Histone availability as a strategy to control gene expression

References

• Corpet A, Almouzni G. Making copies of chromatin: the challenge of nucleosomal organization and epigenetic information. Trends Cell Biol 2009; 19:29-41; PMID:19027300; http://dx.doi.org/10.1016/j.tcb.2008.10.002
   PubMed Web of Science ®Google Scholar
• Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet 2008; 9:843-54; PMID:18927579; http://dx.doi.org/10.1038/nrg2438
   PubMed Web of Science ®Google Scholar
• Han M, Chang M, Kim UJ, Grunstein M. Histone H2B repression causes cell-cycle-specific arrest in yeast: effects on chromosomal segregation, replication, and transcription. Cell 1987; 48:589-97; PMID:3815518; http://dx.doi.org/10.1016/0092-8674(87)90237-6
   PubMed Web of Science ®Google Scholar
• Kim UJ, Han M, Kayne P, Grunstein M. Effects of histone H4 depletion on the cell cycle and transcription of Saccharomyces cerevisiae. Embo J 1988; 7:2211-9; PMID:3046933
   PubMed Web of Science ®Google Scholar
• Saunders MJ, Yeh E, Grunstein M, Bloom K. Nucleosome depletion alters the chromatin structure of Saccharomyces cerevisiae centromeres. Mol Cell Biol 1990; 10:5721-7; PMID:2233714; http://dx.doi.org/10.1128/MCB.10.11.5721
   PubMed Web of Science ®Google Scholar
• Murillo-Pineda M, Cabello-Lobato MJ, Clemente-Ruiz M, Monje-Casas F, Prado F. Defective histone supply causes condensin-dependent chromatin alterations, SAC activation and chromosome decatenation impairment. Nucleic Acids Res 2014; 42:12469-82; PMID:25300489; http://dx.doi.org/10.1093/nar/gku927
   PubMed Web of Science ®Google Scholar
• Ghule PN, Xie RL, Medina R, Colby JL, Jones SN, Lian JB, Stein JL, van Wijnen AJ, Stein GS. Fidelity of histone gene regulation is obligatory for genome replication and stability. Mol Cell Biol 2014; 34:2650-9; PMID:24797072; http://dx.doi.org/10.1128/MCB.01567-13
   PubMed Web of Science ®Google Scholar
• Zhao X, McKillop-Smith S, Muller B. The human histone gene expression regulator HBP/SLBP is required for histone and DNA synthesis, cell cycle progression and cell proliferation in mitotic cells. J Cell Sci 2004; 117:6043-51; PMID:15546920; http://dx.doi.org/10.1242/jcs.01523
   PubMed Web of Science ®Google Scholar
• Wagner EJ, Berkow A, Marzluff WF. Expression of an RNAi-resistant SLBP restores proper S-phase progression. Biochem Soc Trans 2005; 33:471-3; PMID:15916543; http://dx.doi.org/10.1042/BST0330471
   PubMed Web of Science ®Google Scholar
• Barcaroli D, Bongiorno-Borbone L, Terrinoni A, Hofmann TG, Rossi M, Knight RA, Matera AG, Melino G, De Laurenzi V. FLASH is required for histone transcription and S-phase progression. Proc Natl Acad Sci U S A 2006; 103:14808-12; PMID:17003125; http://dx.doi.org/10.1073/pnas.0604227103
   PubMed Web of Science ®Google Scholar
• Sullivan KD, Mullen TE, Marzluff WF, Wagner EJ. Knockdown of SLBP results in nuclear retention of histone mRNA. RNA New York, NY 2009; 15:459-72
   Google Scholar
• Ye X, Franco AA, Santos H, Nelson DM, Kaufman PD, Adams PD. Defective S phase chromatin assembly causes DNA damage, activation of the S phase checkpoint, and S phase arrest. Mol Cell 2003; 11:341-51; PMID:12620223; http://dx.doi.org/10.1016/S1097-2765(03)00037-6
   PubMed Web of Science ®Google Scholar
• Mejlvang J, Feng Y, Alabert C, Neelsen KJ, Jasencakova Z, Zhao X, Lees M, Sandelin A, Pasero P, Lopes M, Groth A. New histone supply regulates replication fork speed and PCNA unloading. J Cell Biol 2014; 204:29-43; PMID:24379417; http://dx.doi.org/10.1083/jcb.201305017
   PubMed Web of Science ®Google Scholar
• Clemente-Ruiz M, Prado F. Chromatin assembly controls replication fork stability. EMBO Rep 2009; 10:790-6; PMID:19465889; http://dx.doi.org/10.1038/embor.2009.67
   PubMed Web of Science ®Google Scholar
• Clemente-Ruiz M, Gonzalez-Prieto R, Prado F. Histone H3K56 acetylation, CAF1, and Rtt106 coordinate nucleosome assembly and stability of advancing replication forks. PLoS Genet 2011; 7:e1002376; PMID:22102830; http://dx.doi.org/10.1371/journal.pgen.1002376.
