المؤلفون: Chapski D. J., Cabaj M., Morselli M., Mason R. J., Soehalim E., Ren S., Pellegrini M., Wang Y., Vondriska T. M., Rosa-Garrido M.

المساهمون: Chapski, D. J., Cabaj, M., Morselli, M., Mason, R. J., Soehalim, E., Ren, S., Pellegrini, M., Wang, Y., Vondriska, T. M., Rosa-Garrido, M.

مصطلحات موضوعية: Chromatin accessibility, CTCF, DNA methylation, Enhancer, Heart failure

العلاقة: info:eu-repo/semantics/altIdentifier/wos/WOS:000709428200007; volume:160; firstpage:73; lastpage:86; numberofpages:14; journal:JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY; http://hdl.handle.net/11381/2904308Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85110632094

الإتاحة: https://doi.org/10.1016/j.yjmcc.2021.07.002Test
http://hdl.handle.net/11381/2904308Test

المؤلفون: Ponte, I., Andrés, M., Jordan, Albert, Roque, Alicia

المساهمون: Ministerio de Economía y Competitividad (España)

مصطلحات موضوعية: Co-regulation, Transcription factors, Subtype functional differentiation, Chromatin compartments, Topologically associated domains (TADs)

العلاقة: #PLACEHOLDER_PARENT_METADATA_VALUE#; info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU2017-82805-C2-2-P; info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/FU2017-82805-C2-1-P; Preprint; http://dx.doi.org/10.1016/j.jmb.2020.166734Test; Sí; Journal of Molecular Biology 433(2): 166734 (2021); http://hdl.handle.net/10261/241515Test; http://dx.doi.org/10.13039/501100003329Test

الإتاحة: https://doi.org/10.1016/j.jmb.2020.166734Test
https://doi.org/10.13039/501100003329Test
http://hdl.handle.net/10261/241515Test

المؤلفون: Kim, Sung-Hak, Park, Jinah, Choi, Moon-Chang, Kim, Hwang-Phill, Park, Jung-Hyun, Jung, Yeonjoo, Lee, Ju-Hee, Oh, Do-Youn, Im, Seock-Ah, Bang, Yung-Jue, Kim, Tae-You

المساهمون: 임석아, Oh, Do-Youn, Im, Seock-Ah, Bang, Yung-Jue, Kim, Tae-You

مصطلحات موضوعية: ICF SYNDROME, METHYLATION PATTERNS, PWWP DOMAIN, PC12 CELLS, PROTEIN, CHROMATIN, DIFFERENTIATION, EXPRESSION, DISEASE, CANCER, DNMT3B, ZHX1, yeast two-hybrid, protein-protein interaction, transcriptional repression

العلاقة: Biochemical and Biophysical Research Communications, Vol.355 No.2, pp.318-323; 119577; https://hdl.handle.net/10371/26983Test; 000244774700005; 2-s2.0-33847155964

الإتاحة: https://doi.org/10.1016/j.bbrc.2007.01.187Test
https://hdl.handle.net/10371/26983Test

المؤلفون: Mammeadov, R., Kuscu, C., Czikora, A., Unlu, H., Tufan, T., Fischer, N.L., Arslan, Åževki

مصطلحات موضوعية: CRISPR, AID (auxin-inducible degron), enhancer-like elements, non-regulatory regions, p300, auxin, histone H3, messenger RNA, MyoD1 protein, octamer transcription factor 4, guide RNA, CRISPR associated protein, E1A associated p300 protein, EP300 protein, human, Article, chromatin, clustered regularly interspaced short palindromic repeat, controlled study, enhancer region, epigenetics, gene control, gene editing, gene expression regulation, HEK293T cell line, human cell, K-562 cell line, mammal cell, priority journal, promoter region

العلاقة: Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı; https://hdl.handle.net/11499/30290Test; https://doi.org/10.1016/j.jmb.2018.08.001Test; 431; 111; 121; 2-s2.0-85051629890; WOS:000456222200009

الإتاحة: https://doi.org/10.1016/j.jmb.2018.08.001Test
https://hdl.handle.net/11499/30290Test

المؤلفون: Cristina Vicente-García, Juan Diego Hernández-Camacho, Jaime J. Carvajal

المساهمون: Association Française contre les Myopathies, Ministerio de Educación, Cultura y Deporte (España), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España)

مصطلحات موضوعية: Gene expression regulation, Post-transcriptional modifications, Gene Expression, Myogenesis, Epigenetics, Cell Biology, Chromatin Assembly and Disassembly, Muscle Development, Muscle, Skeletal, Myogenic regulatory factors, Transcription Factors, Post-translational modifications

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aab8d0b820f1c1b3d97b3b58c298caf5Test
http://hdl.handle.net/10261/286942Test

المؤلفون: CICCARONE, FABIO, ZAMPIERI, Michele, CAIAFA, Paola

المساهمون: Ciccarone, Fabio, Zampieri, Michele, Caiafa, Paola

مصطلحات موضوعية: Chromatin, DNA hydroxymethylation, DNA methylation, Epigenetic regulation, Histone acetylation, Histone methylation, PARP1, PARylation, Developmental Biology, Cell Biology

وصف الملف: ELETTRONICO

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/27908606; info:eu-repo/semantics/altIdentifier/wos/WOS:000395504500015; volume:63; firstpage:123; lastpage:134; numberofpages:12; journal:SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY; http://hdl.handle.net/11573/928070Test; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85008951028; http://www.elsevier.com/inca/publications/store/6/2/2/9/4/4/index.httTest

الإتاحة: https://doi.org/10.1016/j.semcdb.2016.11.010Test
http://hdl.handle.net/11573/928070Test
http://www.elsevier.com/inca/publications/store/6/2/2/9/4/4/index.httTest

المؤلفون: Amemiya, Haley M, Goss, Thomas J, Nye, Taylor M, Hurto, Rebecca L, Simmons, Lyle A, Freddolino, Peter L

مصطلحات موضوعية: bacterial gene regulation, chromatin, gene regulation, nucleoid‐associated proteins, Molecular, Cellular and Developmental Biology, Health Sciences

