Literature DB >> 33823140

p53 mediates target gene association with nuclear speckles for amplified RNA expression.

Katherine A Alexander1, Allison Coté2, Son C Nguyen3, Liguo Zhang4, Omid Gholamalamdari4, Paula Agudelo-Garcia1, Enrique Lin-Shiao5, K M A Tanim1, Joan Lim1, Nicolas Biddle6, Margaret C Dunagin2, Charly R Good1, Mariel R Mendoza5, Shawn C Little7, Andrew Belmont4, Eric F Joyce8, Arjun Raj9, Shelley L Berger10.   

Abstract

Nuclear speckles are prominent nuclear bodies that contain proteins and RNA involved in gene expression. Although links between nuclear speckles and gene activation are emerging, the mechanisms regulating association of genes with speckles are unclear. We find that speckle association of p53 target genes is driven by the p53 transcription factor. Focusing on p21, a key p53 target, we demonstrate that speckle association boosts expression by elevating nascent RNA amounts. p53-regulated speckle association did not depend on p53 transactivation functions but required an intact proline-rich domain and direct DNA binding, providing mechanisms within p53 for regulating gene-speckle association. Beyond p21, a substantial subset of p53 targets have p53-regulated speckle association. Strikingly, speckle-associating p53 targets are more robustly activated and occupy a distinct niche of p53 biology compared with non-speckle-associating p53 targets. Together, our findings illuminate regulated speckle association as a mechanism used by a transcription factor to boost gene expression.
Copyright © 2021 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  chromosome architecture; gene activation; nuclear positioning; nuclear speckles; p21; p53; phase-separated nuclear bodies; transcription; transcription factor

Mesh:

Substances:

Year:  2021        PMID: 33823140      PMCID: PMC8830378          DOI: 10.1016/j.molcel.2021.03.006

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  60 in total

1.  The proline-rich domain of p53 is required for cooperation with anti-neoplastic agents to promote apoptosis of tumor cells.

Authors:  Nicole Baptiste; Philip Friedlander; Xinbin Chen; Carol Prives
Journal:  Oncogene       Date:  2002-01-03       Impact factor: 9.867

2.  Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles.

Authors:  Ryu Miyagawa; Keiko Tano; Rie Mizuno; Yo Nakamura; Kenichi Ijiri; Randeep Rakwal; Junko Shibato; Yoshinori Masuo; Akila Mayeda; Tetsuro Hirose; Nobuyoshi Akimitsu
Journal:  RNA       Date:  2012-02-21       Impact factor: 4.942

3.  A nuclear phosphoinositide kinase complex regulates p53.

Authors:  Suyong Choi; Mo Chen; Vincent L Cryns; Richard A Anderson
Journal:  Nat Cell Biol       Date:  2019-03-18       Impact factor: 28.824

4.  Structural basis for understanding oncogenic p53 mutations and designing rescue drugs.

Authors:  Andreas C Joerger; Hwee Ching Ang; Alan R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2006-10-02       Impact factor: 11.205

5.  Association between active genes occurs at nuclear speckles and is modulated by chromatin environment.

Authors:  Jill M Brown; Joanne Green; Ricardo Pires das Neves; Helen A C Wallace; Andrew J H Smith; Jim Hughes; Nicki Gray; Steve Taylor; William G Wood; Douglas R Higgs; Francisco J Iborra; Veronica J Buckle
Journal:  J Cell Biol       Date:  2008-09-22       Impact factor: 10.539

6.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.

