|
|
|
|
REVIEW
Laboratory of Chromatin Biology, The Rockefeller University, New York, New York 10021, USA
In the universe of science, two worlds have recently collidedthose of RNA and chromatin. The intersection of these two fields has been impending, but evidence for such a meaningful collision has only recently become apparent. In this review, we discuss the implications for noncoding RNAs and the formation of specialized chromatin domains in various epigenetic processes as diverse as dosage compensation, RNA interference-mediated heterochromatin assembly and gene silencing, and programmed DNA elimination. While mechanistic details as to how the RNA and chromatin worlds connect remain unclear, intriguing parallels exist in the overall design and machinery used in model organisms from all eukaryotic kingdoms. The role of potential RNA-binding chromatin-associated proteins will be discussed as one possible link between RNA and chromatin.
[Keywords: RNAi; dosage compensation; heterochromatin; transcriptional gene silencing]
E-MAIL alliscd{at}mail.rockefeller.edu; FAX (212) 327-7849.
![]()
CiteULike
Connotea
Del.icio.us
Digg
Reddit
Technorati What's this?
This article has been cited by other articles:
![]() |
J.-T. Li, Y. Zhang, L. Kong, Q.-R. Liu, and L. Wei Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation Nucleic Acids Res., September 1, 2008; 36(15): 4833 - 4844. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. E. Dinger, P. P. Amaral, T. R. Mercer, K. C. Pang, S. J. Bruce, B. B. Gardiner, M. E. Askarian-Amiri, K. Ru, G. Solda, C. Simons, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation Genome Res., September 1, 2008; 18(9): 1433 - 1445. [Abstract] [Full Text] [PDF] |
||||
![]() |
B.-L. Yin, L. Guo, D.-F. Zhang, W. Terzaghi, X.-F. Wang, T.-T. Liu, H. He, Z.-K. Cheng, and X. W. Deng Integration of Cytological Features with Molecular and Epigenetic Properties of Rice Chromosome 4 Mol Plant, August 8, 2008; (2008) ssn037v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Ganesan and S. M.R. Rao A novel noncoding RNA processed by Drosha is restricted to nucleus in mouse RNA, July 1, 2008; 14(7): 1399 - 1410. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Mohammad, R. R. Pandey, T. Nagano, L. Chakalova, T. Mondal, P. Fraser, and C. Kanduri Kcnq1ot1/Lit1 Noncoding RNA Mediates Transcriptional Silencing by Targeting to the Perinucleolar Region Mol. Cell. Biol., June 1, 2008; 28(11): 3713 - 3728. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. E Dinger, T. R Mercer, and J. S Mattick RNAs as extracellular signaling molecules J. Mol. Endocrinol., April 1, 2008; 40(4): 151 - 159. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. J. Sweeney, P. Campbell, and G. Bosco Drosophila sticky/citron kinase Is a Regulator of Cell-Cycle Progression, Genetically Interacts With Argonaute 1 and Modulates Epigenetic Gene Silencing Genetics, March 1, 2008; 178(3): 1311 - 1325. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Flanagin, J. D. Nelson, D. G. Castner, O. Denisenko, and K. Bomsztyk Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events Nucleic Acids Res., February 11, 2008; 36(3): e17 - e17. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Gendler, T. Paulsen, and C. Napoli ChromDB: The Chromatin Database Nucleic Acids Res., January 11, 2008; 36(suppl_1): D298 - D302. [Abstract] [Full Text] [PDF] |
||||
![]() |