وصف الملف: application/pdf

العلاقة: Amemiya, Haley M; Goss, Thomas J; Nye, Taylor M; Hurto, Rebecca L; Simmons, Lyle A; Freddolino, Peter L (2022). "Distinct heterochromatin‐like domains promote transcriptional memory and silence parasitic genetic elements in bacteria." The EMBO Journal (3): n/a-n/a.; https://hdl.handle.net/2027.42/171627Test; The EMBO Journal; Salvatier J, Wiecki TV, Fonnesbeck C ( 2016 ) Probabilistic programming in Python using PyMC3. PeerJ Compu Sci 2: e55; Sanchez‐Torres V, Hu H, Wood TK ( 2011 ) GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli. Appl Microbiol Biotechnol 90: 651 – 658; Santos‐Zavaleta A, Pérez‐Rueda E, Sánchez‐Pérez M, Velázquez‐Ramírez DA, Collado‐Vides J ( 2019 ) Tracing the phylogenetic history of the Crl regulon through the bacteria and archaea genomes. BMC Genom 20: 299; Scholz SA, Diao R, Wolfe MB, Fivenson EM, Lin XN, Freddolino PL ( 2019 ) High‐resolution mapping of the Escherichia coli chromosome reveals positions of high and low transcription. Cell Syst 8: 212 – 225.e9; Schroeder JW, Simmons LA ( 2013 ) Complete genome sequence of Bacillus subtilis strain PY79. Genome Announc 1: e01085‐13; Shen BA, Landick R ( 2019 ) Transcription of bacterial chromatin. J Mol Biol 431: 4040 – 4066; Shin J‐E, Lin C, Lim HN ( 2016 ) Horizontal transfer of DNA methylation patterns into bacterial chromosomes. Nucleic Acids Res 44: 4460 – 4471; Singh K, Milstein JN, Navarre WW ( 2016 ) Xenogeneic silencing and its impact on bacterial genomes. Annu Rev Microbiol 70: 199 – 213; Singh SS, Singh N, Bonocora RP, Fitzgerald DM, Wade JT, Grainger DC ( 2014 ) Widespread suppression of intragenic transcription initiation by H‐NS. Genes Dev 28: 214 – 219; Smits WK, Grossman AD ( 2010 ) The transcriptional regulator Rok binds A+T‐Rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PLoS Genet 6: e1001207; Sullivan NL, Marquis KA, Rudner DZ ( 2009 ) Recruitment of SMC to the origin by ParB‐parS organizes the origin and promotes efficient chromosome segregation. Cell 137: 697; Thomason LC, Costantino N, Court DL ( 2007 ) E. coli genome manipulation by P1 transduction. Curr Protoc Mol Biol 1: 1.17.1 – 1.17.8; Ueguchi C, Mizuno T ( 1993 ) The Escherichia coli nucleoid protein H‐NS functions directly as a transcriptional repressor. EMBO J 12: 1039 – 1046; Updegrove TB, Zhang A, Storz G ( 2016 ) Hfq: the flexible RNA matchmaker. Curr Opin Microbiol 30: 133 – 138; Valentin‐Hansen P, Eriksen M, Udesen C ( 2004 ) The bacterial Sm‐like protein Hfq: a key player in RNA transactions. Mol Microbiol 51: 1525 – 1533; van der Valk RA, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT ( 2017 ) Mechanism of environmentally driven conformational changes that modulate H‐NS DNA‐bridging activity. Elife 6: e27369; Verma SC, Qian Z, Adhya SL ( 2020 ) Correction: architecture of the Escherichia coli nucleoid. PLoS Genet 16: e1009148; Verzani J ( 2011 ) Getting started with RStudio: an integrated development environment for R. Sebastopol, CA: O’Reilly Media, Inc; Vora T, Hottes AK, Tavazoie S ( 2009 ) Protein occupancy landscape of a bacterial genome. Mol Cell 35: 247 – 253; Walker DM, Freddolino PL, Harshey RM ( 2020 ) A well‐mixed E. coli genome: widespread contacts revealed by tracking mu transposition. Cell 180: 703 – 716.e18; Wang L, Reeves PR ( 1998 ) Organization of Escherichia coli O157 O antigen gene cluster and identification of its specific genes. Infect Immun 66: 3545 – 3551; Wang X, Kim Y, Ma Q, Hong SH, Pokusaeva K, Sturino JM, Wood TK ( 2010 ) Cryptic prophages help bacteria cope with adverse environments. Nat Commun 1: 147; Wang Z, Wang J, Ren G, Li Y, Wang X ( 2016 ) Deletion of the genes waaC, waaF, or waaG in Escherichia coli W3110 disables the flagella biosynthesis. J Basic Microbiol 56: 1021 – 1035; Wasim A, Gupta A, Mondal J ( 2021 ) Mapping the multiscale organisation of Escherichia coli chromosome in a Hi‐C‐integrated model. bioRxiv https://doi.org/10.1101/2020.06.29.178194Test [PREPRINT]; Wickham H ( 2009 ) ggplot2: Elegant graphics for data analysis. Springer Science & Business Media; Wilhelm L, Bürmann F, Minnen A, Shin H‐C, Toseland CP, Oh B‐H, Gruber S ( 2015 ) SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis. Elife 4: e6659; Moazed D ( 2011 ) Mechanisms for the inheritance of chromatin states. Cell 146: 510 – 518; Deatherage DE, Barrick JE ( 2014 ) Identification of mutations in laboratory‐evolved microbes from next‐generation sequencing data using breseq. Methods Mol Biol 1151: 165 – 188; Deng S, Stein RA, Higgins NP ( 2005 ) Organization of supercoil domains and their reorganization by transcription. Mol Microbiol 57: 1511 – 1521; Dillon SC, Dorman CJ ( 2010 ) Bacterial nucleoid‐associated proteins, nucleoid structure and gene expression. Nat Rev Microbiol 8: 185 – 195; Albano M, Smits WK, Ho LTY, Kraigher B, Mandic‐Mulec I, Kuipers OP, Dubnau D ( 2005 ) The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions. J Bacteriol 187: 2010; Al‐Bassam MM, Moyne O, Chapin N, Zengler K ( 2021 ) Nucleoid openness profiling links bacterial genome structure to phenotype. bioRxiv https://doi.org/10.1101/2020.05.07.082990Test [PREPRINT]; Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A ( 1999 ) Growth phase‐dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361 – 6370; Amemiya HM, Schroeder J, Freddolino PL ( 2021 ) Nucleoid‐associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 12: 182 – 218; Anders S, Pyl PT, Huber W ( 2015 ) HTSeq–a Python framework to work with high‐throughput sequencing data. Bioinformatics 31: 166 – 169; Appleman JA, Ross W, Salomon J, Gourse RL ( 1998 ) Activation of Escherichia coli rRNA transcription by FIS during a growth cycle. J Bacteriol 180: 1525 – 1532; Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H ( 2006 ) Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008; Barh D, Azevedo V ( 2017 ) Omics technologies and bio‐engineering: volume 1: towards improving quality of life. Academic Press; Baumler A ( 2006 ) Faculty Opinions recommendation of Selective silencing of foreign DNA with low GC content by the H‐NS protein in Salmonella. Faculty Opinions – Post‐Publication Peer Review of the Biomedical Literature. https://doi.org/10.3410/f.1032929.492954Test; Bausch C, Peekhaus N, Utz C, Blais T, Murray E, Lowary T, Conway T ( 1998 ) Sequence analysis of the GntII (subsidiary) system for gluconate metabolism reveals a novel pathway for L‐idonic acid catabolism in Escherichia coli. J Bacteriol 180: 3704 – 3710; Bausch C, Ramsey M, Conway T ( 2004 ) Transcriptional organization and regulation of the L‐idonic acid pathway (GntII system) in Escherichia coli. J Bacteriol 186: 1388 – 1397; Bokal 4th AJ, Ross W, Gourse RL ( 1995 ) The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J Mol Biol 245: 197 – 207; Boudreau BA, Hron DR, Qin L, van der Valk RA, Kotlajich MV, Dame RT, Landick R ( 2018 ) StpA and Hha stimulate pausing by RNA polymerase by promoting DNA‐DNA bridging of H‐NS filaments. Nucleic Acids Res 46: 5525 – 5546; Cherepanov PP, Wackernagel W ( 1995 ) Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp‐catalyzed excision of the antibiotic‐resistance determinant. Gene 158: 9 – 14; Chintakayala K, Singh SS, Rossiter AE, Shahapure R, Dame RT, Grainger DCE ( 2013 ) coli Fis protein insulates the cbpA gene from uncontrolled transcription. PLoS Genet 9: e1003152; Cho B‐K, Knight EM, Barrett CL, Palsson BØ ( 2008 ) Genome‐wide analysis of Fis binding in Escherichia coli indicates a causative role for A‐/AT‐tracts. Genome Res 18: 900 – 910; Dorman CJ ( 2004 ) H‐NS: a universal regulator for a dynamic genome. Nat Rev Microbiol 2: 391 – 