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Insulator proteins contribute to expression of gene loci repositioned into heterochromatin in the course of Drosophila evolution

https://doi.org/10.1101/802371
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Clustal Omega, Accurate Alignment of Very Large Numbers of Sequences
inferredcites →https://doi.org/10.1007/bf00135277openalex-snapshot
Cytological and linkage maps of Drosophila virilis chromosomes
inferredcites →https://doi.org/10.1007/s004120050389openalex-snapshot
Evidence for an antagonistic relationship between the boundary element-associated factor BEAF and the transcription factor DREF
inferredcites →https://doi.org/10.1016/j.bbagrm.2007.11.011openalex-snapshot
The DRE/DREF transcriptional regulatory system: a master key for cell proliferation
inferredcites →https://doi.org/10.1016/j.cell.2010.09.009openalex-snapshot
Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
inferredcites →https://doi.org/10.1016/j.devcel.2008.02.002openalex-snapshot
Intron Delays and Transcriptional Timing during Development
inferredcites →https://doi.org/10.1016/j.febslet.2013.10.039openalex-snapshot
Chromatin insulators and long‐distance interactions in Drosophila
inferredcites →https://doi.org/10.1016/j.molcel.2005.09.002openalex-snapshot
Antisense Transcription and Heterochromatin at the DM1 CTG Repeats Are Constrained by CTCF
inferredcites →https://doi.org/10.1016/j.molcel.2013.04.018openalex-snapshot
Chromatin Insulators: Linking Genome Organization to Cellular Function
inferredcites →https://doi.org/10.1016/j.plantsci.2015.04.017openalex-snapshot
The enduring mystery of intron-mediated enhancement
inferredcites →https://doi.org/10.1016/j.tcb.2014.08.003openalex-snapshot
Architectural proteins: regulators of 3D genome organization in cell fate
inferredcites →https://doi.org/10.1016/j.tig.2006.04.008openalex-snapshot
Oxymoron no more: the expanding world of heterochromatic genes
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1016/s0378-1119(02)00890-9openalex-snapshot
The DNA replication-related element-binding factor (DREF) is a transcriptional regulator of the Drosophila myb gene
inferredcites →https://doi.org/10.1016/s0378-1119(03)00493-1openalex-snapshot
Transcription control of a gene for Drosophila transcription factor, DREF by DRE and cis-elements conserved between Drosophila melanogaster and virilis
inferredcites →https://doi.org/10.1016/s0960-9822(03)00558-xopenalex-snapshot
Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution
inferredcites →https://doi.org/10.1016/s1937-6448(08)01801-7openalex-snapshot
Chapter 1 Cellular Mechanism for Targeting Heterochromatin Formation in Drosophila
inferredcites →https://doi.org/10.1038/nature05915openalex-snapshot
The complex language of chromatin regulation during transcription
inferredcites →https://doi.org/10.1038/nature06341openalex-snapshot
Evolution of genes and genomes on the Drosophila phylogeny
inferredcites →https://doi.org/10.1038/ncb1580openalex-snapshot
Loss of Drosophila Myb interrupts the progression of chromosome condensation
inferredcites →https://doi.org/10.1038/ng940openalex-snapshot
Selection for short introns in highly expressed genes
inferredcites →https://doi.org/10.1038/nrm3941openalex-snapshot
Histone exchange, chromatin structure and the regulation of transcription
inferredcites →https://doi.org/10.1038/nsmb.1659openalex-snapshot
Chromatin organization marks exon-intron structure
inferredcites →https://doi.org/10.1038/s41467-017-02525-wopenalex-snapshot
High-resolution TADs reveal DNA sequences underlying genome organization in flies
inferredcites →https://doi.org/10.1038/s41598-017-04476-0openalex-snapshot
Identification of introns harboring functional sequence elements through positional conservation
inferredcites →https://doi.org/10.1073/pnas.0503424102openalex-snapshot
Evolution of heterochromatic genes of Drosophila
inferredcites →https://doi.org/10.1073/pnas.0509063102openalex-snapshot
Occupancy of the Drosophila hsp70 promoter by a subset of basal transcription factors diminishes upon transcriptional activation
inferredcites →https://doi.org/10.1073/pnas.0800250105openalex-snapshot
Splicing promotes rapid and efficient mRNA export in mammalian cells
inferredcites →https://doi.org/10.1073/pnas.1207036109openalex-snapshot
Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements
inferredcites →https://doi.org/10.1073/pnas.92.9.3804openalex-snapshot
Transposable elements are stable structural components of Drosophila melanogaster heterochromatin.
