Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation.

Gene regulation is a complex process. Numerous factors appear to be required for the accurate temporal and spatial regulation of each gene. Often these factors are assembled into multiprotein complexes, contributing to specific gene regulation events. Understanding how all these factors are organized in the chromosome and how their function is regulated in vivo is a challenging task. One of the most useful techniques for studying this level of gene regulation is the in vivo fixation by formaldehyde crosslinking of proteins to proteins and proteins to DNA, followed by immunoprecipitation of the fixed material.

[1]  R. Paro,et al.  The polycomb group protein complex of Drosophila melanogaster has different compositions at different target genes , 1997, Molecular and cellular biology.

[2]  K. Luo,et al.  SIR2 and SIR4 interactions differ in core and extended telomeric heterochromatin in yeast. , 1997, Genes & development.

[3]  M. Biggin,et al.  A comparison of in vivo and in vitro DNA‐binding specificities suggests a new model for homeoprotein DNA binding in Drosophila embryos , 1999, The EMBO journal.

[4]  K. Nasmyth,et al.  Loading of an Mcm Protein onto DNA Replication Origins Is Regulated by Cdc6p and CDKs , 1997, Cell.

[5]  R. Paro,et al.  Analysis of chromatin structure by in vivo formaldehyde cross-linking. , 1997, Methods.

[6]  P. V. von Hippel,et al.  Formaldehyde as a probe of DNA structure. I. Reaction with exocyclic amino groups of DNA bases. , 1975, Biochemistry.

[7]  C. Allis,et al.  Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines , 1996, Nature.

[8]  Michael R. Green,et al.  Enhancement of TBP binding by activators and general transcription factors , 1999, Nature.

[9]  H. Kondoh,et al.  A mouse homologue of the Drosophila tumour-suppressor gene l(2)gl controlled by Hox-C8 in vivo , 1993, Nature.

[10]  K. Struhl,et al.  Targeted Recruitment of the Sin3-Rpd3 Histone Deacetylase Complex Generates a Highly Localized Domain of Repressed Chromatin In Vivo , 1998, Molecular and Cellular Biology.

[11]  S. Bell,et al.  Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. , 1999, Genes & development.

[12]  Alexander Varshavsky,et al.  Mapping proteinDNA interactions in vivo with formaldehyde: Evidence that histone H4 is retained on a highly transcribed gene , 1988, Cell.

[13]  K. Zhao,et al.  Visualization of chromosomal domains with boundary element-associated factor BEAF-32 , 1995, Cell.

[14]  P. V. von Hippel,et al.  Formaldehyde as a probe of DNA structure. II. Reaction with endocyclic imino groups of DNA bases. , 1975, Biochemistry.

[15]  M. Solomon,et al.  Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[16]  C. Moorehead.  All rights reserved , 1997 .

[17]  N. Heerema,et al.  Multiplex PCR: critical parameters and step-by-step protocol. , 1997, BioTechniques.

[18]  V. Jackson.  Studies on histone organization in the nucleosome using formaldehyde as a reversible cross-linking agent , 1978, Cell.

[19]  M. Grunstein,et al.  Spreading of transcriptional represser SIR3 from telomeric heterochromatin , 1996, Nature.

[20]  K. Struhl,et al.  Binding of TBP to promoters in vivo is stimulated by activators and requires Pol II holoenzyme , 1999, Nature.

[21]  T. Maniatis,et al.  Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-beta promoter. , 1999, Molecular cell.

[22]  Renato Paro,et al.  Mapping polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin , 1993, Cell.

[23]  C. Allis,et al.  Cell cycle-regulated histone acetylation required for expression of the yeast HO gene. , 1999, Genes & development.

[24]  K. Nasmyth,et al.  Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter. , 1999, Cell.

[25]  R. Evans,et al.  Regulation of Hormone-Induced Histone Hyperacetylation and Gene Activation via Acetylation of an Acetylase , 1999, Cell.

[26]  K. Nasmyth,et al.  Identification of Cohesin Association Sites at Centromeres and along Chromosome Arms , 1999, Cell.

[27]  C. Allis,et al.  A simplified formaldehyde fixation and immunoprecipitation technique for studying protein-DNA interactions. , 1991, Analytical biochemistry.

[28]  J. Lis,et al.  Distribution of GAGA protein on Drosophila genes in vivo. , 1995, Genes & development.

[29]  M. Biggin,et al.  Two homeo domain proteins bind with similar specificity to a wide range of DNA sites in Drosophila embryos. , 1994, Genes & development.

[30]  R. Paro,et al.  Co‐localization of Polycomb protein and GAGA factor on regulatory elements responsible for the maintenance of homeotic gene expression , 1997, The EMBO journal.

[31]  R. Paro,et al.  Binding of Trithorax and Polycomb proteins to the bithorax complex: dynamic changes during early Drosophila embryogenesis , 1998, The EMBO journal.

[32]  J. Broach,et al.  Transcriptional silencing in yeast is associated with reduced nucleosome acetylation. , 1993, Genes & development.

[33]  G Vriend,et al.  New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. , 1998, Genes & development.