400; D’Souza JM, Wang L, Reeves P ( 2002 ) Sequence of the Escherichia coli O26 O antigen gene cluster and identification of O26 specific genes. Gene 297: 123 – 127; Faubladier M, Bouché JP ( 1994 ) Division inhibition gene dicF of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes. J Bacteriol 176: 1150 – 1156; Feng L, Han W, Wang Q, Bastin DA, Wang L ( 2005 ) Characterization of Escherichia coli O86 O‐antigen gene cluster and identification of O86‐specific genes. Vet Microbiol 106: 241 – 248; Francis NJ, Kingston RE ( 2001 ) Mechanisms of transcriptional memory. Nat Rev Mol Cell Biol 2: 409 – 421; Freddolino PL, Amemiya HM, Goss TJ, Tavazoie S ( 2021a ) Dynamic landscape of protein occupancy across the Escherichia coli chromosome. PLoS Biol 19: e3001306; Freddolino PL, Amini S, Tavazoie S ( 2012 ) Newly identified genetic variations in common Escherichia coli MG1655 stock cultures. J Bacteriol 194: 303 – 306; Freddolino PL, Goss TJ, Amemiya HM, Tavazoie S ( 2021b ) Dynamic landscape of protein occupancy across the Escherichia coli chromosome. bioRxiv https://doi.org/10.1101/2020.01.29.924811Test [PREPRINT]; Freddolino PL, Tavazoie S ( 2012 ) Beyond homeostasis: a predictive‐dynamic framework for understanding cellular behavior. Annu Rev Cell Dev Biol 28: 363 – 384; Frenkiel‐Krispin D, Levin‐Zaidman S, Shimoni E, Wolf SG, Wachtel EJ, Arad T et al ( 2001 ) Regulated phase transitions of bacterial chromatin: a non‐enzymatic pathway for generic DNA protection. EMBO J 20: 1184 – 1191; Gómez KM, Rodríguez A, Rodriguez Y, Ramírez AH, Istúriz T ( 2011 ) The subsidiary GntII system for gluconate metabolism in Escherichia coli: alternative induction of the gntV gene. Biol Res 44: 269 – 275; Goodarzi H, Elemento O, Tavazoie S ( 2009 ) Revealing global regulatory perturbations across human cancers. Mol Cell 36: 900 – 911; Grainger DC, Goldberg MD, Lee DJ, Busby SJW ( 2008 ) Selective repression by Fis and H‐NS at the Escherichia coli dps promoter. Mol Microbiol 68: 1366 – 1377; Graumann PL ( 2000 ) Bacillus subtilis SMC is required for proper arrangement of the chromosome and for efficient segregation of replication termini but not for bipolar movement of newly duplicated origin regions. J Bacteriol 182: 6463 – 6471; Harris CR, Millman KJ, van der Walt SJ, Gommers R, Virtanen P, Cournapeau D et al ( 2020 ) Array programming with NumPy. Nature 585: 357 – 362; Hengge R ( 2009 ) Principles of c‐di‐GMP signalling in bacteria. Nat Rev Microbiol 7: 263 – 273; Hoa TT, Tortosa P, Albano M, Dubnau D ( 2002 ) Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK. Mol Microbiol 43: 15 – 26; Hong SH, Wang X, Wood TK ( 2010 ) Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H‐NS of Escherichia coli. Microb Biotechnol 3: 344 – 356; Kahramanoglou C, Seshasayee ASN, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, Luscombe NM ( 2011 ) Direct and indirect effects of H‐NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39: 2073 – 2091; Kotlajich MV, Hron DR, Boudreau BA, Sun Z, Lyubchenko YL, Landick R ( 2015 ) Bridged filaments of histone‐like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria. Elife 4: e4970; Kundu S, Horn PJ, Peterson CL ( 2007 ) SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes Dev 21: 997 – 1004; Lagha M, Ferraro T, Dufourt J, Radulescu O, Mantovani M ( 2017 ) Transcriptional memory in the Drosophila embryo. Mech Dev 145: S137; Landick R, Wade JT, Grainger DC ( 2015 ) H‐NS and RNA polymerase: a love‐hate relationship? Curr Opin Microbiol 24: 53 – 59; Lim CJ, Whang YR, Kenney LJ, Yan J ( 2012 ) Gene silencing H‐NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility. Nucleic Acids Res 40: 3316 – 3328; Link AJ, Phillips D, Church GM ( 1997 ) Methods for generating precise deletions and insertions in the genome of wild‐type Escherichia coli: application to open reading frame characterization. J Bacteriol 179: 6228 – 6237; Linkevicius M, Sandegren L, Andersson DI ( 2013 ) Mechanisms and fitness costs of tigecycline resistance in Escherichia coli. J Antimicrob Chemother 68: 2809 – 2819; Lioy VS, Cournac A, Marbouty M, Duigou S, Mozziconacci J, Espéli O, Boccard F, Koszul R ( 2018 ) Multiscale structuring of the E.coli chromosome by nucleoid‐associated and condensin proteins. Cell 172: 771 – 783.e18; Lucchini S, Rowley G, Goldberg MD, Hurd D, Harrison M, Hinton JCD ( 2006 ) H‐NS mediates the silencing of laterally acquired genes in bacteria. PLoS Pathog 2: e81; Luijsterburg MS, White MF, van Driel R, Dame RT ( 2008 ) The major architects of chromatin: architectural proteins in bacteria, archaea and eukaryotes. Crit Rev Biochem Mol Biol 43: 393 – 418; McQuail J, Switzer A, Burchell L, Wigneshweraraj S ( 2020 ) The RNA‐binding protein Hfq assembles into foci‐like structures in nitrogen starved. J Biol Chem 295: 12355 – 12367; Nagai K ( 2002 ) Faculty Opinions recommendation of Hfq: a bacterial Sm‐like protein that mediates RNA‐RNA interaction. Faculty Opinions – Post‐Publication Peer Review of the Biomedical Literature. https://doi.org/10.3410/f.1003709.40104Test; Nair S, Finkel SE ( 2004 ) Dps protects cells against multiple stresses during stationary phase. J Bacteriol 186: 4192 – 4198; Nakamura K, Ogura Y, Gotoh Y, Hayashi T ( 2021 ) Prophages integrating into prophages: a mechanism to accumulate type III secretion effector genes and duplicate Shiga toxin‐encoding prophages in Escherichia coli. bioRxiv https://doi.org/10.1101/2020.11.04.367953Test [PREPRINT]; Nakao R, Ramstedt M, Wai SN, Uhlin BE ( 2012 ) Enhanced biofilm formation by Escherichia coli LPS mutants defective in Hep biosynthesis. PLoS One 7: e51241; Navarre WW ( 2006 ) Selective silencing of foreign DNA with low GC content by the H‐NS protein in Salmonella. Science 313: 236 – 238; Navarre WW, McClelland M, Libby SJ, Fang FC ( 2007 ) Silencing of xenogeneic DNA by H‐NS—facilitation of lateral gene transfer in bacteria by a defense system that recognizes foreign DNA. Genes Dev 21: 1456 – 1471; Neeli‐Venkata R, Martikainen A, Gupta A, Gonçalves N, Fonseca J, Ribeiro AS ( 2016 ) Robustness of the process of nucleoid exclusion of protein aggregates in Escherichia coli. J Bacteriol 198: 898 – 906; Neidhardt FC, Bloch PL, Smith DF ( 1974 ) Culture medium for enterobacteria. J Bacteriol 119: 736 – 747; Orans J, Kovach AR, Hoff KE, Horstmann NM, Brennan RG ( 2020 ) Crystal structure of an Escherichia coli Hfq Core (residues 2–69)–DNA complex reveals multifunctional nucleic acid binding sites. Nucleic Acids Res 48: 3987 – 3997; Palozola KC, Lerner J, Zaret KS ( 2019 ) A changing paradigm of transcriptional memory propagation through mitosis. Nat Rev Mol Cell Biol 20: 55 – 64; Posfai G ( 2006 ) Emergent properties of reduced‐genome Escherichia coli. Science 312: 1044 – 1046; Postow L, Hardy CD, Arsuaga J, Cozzarelli NR ( 2004 ) Topological domain structure of the Escherichia coli chromosome. Genes Dev 18: 1766 – 1779; Remesh SG, Verma SC, Chen J‐H, Ekman AA, Larabell CA, Adhya S, Hammel M ( 2020 ) Nucleoid remodeling during environmental adaptation is regulated by HU‐dependent DNA bundling. Nat Commun 11: 2905; RStudio ( 2020 ) https://rstudio.comTest/; Rubirés X, Saigi F, Piqué N, Climent N, Merino S, Albertí S, Tomás JM, Regué M ( 1997 ) A gene (wbbL) from Serratia marcescens N28b (O4) complements the rfb‐50 mutation of Escherichia coli K‐12 derivatives. J Bacteriol 179: 7581 – 7586; Salgado H, Martínez‐Flores I, Bustamante VH, Alquicira‐Hernández K, García‐Sotelo JS, García‐Alonso D, Collado‐Vides J ( 2018 ) Using RegulonDB, the Escherichia coli K‐12 gene regulatory transcriptional network database. Curr Protoc Bioinformatics 61: 1.32.1–1.32.30

