The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1

RNA polymerase II (PolII) transcribes RNA within a chromatin context, with nucleosomes acting as barriers to transcription. Despite these barriers, transcription through chromatin in vivo is highly efficient, suggesting the existence of factors that overcome this obstacle. To increase the resolution obtained by standard chromatin immunoprecipitation, we developed a novel strategy using micrococcal nuclease digestion of cross-linked chromatin. We find that the chromatin remodeler Chd1 is recruited to promoter proximal nucleosomes of genes undergoing active transcription, where Chd1 is responsible for the vast majority of PolII-directed nucleosome turnover. The expression of a dominant negative form of Chd1 results in increased stalling of PolII past the entry site of the promoter proximal nucleosomes. We find that Chd1 evicts nucleosomes downstream of the promoter in order to overcome the nucleosomal barrier and enable PolII promoter escape, thus providing mechanistic insight into the role of Chd1 in transcription and pluripotency. DOI: http://dx.doi.org/10.7554/eLife.02042.001

[1]  R. Kornberg,et al.  Isolation of an activator-dependent, promoter-specific chromatin remodeling factor , 2011, Proceedings of the National Academy of Sciences.

[2]  L. Pillus,et al.  Balancing chromatin remodeling and histone modifications in transcription. , 2013, Trends in genetics : TIG.

[3]  O. Rando,et al.  A Key Role for Chd1 in Histone H3 Dynamics at the 3′ Ends of Long Genes in Yeast , 2012, PLoS genetics.

[4]  S. Henikoff,et al.  Epigenome characterization at single base-pair resolution , 2011, Proceedings of the National Academy of Sciences.

[5]  C. Bustamante,et al.  Nucleosomal Elements that Control the Topography of the Barrier to Transcription , 2012, Cell.

[6]  D. Gilmour,et al.  Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor , 2013, The EMBO journal.

[7]  B. Bartholomew,et al.  The INO80 ATP-Dependent Chromatin Remodeling Complex Is a Nucleosome Spacing Factor , 2010, Molecular and Cellular Biology.

[8]  Anjanabha Saha,et al.  Chromatin remodeling through directional DNA translocation from an internal nucleosomal site , 2005, Nature Structural &Molecular Biology.

[9]  S. Khorasanizadeh,et al.  Double chromodomains cooperate to recognize the methylated histone H3 tail , 2005, Nature.

[10]  M. Kashlev,et al.  Nucleosome remodeling induced by RNA polymerase II: loss of the H2A/H2B dimer during transcription. , 2002, Molecular cell.

[11]  J. Lindberg,et al.  Identification of novel CHD1-associated collaborative alterations of genomic structure and functional assessment of CHD1 in prostate cancer , 2012, Oncogene.

[12]  J. Hayes,et al.  Histone dynamics during transcription: exchange of H2A/H2B dimers and H3/H4 tetramers during pol II elongation. , 2006, Results and problems in cell differentiation.

[13]  T. Owen-Hughes,et al.  Evidence for DNA Translocation by the ISWI Chromatin-Remodeling Enzyme , 2003, Molecular and Cellular Biology.

[14]  T. Hughes,et al.  Chromatin- and Transcription-Related Factors Repress Transcription from within Coding Regions throughout the Saccharomyces cerevisiae Genome , 2008, PLoS biology.

[15]  C. Bustamante,et al.  The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes , 2011, Nature Structural &Molecular Biology.

[16]  Jeffrey N. McKnight,et al.  Decoupling nucleosome recognition from DNA binding dramatically alters the properties of the Chd1 chromatin remodeler , 2012, Nucleic acids research.

[17]  Swetansu K. Hota,et al.  Diversity of operation in ATP-dependent chromatin remodelers. , 2011, Biochimica et biophysica acta.

[18]  S. Henikoff,et al.  Chromatin roadblocks to reprogramming 50 years on , 2012, BMC Biology.

[19]  R. Padgett,et al.  Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.

[20]  Andrew Flaus,et al.  Nucleosome mobilization catalysed by the yeast SWI/SNF complex , 1999, Nature.

[21]  B. Maier-Davis,et al.  Selective Removal of Promoter Nucleosomes by the RSC Chromatin Remodeling Complex , 2011, Nature Structural &Molecular Biology.

[22]  Bing Li,et al.  The Role of Chromatin during Transcription , 2007, Cell.

[23]  Cizhong Jiang,et al.  Interaction of transcriptional regulators with specific nucleosomes across the Saccharomyces genome. , 2009, Molecular cell.

[24]  Eran Segal,et al.  Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology , 2010, Genome Biology.

[25]  D. Luse,et al.  Translocation and Transcriptional Arrest during Transcript Elongation by RNA Polymerase II* , 1996, The Journal of Biological Chemistry.

[26]  Sharon E. Torigoe,et al.  ATP-dependent chromatin assembly is functionally distinct from chromatin remodeling , 2013, eLife.

[27]  Danny Reinberg,et al.  Human but Not Yeast CHD1 Binds Directly and Selectively to Histone H3 Methylated at Lysine 4 via Its Tandem Chromodomains* , 2005, Journal of Biological Chemistry.

[28]  J. Brooks,et al.  Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness , 2012, Oncogene.

[29]  Hien G. Tran,et al.  Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes , 2003, The EMBO journal.

