Literature DB >> 31553919

Meta-analysis of Chromatin Programming by Steroid Receptors.

Ville Paakinaho1, Erin E Swinstead2, Diego M Presman3, Lars Grøntved4, Gordon L Hager5.   

Abstract

Transcription factors (TFs) must access chromatin to bind to their response elements and regulate gene expression. A widely accepted model proposes that only a special subset of TFs, pioneer factors, can associate with condensed chromatin and initiate chromatin opening. We previously reported that steroid receptors (SRs), not considered pioneer factors, can assist the binding of an archetypal pioneer, the forkhead box protein 1 (FOXA1), at a subset of receptor-activated enhancers. These findings have been challenged recently, with the suggestion that newly acquired data fully support the prevailing pioneer model. Here, we reexamine our results and confirm the original conclusions. We also analyze and discuss a number of available datasets relevant to chromatin penetration by SRs and find a general consensus supporting our original observations. Hence, we propose that chromatin opening at some sites can be initiated by SRs, with a parallel recruitment of factors often treated as having a unique pioneer function. This Matters Arising paper is in response to Glont et al. (2019), published in Cell Reports. Published by Elsevier Inc.

Entities:  

Keywords:  FOXA1; chromatin; chromatin remodelers; dynamic assisted loading; pioneer factors; steroid receptors; transcription factors

Mesh:

Substances:

Year:  2019        PMID: 31553919      PMCID: PMC6914262          DOI: 10.1016/j.celrep.2019.08.039

Source DB:  PubMed          Journal:  Cell Rep            Impact factor:   9.423


  49 in total

1.  Mutations in the glucocorticoid receptor DNA-binding domain mimic an allosteric effect of DNA.

Authors:  M A van Tilborg; J A Lefstin; M Kruiskamp; J Teuben; R Boelens; K R Yamamoto; R Kaptein
Journal:  J Mol Biol       Date:  2000-08-25       Impact factor: 5.469

2.  FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.

Authors:  Mathieu Lupien; Jérôme Eeckhoute; Clifford A Meyer; Qianben Wang; Yong Zhang; Wei Li; Jason S Carroll; X Shirley Liu; Myles Brown
Journal:  Cell       Date:  2008-03-21       Impact factor: 41.582

3.  Tissue-specific pioneer factors associate with androgen receptor cistromes and transcription programs.

Authors:  Päivi Pihlajamaa; Biswajyoti Sahu; Lauri Lyly; Viljami Aittomäki; Sampsa Hautaniemi; Olli A Jänne
Journal:  EMBO J       Date:  2014-01-22       Impact factor: 11.598

4.  TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome.

Authors:  Hector L Franco; Anusha Nagari; W Lee Kraus
Journal:  Mol Cell       Date:  2015-03-05       Impact factor: 17.970

5.  Transcription factor access is mediated by accurately positioned nucleosomes on the mouse mammary tumor virus promoter.

Authors:  T K Archer; M G Cordingley; R G Wolford; G L Hager
Journal:  Mol Cell Biol       Date:  1991-02       Impact factor: 4.272

6.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Authors:  Ben Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Journal:  Genome Biol       Date:  2009-03-04       Impact factor: 13.583

7.  C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements.

Authors:  Lars Grøntved; Sam John; Songjoon Baek; Ying Liu; John R Buckley; Charles Vinson; Greti Aguilera; Gordon L Hager
Journal:  EMBO J       Date:  2013-05-10       Impact factor: 11.598

8.  Sequence-specific positioning of nucleosomes over the steroid-inducible MMTV promoter.

Authors:  H Richard-Foy; G L Hager
Journal:  EMBO J       Date:  1987-08       Impact factor: 11.598

9.  Cellular reprogramming by the conjoint action of ERα, FOXA1, and GATA3 to a ligand-inducible growth state.

Authors:  Say Li Kong; Guoliang Li; Siang Lin Loh; Wing-Kin Sung; Edison T Liu
Journal:  Mol Syst Biol       Date:  2011-08-30       Impact factor: 11.429

10.  Glucocorticoid receptor quaternary structure drives chromatin occupancy and transcriptional outcome.

Authors:  Ville Paakinaho; Thomas A Johnson; Diego M Presman; Gordon L Hager
Journal:  Genome Res       Date:  2019-07-23       Impact factor: 9.043