   PubMed Web of Science ®Google Scholar
• Prado F, Aguilera A. Partial depletion of histone H4 increases homologous recombination-mediated genetic instability. Mol Cell Biol 2005; 25:1526-36; PMID:15684401; http://dx.doi.org/10.1128/MCB.25.4.1526-1536.2005
   PubMed Web of Science ®Google Scholar
• O'Sullivan RJ, Arnoult N, Lackner DH, Oganesian L, Haggblom C, Corpet A, Almouzni G, Karlseder J. Rapid induction of alternative lengthening of telomeres by depletion of the histone chaperone ASF1. Nat Struct Mol Biol 2014; 21:167-74; PMID:24413054; http://dx.doi.org/10.1038/nsmb.2754
   PubMed Web of Science ®Google Scholar
• Bogenberger JM, Laybourn PJ. Human T Lymphotropic Virus Type 1 protein Tax reduces histone levels. Retrovirology 2008; 5:9; PMID:18237376; http://dx.doi.org/10.1186/1742-4690-5-9
   PubMed Web of Science ®Google Scholar
• Kwak H, Lis JT. Control of Transcriptional Elongation. Annu Rev Genet 2013; 47:501-26; PMID:24050178; http://dx.doi.org/10.1146/annurev-genet-110711-155440
   Web of Science ®Google Scholar
• Venkatesh S, Workman JL. Histone exchange, chromatin structure and the regulation of transcription. Nat Rev Mol Cell Biol 2015; 16:178-89; PMID:25650798; http://dx.doi.org/10.1038/nrm3941
   PubMed Web of Science ®Google Scholar
• Kireeva ML, Hancock B, Cremona GH, Walter W, Studitsky VM, Kashlev M. Nature of the nucleosomal barrier to RNA polymerase II. Mol Cell 2005; 18:97-108; PMID:15808512; http://dx.doi.org/10.1016/j.molcel.2005.02.027
   PubMed Web of Science ®Google Scholar
• Izban MG, Luse DS. Transcription on nucleosomal templates by RNA polymerase II in vitro: inhibition of elongation with enhancement of sequence-specific pausing. Genes Dev 1991; 5:683-96; PMID:2010092; http://dx.doi.org/10.1101/gad.5.4.683
   PubMed Web of Science ®Google Scholar
• Subtil-Rodriguez A, Reyes JC. BRG1 helps RNA polymerase II to overcome a nucleosomal barrier during elongation, in vivo. EMBO Rep 2010; 11:751-7; PMID:20829883; http://dx.doi.org/10.1038/embor.2010.131
   PubMed Web of Science ®Google Scholar
• Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C. Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science 2009; 325:626-8; PMID:19644123; http://dx.doi.org/10.1126/science.1172926
   PubMed Web of Science ®Google Scholar
• Jimeno-Gonzalez S, Ceballos-Chavez M, Reyes JC. A positioned +1 nucleosome enhances promoter-proximal pausing. Nucleic Acids Res 2015; 43:3068-78; PMID:25735750; http://dx.doi.org/10.1093/nar/gkv149
   PubMed Web of Science ®Google Scholar
• Wyrick JJ, Holstege FC, Jennings EG, Causton HC, Shore D, Grunstein M, Lander ES, Young RA. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 1999; 402:418-21; PMID:10586882; http://dx.doi.org/10.1038/46567
   PubMed Web of Science ®Google Scholar
• Gossett AJ, Lieb JD. In vivo effects of histone H3 depletion on nucleosome occupancy and position in Saccharomyces cerevisiae. PLoS Genet 2012; 8:e1002771; PMID:22737086; http://dx.doi.org/10.1371/journal.pgen.1002771
   PubMed Web of Science ®Google Scholar
• Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007; 128:707-19; PMID:17320508; http://dx.doi.org/10.1016/j.cell.2007.01.015