الإتاحة: https://doi.org/10.15252/embj.2021108708Test
https://doi.org/10.1101/2020.06.29.178194Test
https://doi.org/10.1101/2020.05.07.082990Test
https://doi.org/10.3410/f.1032929.492954Test
https://doi.org/10.1101/2020.01.29.924811Test
https://doi.org/10.3410/f.1003709.40104Test
https://doi.org/10.1101/2020.11.04.367953Test
https://hdl.handle.net/2027.42/171627Test

المؤلفون: Bonefas, Katherine M., Iwase, Shigeki

مصطلحات موضوعية: cellular identity, chromatin, epigenetics, germline, neurodevelopment, Molecular, Cellular and Developmental Biology, Health Sciences

وصف الملف: application/pdf

العلاقة: Bonefas, Katherine M.; Iwase, Shigeki (2022). "Soma-to-germline transformation in chromatin-linked neurodevelopmental disorders?." The FEBS Journal (8): 2301-2317.; https://hdl.handle.net/2027.42/172311Test; The FEBS Journal; Strahl BD & Allis CD ( 2000 ) The language of covalent histone modifications. Nature 403, 41 – 45.; Sterpka A & Chen X ( 2018 ) Neuronal and astrocytic primary cilia in the mature brain. Pharmacol Res 137, 114 – 121.; Kempeneers C & Chilvers MA ( 2018 ) To beat, or not to beat, that is question! The spectrum of ciliopathies. Pediatr Pulmonol 53, 1122 – 1129.; Porter ME & Sale WS ( 2000 ) The 9 + 2 axoneme anchors multiple inner arm dyneins and a network of kinases and phosphatases that control motility. J Cell Biol 151, F37 – F42.; Long H & Huang K ( 2019 ) Transport of ciliary membrane proteins. Front Cell Dev Biol 7, 381.; Yu X, Ng CP, Habacher H & Roy S ( 2008 ) Foxj1 transcription factors are master regulators of the motile ciliogenic program. Nat Genet 40, 1445 – 1453.; Ben Khelifa M, Coutton C, Zouari R, Karaouzène T, Rendu J, Bidart M, Yassine S, Pierre V, Delaroche J, Hennebicq S et al. ( 2014 ) Mutations in DNAH1, which encodes an inner arm heavy chain dynein, lead to male infertility from multiple morphological abnormalities of the sperm flagella. Am J Hum Genet 94, 95 – 104.; Ferkol TW & Leigh MW ( 2012 ) Ciliopathies: the central role of cilia in a spectrum of pediatric disorders. J Pediatr 160, 366 – 371.; Zhang Z, Sapiro R, Kapfhamer D, Bucan M, Bray J, Chennathukuzhi V, McNamara P, Curtis A, Zhang M, Blanchette-Mackie EJ et al. ( 2002 ) A sperm-associated WD repeat protein orthologous to Chlamydomonas PF20 associates with Spag6, the mammalian orthologue of Chlamydomonas PF16. Mol Cell Biol 22, 7993 – 8004.; Zhang Z, Tang W, Zhou R, Shen X, Wei Z, Patel AM, Povlishock JT, Bennett J & Strauss JF ( 2007 ) Accelerated mortality from hydrocephalus and pneumonia in mice with a combined deficiency of SPAG6 and SPAG16L reveals a functional interrelationship between the two central apparatus proteins. Cell Motil Cytoskeleton 64, 360 – 376.; Nagarkatti-Gude DR, Jaimez R, Henderson SC, Teves ME, Zhang Z & Strauss JF ( 2011 ) Spag16, an axonemal central apparatus gene, encodes a male germ cell nuclear speckle protein that regulates SPAG16 mRNA expression. PLoS One 6, e20625.; Zhang Z, Kostetskii I, Moss SB, Jones BH, Ho C, Wang H, Kishida T, Gerton GL, Radice GL & Strauss JF ( 2004 ) Haploinsufficiency for the murine orthologue of Chlamydomonas PF20 disrupts spermatogenesis. Proc Natl Acad Sci USA 101, 12946 – 12951.; Yan R, Hu X, Zhang Q, Song L, Zhang M, Zhang Y & Zhao S ( 2015 ) Spag6 negatively regulates neuronal migration during mouse brain development. J Mol Neurosci 57, 463 – 469.; Hu X, Yan R, Cheng X, Song L, Zhang W, Li K & Zhao S ( 2016 ) The function of sperm-associated antigen 6 in neuronal proliferation and differentiation. J Mol Histol 47, 531 – 540.; Sweatt JD ( 2003 ) Mechanisms of Memory, xvii, 400 p. Academic Press, San Diego, CA.; Fu X-F, Cheng S-F, Wang L-Q, Yin S, De Felici M & Shen W ( 2015 ) DAZ family proteins, key players for germ cell development. Int J Biol Sci 11, 1226 – 1235.; Rosario R, Crichton JH, Stewart HL, Childs AJ, Adams IR & Anderson RA ( 2019 ) Dazl determines primordial follicle formation through the translational regulation of Tex14. FASEB J 33, 14221 – 14233.; Chong JA, Tapia-Ramirez J, Kim S, Toledo-Aral JJ, Zheng Y, Boutros MC, Altshuller YM, Frohman MA, Kraner SD & Mandel G ( 1995 ) REST: a mammalian silencer protein that restricts sodium channel gene expression to neurons. Cell 80, 949 – 957.; Chen ZF, Paquette AJ & Anderson DJ ( 1998 ) NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nat Genet 20, 136 – 142.; Hakimi M-A, Bochar DA, Chenoweth J, Lane WS, Mandel G & Shiekhattar R ( 2002 ) A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. Proc Natl Acad Sci USA 99, 7420 – 7425.; Galea I, Bechmann I & Perry VH ( 2007 ) What is immune privilege (not)? Trends Immunol 28, 12 – 18.; Chakradhar S ( 2018 ) Puzzling over privilege: How the immune system protects-and fails-the testes. Nat Med 24, 2 – 5.; Nielsen AY & Gjerstorff MF ( 2016 ) Ectopic expression of testis germ cell proteins in cancer and its potential role in genomic instability. Int J Mol Sci 17, 890.; McCarthy SE, Gillis J, Kramer M, Lihm J, Yoon S, Berstein Y, Mistry M, Pavlidis P, Solomon R, Ghiban E et al. ( 2014 ) De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Mol Psychiatry 19, 652 – 658.; Najmabadi H, Hu H, Garshasbi M, Zemojtel T, Abedini SS, Chen W, Hosseini M, Behjati F, Haas S, Jamali P et al. ( 2011 ) Deep sequencing reveals 50 novel genes for recessive cognitive disorders. Nature 478, 57 – 63.; De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S et al. ( 2014 ) Synaptic, transcriptional and chromatin genes disrupted in autism. Nature 515, 209 – 215.; Pocklington AJ, O’Donovan M & Owen MJ ( 2014 ) The synapse in schizophrenia. Eur J Neurosci 39, 1059 – 1067.; Akbarian S ( 2014 ) Epigenetic mechanisms in schizophrenia. Dialogues Clin Neurosci 16, 405 – 417.; Ropers HH ( 2010 ) Genetics of early onset cognitive impairment. Annu Rev Genomics Hum Genet 11, 161 – 187.; Vallianatos CN & Iwase S ( 2015 ) Disrupted intricacy of histone H3K4 methylation in neurodevelopmental disorders. Epigenomics 7, 503 – 519.; Garay PM, Wallner MA & Iwase S ( 2016 ) Yin-yang actions of histone methylation regulatory complexes in the brain. Epigenomics 8, 1689 – 1708.; Iwase S, Bérubé NG, Zhou Z, Kasri NN, Battaglioli E, Scandaglia M & Barco A ( 2017 ) Epigenetic etiology of intellectual disability. J Neurosci 37, 10773 – 10782.; Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE et al. ( 2014 ) The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216 – 221.; Gabriele M, Tobon AL, D’Agostino G & Testa G ( 2018 ) The chromatin basis of neurodevelopmental disorders: rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 84, 306 – 327.; Bagni C & Zukin RS ( 2019 ) A synaptic perspective of fragile X syndrome and autism spectrum disorders. Neuron 101, 1070 – 1088.; Nishiyama J ( 2019 ) Plasticity of dendritic spines: molecular function