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Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary by Colin D. Malone and others (2009)

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Authors include Colin D. Malone.

doi.org/10.1016/j.cell.2009.03.040

cell 137, pp. 522–535. Nine pathway mutants, small-RNA populations and Piwi localization distinguish germline and somatic ovarian pathways.

DNA-guided DNA interference by a prokaryotic Argonaute by Daan C. Swarts and others (2014)

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Authors include Daan C. Swarts.

doi.org/10.1038/nature12971

Nature 507, pp. 258–261. Figures 1–4: plasmid restriction, DNA guides and Complementary DNA cleavage distinguish a bacterial defence system from RNA-guided RNA interference.

ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation by Daniel Zilberman and others (2003)

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Authors include Daniel Zilberman.

doi.org/10.1126/science.1079695

Science 299, pp. 716–719. AGO4 mutants test small-RNA-associated chromatin regulation at SUPERMAN and AtSN1.

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piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans by Alyson Ashe and others (2012)

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Authors include Alyson Ashe.

doi.org/10.1016/j.cell.2012.06.018

cell 150, pp. 88–99. Trigger removal and nuclear RNAi/chromatin mutants distinguish establishment from maintenance.

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Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes by Toshiaki Watanabe and others (2008)

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Authors include Toshiaki Watanabe.

doi.org/10.1038/nature06908

Nature 453, pp. 539–543. Small-RNA sequencing and Dicer/Ago2 loss establish endogenous siRNA roles in oocytes.

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A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice by Alexei A. Aravin and others (2008)

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Authors include Alexei A. Aravin.

doi.org/10.1016/j.molcel.2008.09.003

Molecular cell 31, pp. 785–799. Fetal-germ-cell MILI/MIWI2 localization, piRNAs and methylation-pathway mutants establish ordering.

An epigenetic role for maternally inherited piRNAs in transposon silencing by Julius Brennecke and others (2008)

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Authors include Julius Brennecke.

doi.org/10.1126/science.1165171

Science 322, pp. 1387–1392. Reciprocal crosses link maternal piRNAs to transposon control and hybrid dysgenesis.

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Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila by Julius Brennecke and others (2007)

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Authors include Julius Brennecke.

doi.org/10.1016/j.cell.2007.01.043

cell 128, pp. 1089–1103. Piwi-family immunoprecipitation and small-RNA sequencing identify clusters and complementary piRNA populations.

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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 by Rosalind C. Lee and others (1993)

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doi.org/10.1016/0092-8674(93)90529-Y

cell 75, pp. 843–854. Transformation rescue, small-RNA detection and target complementarity establish a developmental regulatory RNA.

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans by Andrew Fire and others (1998)

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Nature 391, pp. 806–811. Double-stranded versus single-stranded RNA injection controls establish potent sequence-specific interference.

Excised linear introns regulate growth in yeast by Jeffrey T. Morgan and others (2019)

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scGen predicts single-cell perturbation responses by Mohammad Lotfollahi and others (2019, 10.1038/s41592-019-0494-8)

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Gene name errors are widespread in the scientific literature by Mark Ziemann and others (2016, 10.1186/s13059-016-1044-7)

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RNase H2-initiated ribonucleotide excision repair by Justin L. Sparks and others

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Molecular biological cell 47, 980–986 (2012). Publisher record. Primary article or institutional bibliographic record.

Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair by Micheline Strand and others

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Nature 365, 274–276 (1993). Publisher record. Primary article or institutional bibliographic record.

Human mismatch repair: reconstitution of a nick-directed bidirectional reaction by Nicoleta Constantin and others

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Journal of Biological Chemistry 280, 39752–39761 (2005). Publisher record. Primary article or institutional bibliographic record.

The origin and behavior of mutable loci in maize by Barbara McClintock (1950)

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By Barbara McClintock. PNAS 36, pp. 344–355; genetic and cytological evidence for mobile controlling elements.

Genomic imprinting and the strange case of the insulin-like growth factor II receptor by David Haig and C. Graham (1991)

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Primary publication or institutional full text.

By David Haig, C. Graham. Cell 64, pp. 1045–1046; original kinship-conflict interpretation of imprinted growth regulation.

