DNA binding specificity in-vivo

Project Information

bInDR

Grant agreement ID: 101018688

DOI

10.3030/101018688

Project closed

EC signature date 19 May 2021

Start date 1 June 2021

End date 31 May 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 500 000,00

EU contribution

€ 2 500 000,00

Coordinated by

WEIZMANN INSTITUTE OF SCIENCE
Israel

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (14)

Intrinsically disordered regions as facilitators of the transcription factor target search

Author(s): Felix Jonas, Yoav Navon, Naama Barkai
Published in: Nature Reviews Genetics, Issue 26, 2025, Page(s) 424-435, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-025-00816-3

Complementary strategies for directing in vivo transcription factor binding through DNA binding domains and intrinsically disordered regions

Author(s): Divya Krishna Kumar, Felix Jonas, Tamar Jana, Sagie Brodsky, Miri Carmi, Naama Barkai
Published in: Molecular Cell, Issue 83, 2026, Page(s) 1462-1473.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2023.04.002

Spatially resolved profiling of steroid nuclear receptors reveals a role for the disordered N-terminal domains in genome targeting and AP-1 interaction

Author(s): Inbal Zigdon, Achinoam Shoham, Vladimir Mindel, Wajd Manadre, David Jan, Beniamin Krupkin, Dekel Yahav Har-Shai, Yaron Antebi, Naama Barkai
Published in: Genome Research, 2026, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.280896.125

The architecture of binding cooperativity between densely bound transcription factors

Author(s): Offir Lupo, Divya Krishna Kumar, Rotem Livne, Michal Chappleboim, Idan Levy, Naama Barkai
Published in: Cell Systems, Issue 14, 2025, Page(s) 732-745.e5, ISSN 2405-4712
Publisher: Elsevier BV
DOI: 10.1016/j.cels.2023.06.010

The molecular grammar of protein disorder guiding genome-binding locations

Author(s): Felix Jonas, Miri Carmi, Beniamin Krupkin, Joseph Steinberger, Sagie Brodsky, Tamar Jana, Naama Barkai
Published in: Nucleic Acids Research, Issue 51, 2023, Page(s) 4831-4844, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad184

Evolution of transcription factor binding through sequence variations and turnover of binding sites

Author(s): Gat Krieger, Offir Lupo, Patricia Wittkopp, Naama Barkai
Published in: Genome Research, 2021, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.276715.122

Engineering intrinsically disordered regions for guiding genome navigation

Author(s): Jing Liu, Divya Krishna Kumar, Bohdana Hurieva, Felix Jonas, Naama Barkai
Published in: Molecular Cell, Issue 86, 2026, Page(s) 851-867.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2026.01.019

Design principles of transcription factors with intrinsically disordered regions

Author(s): Wencheng Ji, Ori Hachmo, Naama Barkai, Ariel Amir
Published in: eLife, Issue 14, 2026, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.104956

Disordered sequences of transcription factors regulate genomic binding by integrating diverse sequence grammars and interaction types

Author(s): Bohdana Hurieva, Divya Krishna Kumar, Rotem Morag, Offir Lupo, Miri Carmi, Naama Barkai, Felix Jonas
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 8763-8777, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae521

Selective association of short tandem repeats with DNA-binding domains and intrinsically disordered regions of transcription factors

Author(s): Matan Vidavski, Sagie Brodsky, Wajd Manadre, Tamar Jana Lang, Vladimir Mindel, Yoav Navon, Naama Barkai
Published in: Cell Systems, Issue 16, 2025, Page(s) 101349, ISSN 2405-4712
Publisher: Elsevier BV
DOI: 10.1016/j.cels.2025.101349

Intrinsically disordered regions of the Msn2 transcription factor encode multiple functions using interwoven sequence grammars

Author(s): Vladimir Mindel, Sagie Brodsky, Aileen Cohen, Wajd Manadre, Felix Jonas, Miri Carmi, Naama Barkai
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 2260-2272, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkad1191

Rtt109 promotes nucleosome replacement ahead of the replication fork

Author(s): Felix Jonas , Gilad Yaakov , Naama Barkai
Published in: Genome Research, 2022, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.276674.122

Massively parallel binding assay (MPBA) reveals limited transcription factor binding cooperativity, challenging models of specificity

Author(s): Tamar Jana Lang, Sagie Brodsky, Wajd Manadre, Matan Vidavski, Gili Valinsky, Vladimir Mindel, Guy Ilan, Miri Carmi, Felix Jonas, Naama Barkai
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 12227-12243, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae846

Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors

Author(s): Vladimir Mindel, Sagie Brodsky, Hadas Yung, Wajd Manadre, Naama Barkai
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 12093-12111, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae718