Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells.

[1]  Maksims Fiosins,et al.  Oasis 2: improved online analysis of small RNA-seq data , 2018, BMC Bioinformatics.

[2]  Hsien-Da Huang,et al.  miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions , 2017, Nucleic Acids Res..

[3]  V. Wysocki,et al.  Human Argonaute3 has slicer activity , 2017, Nucleic acids research.

[4]  T. Vuorenmaa,et al.  Analysis of primary microRNA loci from nascent transcriptomes reveals regulatory domains governed by chromatin architecture , 2017, Nucleic acids research.

[5]  K. Mulder,et al.  Reactivity of human AGO2 monoclonal antibody 11A9 with the SWI/SNF complex: A case study for rigorously defining antibody selectivity , 2017, Scientific Reports.

[6]  Marc A. Martí-Renom,et al.  Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors , 2017, PLoS Comput. Biol..

[7]  D. Reinberg,et al.  RNA Binding to CBP Stimulates Histone Acetylation and Transcription , 2017, Cell.

[8]  J. Rinn,et al.  "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. , 2016, Molecular cell.

[9]  David S. Wishart,et al.  Heatmapper: web-enabled heat mapping for all , 2016, Nucleic Acids Res..

[10]  François Serra,et al.  Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling , 2016, bioRxiv.

[11]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[12]  Aaron T. L. Lun,et al.  diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data , 2015, BMC Bioinformatics.

[13]  P. Avner,et al.  Xist localization and function: new insights from multiple levels , 2015, Genome Biology.

[14]  Wouter de Laat,et al.  Getting the genome in shape: the formation of loops, domains and compartments , 2015, Genome Biology.

[15]  D. Corey,et al.  Reduced Expression of Argonaute 1, Argonaute 2, and TRBP Changes Levels and Intracellular Distribution of RNAi Factors , 2015, Scientific Reports.

[16]  Eduardo Eyras,et al.  A chromatin code for alternative splicing involving a putative association between CTCF and HP1α proteins , 2015, BMC Biology.

[17]  Cameron S. Osborne,et al.  The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements , 2015, Genome research.

[18]  G. Macino,et al.  ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites , 2015, Nucleic acids research.

[19]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[20]  J. Valcárcel,et al.  Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells , 2014, Proceedings of the National Academy of Sciences.

[21]  P. Kantoff,et al.  Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation , 2014, Proceedings of the National Academy of Sciences.

[22]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[23]  David R. Kelley,et al.  Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre , 2014, Nature Structural &Molecular Biology.

[24]  Miguel Beato,et al.  bwtool: a tool for bigWig files , 2014, Bioinform..

[25]  Jesse R. Dixon,et al.  Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells , 2013, Proceedings of the National Academy of Sciences.

[26]  Boris Lenhard,et al.  Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments , 2013, Genome research.

[27]  G. Schroth,et al.  Cohesin-mediated interactions organize chromosomal domain architecture , 2013, The EMBO journal.

[28]  L. Grøntved,et al.  eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. , 2013, Molecular cell.

[29]  Vladimir B. Bajic,et al.  HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data , 2013, Bioinform..

[30]  Hao Li,et al.  Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells , 2013, PLoS genetics.

[31]  M. Rosenfeld,et al.  LncRNA-Dependent Mechanisms of Androgen Receptor-regulated Gene Activation Programs , 2013, Nature.

[32]  C. Danko,et al.  Enhancer transcripts mark active estrogen receptor binding sites , 2013, Genome research.

[33]  G. Meister.  Argonaute proteins: functional insights and emerging roles , 2013, Nature Reviews Genetics.

[34]  William Stafford Noble,et al.  Integrative annotation of chromatin elements from ENCODE data , 2012, Nucleic acids research.

[35]  Andrew D. Smith,et al.  Site identification in high-throughput RNA-protein interaction data , 2012, Bioinform..

[36]  G. Natoli,et al.  Noncoding transcription at enhancers: general principles and functional models. , 2012, Annual review of genetics.

[37]  J. Dekker,et al.  Hi-C: a comprehensive technique to capture the conformation of genomes. , 2012, Methods.

[38]  Annick Harel-Bellan,et al.  Argonaute proteins couple chromatin silencing to alternative splicing , 2012, Nature Structural &Molecular Biology.

[39]  Bronwen L. Aken,et al.  GENCODE: The reference human genome annotation for The ENCODE Project , 2012, Genome research.

[40]  P. Cohen,et al.  AGO4 regulates entry into meiosis and influences silencing of sex chromosomes in the male mouse germline. , 2012, Developmental cell.

[41]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[42]  Giacomo Cavalli,et al.  Polycomb: a paradigm for genome organization from one to three dimensions. , 2012, Current opinion in cell biology.

[43]  J. Sedat,et al.  Spatial partitioning of the regulatory landscape of the X-inactivation centre , 2012, Nature.

[44]  Jesse R. Dixon,et al.  Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.

[45]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[46]  Michael S. Becker,et al.  Spatial Organization of the Mouse Genome and Its Role in Recurrent Chromosomal Translocations , 2012, Cell.

[47]  Piero Carninci,et al.  5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing , 2012, Nature Protocols.

[48]  Piero Carninci,et al.  Chromatin-associated RNAi components contribute to transcriptional regulation in Drosophila , 2011, Nature.

[49]  G. Hannon,et al.  Ancestral roles of small RNAs: an Ago-centric perspective. , 2011, Cold Spring Harbor perspectives in biology.

[50]  Peter J. Bickel,et al.  Measuring reproducibility of high-throughput experiments , 2011, 1110.4705.

[51]  Ryan K. Dale,et al.  RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. , 2011, Genes & development.

[52]  Leighton J. Core,et al.  A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells , 2011, Cell.

[53]  V. Corces,et al.  Enhancer function: new insights into the regulation of tissue-specific gene expression , 2011, Nature Reviews Genetics.

[54]  Piero Carninci,et al.  NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. , 2011, Cold Spring Harbor protocols.

[55]  Mark Groudine,et al.  Functional and Mechanistic Diversity of Distal Transcription Enhancers , 2011, Cell.

[56]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[57]  G. Kreiman,et al.  Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.

[58]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[59]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[60]  A. Lassar,et al.  Id3 is a direct transcriptional target of Pax7 in quiescent satellite cells. , 2009, Molecular biology of the cell.

[61]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[62]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[63]  Shinsei Minoshima,et al.  Identification of eight members of the Argonaute family in the human genome. , 2003, Genomics.

[64]  Xiaofeng Cao,et al.  ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation , 2003, Science.

[65]  Ira M. Hall,et al.  Regulation of Heterochromatic Silencing and Histone H3 Lysine-9 Methylation by RNAi , 2002, Science.

[66]  J. Nickerson,et al.  Chromatin architecture and nuclear RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[67]  D. Holmes,et al.  Chromosomal RNA: Its Properties , 1972, Science.