Chromatin organization marks exon-intron structure
Schwartz, Schraga, Meshorer, Eran, Ast, Gil·2009·Nature Structural & Molecular Biology
Cited by (635)
Items 301–400 of 635
- Dissecting relative contributions ofcis- andtrans-determinants to nucleosome distribution by comparingTetrahymenamacronuclear and micronuclear chromatinJie Xiong, Shan Gao, Wen Dui, Wentao Yang, Xiao Chen, Sean D. Taverna, Ronald E. Pearlman, Wendy Ashlock, Wei Miao, Yifan Liu · 2016 · Nucleic Acids Research
- Cotranscriptional splicing efficiencies differ within genes and between cell typesKaran Bedi, Brian Magnuson, Ishwarya Venkata Narayanan, Michelle T. Paulsen, Thomas E. Wilson, Mats E. Ljungman · 2021 · RNA
- Coupling polymerase pausing and chromatin landscapes for precise regulation of transcriptionDaniel A. Gilchrist, Karen Adelman · 2012 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Exon 11 Skipping of E-Cadherin RNA Downregulates Its Expression in Head and Neck Cancer CellsSanjai Sharma, Wei Liao, Xiaofeng C. Zhou, David T. Wong, Alan K. Lichtenstein · 2011 · Molecular Cancer Therapeutics
- Regulation of Alternative Pre-mRNA SplicingMiguel B. Coelho, Christopher W. J. Smith · 2014 · Methods in molecular biology
- Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thalianaWaqas Khokhar, Musa A. Hassan, Anireddy S. N. Reddy, Saurabh Chaudhary, Ibtissam Jabre, Lee James Byrne, Naeem Hasan Syed · 2019 · Frontiers in Plant Science
- The impact of biological sex on alternative splicingGuy Karlebach, Diogo F. T. Veiga, Anne Deslattes Mays, Christina Chatzipantsiou, Pablo Prieto Barja, Maria Chatzou, Anil K Kesarwani, Daniel Daniš, Georgios Kararigas, Xingmin Zhang et al. · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
- Computational analysis of associations between alternative splicing and histone modificationsYuki Shindo, Tadasu Nozaki, Rintaro Saito, Masaru Tomita · 2013 · FEBS Letters
- Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide compositionAkinori Awazu · 2016 · Bioinformatics
- Epigenetics in Social InsectsKarl M. Glastad, Linh M. Chau, M. Goodisman · 2015 · Advances in insect physiology
- Context-dependent splicing regulationShengdong Ke, Lawrence A. Chasin · 2011 · RNA Biology
- Modulation of nuclear REST by alternative splicing: a potential therapeutic target for Huntington's diseaseGuo‐Lin Chen, Qi Ma, Dharmendra B. Goswami, Jianyu Shang, Gregory M. Miller · 2017 · Journal of Cellular and Molecular Medicine
- Characterizing the interplay between gene nucleotide composition bias and splicingSébastien Lemaire, Nicolas Fontrodona, Jean-Baptiste Claude, Hélène Polvèche, Fabien Aubé, Laurent Modolo, Cyril F. Bourgeois, Franck Mortreux, Didier Auboeuf · 2019 · Genome biology
- Nucleosome landscape reflects phenotypic differences in Trypanosoma cruzi life formsAlex Ranieri Jerônimo Lima, Christiane B. de Araujo, Saloê Bispo Poubel, José Salvatore Leister Patané, Ariel Mariano Silber, Maria Carolina Elias, Júlia Pinheiro Chagas da Cunha · 2021 · PLoS Pathogens
- KDM3A regulates alternative splicing of cell-cycle genes following DNA damageMai Baker, Mayra Petasny, Nadeen Taqatqa, Mercedes Bentata, Gillian Kay, Eden Engal, Yuval Nevo, Ahmad Siam, Sara Dahan, Maayan Salton · 2021 · RNA
- Multiple functions of SWI/SNF chromatin remodeling complex in plant-pathogen interactionsYunqing Jian, Won‐Bo Shim, Zhonghua Ma · 2021 · Stress Biology
- Characterizing crosstalk in epigenetic signaling to understand disease physiologyJoanna K. Lempiäinen, Benjamin Aaron Garcia · 2023 · Biochemical Journal
- Position-dependent effects of RNA-binding proteins in the context of co-transcriptional splicingTimur Horn, Alison R Gosliga, Congxin Li, Mihaela Enculescu, Stefan Legewie · 2023 · npj Systems Biology and Applications