and dysfunction in neurodevelopmental disorders. Psychiatry Clin Neurosci 73, 541 – 550.; Noble D ( 2015 ) Conrad Waddington and the origin of epigenetics. J Exp Biol 218, 816 – 818.; Kassis JA, Kennison JA & Tamkun JW ( 2017 ) Polycomb and trithorax group genes in Drosophila. Genetics 206, 1699 – 1725.; Lewis EB ( 1978 ) A gene complex controlling segmentation in Drosophila. Nature 276, 565 – 570.; Kennison JA & Tamkun JW ( 1988 ) Dosage-dependent modifiers of polycomb and antennapedia mutations in Drosophila. Proc Natl Acad Sci USA 85, 8136 – 8140.; Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Patnaik D, Pradhan S, Goodrich J, Schubert I et al. ( 2004 ) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23, 4286 – 4296.; Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK et al. ( 2006 ) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441, 349 – 353.; Czermin B, Melfi R, McCabe D, Seitz V, Imhof A & Pirrotta V ( 2002 ) Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal polycomb sites. Cell 111, 185 – 196.; Milne TA, Briggs SD, Brock HW, Martin ME, Gibbs D, Allis CD & Hess JL ( 2002 ) MLL targets SET domain methyltransferase activity to Hox gene promoters. Mol Cell 10, 1107 – 1117.; Ingham PW ( 1981 ) Trithorax: a new homoeotic mutation of Drosophila melanogaster: II. The role of trx. Wilhelm Roux Arch Dev Biol 190, 365 – 369.; Ingham PW ( 1985 ) A clonal analysis of the requirement for the trithorax gene in the diversification of segments in Drosophila. J Embryol Exp Morphol 89, 349 – 365.; Hirabayashi Y, Suzki N, Tsuboi M, Endo TA, Toyoda T, Shinga J, Koseki H, Vidal M & Gotoh Y ( 2009 ) Polycomb limits the neurogenic competence of neural precursor cells to promote astrogenic fate transition. Neuron 63, 600 – 613.; Delgado RN, Mansky B, Ahanger SH, Lu C, Andersen RE, Dou Y, Alvarez-Buylla A & Lim DA ( 2020 ) Maintenance of neural stem cell positional identity by mixed-lineage leukemia 1. Science 368, 48 – 53.; Guarnieri FC, de Chevigny A, Falace A & Cardoso C ( 2018 ) Disorders of neurogenesis and cortical development. Dialogues Clin Neurosci 20, 255 – 266.; Lee TW & Katz DJ ( 2020 ) Hansel, Gretel, and the consequences of failing to remove histone methylation breadcrumbs. Trends Genet 36, 160 – 176.; Kwan KY, Sestan N & Anton ES ( 2012 ) Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex. Development 139, 1535 – 1546.; Corley M & Kroll KL ( 2015 ) The roles and regulation of polycomb complexes in neural development. Cell Tissue Res 359, 65 – 85.; Iwase S, Brookes E, Agarwal S, Badeaux AI, Ito H, Vallianatos CN, Tomassy GS, Kasza T, Lin G, Thompson A et al. ( 2016 ) A mouse model of X-linked intellectual disability associated with impaired removal of histone methylation. Cell Rep 14, 1000 – 1009.; Vallianatos CN, Raines B, Porter RS, Bonefas KM, Wu MC, Garay PM, Collette KM, Seo YA, Dou Y, Keegan CE et al. ( 2020 ) Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. Commun Biol 3, 278.; Ben-Shachar S, Chahrour M, Thaller C, Shaw CA & Zoghbi HY ( 2009 ) Mouse models of MeCP2 disorders share gene expression changes in the cerebellum and hypothalamus. Hum Mol Genet 18, 2431 – 2442.; Scandaglia M, Lopez-Atalaya JP, Medrano-Fernandez A, Lopez-Cascales MT, del Blanco B, Lipinski M, Benito E, Olivares R, Iwase S, Shi Y et al. ( 2017 ) Loss of Kdm5c causes spurious transcription and prevents the fine-tuning of activity-regulated enhancers in neurons. Cell Rep 21, 47 – 59.; Velasco G, Hube F, Rollin J, Neuillet D, Philippe C, Bouzinba-Segard H, Galvani A, Viegas-Pequignot E & Francastel C ( 2010 ) Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues. Proc Natl Acad Sci USA 107, 9281 – 9286.; Samaco RC, Mandel-Brehm C, McGraw CM, Shaw CA, McGill BE & Zoghbi HY ( 2012 ) Crh and Oprm1 mediate anxiety-related behavior and social approach in a mouse model of MECP2 duplication syndrome. Nat Genet 44, 206 – 211.; Gill ME, Hu Y-C, Lin Y & Page DC ( 2011 ) Licensing of gametogenesis, dependent on RNA binding protein DAZL, as a gateway to sexual differentiation of fetal germ cells. Proc Natl Acad Sci USA 108, 7443 – 7448.; Fujiwara Y, Komiya T, Kawabata H, Sato M, Fujimoto H, Furusawa M & Noce T ( 1994 ) Isolation of a DEAD-family protein gene that encodes a murine homolog of Drosophila vasa and its specific expression in germ cell lineage. Proc Natl Acad Sci USA 91, 12258 – 12262.; Alciaturi J, Anesetti G, Irigoin F, Skowronek F & Sapiro R ( 2019 ) Distribution of sperm antigen 6 (SPAG6) and 16 (SPAG16) in mouse ciliated and non-ciliated tissues. J Mol Histol 50, 189 – 202.; Deaton AM & Bird A ( 2011 ) CpG islands and the regulation of transcription. Genes Dev 25, 1010 – 1022.; Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, Rebhan M & Schübeler D ( 2007 ) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457 – 466.; Shen L, Kondo Y, Guo YI, Zhang J, Zhang LI, Ahmed S, Shu J, Chen X, Waterland RA & Issa J-P ( 2007 ) Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet 3, 2023 – 2036.; Walton EL, Francastel C & Velasco G ( 2014 ) Dnmt3b prefers germ line genes and centromeric regions: lessons from the ICF syndrome and cancer and implications for diseases. Biology (Basel) 3, 578 – 605.; Hagleitner MM, Lankester A, Maraschio P, Hultén M, Fryns JP, Schuetz C, Gimelli G, Davies EG, Gennery A, Belohradsky BH et al. ( 2008 ) Clinical spectrum of immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome). J Med Genet 45, 93 – 99.; Kiaee F, Zaki-Dizaji M, Hafezi N, Almasi-Hashiani A, Hamedifar H, Sabzevari A, Shirkani A, Zian Z, Jadidi-Niaragh F, Aghamahdi F et al. ( 2020 ) Clinical, immunologic, and molecular spectrum of patients with immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome: a systematic review. Endocr Metab Immune Disord Drug Targets 21, 664 – 672.; Velasco G, Walton EL, Sterlin D, Hédouin S, Nitta H, Ito Y, Fouyssac F, Mégarbané A, Sasaki H, Picard C et al. ( 2014 ) Germline genes hypomethylation and expression define a molecular signature in peripheral blood of ICF patients: implications for diagnosis and etiology. Orphanet J Rare Dis 9, 56.; Lewis JD, Meehan RR, Henzel WJ, Maurer-Fogy I, Jeppesen P, Klein F & Bird A ( 1992 ) Purification, sequence, and cellular localization of a novel chromosomal protein that binds to methylated DNA. Cell 69, 905 – 914.; Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U & Zoghbi HY ( 1999 ) Rett syndrome is caused by mutations in X-linked MECP2, encoding methyl-CpG-binding protein 2. Nat Genet 23, 185 – 188.; Lyst MJ & Bird A ( 2015 ) Rett syndrome: a complex disorder with simple roots. Nat Rev Genet 16, 261 – 275.; Van Esch H ( 2012 ) MECP2 duplication syndrome. Mol Syndromol 2, 128 – 136.; Lagger S, Connelly JC, Schweikert G, Webb S, Selfridge J, Ramsahoye BH, Yu M, He C, Sanguinetti G, Sowers