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  13 in total

1.  FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer.

Authors:  Amaia Arruabarrena-Aristorena; Jesper L V Maag; Srushti Kittane; Yanyan Cai; Wouter R Karthaus; Erik Ladewig; Jane Park; Srinivasaraghavan Kannan; Lorenzo Ferrando; Emiliano Cocco; Sik Y Ho; Daisylyn S Tan; Mirna Sallaku; Fan Wu; Barbara Acevedo; Pier Selenica; Dara S Ross; Matthew Witkin; Charles L Sawyers; Jorge S Reis-Filho; Chandra S Verma; Ralf Jauch; Richard Koche; José Baselga; Pedram Razavi; Eneda Toska; Maurizio Scaltriti
Journal:  Cancer Cell       Date:  2020-09-03       Impact factor: 31.743

2.  Nonlinear relationship between chromatin accessibility and estradiol-regulated gene expression.

Authors:  Duojiao Chen; Taylor M Parker; Poornima Bhat-Nakshatri; Xiaona Chu; Yunlong Liu; Yue Wang; Harikrishna Nakshatri
Journal:  Oncogene       Date:  2021-01-08       Impact factor: 9.867

Review 3.  Generating specificity in genome regulation through transcription factor sensitivity to chromatin.

Authors:  Luke Isbel; Ralph S Grand; Dirk Schübeler
Journal:  Nat Rev Genet       Date:  2022-07-12       Impact factor: 59.581

Review 4.  Pioneer factors as master regulators of the epigenome and cell fate.

Authors:  Aurelio Balsalobre; Jacques Drouin
Journal:  Nat Rev Mol Cell Biol       Date:  2022-03-09       Impact factor: 113.915

Review 5.  Shaping Chromatin States in Prostate Cancer by Pioneer Transcription Factors.

Authors:  William Hankey; Zhong Chen; Qianben Wang
Journal:  Cancer Res       Date:  2020-02-24       Impact factor: 12.701

Review 6.  Pioneering the developmental frontier.

Authors:  Elizabeth D Larson; Audrey J Marsh; Melissa M Harrison
Journal:  Mol Cell       Date:  2021-03-08       Impact factor: 17.970

7.  Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors.

Authors:  Ryan J Geusz; Allen Wang; Dieter K Lam; Nicholas K Vinckier; Konstantinos-Dionysios Alysandratos; David A Roberts; Jinzhao Wang; Samy Kefalopoulou; Araceli Ramirez; Yunjiang Qiu; Joshua Chiou; Kyle J Gaulton; Bing Ren; Darrell N Kotton; Maike Sander
Journal:  Nat Commun       Date:  2021-11-17       Impact factor: 14.919

8.  IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis.

Authors:  Rasmus Siersbæk; Valentina Scabia; Sankari Nagarajan; Igor Chernukhin; Evangelia K Papachristou; Rebecca Broome; Simon J Johnston; Stacey E P Joosten; Andrew R Green; Sanjeev Kumar; Julia Jones; Soleilmane Omarjee; Ruben Alvarez-Fernandez; Silvia Glont; Sarah J Aitken; Kamal Kishore; Danya Cheeseman; Emad A Rakha; Clive D'Santos; Wilbert Zwart; Alasdair Russell; Cathrin Brisken; Jason S Carroll
Journal:  Cancer Cell       Date:  2020-07-16       Impact factor: 31.743

Review 9.  The estrogen receptor/GATA3/FOXA1 transcriptional network: lessons learned from breast cancer.

Authors:  Elizabeth M Martin; Krystal A Orlando; Kosuke Yokobori; Paul A Wade
Journal:  Curr Opin Struct Biol       Date:  2021-07-02       Impact factor: 6.809

10.  Chromatin-directed proteomics-identified network of endogenous androgen receptor in prostate cancer cells.

Authors:  Kaisa-Mari Launonen; Ville Paakinaho; Gianluca Sigismondo; Marjo Malinen; Reijo Sironen; Jaana M Hartikainen; Hanna Laakso; Tapio Visakorpi; Jeroen Krijgsveld; Einari A Niskanen; Jorma J Palvimo
Journal:  Oncogene       Date:  2021-06-14       Impact factor: 9.867

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