- Prp40 and early events in splice site definitionSoraya Becerra, Eduardo Andrés‐León, Silvia Prieto‐Sánchez, Cristina Hernández-Munaín, Carlos Suñé · 2015 · Wiley Interdisciplinary Reviews - RNA
- RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human DiseasesAmber R. Willbanks, Shaun Wood, Jason Xiaojun Cheng · 2021 · Genes
- Corrigendum: Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells.Camilla Iannone, Andy Pohl, Panagiotis Papasaikas, Daniel Soronellas, Guillermo Pablo Vicent, Miguel Beato, Juan Valcárcel · 2015 · PubMed Central
- Narrow H3K4me2 is required for chicken PGC formationChen Yu Zhang, Qisheng Zuo, Man Wang, Hao Chen, Nana He, Jing Jin, Tingting Li, Jingyi Jiang, Xia Yuan, Jiancheng Li et al. · 2020 · Journal of Cellular Physiology
- Regulation of alternative splicing: Functional interplay with epigenetic modifications and its implication to cancerNing Wang, Yue Hu, Zefeng Wang · 2023 · Wiley Interdisciplinary Reviews - RNA
- CAG repeat expansion in the Huntington’s disease gene shapes linear and circular RNAs biogenesisDilara Ayyildiz, Alan Monziani, Takshashila Tripathi, Jessica Döring, Guendalina Bergonzoni, Emanuela Kerschbamer, Francesca Di Leva, Elia Pennati, Luisa Donini, Marina V. Kovalenko et al. · 2023 · PLoS Genetics
- H2B ubiquitylation modulates spliceosome assembly and function in budding yeastLucas Hérissant, Erica A. Moehle, Diego Bertaccini, Alain VAN DORSSELAER, Christine Schaeffer‐Reiss, Christine Guthrie, Catherine Dargemont · 2014 · Biology of the Cell
- Connecting the dots: chromatin and alternative splicing in EMTJessica A. Warns, James Davie, Archana Dhasarathy · 2015 · Biochemistry and Cell Biology
- Histone Modifications Are Associated with Transcript Isoform Diversity in Normal and Cancer CellsOndřej Podlaha, Subhajyoti De, Mithat Gönen, Franziska Michor A · 2014 · PLoS Computational Biology
- CTCF: from insulators to alternative splicing regulationAlberto Rodolfo Kornblihtt · 2012 · Cell Research
- Introns Structure Patterns of Variation in Nucleotide Composition in Arabidopsis thaliana and Rice Protein-Coding GenesAdrienne Ressayre, Sylvain Glémin, Pierre Montalent, Laurana Serres-Giardi, Christine Dillmann, Johann Joets · 2015 · Genome Biology and Evolution
- Crop epigenetics and the molecular hardware of genotype × environment interactionsGraham J.W. King · 2015 · Frontiers in Plant Science
- Genome-Wide Identification of the CrRLK1L Subfamily and Comparative Analysis of Its Role in the Legume-Rhizobia SymbiosisJorge Solís-Miranda, Citlali Fonseca-García, Noreide Nava, Ronal Pacheco, Carmen Quinto · 2020 · Genes
- Quantification of somatic mutation flow across individual cell division events by lineage sequencingYehuda Brody, Robert J. Kimmerling, Yosef E. Maruvka, David I. Benjamin, Joshua J. Elacqua, Nicholas J. Haradhvala, Jaegil Kim, Kent William Mouw, Kristjana Frangaj, Amnon Koren et al. · 2018 · Genome Research
- TALE-directed local modulation of H3K9 methylation shapes exon recognitionNicole I. Bieberstein, Eva Kozáková, Martina Huranová, Prasoon Kumar Thakur, Zuzana Krchňáková, Michaela Krausová, Fernando Carrillo Oesterreich, David Staněk · 2016 · Scientific Reports
- Well-positioned nucleosomes punctuate polycistronic pol II transcription units and flank silent VSG gene arrays in Trypanosoma bruceiJohannes Petrus Maree, Megan L. Povelones, David J. Clark, Gloria Rudenko, Hugh‐G. Patterton · 2017 · Epigenetics & Chromatin
- GC‐content biases in protein‐coding genes act as an “mRNA identity” feature for nuclear exportAlexander F. Palazzo, Yoon Mo Kang · 2020 · BioEssays
- Chromatin: The Final Frontier in Splicing Regulation?Kristi L. Fox-Walsh, Xiang‐Dong Fu · 2010 · Developmental Cell
- The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell MetabolismGiuseppe Biamonti, Lucia Maita, Alessandra Montecucco · 2018 · Frontiers in Oncology