Parental imprinting of the mouse insulin-like growth factor II gene by Thomas M. DeChiara and others (1991)

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By Thomas M. DeChiara. Cell 64, pp. 849–859; parental transmission of targeted Igf2 disruption and growth.

Organization of Chromatin by Intrinsic and Regulated Phase Separation by Bryan A. Gibson and others (2019)

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Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions by Stephen E. Farr and others (2021)

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Chromosome Engineering Allows the Efficient Isolation of Vertebrate Neocentromeres by Wei-Hao Shang and others (2013)

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Birth, evolution, and transmission of satellite-free mammalian centromeric domains by Solomon G. Nergadze and others (2018)

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Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences by Wei-Hao Shang and others (2010)

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Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system by Baohui Chen and others (2013)

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In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition by Carmen C. Robinett and others (1996)

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Dynamics of ribosome scanning and recycling revealed by translation complex profiling by Stuart K. Archer and others

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Nature 535, 570–574 (2016). Publisher record. Primary article or institutional record.

The translational landscape of mTOR signalling steers cancer initiation and metastasis by Andrew C. Hsieh and others

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Nature 485, 55–61 (2012). Publisher record. Primary article or institutional record.

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution by Sooncheol Lee and others

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PNAS 109, E2424–E2432 (2012). Publisher record. Primary article or institutional record.

Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes by Nicholas T. Ingolia and others

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biological cell 147, 789–802 (2011). Publisher record. Primary article or institutional record.

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling by Nicholas T. Ingolia and others

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Science 324, 218–223 (2009). Publisher record. Primary article or institutional record.

Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase by Bas van Steensel and Steven Henikoff

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Nature Biotechnology 18, 424–428 (2000). Publisher record. Primary article or institutional record.

Cohesin loss eliminates all loop domains by Suhas S. P. Rao and others

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biological cell 171, 305–320.e24 (2017). Publisher record. Primary article or institutional record.

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping by Suhas S. P. Rao and others

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biological cell 159, 1665–1680 (2014). Publisher record. Primary article or institutional record.

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells by Horng D. Ou and others

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Science 357, eaag0025 (2017). Publisher record. Primary article or institutional record.

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position by Jason D. Buenrostro and others

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Nature Methods 10, 1213–1218 (2013). Publisher record. Primary article or institutional record.

Crystal structure of the nucleosome core particle at 2.8 Å resolution by Karolin Luger and others

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Nature 389, 251–260 (1997). Publisher record. Primary article or institutional record.

G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits by Nancy Kedersha and others

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Journal of biological cell Biology 212, 845–860 (2016). Publisher record. Primary article or institutional record.

Single-Molecule Imaging Reveals Translation of mRNAs Localized to Stress Granules by Daniel Mateju and others

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biological cell 183, 1801–1812.e13 (2020). Publisher record. Primary article or institutional record.

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB by Miriam Llorian and others

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Nature Structural & Molecular Biology 17, 1114–1123 (2010). Publisher record. Primary article or institutional record.

RNA looping by PTB: evidence using FRET and NMR spectroscopy for a role in splicing repression by Rajan Lamichhane and others

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PNAS 107, 4105–4110 (2010). Publisher record. Primary article or institutional record.

Structure of PTB bound to RNA: specific binding and implications for splicing regulation by Florian C. Oberstrass and others

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Science 309, 2054–2057 (2005). Publisher record. Primary article or institutional record.

Splicing regulation at the second catalytic step by Sex-lethal involves 3′ splice site recognition by SPF45 by María José Lallena and others

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biological cell 109, 285–296 (2002). Publisher record. Primary article or institutional record.

The protein Sex-lethal antagonizes the splicing factor U2AF to regulate alternative splicing of transformer pre-mRNA by Juan Valcárcel and others

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Nature 362, 171–175 (1993). Publisher record. Primary article or institutional record.

Identification of a novel iron-responsive element in murine and human erythroid delta-aminolevulinic acid synthase mRNA by Thomas Dandekar and others

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EMBO Journal 10, 1903–1909 (1991). Publisher record. Primary article or institutional record.

Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation by Sergi Puig and others

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biological cell 120, 99–110 (2005). Publisher record. Primary article or institutional record.