   PubMed Web of Science ®Google Scholar
• Prado F, Koop R, Beato M. Accurate chromatin organization of the mouse mammary tumor virus promoter determines the nature of the synergism between transcription factors. J Biol Chem 2002; 277:4911-7; PMID:11733499; http://dx.doi.org/10.1074/jbc.M110094200
   PubMed Web of Science ®Google Scholar
• Chavez S, Beato M. Nucleosome-mediated synergism between transcription factors on the mouse mammary tumor virus promoter. Proc Natl Acad Sci U S A 1997; 94:2885-90; PMID:9096316; http://dx.doi.org/10.1073/pnas.94.7.2885
   PubMed Web of Science ®Google Scholar
• Spies N, Nielsen CB, Padgett RA, Burge CB. Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 2009; 36:245-54; PMID:19854133; http://dx.doi.org/10.1016/j.molcel.2009.10.008
   PubMed Web of Science ®Google Scholar
• Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 2009; 19:1732-41; PMID:19687145; http://dx.doi.org/10.1101/gr.092353.109
   PubMed Web of Science ®Google Scholar
• Tilgner H, Nikolaou C, Althammer S, Sammeth M, Beato M, Valcarcel J, Guigo R. Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 2009; 16:996-1001; PMID:19684599; http://dx.doi.org/10.1038/nsmb.1658
   PubMed Web of Science ®Google Scholar
• Nahkuri S, Taft RJ, Mattick JS. Nucleosomes are preferentially positioned at exons in somatic and sperm cells. Cell Cycle Georgetown, Tex 2009; 8:3420-4
   Google Scholar
• Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 2009; 16:990-5; PMID:19684600; http://dx.doi.org/10.1038/nsmb.1659
   PubMed Web of Science ®Google Scholar
• Jimeno-Gonzalez S, Payan-Bravo L, Munoz-Cabello AM, Guijo M, Gutierrez G, Prado F, Reyes JC. Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing. Proc Natl Acad Sci U S A 2015; 112:14840-5; PMID:26578803; http://dx.doi.org/10.1073/pnas.1506760112
   PubMed Web of Science ®Google Scholar
• McKittrick E, Gafken PR, Ahmad K, Henikoff S. Histone H3.3 is enriched in covalent modifications associated with active chromatin. Proc Natl Acad Sci U S A 2004; 101:1525-30; PMID:14732680; http://dx.doi.org/10.1073/pnas.0308092100
   PubMed Web of Science ®Google Scholar
• Chen P, Zhao J, Wang Y, Wang M, Long H, Liang D, Huang L, Wen Z, Li W, Li X et al., H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin. Genes Dev 2013; 27:2109-24; PMID:24065740; http://dx.doi.org/10.1101/gad.222174.113
   PubMed Web of Science ®Google Scholar
• Carrillo Oesterreich F, Herzel L, Straube K, Hujer K, Howard J, Neugebauer KM. Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. Cell 2016; 165:372-381; PMID:27020755; http://dx.doi.org/10.1016/j.cell.2016.02.045
   PubMed Web of Science ®Google Scholar
• de la Mata M, Alonso CR, Kadener S, Fededa JP, Blaustein M, Pelisch F, Cramer P, Bentley D, Kornblihtt AR. A slow RNA polymerase II affects alternative splicing in vivo. Mol Cell 2003; 12:525-32; PMID:14536091; http://dx.doi.org/10.1016/j.molcel.2003.08.001
   PubMed Web of Science ®Google Scholar