- Mass spectrometry and biochemical analysis of RNA polymerase II: targeting by protein phosphatase-1Marina Jerebtsova, Sergey A. Klotchenko, Т. О. Артамонова, Tatiana Ammosova, Kareem N. Washington, Vladimir V. Egorov, Aram A. Shaldzhyan, Maria V. Sergeeva, Evgeny A. Zatulovskiy, Olga A. Temkina et al. · 2010 · Molecular and Cellular Biochemistry
- Exploratory analysis of genomic segmentations with SegtoolsOrion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine G. Le Roch, William Stafford Noble · 2011 · BMC Bioinformatics
- A Minimal Set of Tissue-Specific Hypomethylated CpGs Constitute Epigenetic Signatures of Developmental ProgrammingAlejandro Colaneri, Tianyuan Wang, Vijayakanth Pagadala, Jaya Kittur, Nickolas G. Staffa, Shyamal D. Peddada, ELVIRA M. ISGANAITIS, Mary‐Elizabeth Patti, Lutz Birnbaumer · 2013 · PLoS ONE
- The epigenetic landscape of oligodendrocyte lineage cellsIpek Selcen, Emily Prentice, Patrizia Casaccia · 2023 · Annals of the New York Academy of Sciences
- Systems analysis of alternative splicing and its regulationXinshu Grace Xiao, Jae‐Hyung Lee · 2010 · WIREs Systems Biology and Medicine
- Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer CellsChang Pyo Hong, Moon Kyung Choe, Tae‐Young Roh · 2012 · Genomics & Informatics
- ArchAlign: Coordinate-free chromatin alignment reveals novel architecturesWilliam Lai, Michael Joseph Buck · 2010 · Genome biology
- Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell linesChe-yu Lee, Liang Chen · 2013 · Bioinformatics
- Effect of epigenetic histone modifications on E-cadherin splicing and expression in lung cancer.Wei Liao, Gwen Jordaan, Minu K. Srivastava, Steven M. Dubinett, Sherven P. Sharma, Sanjai Sharma · 2013 · Europe PMC (PubMed Central)
- Shaping the Arabidopsis Transcriptome through Alternative SplicingDorothee Staiger · 2015 · Advances in Botany
- Dynamic alterations in methylation of global DNA and growth-related genes in large yellow croaker (Larimichthys crocea) in response to starvation stressYu Zhang, Weiliang Shen, Mingyue Cao, Juan Li, Baoxiao Zheng, Zhengjia Lou, Baoying Qian, Liangyi Xue · 2018 · Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology
- Histone H1.5 binds over splice sites in chromatin and regulates alternative splicingOhad Glaich, Yodfat Leader, Galit Lev-Maor, Gil Ast · 2019 · Nucleic Acids Research
- Bioinformatics identification of splice site signals and prediction of mutation effectsFrançois-Olivier Desmet, Dalil Hamroun, Gwenaëlle Collod‐Béroud, Mireille Claustres, Christophe Béroud · 2010 · HAL
- Silencing by the HUSH Epigenetic Transcriptional Repressor ComplexPaul J. Lehner · 2025 · Annual Review of Biochemistry
- Centromeric and pericentric transcription and transcripts: their intricate relationships, regulation, and functionsJing Zhu, Qiao Guo, Minjun W. Choi, Zhoubin Liang, Karen Wing Yee Yuen · 2023 · Chromosoma
- Global remodeling of nucleosome positions in C. elegansGeorge Locke, Devorah M. Haberman, Steven Johnson, Alexandre V. Morozov · 2013 · BMC Genomics
- Genetic and epigenetic variants contributing to clofarabine cytotoxicityMichael T. Eadon, Heather E. Wheeler, Amy L. Stark, Xu Zhang, Erika L. Moen, Shannon M. Delaney, Hae Kyung Im, Patrick N. Cunningham, Wei Zhang, M. Eileen Dolan · 2013 · Human Molecular Genetics
- Epigenetics at the base of alternative splicing changes that promote colorectal cancerAlberto Rodolfo Kornblihtt · 2017 · Journal of Clinical Investigation
- Transcription of intragenic CpG islands influences spatiotemporal host gene pre-mRNA processingSamuele M. Amante, Bertille Montibus, Michael Cowley, Nikolaos Barkas, Jessica Setiadi, Heba Saadeh, Joanna Giemza, S. Contreras, Karin Fleischanderl, Reiner Schulz et al. · 2020 · Nucleic Acids Research
