Literature DB >> 25311126

Purification of proteins on newly synthesized DNA using iPOND.

Huzefa Dungrawala1, David Cortez.   

Abstract

The replisome is a large protein machine containing multiple enzymatic activities needed to complete DNA replication. In addition to helicase and polymerases needed for copying the DNA, the replisome also contains proteins like DNA methyltransferases, histone chaperones, and chromatin modifying enzymes to couple DNA replication with chromatin deposition and establishment of the epigenetic code. In addition, since template DNA strands often contain DNA damage or other roadblocks to the replication machinery, replication stress response proteins associate with the replisome to stabilize, repair, and restart stalled replication forks. Hundreds of proteins are needed to accomplish these tasks. Identifying these proteins, monitoring their posttranslational modifications, and understanding how their activities are coordinated is essential to understand how the genome and epigenome are duplicated rapidly, completely, and accurately every cell division cycle. Here we describe an updated iPOND (isolation of proteins on nascent DNA) method to facilitate these analyses.

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Year:  2015        PMID: 25311126      PMCID: PMC4384176          DOI: 10.1007/978-1-4939-1680-1_10

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  6 in total

1.  Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry.

Authors:  Bianca M Sirbu; W Hayes McDonald; Huzefa Dungrawala; Akosua Badu-Nkansah; Gina M Kavanaugh; Yaoyi Chen; David L Tabb; David Cortez
Journal:  J Biol Chem       Date:  2013-09-18       Impact factor: 5.157

2.  Analysis of protein dynamics at active, stalled, and collapsed replication forks.

Authors:  Bianca M Sirbu; Frank B Couch; Jordan T Feigerle; Srividya Bhaskara; Scott W Hiebert; David Cortez
Journal:  Genes Dev       Date:  2011-06-15       Impact factor: 11.361

3.  A proteomic characterization of factors enriched at nascent DNA molecules.

Authors:  Andres J Lopez-Contreras; Isabel Ruppen; Maria Nieto-Soler; Matilde Murga; Sara Rodriguez-Acebes; Silvia Remeseiro; Sara Rodrigo-Perez; Ana M Rojas; Juan Mendez; Javier Muñoz; Oscar Fernandez-Capetillo
Journal:  Cell Rep       Date:  2013-03-28       Impact factor: 9.423

4.  Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA.

Authors:  Bianca M Sirbu; Frank B Couch; David Cortez
Journal:  Nat Protoc       Date:  2012-03-01       Impact factor: 13.491

5.  A chemical method for fast and sensitive detection of DNA synthesis in vivo.

Authors:  Adrian Salic; Timothy J Mitchison
Journal:  Proc Natl Acad Sci U S A       Date:  2008-02-12       Impact factor: 11.205

6.  Histone acetyl transferase 1 is essential for mammalian development, genome stability, and the processing of newly synthesized histones H3 and H4.

Authors:  Prabakaran Nagarajan; Zhongqi Ge; Bianca Sirbu; Cheryl Doughty; Paula A Agudelo Garcia; Michaela Schlederer; Anthony T Annunziato; David Cortez; Lukas Kenner; Mark R Parthun
Journal:  PLoS Genet       Date:  2013-06-06       Impact factor: 5.917

  6 in total
  29 in total

1.  USP1 Is Required for Replication Fork Protection in BRCA1-Deficient Tumors.

Authors:  Kah Suan Lim; Heng Li; Emma A Roberts; Emily F Gaudiano; Connor Clairmont; Larissa Alina Sambel; Karthikeyan Ponnienselvan; Jessica C Liu; Chunyu Yang; David Kozono; Kalindi Parmar; Timur Yusufzai; Ning Zheng; Alan D D'Andrea
Journal:  Mol Cell       Date:  2018-12-20       Impact factor: 17.970

2.  WRNIP1 protects stalled forks from degradation and promotes fork restart after replication stress.

Authors:  Giuseppe Leuzzi; Veronica Marabitti; Pietro Pichierri; Annapaola Franchitto
Journal:  EMBO J       Date:  2016-05-30       Impact factor: 11.598

3.  HUWE1 interacts with PCNA to alleviate replication stress.

Authors:  Katherine N Choe; Claudia M Nicolae; Daniel Constantin; Yuka Imamura Kawasawa; Maria Rocio Delgado-Diaz; Subhajyoti De; Raimundo Freire; Veronique Aj Smits; George-Lucian Moldovan
Journal:  EMBO Rep       Date:  2016-05-04       Impact factor: 8.807

Review 4.  Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq.

Authors:  Nataliya Petryk; Nazaret Reverón-Gómez; Cristina González-Aguilera; Maria Dalby; Robin Andersson; Anja Groth
Journal:  Nat Protoc       Date:  2021-08-06       Impact factor: 13.491

Review 5.  Proteomic Analyses of the Eukaryotic Replication Machinery.

Authors:  David Cortez
Journal:  Methods Enzymol       Date:  2017-04-06       Impact factor: 1.600

6.  Identification of cellular proteins associated with human cytomegalovirus (HCMV) DNA replication suggests novel cellular and viral interactions.

Authors:  Salomé Manska; Cyprian C Rossetto
Journal:  Virology       Date:  2021-11-22       Impact factor: 3.616

Review 7.  Hallmarks of DNA replication stress.

Authors:  Sneha Saxena; Lee Zou
Journal:  Mol Cell       Date:  2022-06-16       Impact factor: 19.328

8.  The Replication Checkpoint Prevents Two Types of Fork Collapse without Regulating Replisome Stability.

Authors:  Huzefa Dungrawala; Kristie L Rose; Kamakoti P Bhat; Kareem N Mohni; Gloria G Glick; Frank B Couch; David Cortez
Journal:  Mol Cell       Date:  2015-09-10       Impact factor: 17.970

9.  PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells.

Authors:  Jae Jin Kim; Seo Yun Lee; Ji-Hye Choi; Hyun Goo Woo; Blerta Xhemalce; Kyle M Miller
Journal:  Mol Cell       Date:  2020-09-22       Impact factor: 17.970

10.  Isomerization of BRCA1-BARD1 promotes replication fork protection.

Authors:  Manuel Daza-Martin; Katarzyna Starowicz; Mohammed Jamshad; Stephanie Tye; George E Ronson; Hannah L MacKay; Anoop Singh Chauhan; Alexandra K Walker; Helen R Stone; James F J Beesley; Jennifer L Coles; Alexander J Garvin; Grant S Stewart; Thomas J McCorvie; Xiaodong Zhang; Ruth M Densham; Joanna R Morris
Journal:  Nature       Date:  2019-07-03       Impact factor: 49.962

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