute of Molecular and Cellular Biology SD RAS, Lavrentyev Ave., 8/2, Novosibirsk, 630090, Russian Federation
Institute of Cytology and Genetics SD RAS, Lavrentyev Ave., 10, Novosibirsk, 630090, Russian Federation
Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, 354340, Russian Federation
Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, Novosibirsk, 630090, Russian Federation
School of Medicine, Nazarbayev University, 5/1 Kerei, Zhanibek Khandar Street, Astana, 010000, Kazakhstan
Epigenetics Laboratory
Institute of Molecular and Cellular Biology SD RAS
Institute of Cytology and Genetics SD RAS
Scientific Center for Genetics and Life Sciences
Department of Natural Sciences
School of Medicine
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