- Role of Viral Ribonucleoproteins in Human Papillomavirus Type 16 Gene ExpressionNaoko Kajitani, Stefan Schwartz · 2020 · Viruses
- Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene NetworksAngelika Voronova, Martha Rendón‐Anaya, Pär K. Ingvarsson, Ruslan N. Kalendar, Dainis Edgars Rungis · 2020 · Genes
- Histone and RNA-binding protein interaction creates crosstalk network for regulation of alternative splicingYong‐Eun Kim, Chungoo Park, Kyoon Eon Kim, Kee Kwang Kim · 2018 · Biochemical and Biophysical Research Communications
- Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongationCorina Pascal, Jonathan Zonszain, Ofir Hameiri, Chen Gargi-Levi, Galit Lev-Maor, Luna Tammer, Tamar Levy, Anan Tarabeih, Vanessa Rachel Roy, Stav Ben-Salmon et al. · 2023 · Molecular Cell
- Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genesTonglaga Bao, Hong Li, Xiaoqing Zhao, Guoqing Liu · 2012 · Chromosome Research
- DNA Repair in Nucleosomes: Insights from Histone Modifications and MutantsKathiresan Selvam, John J. Wyrick, Michael A. Parra · 2024 · International Journal of Molecular Sciences
- The Functional Relationship Between RNA Splicing and the Chromatin LandscapeJuan-Carlos Yustis, Maëva Devoucoux, Jacques Côté · 2024 · Journal of Molecular Biology
- Analysis of complex fluids using microfluidics: the particular case of DNA/polycations assembliesAdriana Cristina Toma, Rolf Dootz, Thomas Pfohl · 2013 · Journal of Physics D Applied Physics
- First Come, First Served: Sui Generis Features of the First IntronDavid Zalabák, Yoshihisa Ikeda · 2020 · Plants
- Compositional Features and Codon Usage Pattern of Genes Associated with Anxiety in HumanArif Uddin · 2020 · Molecular Neurobiology
- Comprehensive Analysis of Alternative Splicing in Digitalis purpurea by Strand-Specific RNA-SeqBin Wu, Fengmei Suo, Wanjun Lei, Lianfeng Gu · 2014 · PLoS ONE
- Stochastic Variation in DNA Methylation Modulates Nucleosome Occupancy and Alternative Splicing in Arabidopsis thalianaIbtissam Jabre, Saurabh Chaudhary, Cornelia M. Wilson, Dorothee Staiger, Naeem Hasan Syed · 2022 · Plants
- Modeling Exon Expression Using Histone ModificationsShijia Zhu, Guohua Wang, Bo Liu, Yadong Wang · 2013 · PLoS ONE
- Epigenetic Regulation in Cell Reprogramming Revealed by Genome-Wide AnalysisChang Pyo Hong, Jihwan Park, Tae‐Young Roh · 2011 · Epigenomics
- Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatmentCharles A. Lambert, Nancy Garbacki, Alain Colige · 2017 · The International Journal of Biochemistry & Cell Biology
- DNMT3B shapes the mCA landscape and regulates mCG for promoter bivalency in human embryonic stem cellsHong Kee Tan, Chan-Shuo Wu, Jia Li, Zi Hui Tan, Jordan R Hoffman, Christopher J. Fry, Henry He Yang, Annalisa Di Ruscio, Daniel Geoffrey Tenen · 2019 · Nucleic Acids Research
- Epigenetics in Necrotizing EnterocolitisJayasree Nair, Akhil Maheshwari · 2021 · Current Pediatric Reviews
- The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulationHenrik Lindehell, Alexander Glotov, Eshagh Dorafshan, Yuri B. Schwartz, Jan Larsson · 2021 · Science Advances
- Chromatin structure and pre-mRNA processing work togetherSilvia Jimeno-González, José C. Reyes · 2016 · Transcription
- Genome stability versus transcript diversityBrian Magnuson, Karan Bedi, Mats E. Ljungman · 2016 · DNA repair
- Human exonization through differential nucleosome occupancyYumei Li, Chen Li, Shuxian Li, Qi Peng, Ni A. An, Aibin He, Chuan‐Yun Li · 2018 · Proceedings of the National Academy of Sciences
- Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogasterPhilge Philip, Fredrik H. Pettersson, Per Stenberg · 2012 · BMC Genomics
- Analysis of codon usage of Horseshoe Bat Hepatitis B virus and its hostBornali Deb, Arif Uddin, Supriyo Chakraborty · 2021 · Virology