Authors:  Michael I Love; Wolfgang Huber; Simon Anders
Journal:  Genome Biol       Date:  2014       Impact factor: 13.583

7.  HTSeq--a Python framework to work with high-throughput sequencing data.

Authors:  Simon Anders; Paul Theodor Pyl; Wolfgang Huber
Journal:  Bioinformatics       Date:  2014-09-25       Impact factor: 6.937

8.  Visualizing adenosine-to-inosine RNA editing in single mammalian cells.

Authors:  Ian A Mellis; Rohit Gupte; Arjun Raj; Sara H Rouhanifard
Journal:  Nat Methods       Date:  2017-06-12       Impact factor: 28.547

9.  CRISPR/Cas9-mediated knock-in of an optimized TetO repeat for live cell imaging of endogenous loci.

Authors:  Ipek Tasan; Gabriela Sustackova; Liguo Zhang; Jiah Kim; Mayandi Sivaguru; Mohammad HamediRad; Yuchuan Wang; Justin Genova; Jian Ma; Andrew S Belmont; Huimin Zhao
Journal:  Nucleic Acids Res       Date:  2018-09-28       Impact factor: 16.971

10.  TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.

Authors:  Liguo Zhang; Yang Zhang; Yu Chen; Omid Gholamalamdari; Yuchuan Wang; Jian Ma; Andrew S Belmont
Journal:  Genome Res       Date:  2020-12-18       Impact factor: 9.043

View more
  9 in total

Review 1.  Nuclear compartmentalization as a mechanism of quantitative control of gene expression.

Authors:  Prashant Bhat; Drew Honson; Mitchell Guttman
Journal:  Nat Rev Mol Cell Biol       Date:  2021-08-02       Impact factor: 94.444

Review 2.  Nuclear speckles - a driving force in gene expression.

Authors:  Gabriel P Faber; Shani Nadav-Eliyahu; Yaron Shav-Tal
Journal:  J Cell Sci       Date:  2022-07-05       Impact factor: 5.235

Review 3.  It's Just a Phase: Exploring the Relationship Between mRNA, Biomolecular Condensates, and Translational Control.

Authors:  Dylan M Parker; Lindsay P Winkenbach; Erin Osborne Nishimura
Journal:  Front Genet       Date:  2022-06-27       Impact factor: 4.772

4.  Transcriptional Dynamics of DNA Damage Responsive Genes in Circulating Leukocytes during Radiotherapy.

Authors:  Lourdes Cruz-Garcia; Farah Nasser; Grainne O'Brien; Jakub Grepl; Volodymyr Vinnikov; Viktor Starenkiy; Sergiy Artiukh; Svetlana Gramatiuk; Christophe Badie
Journal:  Cancers (Basel)       Date:  2022-05-26       Impact factor: 6.575

5.  Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis.

Authors:  William Dion; Heather Ballance; Jane Lee; Yinghong Pan; Saad Irfan; Casey Edwards; Michelle Sun; Jing Zhang; Xin Zhang; Silvia Liu; Bokai Zhu
Journal:  Sci Adv       Date:  2022-01-05       Impact factor: 14.136

Review 6.  14-3-3 Proteins are Potential Regulators of Liquid-Liquid Phase Separation.

Authors:  Xianlong Huang; Zhiwen Zheng; Yixin Wu; Meng Gao; Zhengding Su; Yongqi Huang
Journal:  Cell Biochem Biophys       Date:  2022-02-10       Impact factor: 2.989

7.  Revealing RCOR2 as a regulatory component of nuclear speckles.

Authors:  Carlos Rivera; Daniel Verbel-Vergara; Duxan Arancibia; Anna Lappala; Marcela González; Fabián Guzmán; Gianluca Merello; Jeannie T Lee; María Estela Andrés
Journal:  Epigenetics Chromatin       Date:  2021-11-24       Impact factor: 4.954

Review 8.  Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis).

Authors:  Jekaterina Erenpreisa; Jekabs Krigerts; Kristine Salmina; Bogdan I Gerashchenko; Talivaldis Freivalds; Reet Kurg; Ruth Winter; Matthias Krufczik; Pawel Zayakin; Michael Hausmann; Alessandro Giuliani
Journal:  Cells       Date:  2021-06-23       Impact factor: 6.600

Review 9.  Higher-order organization of biomolecular condensates.

Authors:  Charlotte M Fare; Alexis Villani; Lauren E Drake; James Shorter
Journal:  Open Biol       Date:  2021-06-16       Impact factor: 6.411

  9 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.