• Dujardin G, Lafaille C, de la Mata M, Marasco LE, Munoz MJ, Le Jossic-Corcos C, Corcos L, Kornblihtt AR. How slow RNA polymerase II elongation favors alternative exon skipping. Mol Cell 2014; 54:683-90; PMID:24793692; http://dx.doi.org/10.1016/j.molcel.2014.03.044
   PubMed Web of Science ®Google Scholar
• Fong N, Kim H, Zhou Y, Ji X, Qiu J, Saldi T, Diener K, Jones K, Fu XD, Bentley DL. Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate. Genes Dev 2014; 28:2663-76; PMID:25452276; http://dx.doi.org/10.1101/gad.252106.114
   PubMed Web of Science ®Google Scholar
• Saltzman AL, Kim YK, Pan Q, Fagnani MM, Maquat LE, Blencowe BJ. Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol 2008; 28:4320-30; PMID:18443041; http://dx.doi.org/10.1128/MCB.00361-08
   PubMed Web of Science ®Google Scholar
• Saltzman AL, Pan Q, Blencowe BJ. Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev 2011; 25:373-84; PMID:21325135; http://dx.doi.org/10.1101/gad.2004811
   PubMed Web of Science ®Google Scholar
• Gunjan A, Paik J, Verreault A. The emergence of regulated histone proteolysis. Curr Opin Genet Dev 2006; 16:112-8; PMID:16510276; http://dx.doi.org/10.1016/j.gde.2006.02.010
   PubMed Web of Science ®Google Scholar
• O'Sullivan RJ, Kubicek S, Schreiber SL, Karlseder J. Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres. Nat Struct Mol Biol 2010; 17:1218-25; PMID:20890289; http://dx.doi.org/10.1038/nsmb.1897
   PubMed Web of Science ®Google Scholar
• Liang D, Burkhart SL, Singh RK, Kabbaj MH, Gunjan A. Histone dosage regulates DNA damage sensitivity in a checkpoint-independent manner by the homologous recombination pathway. Nucleic Acids Res 2012; 40:9604-20; PMID:22850743; http://dx.doi.org/10.1093/nar/gks722
   PubMed Web of Science ®Google Scholar
• Platt JM, Ryvkin P, Wanat JJ, Donahue G, Ricketts MD, Barrett SP, Waters HJ, Song S, Chavez A, Abdallah KO, Master SR, Wang LS, Johnson FB. Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence. Genes Dev 2013; 27:1406-20; PMID:23756653; http://dx.doi.org/10.1101/gad.218776.113
   PubMed Web of Science ®Google Scholar
• Ivanov A, Pawlikowski J, Manoharan I, van Tuyn J, Nelson DM, Rai TS, Shah PP, Hewitt G, Korolchuk VI, Passos JF, Wu H, Berger SL, Adams PD. Lysosome-mediated processing of chromatin in senescence. J Cell Biol 2013; 202:129-43; PMID:23816621; http://dx.doi.org/10.1083/jcb.201212110
   PubMed Web of Science ®Google Scholar
• Rai TS, Cole JJ, Nelson DM, Dikovskaya D, Faller WJ, Vizioli MG, Hewitt RN, Anannya O, McBryan T, Manoharan I, et al. HIRA orchestrates a dynamic chromatin landscape in senescence and is required for suppression of neoplasia. Genes Dev 2014; 28:2712-25; PMID:25512559; http://dx.doi.org/10.1101/gad.247528.114
   PubMed Web of Science ®Google Scholar
• Rogakou EP, Sekeri-Pataryas KE. Histone variants of H2A and H3 families are regulated during in vitro aging in the same manner as during differentiation. Exp Gerontol 1999; 34:741-54; PMID:10579635; http://dx.doi.org/10.1016/S0531-5565(99)00046-7
   PubMed Web of Science ®Google Scholar
• Tissenbaum HA, Guarente L. Model organisms as a guide to mammalian aging. Dev Cell 2002; 2:9-19; PMID:11782310; http://dx.doi.org/10.1016/S1534-5807(01)00098-3