[30]  Michelle D. Wang,et al.  Synergistic action of RNA polymerases in overcoming the nucleosomal barrier , 2010, Nature Structural &Molecular Biology.

[31]  Christopher B. Burge,et al.  c-Myc Regulates Transcriptional Pause Release , 2010, Cell.

[32]  T. Owen-Hughes,et al.  Analysis of Nucleosome Repositioning by Yeast ISWI and Chd1 Chromatin Remodeling Complexes* , 2006, Journal of Biological Chemistry.

[33]  B. Cairns.  The logic of chromatin architecture and remodelling at promoters , 2009, Nature.

[34]  S. Henikoff,et al.  Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones , 2010, Science.

[35]  S. Henikoff,et al.  Doxorubicin Enhances Nucleosome Turnover around Promoters , 2013, Current Biology.

[36]  H. Madhani,et al.  Mechanisms that Specify Promoter Nucleosome Location and Identity , 2009, Cell.

[37]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[38]  M. Zofall,et al.  Topography of the ISW2–nucleosome complex: insights into nucleosome spacing and chromatin remodeling , 2004, The EMBO journal.

[39]  M. Zofall,et al.  Functional Role of Extranucleosomal DNA and the Entry Site of the Nucleosome in Chromatin Remodeling by ISW2 , 2004, Molecular and Cellular Biology.

[40]  K. Struhl,et al.  Mechanisms of transcriptional activation in vivo: two steps forward. , 1996, Trends in genetics : TIG.

[41]  Stephan C. Schuster,et al.  Nucleosome organization in the Drosophila genome , 2008, Nature.

[42]  Vijender Singh,et al.  The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains , 2011, The EMBO journal.

[43]  G. Hartzog,et al.  Histone H3K4 and K36 Methylation, Chd1 and Rpd3S Oppose the Functions of Saccharomyces cerevisiae Spt4–Spt5 in Transcription , 2010, Genetics.

[44]  Carl Wu,et al.  The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. , 2000, Molecular cell.

[45]  Nicola J. Rinaldi,et al.  Global position and recruitment of HATs and HDACs in the yeast genome. , 2004, Molecular cell.

[46]  Michael T. McManus,et al.  Chd1 regulates open chromatin and pluripotency of embryonic stem cells , 2009, Nature.

[47]  J. Lis,et al.  Rapid, Transcription-Independent Loss of Nucleosomes over a Large Chromatin Domain at Hsp70 Loci , 2008, Cell.

[48]  J. Lis,et al.  Overcoming the nucleosome barrier during transcript elongation. , 2012, Trends in genetics : TIG.

[49]  A. Bird,et al.  A Temporal Threshold for Formaldehyde Crosslinking and Fixation , 2009, PloS one.

[50]  R. Kornberg,et al.  Nucleosomes inhibit the initiation of transcription but allow chain elongation with the displacement of histones , 1987, Cell.

[51]  E. Segal,et al.  What controls nucleosome positions? , 2009, Trends in genetics : TIG.

[52]  J. Tamkun,et al.  Genetic and cytological analysis of Drosophila chromatin-remodeling factors. , 2004, Methods in enzymology.

[53]  Carlos Bustamante,et al.  Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II , 2009, Science.

[54]  Geoffrey J. Barton,et al.  A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization , 2011, Science.

[55]  M. Zofall,et al.  Chromatin remodeling by ISW2 and SWI/SNF requires DNA translocation inside the nucleosome , 2006, Nature Structural &Molecular Biology.

[56]  M. Ardehali,et al.  Tracking rates of transcription and splicing in vivo , 2009, Nature Structural &Molecular Biology.

[57]  Jeffrey N. McKnight,et al.  Extranucleosomal DNA Binding Directs Nucleosome Sliding by Chd1 , 2011, Molecular and Cellular Biology.

[58]  C. Gustafsson,et al.  A genome‐wide role for CHD remodelling factors and Nap1 in nucleosome disassembly , 2007, The EMBO journal.

[59]  Daria A. Gaykalova,et al.  Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II , 2009, Nature Structural &Molecular Biology.

[60]  Tamás Fischer,et al.  Chd1 chromatin remodelers maintain nucleosome organization and repress cryptic transcription , 2012, EMBO reports.

[61]  M. Groudine,et al.  Promoter-proximal pausing of RNA polymerase II defines a general rate-limiting step after transcription initiation. , 1995, Genes & development.

[62]  J. Workman,et al.  Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange , 2012, Nature Structural &Molecular Biology.

[63]  B. Pugh,et al.  Genome-wide structure and organization of eukaryotic pre-initiation complexes , 2011, Nature.

[64]  Steven Henikoff,et al.  ISWI and CHD chromatin remodelers bind to promoters but act in gene bodies , 2013, Epigenetics & Chromatin.

[65]  J. Gurdon,et al.  HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes , 2012, Epigenetics & Chromatin.

[66]  J. Broach,et al.  Chromatin remodelers clear nucleosomes from intrinsically unfavorable sites to establish nucleosome-depleted regions at promoters , 2011, Molecular biology of the cell.

[67]  R. Young,et al.  A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells , 2007, Cell.

[68]  A. DePace,et al.  Genetic analysis of brahma: the Drosophila homolog of the yeast chromatin remodeling factor SWI2/SNF2. , 1998, Genetics.

[69]  J. T. Kadonaga,et al.  Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly , 2005, Nature Structural &Molecular Biology.