Dual-initiation promoters with intertwined canonical and TCT/TOP transcription start sites diversify transcript processing

[1]  Vanja Haberle,et al.  Transcriptional cofactors display specificity for distinct types of core promoters , 2019, Nature.

[2]  D. Onichtchouk,et al.  Maternal Nanog is required for zebrafish embryo architecture and for cell viability during gastrulation , 2018, Development.

[3]  Xosé M. Fernández-Suárez,et al.  The 2018 Nucleic Acids Research database issue and the online molecular biology database collection , 2017, Nucleic Acids Res..

[4]  S. Hubbard,et al.  Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses , 2017, Genome Biology.

[5]  S. Hubbard,et al.  Dynamic changes in eIF4F-mRNA interactions revealed by global analyses of environmental stress responses , 2017, Genome Biology.

[6]  Ran Elkon,et al.  Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation , 2017, Cell.

[7]  Han Rauwerda,et al.  UvA-DARE ( Digital Academic Repository ) Linking Maternal and Somatic 5 S rRNA types with Different Sequence-Specific Non-LTR Retrotransposons , 2017 .

[8]  I. Ulitsky,et al.  Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress , 2017, eLife.

[9]  D. Karolchik,et al.  The UCSC Genome Browser database: 2017 update , 2016, Nucleic Acids Res..

[10]  Yue Wang,et al.  Long non-coding RNA GAS5 controls human embryonic stem cell self-renewal by maintaining NODAL signalling , 2016, Nature Communications.

[11]  C. Benner,et al.  Nascent RNA sequencing reveals distinct features in plant transcription , 2016, Proceedings of the National Academy of Sciences.

[12]  Wei Chen,et al.  Pervasive isoform‐specific translational regulation via alternative transcription start sites in mammals , 2016, Molecular systems biology.

[13]  J. Pelletier,et al.  nanoCAGE reveals 5′ UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs , 2016, Genome research.

[14]  Piero Carninci,et al.  Transcriptional, post-transcriptional and chromatin-associated regulation of pri-miRNAs, pre-miRNAs and moRNAs , 2015, Nucleic acids research.

[15]  Oded Meyuhas,et al.  The race to decipher the top secrets of TOP mRNAs. , 2015, Biochimica et biophysica acta.

[16]  Masahiro Morita,et al.  La-related Protein 1 (LARP1) Represses Terminal Oligopyrimidine (TOP) mRNA Translation Downstream of mTOR Complex 1 (mTORC1)* , 2015, The Journal of Biological Chemistry.

[17]  Martina Rath,et al.  Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation , 2014, Nature.

[18]  Boris Lenhard,et al.  CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses , 2015, Nucleic acids research.

[19]  A. Sandelin,et al.  Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes , 2014, Genes & development.

[20]  André L. Martins,et al.  Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers , 2014, Nature Genetics.

[21]  Julia Zeitlinger,et al.  TRF2, but not TBP, mediates the transcription of ribosomal protein genes , 2014, Genes & development.

[22]  E. O’Shea,et al.  Promoter sequences direct cytoplasmic localization and translation of mRNAs during starvation in yeast , 2014, Nature.

[23]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[24]  Nan Li,et al.  Two independent transcription initiation codes overlap on vertebrate core promoters , 2014, Nature.

[25]  I. Dawid.  Faculty Opinions recommendation of Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition. , 2013 .

[26]  Miler T. Lee,et al.  Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition , 2013, Nature.

[27]  Boris Lenhard,et al.  Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis , 2013, Genome research.

[28]  Steven A. Harvey,et al.  Identification of the zebrafish maternal and paternal transcriptomes , 2013, Development.

[29]  Stefan Stamm,et al.  Processing of snoRNAs as a new source of regulatory non‐coding RNAs , 2013, BioEssays : news and reviews in molecular, cellular and developmental biology.

