Chromatin immunoprecipitation indirect peaks highlight long-range interactions of insulator proteins and Pol II pausing.
Eukaryotic chromosomes are partitioned into topologically associating domains (TADs) that are demarcated by distinct insulator-binding proteins (IBPs) in Drosophila. Whether IBPs regulate specific long-range contacts and how this may impact gene expression remains unclear. Here we identify "indirect peaks" of multiple IBPs that represent their distant sites of interactions through long-range contacts. Indirect peaks depend on protein-protein interactions among multiple IBPs and their common cofactors, including CP190, as confirmed by high-resolution analyses of long-range contacts. Mutant IBPs unable to interact with CP190 impair long-range contacts as well as the expression of hundreds of distant genes that are specifically flanked by indirect peaks. Regulation of distant genes strongly correlates with RNAPII pausing, highlighting how this key transcriptional stage may trap insulator-based long-range interactions. Our data illustrate how indirect peaks may decipher gene regulatory networks through specific long-range interactions.
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Jun
J
Liang
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Laurent
L
Lacroix
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Adrien
A
Gamot
Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20824, USA.
Suresh
S
Cuddapah
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Sophie
S
Queille
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Priscillia
P
Lhoumaud
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Pierre
P
Lepetit
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France; INRA, UMR444- GeT-PlaGe, Genotoul, 31326 Toulouse, France.
Pascal G P
PG
Martin
Centre de Biochimie Structurale, CNRS, 34090 Montpellier, France.
Jutta
J
Vogelmann
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Franck
F
Court
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Magali
M
Hennion
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France.
Gaël
G
Micas
Platform Proteomic Fonctionnelle, IGF, CNRS, 34060 Montpellier, France.
Serge
S
Urbach
INRA, UMR444- GeT-PlaGe, Genotoul, 31326 Toulouse, France.
Olivier
O
Bouchez
Centre de Biochimie Structurale, CNRS, 34090 Montpellier, France.
Marcelo
M
Nöllmann
Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health (NIH), Bethesda, MD 20824, USA.
Keji
K
Zhao
Physics Department, Simon Fraser University (SFU), Burnaby, BC V5A 1S6, Canada.
Eldon
E
Emberly
Laboratoire de Biologie Moléculaire Eucaryote (LBME), CNRS, Université de Toulouse (UPS), 31000 Toulouse, France. Electronic address: cuvier@ibcg.biotoul.fr.
Olivier
O
Cuvier
D000818:Animals; D001665:Binding Sites; D000076246:CCCTC-Binding Factor; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004268:DNA-Binding Proteins / Q000378:metabolism; D029721:Drosophila Proteins / Q000378:metabolism; D004331:Drosophila melanogaster; D005136:Eye Proteins / Q000378:metabolism; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D038101:Insulator Elements / Q000502:physiology*; D009154:Mutation; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D025941:Protein Interaction Mapping; D034622:RNA Interference; D012319:RNA Polymerase II / Q000378:metabolism*; D012097:Repressor Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism
C452919:BEAF-32 protein, Drosophila; D000076246:CCCTC-Binding Factor; C524946:CTCF protein, Drosophila; D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; D005136:Eye Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C063460:Trl protein, Drosophila; D012319:RNA Polymerase II