V. K. Rajasekhar and M. Begemann Concise Review: Roles of Polycomb Group Proteins in Development and Disease: A Stem Cell Perspective Stem Cells, October 1, 2007; 25(10): 2498 - 2510. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Pheasant and J. S. Mattick Raising the estimate of functional human sequences Genome Res., September 1, 2007; 17(9): 1245 - 1253. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Royo, E. Basyuk, V. Marty, M. Marques, E. Bertrand, and J. Cavaille Bsr, a Nuclear-retained RNA with Monoallelic Expression Mol. Biol. Cell, August 1, 2007; 18(8): 2817 - 2827. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. F. Mehler and J. S. Mattick Noncoding RNAs and RNA Editing in Brain Development, Functional Diversification, and Neurological Disease Physiol Rev, July 1, 2007; 87(3): 799 - 823. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. S. Judelson and S. Tani Transgene-Induced Silencing of the Zoosporogenesis-Specific NIFC Gene Cluster of Phytophthora infestans Involves Chromatin Alterations Eukaryot. Cell, July 1, 2007; 6(7): 1200 - 1209. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Liu, S. D. Taverna, T. L. Muratore, J. Shabanowitz, D. F. Hunt, and C. D. Allis RNAi-dependent H3K27 methylation is required for heterochromatin formation and DNA elimination in Tetrahymena Genes & Dev., June 15, 2007; 21(12): 1530 - 1545. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Stalder and O. Muhlemann Transcriptional Silencing of Nonsense Codon-containing Immunoglobulin {micro} Genes Requires Translation of Its mRNA J. Biol. Chem., June 1, 2007; 282(22): 16079 - 16085. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Neumann, H. Yan, and J. Jiang The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference Genetics, June 1, 2007; 176(2): 749 - 761. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Fazi, G. Zardo, V. Gelmetti, L. Travaglini, A. Ciolfi, L. Di Croce, A. Rosa, I. Bozzoni, F. Grignani, F. Lo-Coco, et al. Heterochromatic gene repression of the retinoic acid pathway in acute myeloid leukemia Blood, May 15, 2007; 109(10): 4432 - 4440. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. S. Mattick A new paradigm for developmental biology J. Exp. Biol., May 1, 2007; 210(9): 1526 - 1547. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Inaoka, Y. Fukuoka, and I. S. Kohane Evidence of spatially bound gene regulation in Mus musculus: Decreased gene expression proximal to microRNA genomic location PNAS, March 20, 2007; 104(12): 5020 - 5025. [Abstract] [Full Text] [PDF] |
||||
![]() |
B. A. Garcia, S. B. Hake, R. L. Diaz, M. Kauer, S. A. Morris, J. Recht, J. Shabanowitz, N. Mishra, B. D. Strahl, C. D. Allis, et al. Organismal Differences in Post-translational Modifications in Histones H3 and H4 J. Biol. Chem., March 9, 2007; 282(10): 7641 - 7655. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Sessa, A. Breiling, G. Lavorgna, L. Silvestri, G. Casari, and V. Orlando Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster RNA, February 1, 2007; 13(2): 223 - 239. [Abstract] [Full Text] [PDF] |
||||
![]() |
T. Sado, Y. Hoki, and H. Sasaki Tsix defective in splicing is competent to establish Xist silencing Development, December 15, 2006; 133(24): 4925 - 4931. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Katic and I. Greenwald EMB-4: A Predicted ATPase That Facilitates lin-12 Activity in Caenorhabditis elegans Genetics, December 1, 2006; 174(4): 1907 - 1915. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. M. Checchi and W. G. Kelly emb-4 Is a Conserved Gene Required for Efficient Germline-Specific Chromatin Remodeling During Caenorhabditis elegans Embryogenesis Genetics, December 1, 2006; 174(4): 1895 - 1906. [Abstract] [Full Text] [PDF] |
||||
![]() |
H.-R. Lee, P. Neumann, J. Macas, and J. Jiang Transcription and Evolutionary Dynamics of the Centromeric Satellite Repeat CentO in Rice Mol. Biol. Evol., December 1, 2006; 23(12): 2505 - 2520. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. P. Sripathy, J. Stevens, and D. C. Schultz The KAP1 Corepressor Functions To Coordinate the Assembly of De Novo HP1-Demarcated Microenvironments of Heterochromatin Required for KRAB Zinc Finger Protein-Mediated Transcriptional Repression Mol. Cell. Biol., November 15, 2006; 26(22): 8623 - 8638. [Abstract] [Full Text] [PDF] |
||||
![]() |
Y. Yabuta, K. Kurimoto, Y. Ohinata, Y. Seki, and M. Saitou Gene Expression Dynamics During Germline Specification in Mice Identified by Quantitative Single-Cell Gene Expression Profiling Biol Reprod, November 1, 2006; 75(5): 705 - 716. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Navarro, D. R. Page, P. Avner, and C. Rougeulle Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes & Dev., October 15, 2006; 20(20): 2787 - 2792. [Abstract] [Full Text] [PDF] |
