3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages.

Autor: Murphy D; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.; Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA., Salataj E; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA., Di Giammartino DC; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.; 3D Chromatin Conformation and RNA Genomics Laboratory, Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy., Rodriguez-Hernaez J; Department of Pathology, New York University Langone Health, New York, NY, USA.; Department of Medicine, New York University Langone Health, New York, NY, USA.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA., Kloetgen A; Department of Pathology, New York University Langone Health, New York, NY, USA.; Department of Medicine, New York University Langone Health, New York, NY, USA.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA., Garg V; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA., Char E; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA., Uyehara CM; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA., Ee LS; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA., Lee U; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA., Stadtfeld M; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA., Hadjantonakis AK; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA., Tsirigos A; Department of Pathology, New York University Langone Health, New York, NY, USA. Aristotelis.Tsirigos@nyulangone.org.; Department of Medicine, New York University Langone Health, New York, NY, USA. Aristotelis.Tsirigos@nyulangone.org.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA. Aristotelis.Tsirigos@nyulangone.org., Polyzos A; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. app2001@med.cornell.edu., Apostolou E; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA. efa2001@med.cornell.edu.

Publikováno v: Nature structural & molecular biology [Nat Struct Mol Biol] 2024 Jan; Vol. 31 (1), pp. 125-140. Date of Electronic Publication: 2023 Dec 05.

Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.

Autor: Murphy D; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Salataj E; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Di Giammartino DC; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States.; 3D Chromatin Conformation and RNA genomics laboratory, Instituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy (current affiliation)., Rodriguez-Hernaez J; Department of Pathology, New York University Langone Health, New York, NY 10016, USA.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA., Kloetgen A; Department of Pathology, New York University Langone Health, New York, NY 10016, USA.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA., Garg V; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA., Char E; Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, 10065, New York, USA., Uyehara CM; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Ee LS; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Lee U; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Stadtfeld M; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Hadjantonakis AK; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA., Tsirigos A; Department of Pathology, New York University Langone Health, New York, NY 10016, USA.; Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA., Polyzos A; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States., Apostolou E; Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2023 Jul 19. Date of Electronic Publication: 2023 Jul 19.

Opportunistic binding of EcR to open chromatin drives tissue-specific developmental responses.

Autor: Uyehara CM; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599., Leatham-Jensen M; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599., McKay DJ; Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.; Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2022 Oct 04; Vol. 119 (40), pp. e2208935119. Date of Electronic Publication: 2022 Sep 26.

Transcriptional repression and enhancer decommissioning silence cell cycle genes in postmitotic tissues.

Autor: Fogarty, Elizabeth A¹ (AUTHOR), Buchert, Elli M¹ (AUTHOR), Ma, Yiqin¹ (AUTHOR), Nicely, Ava B¹ (AUTHOR), Buttitta, Laura A¹ (AUTHOR) buttitta@umich.edu

Publikováno v: G3: Genes | Genomes | Genetics. Oct2024, Vol. 14 Issue 10, p1-19. 19p.

Super-enhancer omics in stem cell.

Autor: Ma, Hongying^1,2 (AUTHOR), Qu, Jian^3,4 (AUTHOR), Pang, Zicheng^1,5 (AUTHOR), Luo, Jian^1,2 (AUTHOR), Yan, Min^1,2 (AUTHOR), Xu, Weixin³ (AUTHOR), Zhuang, Haihui³ (AUTHOR), Liu, Linxin⁶ (AUTHOR), Qu, Qiang^1,2,6 (AUTHOR) quqiang@csu.edu.cn

Publikováno v: Molecular Cancer. 8/1/2024, Vol. 23 Issue 1, p1-23. 23p.