LC et al. ( 2017 ) MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet 13, e1006793.; Gabel HW, Kinde B, Stroud H, Gilbert CS, Harmin DA, Kastan NR, Hemberg M, Ebert DH & Greenberg ME ( 2015 ) Disruption of DNA-methylation-dependent long gene repression in Rett syndrome. Nature 522, 89 – 93.; Liu KE, Xu C, Lei M, Yang A, Loppnau P, Hughes TR & Min J ( 2018 ) Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. J Biol Chem 293, 7344 – 7354.; Sperlazza MJ, Bilinovich SM, Sinanan LM, Javier FR & Williams DC ( 2017 ) Structural basis of MeCP2 distribution on non-CpG methylated and hydroxymethylated DNA. J Mol Biol 429, 1581 – 1594.; Tillotson R, Cholewa-Waclaw J, Chhatbar K, Connelly JC, Kirschner SA, Webb S, Koerner MV, Selfridge J, Kelly DA, De Sousa D et al. ( 2021 ) Neuronal non-CG methylation is an essential target for MeCP2 function. Mol Cell 81, 1260 – 1275.e12.; Tudor M, Akbarian S, Chen RZ & Jaenisch R ( 2002 ) Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci USA 99, 15536 – 15541.; Horvath PM & Monteggia LM ( 2018 ) MeCP2 as an activator of gene expression. Trends Neurosci 41, 72 – 74.; Chahrour M, Jung SY, Shaw C, Zhou X, Wong STC, Qin J & Zoghbi HY ( 2008 ) MeCP2, a key contributor to neurological disease, activates and represses transcription. Science 320, 1224 – 1229.; Chen Z & Zhang Y ( 2020 ) Role of mammalian DNA methyltransferases in development. Annu Rev Biochem 89, 135 – 158.; Tachibana M, Sugimoto K, Nozaki M, Ueda J, Ohta T, Ohki M, Fukuda M, Takeda N, Niida H, Kato H et al. ( 2002 ) G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis. Genes Dev 16, 1779 – 1791.; Tachibana M, Ueda J, Fukuda M, Takeda N, Ohta T, Iwanari H, Sakihama T, Kodama T, Hamakubo T & Shinkai Y ( 2005 ) Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes & Development 19, 815 – 826. http://dx.doi.org/10.1101/gad.1284005Test; Shinkai Y & Tachibana M ( 2011 ) H3K9 methyltransferase G9a and the related molecule GLP. Genes Dev 25, 781 – 788.; Kleefstra T, Smidt M, Banning MJG, Oudakker AR, Esch HV, de Brouwer APM, Nillesen W, Sistermans EA, Hamel BCJ, Bruijn DD et al. ( 2005 ) Disruption of the gene euchromatin histone methyl transferase1 (Eu-HMTase1) is associated with the 9q34 subtelomeric deletion syndrome. J Med Genet 42, 299 – 306.; Kleefstra T, Brunner HG, Amiel J, Oudakker AR, Nillesen WM, Magee A, Geneviève D, Cormier-Daire V, van Esch H, Fryns J-P et al. ( 2006 ) Loss-of-function mutations in euchromatin histone methyl transferase 1 (EHMT1) cause the 9q34 subtelomeric deletion syndrome. Am J Hum Genet 79, 370 – 377.; Schaefer A, Sampath SC, Intrator A, Min A, Gertler TS, Surmeier DJ, Tarakhovsky A & Greengard P ( 2009 ) Control of cognition and adaptive behavior by the GLP/G9a epigenetic suppressor complex. Neuron 64, 678 – 691.; Koubova J, Hu Y-C, Bhattacharyya T, Soh YQS, Gill ME, Goodheart ML, Hogarth CA, Griswold MD & Page DC ( 2014 ) Retinoic acid activates two pathways required for meiosis in mice. PLoS Genet 10, e1004541.; Li H, Liang Z, Yang J, Wang D, Wang H, Zhu M, Geng B & Xu EY ( 2019 ) DAZL is a master translational regulator of murine spermatogenesis. Natl Sci Rev 6, 455 – 468.; Ruggiu M, Speed R, Taggart M, McKay SJ, Kilanowski F, Saunders P, Dorin J & Cooke HJ ( 1997 ) The mouse Dazla gene encodes a cytoplasmic protein essential for gametogenesis. Nature 389, 73 – 77.; Cenik BK & Shilatifard A ( 2021 ) COMPASS and SWI/SNF complexes in development and disease. Nat Rev Genet 22, 38 – 58.; Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, Qi HH, Whetstine J, Bonni A, Roberts TM & Shi Y ( 2007 ) The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases. Cell 128, 1077 – 1088.; Vermeulen M, Mulder KW, Denissov S, Pijnappel WWMP, van Schaik FMA, Varier RA, Baltissen MPA, Stunnenberg HG, Mann M & Timmers HTM ( 2007 ) Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 131, 58 – 69.; Tahiliani M, Mei P, Fang R, Leonor T, Rutenberg M, Shimizu F, Li J, Rao A & Shi Y ( 2007 ) The histone H3K4 demethylase SMCX links REST target genes to X-linked mental retardation. Nature 447, 601 – 605.; Claes S, Devriendt K, Goethem GV, Roelen L, Meireleire J, Raeymaekers P, Cassiman JJ & Fryns JP ( 2000 ) Novel syndromic form of X-linked complicated spastic paraplegia. Am J Med Genet 94, 1 – 4.; Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A, Janecke AR, Tariverdian G, Chelly J, Fryns J et al. ( 2005 ) Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation. Am J Hum Genet 76, 227 – 236.; Belalcazar HM, Hendricks EL, Zamurrad S, Liebl FLW & Secombe J ( 2021 ) The histone demethylase KDM5 is required for synaptic structure and function at the Drosophila neuromuscular junction. Cell Rep 34, 108753.; Chen K, Luan X, Liu Q, Wang J, Chang X, Snijders AM, Mao J-H, Secombe J, Dan Z, Chen J-H et al. ( 2019 ) Drosophila histone demethylase KDM5 regulates social behavior through immune control and gut microbiota maintenance. Cell Host Microbe 25, 537 – 552.e8.; Drelon C, Rogers MF, Belalcazar HM & Secombe J ( 2019 ) The histone demethylase KDM5 controls developmental timing in Drosophila by promoting prothoracic gland endocycles. Development 146, dev182568.; Hatch HAM, Belalcazar HM, Marshall OJ & Secombe J ( 2021 ) A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. Elife 10, e63886.; Liu X & Secombe J ( 2015 ) The histone demethylase KDM5 activates gene expression by recognizing chromatin context through its PHD reader motif. Cell Rep 13, 2219 – 2231.; Secombe J, Li L, Carlos L & Eisenman RN ( 2007 ) The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth. Genes Dev 21, 537 – 551.; Zamurrad S, Hatch HAM, Drelon C, Belalcazar HM & Secombe J ( 2018 ) A Drosophila model of intellectual disability caused by mutations in the histone demethylase KDM5. Cell Rep 22, 2359 – 2369.; Magnúsdóttir E & Surani MA ( 2014 ) How to make a primordial germ cell. Development 141, 245 – 252.; Günesdogan U, Magnúsdóttir E & Surani MA ( 2014 ) Primordial germ cell specification: a context-dependent cellular differentiation event [corrected]. Philos Trans R Soc Lond B Biol Sci 369, 20130543.; Kurimoto K, Yabuta Y, Hayashi K, Ohta H, Kiyonari H, Mitani T, Moritoki Y, Kohri K, Kimura H, Yamamoto T et al. ( 2015 ) Quantitative dynamics of chromatin remodeling during germ cell specification from mouse embryonic stem cells. Cell Stem Cell 16, 517 – 532.; Borgel J, Guibert S, Li Y, Chiba H, Schübeler D, Sasaki H, Forné T & Weber M ( 2010 ) Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet 42, 1093 – 1100.; Zylicz JJ, Dietmann S, Günesdogan U, Hackett JA, Cougot D, Lee C & Surani MA ( 2015 ) Chromatin dynamics and the role of G9a in gene regulation and enhancer silencing during early mouse development. Elife 4, e09571.; Liu M, Zhu Y, Xing F, Liu S, Xia Y, Jiang Q & Qin J ( 