Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins.

Scientific Reports
Sergei Yu FunikovMichael B Evgen'ev

Abstract

Pericentromeric heterochromatin is generally composed of repetitive DNA forming a transcriptionally repressive environment. Dozens of genes were embedded into pericentromeric heterochromatin during evolution of Drosophilidae lineage while retaining activity. However, factors that contribute to insusceptibility of gene loci to transcriptional silencing remain unknown. Here, we find that the promoter region of genes that can be embedded in both euchromatin and heterochromatin exhibits a conserved structure throughout the Drosophila phylogeny and carries motifs for binding of certain chromatin remodeling factors, including insulator proteins. Using ChIP-seq data, we demonstrate that evolutionary gene relocation between euchromatin and pericentric heterochromatin occurred with preservation of sites of insulation of BEAF-32 in evolutionarily distant species, i.e. D. melanogaster and D. virilis. Moreover, promoters of virtually all protein-coding genes located in heterochromatin in D. melanogaster are enriched with insulator proteins BEAF-32, GAF and dCTCF. Applying RNA-seq of a BEAF-32 mutant, we show that the impairment of BEAF-32 function has a complex effect on gene expression in D. melanogaster, affecting even those genes that l...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 25, 1995·Proceedings of the National Academy of Sciences of the United States of America·S PimpinelliM Gatti
Jan 1, 1994·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·D J States, W Gish
May 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·Félix Recillas-TargaGary Felsenfeld
Sep 17, 2002·Briefings in Bioinformatics·Christian J A SigristPhilipp Bucher
Jun 1, 2004·Proceedings of the National Academy of Sciences of the United States of America·Timur M Yusufzai, Gary Felsenfeld
Jul 22, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jiro C YasuharaBarbara T Wakimoto
Dec 7, 2005·Proceedings of the National Academy of Sciences of the United States of America·Lyubov A LebedevaLàszlò Tora
May 2, 2006·Genetics·Sandra R SchulzeBarry M Honda
May 13, 2006·Trends in Genetics : TIG·Jiro C Yasuhara, Barbara T Wakimoto
Feb 28, 2007·Genome Biology·Shobhit GuptaWilliam Stafford Noble
Apr 24, 2007·Nature Cell Biology·J Robert ManakJoseph S Lipsick
May 8, 2007·Molecular Biology and Evolution·Ziheng Yang
Jun 7, 2007·PLoS Biology·José M RanzCasey M Bergman
Nov 13, 2007·Nature·UNKNOWN Drosophila 12 Genomes ConsortiumIain MacCallum
Dec 25, 2007·Biochimica Et Biophysica Acta·Akio MatsukageMasamitsu Yamaguchi
Jul 16, 2008·Genetics·Arjun BhutkarWilliam M Gelbart
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Feb 14, 2009·International Review of Cell and Molecular Biology·Joel C Eissenberg, Gunter Reuter
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Apr 11, 2009·PLoS Genetics·Bayly S WheelerKristin C Scott
May 22, 2009·Nucleic Acids Research·Timothy L BaileyWilliam S Noble
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jun 23, 2009·Genome Research·Martin KrzywinskiMarco A Marra

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Datasets Mentioned

BETA
MN481598

Methods Mentioned

BETA
ChIP-seq
RNA-seq
PCR
dissection

Software Mentioned

deepTools
MEGA
TFBSTools
R
OnTheFly
PAL2NAL
MACS
GSEA ( Gene Set Enrichment Analysis
codeml
edgeR

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.