inferredcites →https://doi.org/10.1080/19336934.2016.1225634openalex-snapshot
Trans-inactivation: Repression in a wrong place
inferredcites →https://doi.org/10.1089/cmb.1994.1.39openalex-snapshot
QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification
inferredcites →https://doi.org/10.1093/bib/3.3.265openalex-snapshot
PROSITE: A documented database using patterns and profiles as motif descriptors
inferredcites →https://doi.org/10.1093/bib/bbs017openalex-snapshot
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
inferredcites →https://doi.org/10.1093/bioinformatics/btp033openalex-snapshot
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btu808openalex-snapshot
Kablammo: an interactive, web-based BLAST results visualizer
inferredcites →https://doi.org/10.1093/emboj/21.4.675openalex-snapshot
Myb controls G2/M progression by inducing cyclin B expression in the Drosophila eye imaginal disc
inferredcites →https://doi.org/10.1093/genetics/125.1.141openalex-snapshot
The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/127.3.553openalex-snapshot
Cytogenetic analysis of the second chromosome heterochromatin of Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/128.4.785openalex-snapshot
The effect of modifiers of position-effect variegation on the variegation of heterochromatic genes of Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/134.1.277openalex-snapshot
The role of heterochromatin in the expression of a heterochromatic gene, the rolled locus of Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/140.3.1033openalex-snapshot
Cis-effects of heterochromatin on heterochromatic and euchromatic gene activity in Drosophila melanogaster.
inferredcites →https://doi.org/10.1093/genetics/155.2.699openalex-snapshot
Heterochromatin Protein 1 Is Required for the Normal Expression of Two Heterochromatin Genes in Drosophila
inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot
PAML 4: Phylogenetic Analysis by Maximum Likelihood
inferredcites →https://doi.org/10.1093/molbev/msu226openalex-snapshot
Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila
inferredcites →https://doi.org/10.1093/molbev/msy096openalex-snapshot
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
inferredcites →https://doi.org/10.1093/nar/22.22.4673openalex-snapshot
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
inferredcites →https://doi.org/10.1093/nar/gkl315openalex-snapshot
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments
inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot
MEME SUITE: tools for motif discovery and searching
inferredcites →https://doi.org/10.1093/nar/gks1067openalex-snapshot
New and continuing developments at PROSITE
inferredcites →https://doi.org/10.1093/nar/gkt1165openalex-snapshot
OnTheFly: a database of Drosophila melanogaster transcription factors and their binding sites
inferredcites →https://doi.org/10.1093/nar/gkt158openalex-snapshot
HP1a, Su(var)3-9, SETDB1 and POF stimulate or repress gene expression depending on genomic position, gene length and expression pattern in Drosophila melanogaster
inferredcites →https://doi.org/10.1093/nar/gku365openalex-snapshot
deepTools: a flexible platform for exploring deep-sequencing data
inferredcites →https://doi.org/10.1093/nar/gkw371openalex-snapshot
Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long-range interactions inDrosophila
inferredcites →https://doi.org/10.1093/nar/gky957openalex-snapshot
REDfly: the transcriptional regulatory element database for Drosophila
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040023openalex-snapshot
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
inferredcites →https://doi.org/10.1101/cshperspect.a017780openalex-snapshot
Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila
inferredcites →https://doi.org/10.1101/gad.12.18.2852openalex-snapshot
Loss of transcriptional activity of a transgene is accompanied by DNA methylation and histone deacetylation and is prevented by insulators
inferredcites →https://doi.org/10.1101/gad.1643208openalex-snapshot
NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly
inferredcites →https://doi.org/10.1101/gad.1798209openalex-snapshot
Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions
inferredcites →https://doi.org/10.1101/gr.092759.109openalex-snapshot
Circos: An information aesthetic for comparative genomics
inferredcites →https://doi.org/10.1101/gr.110098.110openalex-snapshot
Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
inferredcites →https://doi.org/10.1101/gr.138156.112openalex-snapshot
Nature and function of insulator protein binding sites in the Drosophila genome
inferredcites →https://doi.org/10.1101/gr.174169.114openalex-snapshot
Two new insulator proteins, Pita and ZIPIC, target CP190 to chromatin
inferredcites →https://doi.org/10.1101/sqb.2010.75.039openalex-snapshot
Drosophila Heat Shock System as a General Model to Investigate Transcriptional Regulation