Iron-responsive elements: regulatory RNA sequences that control mRNA levels and translation by John L. Casey and others

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Science 240, 924–928 (1988). Publisher record. Primary article or institutional record.

Identification of the iron-responsive element for the translational regulation of human ferritin mRNA by Matthias W. Hentze and others

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Science 238, 1570–1573 (1987). Publisher record. Primary article or institutional record.

An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis by Ameen A. Salahudeen and others

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Science 326, 722–726 (2009). Publisher record. Primary article or institutional record.

Cellular regulation of the iron-responsive element binding protein: disassembly of the cubane iron-sulfur cluster results in high-affinity RNA binding by David J. Haile and others

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PNAS 89, 11735–11739 (1992). Publisher record. Primary article or institutional record.

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites by Peter J. Skene and Steven Henikoff

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eLife 6, e21856 (2017). Publisher record. Primary article or institutional record.

GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets by Joerg E. Braun and others

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Molecular biological cell 44, 120–133 (2011). Publisher record. Primary article or institutional record.

Human Upf proteins target an mRNA for nonsense-mediated decay when bound downstream of a termination codon by Jens Lykke-Andersen and others

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biological cell 103, 1121–1131 (2000). Publisher record. Primary article or institutional record.

mRNA stabilization by poly(A) binding protein is independent of poly(A) and requires translation by Jeffery M. Coller and others

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genes & Development 12, 3226–3235 (1998). Publisher record. Primary article or institutional record.

The role of the iron responsive element in the control of ferroportin1/IREG1/MTP1 gene expression by Athina Lymboussaki and others

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Journal of Hepatology 39, 710–715 (2003). Publisher record. Primary article or institutional record.

Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP by Markus Hafner and others (2010)

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doi.org/10.1016/j.cell.2010.03.009

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP) by Eric L. Van Nostrand and others (2016)

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doi.org/10.1038/nmeth.3810

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution by Julian König and others (2010)

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doi.org/10.1038/nsmb.1838

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+ by Chee-Huat Linus Eng and others (2019)

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doi.org/10.1038/s41586-019-1049-y

Spatially resolved, highly multiplexed RNA profiling in single cells by Kok Hao Chen and others (2015)

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doi.org/10.1126/science.aaa6090

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution by Samuel G. Rodriques and others (2019)

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doi.org/10.1126/science.aaw1219

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics by Patrik L. Ståhl and others (2016)

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doi.org/10.1126/science.aaf2403

Structure and function of the feed-forward loop network motif by Shmoolik Mangan and Uri Alon (2003)

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doi.org/10.1073/pnas.2133841100

DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution by Willem P. C. Stemmer

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PNAS 91, 10747–10751 (1994). Publisher record. Primary article or institutional bibliographic record.

Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis by Bernhard Virnekas and others

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Nucleic Acids Research 22, 5600–5607 (1994). Publisher record. Primary article or institutional bibliographic record.

Randomization of genes by PCR mutagenesis by R. Craig Cadwell and Gerald F. Joyce

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PCR Methods and Applications 2, 28–33 (1992). Publisher record. Primary article or institutional bibliographic record.

Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches by Susanne Ude and others

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Science 339, 82–85 (2013). Publisher record. Primary article or institutional bibliographic record.

EF-P is essential for rapid synthesis of proteins containing consecutive proline residues by Lili K. Doerfel and others

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Science 339, 85–88 (2013). Publisher record. Primary article or institutional bibliographic record.

Genome-defence small RNAs exapted for epigenetic mating-type inheritance by Deepankar Pratap Singh and others (2014, 10.1038/nature13318)

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First author: Deepankar Pratap Singh.

Primary research: pubmed.ncbi.nlm.nih.gov/24805235/

Cited passages: Singh and colleagues, 2014, abstract and mtA promoter-excision results.

Selecting One of Several Mating Types through Gene Segment Joining and Deletion in Tetrahymena thermophila by Marcella D. Cervantes and others (2013, 10.1371/journal.pbio.1001518)

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First author: Marcella D. Cervantes.

Primary research: journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001518

Cited passages: Cervantes and colleagues, 2013, results on germline versus somatic mating-type gene organization.

Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia by R. K. Saiki and others (1985, 10.1126/science.2999980)

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First author: R. K. Saiki.