||||
![]() |
J.-H. Shin and Z. Kelman The Replicative Helicases of Bacteria, Archaea, and Eukarya Can Unwind RNA-DNA Hybrid Substrates J. Biol. Chem., September 15, 2006; 281(37): 26914 - 26921. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. P. Christov, T. J. Gardiner, D. Szuts, and T. Krude Functional Requirement of Noncoding Y RNAs for Human Chromosomal DNA Replication. Mol. Cell. Biol., September 1, 2006; 26(18): 6993 - 7004. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Imhof Epigenetic regulators and histone modification Brief Funct Genomic Proteomic, September 1, 2006; 5(3): 222 - 227. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Li, J. E. Mueller, and M. Bryk Sir2 Represses Endogenous Polymerase II Transcription Units in the Ribosomal DNA Nontranscribed Spacer Mol. Biol. Cell, September 1, 2006; 17(9): 3848 - 3859. [Abstract] [Full Text] [PDF] |
||||
![]() |
A.-K. Souid, C. Gao, L. Wang, E. Milgrom, and W.-C. W. Shen ELM1 Is Required for Multidrug Resistance in Saccharomyces cerevisiae Genetics, August 1, 2006; 173(4): 1919 - 1937. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Sundaram, B. Echalier, W. Han, D. Hull, and L. Timmons ATP-binding Cassette Transporters Are Required for Efficient RNA Interference in Caenorhabditis elegans Mol. Biol. Cell, August 1, 2006; 17(8): 3678 - 3688. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. S. Dimitrova Nuclear transcription is essential for specification of mammalian replication origins. Genes Cells, July 1, 2006; 11(7): 829 - 844. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Bouzinba-Segard, A. Guais, and C. Francastel Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function PNAS, June 6, 2006; 103(23): 8709 - 8714. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Wang, N. Koyama, H. Nishida, T. Haraguchi, W. Reith, and T. Tsukamoto The assembly and maintenance of heterochromatin initiated by transgene repeats are independent of the RNA interference pathway in Mammalian cells. Mol. Cell. Biol., June 1, 2006; 26(11): 4028 - 4040. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. S. Mattick and I. V. Makunin Non-coding RNA. Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R17 - R29. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Buszczak and A. C. Spradling The Drosophila P68 RNA helicase regulates transcriptional deactivation by promoting RNA release from chromatin Genes & Dev., April 15, 2006; 20(8): 977 - 989. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Richard, A. M. Kiss, X. Darzacq, and T. Kiss Cotranscriptional Recognition of Human Intronic Box H/ACA snoRNAs Occurs in a Splicing-Independent Manner. Mol. Cell. Biol., April 1, 2006; 26(7): 2540 - 2549. [Abstract] [Full Text] [PDF] |
||||
![]() |
E. Bernstein, E. M. Duncan, O. Masui, J. Gil, E. Heard, and C. D. Allis Mouse polycomb proteins bind differentially to methylated histone h3 and RNA and are enriched in facultative heterochromatin. Mol. Cell. Biol., April 1, 2006; 26(7): 2560 - 2569. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Kotaja, S. N. Bhattacharyya, L. Jaskiewicz, S. Kimmins, M. Parvinen, W. Filipowicz, and P. Sassone-Corsi The chromatoid body of male germ cells: Similarity with processing bodies and presence of Dicer and microRNA pathway components PNAS, February 21, 2006; 103(8): 2647 - 2652. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. D. Nelson, O. Denisenko, P. Sova, and K. Bomsztyk Fast chromatin immunoprecipitation assay Nucleic Acids Res., January 5, 2006; 34(1): e2 - e2. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. A. Martens, P.-Y. J. Wu, and F. Winston Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae Genes & Dev., November 15, 2005; 19(22): 2695 - 2704. [Abstract] [Full Text] [PDF] |
||||