inferredcites →https://doi.org/10.1105/tpc.17.00020openalex-snapshot
Intron DNA Sequences Can Be More Important Than the Proximal Promoter in Determining the Site of Transcript Initiation
inferredcites →https://doi.org/10.1128/mcb.01748-08openalex-snapshot
Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription
inferredcites →https://doi.org/10.1186/1471-2148-7-192openalex-snapshot
Patterns of intron gain and conservation in eukaryotic genes
inferredcites →https://doi.org/10.1186/1471-2148-7-87openalex-snapshot
Molecular phylogeny of the Drosophila obscura species group, with emphasis on the Old World species
inferredcites →https://doi.org/10.1186/gb-2007-8-2-r24openalex-snapshot
Quantifying similarity between motifs
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1242/jeb.143008openalex-snapshot
Phylogeny, environment and sexual communication across the Drosophila genus
inferredcites →https://doi.org/10.1242/jeb.204.13.2331openalex-snapshot
Evolution of water balance in the genusDrosophila
inferredcites →https://doi.org/10.1261/rna.5250403openalex-snapshot
A quantitative analysis of intron effects on mammalian gene expression
inferredcites →https://doi.org/10.1371/journal.pbio.0050152openalex-snapshot
Principles of Genome Evolution in the Drosophila melanogaster Species Group
inferredcites →https://doi.org/10.1371/journal.pcbi.0010043openalex-snapshot
ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun
inferredcites →https://doi.org/10.1371/journal.pgen.0030038openalex-snapshot
High-Resolution Mapping Reveals Links of HP1 with Active and Inactive Chromatin Components
inferredcites →https://doi.org/10.1371/journal.pgen.0040016openalex-snapshot
Molecular Landscape of Modified Histones in Drosophila Heterochromatic Genes and Euchromatin-Heterochromatin Transition Zones
inferredcites →https://doi.org/10.1371/journal.pgen.1000453openalex-snapshot
The Impact of Local Genome Sequence on Defining Heterochromatin Domains
inferredcites →https://doi.org/10.1371/journal.pgen.1002954openalex-snapshot
Enrichment of HP1a on Drosophila Chromosome 4 Genes Creates an Alternate Chromatin Structure Critical for Regulation in this Heterochromatic Domain
inferredcites →https://doi.org/10.1371/journal.pgen.1003061openalex-snapshot
HP1a Recruitment to Promoters Is Independent of H3K9 Methylation in Drosophila melanogaster
inferredcites →https://doi.org/10.1371/journal.pgen.1006212openalex-snapshot
Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila
inferredcites →https://doi.org/10.1371/journal.pone.0012339openalex-snapshot
Complex Exon-Intron Marking by Histone Modifications Is Not Determined Solely by Nucleosome Distribution
inferredcites →https://doi.org/10.1371/journal.pone.0113010openalex-snapshot
On the Evolution of Yeti, a Drosophila melanogaster Heterochromatin Gene
inferredcites →https://doi.org/10.1371/journal.pone.0173602openalex-snapshot
The GAGA factor regulatory network: Identification of GAGA factor associated proteins
inferredcites →https://doi.org/10.1371/journal.pone.0203843openalex-snapshot
4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin
inferredcites →https://doi.org/10.1534/g3.119.0003openalex-snapshot
Genetic and Molecular Analysis of Essential Genes in Centromeric Heterochromatin of the Left Arm of Chromosome 3 inDrosophila melanogaster
inferredcites →https://doi.org/10.1534/genetics.106.056069openalex-snapshot
Heterochromatic Genes in Drosophila: A Comparative Analysis of Two Genes
inferredcites →https://doi.org/10.1534/genetics.107.086074openalex-snapshot
Polytene Chromosomal Maps of 11 Drosophila Species: The Order of Genomic Scaffolds Inferred From Genetic and Physical Maps
inferredcites →https://doi.org/10.1534/genetics.107.086108openalex-snapshot
Chromosomal Rearrangement Inferred From Comparisons of 12 Drosophila Genomes
inferredcites →https://doi.org/10.1534/genetics.110.117259openalex-snapshot
Essential Loci in Centromeric Heterochromatin of Drosophila melanogaster. I: The Right Arm of Chromosome 2
inferredcites →https://doi.org/10.1534/genetics.115.181693openalex-snapshot
The Differences BetweenCis- andTrans-Gene Inactivation Caused by Heterochromatin inDrosophila
inferredcites →https://doi.org/10.1534/genetics.117.300583openalex-snapshot
Phylogeny of the Genus Drosophila
inferredcites →https://doi.org/10.3389/fgene.2014.00028openalex-snapshot
Mechanisms and proteins involved in long-distance interactions
inferredcites →https://doi.org/10.4161/cc.24742openalex-snapshot
Dynamic changes in the genomic localization of DNA replication-related element binding factor during the cell cycle

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1186/s13100-020-0205-0openalex-snapshot
Hybrid dysgenesis in Drosophila virilis results in clusters of mitotic recombination and loss-of-heterozygosity but leaves meiotic recombination unaltered
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