KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal Vostok antibody | This paper | N/A |
| Rabbit polyclonal GAF antibody | Erokhin et al., 2015 38 | N/A |
| Rabbit polyclonal CP190 antibody | Mazina et al., 2020 39 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| DSG (disuccinimidyl glutarate) | Thermo Fisher Scientific | 20593 |
| EGS (ethylene glycol bis(succinimidyl succinate)) | Thermo Fisher Scientific | 21565 |
| E. coli Spike-in DNA | EpiCypher | 18–1401 |
| Ampure XP beads | Beckman Coulter | A63880 |
| Hoechst 33342 | Sigma-Aldrich | 23491–52-3 |
| UltraPure™ SSC, 20X | Thermo Fisher Scientific | 15557044 |
| ProLong Gold Antifade Mountant | Thermo Fisher Scientific | P36934 |
| Critical commercial assays | ||
| HCR buffer set | Molecular Instruments | www.molecularinstruments.com |
| HCR B3 amplifier | Molecular Instruments | www.molecularinstruments.com |
| HCR B4 amplifier | Molecular Instruments | www.molecularinstruments.com |
| Deposited data | ||
| Micro-C for Vostok mutants in the larvae brains | This study, GEO | GSE285744 |
| Micro-C for yw control line and GAF-ΔPOZ in the larvae brains | Xiao et al., 2023 8 | GSE228095 |
| RNA-seq for Vostok mutants and yw control line in the larvae brains | This study, GEO | GSE285744 |
| Vostok and GAF ChIP-seq for Vostok mutants and yw control line in the larvae brains |
This study, GEO | GSE285842 |
| Unprocessed Original Images for Western blot | This study, Mendeley data | DOI:10.17632/8nd5hdc3md.1 |
| Microscopy images | This study, Mendeley data | DOI:10.17632/km724c2kpt.1 |
| Github code deposition: Codes for differential loop strength analysis, differential gene expression, aggregation plot, “changed boundary regions” analyses, and other figure plotting | This study, Zenodo data | DOI:10.5281/zenodo.15358274 |
| Experimental models: Organisms/strains | ||
| Drosophila melanogaster/ halo-GAF-ΔPOZ/TM6B | Tang et al., 2022 40 | N/A |
| Drosophila melanogaster/ Vostok-mutants/TM6B | This study | N/A |
| Oligonucleotides | ||
| Pvf3-L probe | This study, table S4 | N/A |
| Pvf3-S probe | This study, table S5 | N/A |
| Software and algorithms | ||
| BWA | Li and Durbin, 2009 41 | https://bio-bwa.sourceforge.net/ |
| pairtools | Goloborodko et al., 2019 42 | https://github.com/open2c/pairtools |
| Cooler | Abdennur and Mirny, 2020 43 | https://github.com/open2c/cooler |
| Mustache | Ardakany et al., 2020 44 | https://github.com/ay-lab/mustache |
| BEDtools | Quinlan and Hall, 2010 45 | https://bedtools.readthedocs.io/en/latest/ |
| DESeq2 | Love et al., 2017 46 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| ggplot2 | Villanueva and Chen, 2019 47 | https://ggplot2.tidyverse.org/ |
| cooltools | Abdennur et al., 2024 48 | https://github.com/open2c/cooltools |
| deepTools | Ramírez et al., 2016 49 | https://deeptools.readthedocs.io/en/develop/ |
| MEME | Timothy et al., 2015 50 | https://meme-suite.org/meme/tools/meme |
| MEME-ChIP | Machanick et al., 2011 21 | https://meme-suite.org/meme/tools/meme-chip |
| FIMO | Grant et al., 2011 51 | https://meme-suite.org/meme/tools/fimo |
| Tomtom Motif Comparison Tool | Gupta et al., 2007 52 | https://meme-suite.org/meme/tools/tomtom |
| Salmon | Patro et al., 2017 53 | https://combine-lab.github.io/salmon/ |
| nf-core/RNA-seq | Ewels et al., 2020 54 | https://nf-co.re/rnaseq/3.18.0/ |
| Bowtie2 | Langmead and Salzberg, 2012 55 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| HISAT2 | Kim et al., 2015 56 | http://daehwankimlab.github.io/hisat2/ |
| SAMtools | Danecek et al., 2021 57 | http://www.htslib.org/ |
| MACS2 | Zhang et al., 2008 58 | https://github.com/macs3-project/MACS |
| UCSC-tools | Kuhn et al., 2013 59 | https://genome.ucsc.edu/util.html |
| RNASTAR | Widmann et al., 2012 60 | https://github.com/alexdobin/STAR |
| ImageJ | Collins, 2007 61 | https://imagej.nih.gov/ij/ |
| Easy_HCR | Elagoz et al., 2022 62,63 | https://github.com/SeuntjensLab/Easy_HCR?tab=readme-ov-file |