- SUMOylation regulates pre‐mRNA splicing to overcome DNA damage in fungiYunqing Jian, Xia Chen, Kewei Sun, Zunyong Liu, Danni Cheng, Jie Cao, Jianzhao Liu, Xiaofei Cheng, Liang Wu, Feng Zhang et al. · 2022 · New Phytologist
- Chromatin structure characteristics of pre-miRNA genomic sequencesShijia Zhu, Qinghua Jiang, Guohua Wang, Bo Liu, Mingxiang Teng, Yadong Wang · 2011 · BMC Genomics
- New Insights from Existing Sequence Data: Generating Breakthroughs without a PipetteAlex M. Plocik, Brenton R. Graveley · 2013 · Molecular Cell
- Genetic variations and alternative splicing: the Glioma associated oncogene 1, GLI1Peter G. Zaphiropoulos · 2012 · Frontiers in Genetics
- Long range chromatin organizationLuciana I. Gómez Acuña, Alberto Rodolfo Kornblihtt · 2014 · Transcription
- Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cellsYoshihiro Ohta, Tatsuhiko Kodama, Sigeo Ihara · 2011 · Physical Review E
- Regulation by alternative splicingYair Aaronson, Eran Meshorer · 2013 · Nature
- Combined single-cell profiling of chromatin–transcriptome and splicing across brain cell types, regions and disease stateWen Hu, Careen Foord, Justine Hsu, Li Fan, Michael J. Corley, Samantha N. Lanjewar, Siwei Xu, Natan Belchikov, Yi He, Alina P.S. Pang et al. · 2025 · Nature Biotechnology
- High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAsPinki Dey, John S. Mattick · 2021 · Epigenetics & Chromatin
- Alternative splicing diversifies the skeletal muscle transcriptome during prolonged spaceflightMason Henrich, Pin Ha, Yuanyuan Wang, Kang Ting, Louis Stodieck, Chia B. Soo, John S. Adams, Rene F. Chun · 2022 · Skeletal Muscle
- Histone Marks-Dependent Effect on Alternative Splicing: New Perspectives for Targeted Splicing Modulation in Cancer?Carol Imbriano, Silvia Belluti · 2022 · International Journal of Molecular Sciences
- Alternative Splicing in the Regulatory Circuit of Plant Temperature ResponseRong Xue, Ruirui Mo, Dongkai Cui, Wencong Cheng, Haoyu Wang, Jinxia Qin, Zhenshan Liu · 2023 · International Journal of Molecular Sciences
- Nucleosome organization in sequences of alternative events in human genomeHuan Huang, Shuangxin Yu, Hongde Liu, Xiao Song Sun · 2012 · Biosystems
- Chromatin computation: Epigenetic inheritance as a pattern reconstruction problemChristian Arnold, Peter Florian Stadler, Sonja J. Prohaska · 2013 · Journal of Theoretical Biology
- DNA Methylation is Associated with an Increased Level of Conservation at Nondegenerate Nucleotides in MammalsTrees‐Juen Chuang, Feng‐Chi Chen · 2013 · Molecular Biology and Evolution
- Transcriptional control of embryonic and induced pluripotent stem cells.M. Guenther · 2011 · Epigenomics
- Conservation and divergence of the histone code in nucleomorphsGeorgi K. Marinov, Michael Lynch · 2016 · Biology Direct
- Epigenetic silencing of OR and TAS2R genes expression in human orbitofrontal cortex at early stages of sporadic Alzheimer’s diseaseVictória Cunha Alves, Joana Figueiro‐Silva, Isidró Ferrer, Eva Carro · 2023 · Cellular and Molecular Life Sciences
- Histone modifications involved in cassette exon inclusions: a quantitative and interpretable analysisHui Liu, Ting Jin, Jihong Guan, Shuigeng Zhou · 2014 · BMC Genomics
- Molecular identification of the dominant-negative, splicing isoform of the two-pore domain K+ channel K2P5.1 in lymphoid cells and enhancement of its expression by splicing inhibitionKyoko Endo, Natsumi Kurokawa, Hiroaki Kito, Sawa Nakakura, Masanori Fujii, Susumu Ohya · 2015 · Biochemical Pharmacology
- Alternatively spliced MEFV transcript lacking exon 2 and its protein isoform pyrin-2d implies an epigenetic regulation of the gene in inflammatory cell culture modelsGökçe Çelikyapi Erdem, Sule Erdemir, İrem Abacı, Aslı Kireçtepe Aydın, Elif Everest, Eda Tahir Turanlı · 2017 · Genetics and Molecular Biology