2020 ) The polycomb group protein PCGF6 mediates germline gene silencing by recruiting histone-modifying proteins to target gene promoters. J Biol Chem 295, 9712 – 9724.; Gao Z, Zhang J, Bonasio R, Strino F, Sawai A, Parisi F, Kluger Y & Reinberg D ( 2012 ) PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes. Mol Cell 45, 344 – 356.; Qin J, Whyte W, Anderssen E, Apostolou E, Chen H-H, Akbarian S, Bronson R, Hochedlinger K, Ramaswamy S, Young R et al. ( 2012 ) The polycomb group protein L3mbtl2 assembles an atypical PRC1-family complex that is essential in pluripotent stem cells and early development. Cell Stem Cell 11, 319 – 332.; Endoh M, Endo TA, Shinga J, Hayashi K, Farcas A, Ma K, Ito S, Sharif J, Endoh T, Onaga N et al. ( 2017 ) PCGF6-PRC1 suppresses premature differentiation of mouse embryonic stem cells by regulating germ cell-related genes. Elife 6, e21064.; Huang Y, Zhao W, Wang C, Zhu Y, Liu M, Tong H, Xia Y, Jiang Q & Qin J ( 2018 ) Combinatorial control of recruitment of a variant PRC1.6 complex in embryonic stem cells. Cell Rep 22, 3032 – 3043.; Stielow B, Finkernagel F, Stiewe T, Nist A & Suske G ( 2018 ) L3MBTL2 and E2F6 determine genomic binding of the non-canonical polycomb repressive complex PRC1.6. PLoS Genet 14, e1007193.; Maeda I, Okamura D, Tokitake Y, Ikeda M, Kawaguchi H, Mise N, Abe K, Noce T, Okuda A & Matsui Y ( 2013 ) Max is a repressor of germ cell-related gene expression in mouse embryonic stem cells. Nat Commun 4, 1754.; Pohlers M, Truss M, Frede U, Scholz A, Strehle M, Kuban R-J, Hoffmann B, Morkel M, Birchmeier C & Hagemeier C ( 2005 ) A role for E2F6 in the restriction of male-germ-cell-specific gene expression. Curr Biol 15, 1051 – 1057.; Leseva M, Santostefano KE, Rosenbluth AL, Hamazaki T & Terada N ( 2013 ) E2f6-mediated repression of the meiotic Stag3 and Smc1β genes during early embryonic development requires Ezh2 and not the de novo methyltransferase Dnmt3b. Epigenetics 8, 873 – 884.; van den Heuvel S & Dyson NJ ( 2008 ) Conserved functions of the pRB and E2F families. Nat Rev Mol Cell Biol 9, 713 – 724.; Korenjak M, Taylor-Harding B, Binné UK, Satterlee JS, Stevaux O, Aasland R, White-Cooper H, Dyson N & Brehm A ( 2004 ) Native E2F/RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes. Cell 119, 181 – 193.; Lewis PW, Beall EL, Fleischer TC, Georlette D, Link AJ & Botchan MR ( 2004 ) Identification of a Drosophila Myb-E2F2/RBF transcriptional repressor complex. Genes Dev 18, 2929 – 2940.; Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS & DeCaprio JA ( 2007 ) Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell 26, 539 – 551.; Burkhart DL & Sage J ( 2008 ) Cellular mechanisms of tumour suppression by the retinoblastoma gene. Nat Rev Cancer 8, 671 – 682.; Wang D, Kennedy S, Conte D Jr, Kim JK, Gabel HW, Kamath RS, Mello CC & Ruvkun G ( 2005 ) Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants. Nature 436, 593 – 597.; Wu X, Shi Z, Cui M, Han M & Ruvkun G ( 2012 ) Repression of germline RNAi pathways in somatic cells by retinoblastoma pathway chromatin complexes. PLoS Genet 8, e1002542.; Janic A, Mendizabal L, Llamazares S, Rossell D & Gonzalez C ( 2010 ) Ectopic expression of germline genes drives malignant brain tumor growth in Drosophila. Science 330, 1824 – 1827.; Sowpati DT, Ramamoorthy S & Mishra RK ( 2015 ) Expansion of the polycomb system and evolution of complexity. Mech Dev 138 ( Pt 2 ), 97 – 112.; Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA, McCann JL, McDougle RM, Carpenter MA, Martens JW, Span PN et al. ( 2020 ) Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. Elife 9, e61287.; Morris EJ & Dyson NJ ( 2001 ) Retinoblastoma protein partners. Adv Cancer Res 82, 1 – 54.; Luger K, Mäder AW, Richmond RK, Sargent DF & Richmond TJ ( 1997 ) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251 – 260.; Li B, Qing T, Zhu J, Wen Z, Yu Y, Fukumura R, Zheng Y, Gondo Y & Shi L ( 2017 ) A comprehensive mouse transcriptomic BodyMap across 17 tissues by RNA-seq. Sci Rep 7, 4200.; GTEx Consortium ( 2015 ) Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648 – 660.; Baudat F, Imai Y & de Massy B ( 2013 ) Meiotic recombination in mammals: localization and regulation. Nat Rev Genet 14, 794 – 806.; Zickler D, Kleckner N ( 2015 ) Recombination, pairing, and synapsis of homologs during meiosis. Cold Spring Harb Perspect Biol 7, a016626.; Soh YQS, Junker JP, Gill ME, Mueller JL, van Oudenaarden A & Page DC ( 2015 ) A gene regulatory program for meiotic prophase in the fetal ovary. PLoS Genet 11, e1005531.; Suzuki A, Hirasaki M, Hishida T, Wu J, Okamura D, Ueda A, Nishimoto M, Nakachi Y, Mizuno Y, Okazaki Y et al. ( 2016 ) Loss of MAX results in meiotic entry in mouse embryonic and germline stem cells. Nat Commun 7, 11056.; Folco HD, Chalamcharla VR, Sugiyama T, Thillainadesan G, Zofall M, Balachandran V, Dhakshnamoorthy J, Mizuguchi T & Grewal SIS ( 2017 ) Untimely expression of gametogenic genes in vegetative cells causes uniparental disomy. Nature 543, 126 – 130.; Volpe TA, Kidner C, Hall IM, Teng G, Grewal SIS & Martienssen RA ( 2002 ) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833 – 1837.; Volpe T, Schramke V, Hamilton GL, White SA, Teng G, Martienssen RA & Allshire RC ( 2003 ) RNA interference is required for normal centromere function in fission yeast. Chromosome Res 11, 137 – 146.; Lee J, Iwai T, Yokota T & Yamashita M ( 2003 ) Temporally and spatially selective loss of Rec8 protein from meiotic chromosomes during mammalian meiosis. J Cell Sci 116 ( Pt 13 ), 2781 – 2790.; Engel E & DeLozier-Blanchet CD ( 1991 ) Uniparental disomy, isodisomy, and imprinting: probable effects in man and strategies for their detection. Am J Med Genet 40, 432 – 439.; Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Calcar SV, Qu C, Ching KA et al. ( 2007 ) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39, 311 – 318.; Barski A, Cuddapah S, Cui K, Roh T, Schones DE, Wang Z, Wei G, Chepelev I & Zhao K ( 2007 ) High-resolution profiling of histone methylations in the human genome. Cell 129, 823 – 837.; Powers NR, Parvanov ED, Baker CL, Walker M, Petkov PM & Paigen K ( 2016 ) The meiotic recombination activator PRDM9 trimethylates both H3K36 and H3K4 at recombination hotspots in vivo. PLoS Genet 12, e1006146.; D’Gama AM & Walsh CA ( 2018 ) Somatic mosaicism and neurodevelopmental disease. Nat Neurosci 21, 1504 – 1514.; Zylka MJ, Simon JM & Philpot BD ( 2015 ) Gene length matters in neurons. Neuron 86, 353 – 355.; Wei P-C, Chang A, Kao J, Du Z, Meyers R, Alt F & Schwer B ( 2016 ) Long neural genes harbor recurrent DNA break clusters in neural stem/progenitor cells. Cell 164, 644 – 655.; Guemez-Gamboa A, Coufal NG & Gleeson JG ( 2014 ) Primary cilia in the developing and mature brain. Neuron 82, 511 – 521.