   PubMed Web of Science ®Google Scholar
• Feser J, Truong D, Das C, Carson JJ, Kieft J, Harkness T, Tyler JK. Elevated histone expression promotes life span extension. Mol Cell 2010; 39:724-35; PMID:20832724; http://dx.doi.org/10.1016/j.molcel.2010.08.015
   PubMed Web of Science ®Google Scholar
• Hu Z, Chen K, Xia Z, Chavez M, Pal S, Seol JH, Chen CC, Li W, Tyler JK. Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes Dev 2014; 28:396-408; PMID:24532716; http://dx.doi.org/10.1101/gad.233221.113
   PubMed Web of Science ®Google Scholar
• Liu L, Cheung TH, Charville GW, Hurgo BM, Leavitt T, Shih J, Brunet A, Rando TA. Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging. Cell reports 2013; 4:189-204; PMID:23810552; http://dx.doi.org/10.1016/j.celrep.2013.05.043
   PubMed Web of Science ®Google Scholar
• Rodriguez SA, Grochova D, McKenna T, Borate B, Trivedi NS, Erdos MR, Eriksson M. Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging. Aging cell 2016; 15:267-78; PMID:26685868; http://dx.doi.org/10.1111/acel.12433
   PubMed Web of Science ®Google Scholar
• Mazin P, Xiong J, Liu X, Yan Z, Zhang X, Li M, He L, Somel M, Yuan Y, Phoebe Chen YP, et al. Widespread splicing changes in human brain development and aging. Mol System Biol 2013; 9:633; PMID:23340839; http://dx.doi.org/10.1038/msb.2012.67
   PubMed Web of Science ®Google Scholar
• Tollervey JR, Wang Z, Hortobagyi T, Witten JT, Zarnack K, Kayikci M, Clark TA, Schweitzer AC, Rot G, Curk T, et al. Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res 2011; 21:1572-82; PMID:21846794; http://dx.doi.org/10.1101/gr.122226.111
   PubMed Web of Science ®Google Scholar
• Harries LW, Hernandez D, Henley W, Wood AR, Holly AC, Bradley-Smith RM, Yaghootkar H, Dutta A, Murray A, Frayling TM, et al. Human aging is characterized by focused changes in gene expression and deregulation of alternative splicing. Aging Cell 2011; 10:868-78; PMID:21668623; http://dx.doi.org/10.1111/j.1474-9726.2011.00726.x
   PubMed Web of Science ®Google Scholar
• Holly AC, Melzer D, Pilling LC, Fellows AC, Tanaka T, Ferrucci L, Harries LW. Changes in splicing factor expression are associated with advancing age in man. Mechan Age Dev 2013; 134:356-66; PMID:23747814; http://dx.doi.org/10.1016/j.mad.2013.05.006
   PubMed Web of Science ®Google Scholar
• O'Sullivan RJ, Karlseder J. The great unravelling: chromatin as a modulator of the aging process. Trends Biochem Sci 2012; 37:466-76; PMID:22959736; http://dx.doi.org/10.1016/j.tibs.2012.08.001
   PubMed Web of Science ®Google Scholar
• Graves RA, Marzluff WF, Giebelhaus DH, Schultz GA. Quantitative and qualitative changes in histone gene expression during early mouse embryo development. Proc Natl Acad Sci U S A 1985; 82:5685-9; PMID:3862090; http://dx.doi.org/10.1073/pnas.82.17.5685
   PubMed Web of Science ®Google Scholar
• Karnavas T, Pintonello L, Agresti A, Bianchi ME. Histone content increases in differentiating embryonic stem cells. Front Physiol 2014; 5:330; PMID:25221520; http://dx.doi.org/10.3389/fphys.2014.00330
   PubMed Web of Science ®Google Scholar