[30]  D. Sabatini,et al.  A unifying model for mTORC1-mediated regulation of mRNA translation , 2012, Nature.

[31]  A. Sandelin,et al.  Metazoan promoters: emerging characteristics and insights into transcriptional regulation , 2012, Nature Reviews Genetics.

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

[33]  Nicholas T. Ingolia,et al.  The translational landscape of mTOR signalling steers cancer initiation and metastasis , 2012, Nature.

[34]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[35]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[36]  Piero Carninci,et al.  Genome-wide analysis of promoter architecture in Drosophila melanogaster. , 2011, Genome research.

[37]  Michael Y. Galperin,et al.  The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2010, Nucleic Acids Res..

[38]  Peter J. Bickel,et al.  The Developmental Transcriptome of Drosophila melanogaster , 2010, Nature.

[39]  B. Graveley.  The developmental transcriptome of Drosophila melanogaster , 2010, Nature.

[40]  D. Corcoran,et al.  The TCT motif, a key component of an RNA polymerase II transcription system for the translational machinery. , 2010, Genes & development.

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

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

[43]  Sean R. Eddy,et al.  Infernal 1.0: inference of RNA alignments , 2009, Bioinform..

[44]  Robert D. Finn,et al.  Rfam: updates to the RNA families database , 2008, Nucleic Acids Res..

[45]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[46]  Yi Wen Kong,et al.  The mechanism of micro-RNA-mediated translation repression is determined by the promoter of the target gene , 2008, Proceedings of the National Academy of Sciences.

[47]  K. Nakai,et al.  Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics , 2008, Nucleic acids research.

[48]  Peter F. Stadler,et al.  SnoReport: computational identification of snoRNAs with unknown targets , 2008, Bioinform..

[49]  Marco Ferg,et al.  The TATA-binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish , 2007, The EMBO journal.

[50]  Robert Gentleman,et al.  Using GOstats to test gene lists for GO term association , 2007, Bioinform..

[51]  Martin S. Taylor,et al.  Genome-wide analysis of mammalian promoter architecture and evolution , 2006, Nature Genetics.

[52]  T. Kiss,et al.  Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. , 2006, Cold Spring Harbor symposia on quantitative biology.

[53]  J. Makarova,et al.  Noncoding RNA of U87 host gene is associated with ribosomes and is relatively resistant to nonsense-mediated decay. , 2005, Gene.

[54]  J. Martial,et al.  sox4b is a key player of pancreatic alpha cell differentiation in zebrafish. , 2005, Developmental biology.

[55]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[56]  R. Perry.  BMC Evolutionary Biology BioMed Central Research article The architecture of mammalian ribosomal protein promoters , 2005 .

[57]  I. Bozzoni,et al.  TOP promoter elements control the relative ratio of intron-encoded snoRNA versus spliced mRNA biosynthesis. , 2004, Journal of molecular biology.

[58]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[59]  G. Rubin,et al.  Computational analysis of core promoters in the Drosophila genome , 2002, Genome Biology.

[60]  S. Eddy,et al.  A computational screen for methylation guide snoRNAs in yeast. , 1999, Science.

[61]  J. Steitz,et al.  Classification of gas5 as a Multi-Small-Nucleolar-RNA (snoRNA) Host Gene and a Member of the 5′-Terminal Oligopyrimidine Gene Family Reveals Common Features of snoRNA Host Genes , 1998, Molecular and Cellular Biology.

[62]  W. Filipowicz,et al.  The Host Gene for Intronic U17 Small Nucleolar RNAs in Mammals Has No Protein-Coding Potential and Is a Member of the 5′-Terminal Oligopyrimidine Gene Family , 1998, Molecular and Cellular Biology.

[63]  M. Bortolin,et al.  Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. , 1998, RNA.

[64]  G. Hauptmann,et al.  Two-color whole-mount in situ hybridization to vertebrate and Drosophila embryos. , 1994, Trends in genetics : TIG.