الإتاحة: https://doi.org/10.1111/febs.16196Test
https://hdl.handle.net/2027.42/172311Test

المؤلفون: Wollman, Adam J.M., Hedlund, Erik G., Shashkova, Sviatlana, Leake, Mark C.

المصدر: Methods (San Diego, Calif.)

مصطلحات موضوعية: Saccharomyces cerevisiae Proteins, EMCCD, electron multiplying charge-coupled device, Intravital Microscopy, FISH, fluorescence in situ hybridization, Green Fluorescent Proteins, PBS, phosphate-buffered saline, Saccharomyces cerevisiae, Article, Imaging, Three-Dimensional, Genes, Reporter, Transcription factors, GFP, green fluorescent protein, Fluorescent Dyes, Cell Nucleus, Spatial Analysis, Single-molecule, ChIP-Seq, chromatin immunoprecipitation-sequencing, Single Molecule Imaging, Gene regulation, Repressor Proteins, Microscopy, Fluorescence, Super-resolution, RT, room temperature, Nucleic Acid Conformation, MSD, mean square displacement, Chromosomes, Fungal, Genome, Fungal, Single-Cell Analysis, PSF, point spread function, Yeast genome, Transcription

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=pmid________::420767b3afbfddcf728031cccb128da6Test
http://europepmc.org/articles/PMC6971689Test

المؤلفون: Schmolka, Nina, Silva-Santos, Bruno, Gomes, Anita Q.

مصطلحات موضوعية: Chromatin, Histone methylation, DNA methylation, lncRNAs, miRNAs, T-cell differentiation, B-cell differentiation, Gene expression regulation

العلاقة: https://www.sciencedirect.com/science/article/pii/B9780128179642000046Test; Schmolka N, Silva-Santos B, Gomes AQ. Epigenetic mechanisms in the regulation of lymphocyte differentiation. In: Kabelitz D, Bhat J, editors. Epigenetics of the immune system. San Diego: Academic Press; 2020. p. 77-116.; http://hdl.handle.net/10400.21/12109Test

الإتاحة: https://doi.org/10.1016/B978-0-12-817964-2.00004-6Test
http://hdl.handle.net/10400.21/12109Test