Primary research: pubmed.ncbi.nlm.nih.gov/2999980/

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CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes by Luke A. Gilbert and others (2013, 10.1016/j.cell.2013.06.044)

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First author: Luke A. Gilbert.

Primary research: pmc.ncbi.nlm.nih.gov/articles/PMC3770145/

Cited passages: Gilbert and colleagues, 2013, results on dCas9-based repression and activation in eukaryotic cells.

Multiplex genome engineering using CRISPR/Cas systems by Le Cong and others (2013, 10.1126/science.1231143)

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First author: Le Cong.

Primary research: pmc.ncbi.nlm.nih.gov/articles/PMC3795411/

Cited passages: Cong and colleagues, 2013, abstract and results on endogenous mammalian targeting.

Alternative splicing of METTL3 explains apparently METTL3-independent m6A modifications in mRNA by Hui Xian Poh and others (2022)

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Hui Xian Poh and coauthors.

doi.org/10.1371/journal.pbio.3001683

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore by Ploy N. Pratanwanich and others (2021)

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Ploy N. Pratanwanich and coauthors.

doi.org/10.1038/s41587-021-00949-w

The AAUAAA sequence is required both for cleavage and for polyadenylation of simian virus 40 pre-mRNA in vitro by David Zarkower and others (1986)

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Original research by David Zarkower and colleagues.

doi.org/10.1128/MCB.6.7.2317

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Accurate cleavage and polyadenylation of exogenous RNA substrate by Claire L. Moore and Phillip A. Sharp (1985)

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Original research by Claire L. Moore and Phillip A. Sharp.

doi.org/10.1016/S0092-8674(85)80065-9

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Structure of the bacterial RNA polymerase promoter specificity sigma subunit by Elizabeth A. Campbell and others (2002)

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Original research by Elizabeth A. Campbell and colleagues.

doi.org/10.1016/S1097-2765(02)00470-7

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FourU: a novel type of RNA thermometer in Salmonella by Torsten Waldminghaus and others (2007)

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First author: Torsten Waldminghaus.

Primary source: pubmed.ncbi.nlm.nih.gov/17630972/

Relevant passages: Abstract and results on the agsA 5′ untranslated-region thermometer.

Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression by Wade Winkler and others (2002)

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First author: Wade Winkler.

Primary source: pubmed.ncbi.nlm.nih.gov/12410317/

Relevant passages: Abstract and pp. 952–956, direct metabolite binding by regulatory RNA.

Structural basis of transcription activation: the CAP-alpha CTD-DNA complex by Brian Benoff and others (2002)

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First author: Brian Benoff.

Primary source: pubmed.ncbi.nlm.nih.gov/12202833/

Relevant passages: pp. 1562–1566, CAP–alpha-domain contact and transcription-activation complex.

A mediator required for activation of RNA polymerase II transcription in vitro by Peter M. Flanagan and others (1991, 10.1038/350436a0)

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First author: Peter M. Flanagan.

Primary source: pubmed.ncbi.nlm.nih.gov/2011193/

Relevant passages: Abstract and pp. 436–438, biochemical requirement for mediator activity.

Sequence-specific recognition of double helical nucleic acids by proteins by Nadrian C. Seeman and others (1976, 10.1073/pnas.73.3.804)

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First author: Nadrian C. Seeman.

Primary source: williams.chemistry.gatech.edu/course_Information/nucleic_acid_biochem/articles/rich_pnas_1976.pdf

Relevant passages: pp. 804–808, accessibility of base-edge recognition patterns.

Molecular structure of a left-handed double helical DNA fragment at atomic resolution by A. H.-J. Wang and others (1979, 10.1038/282680a0)

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First author: A. H.-J. Wang.

Primary source: doi.org/10.1038/282680a0

Relevant passages: pp. 680–686, alternating CG duplex and left-handed structure.

Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes by F. William Studier and others (1986, 10.1016/0022-2836(86)90385-2)

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First author: F. William Studier.

Primary source: pubmed.ncbi.nlm.nih.gov/3537305/

Relevant passages: Abstract and pp. 113–130, inducible selective expression.

Independent and stochastic action of DNA polymerases in the replisome by James E. Graham and others (2017)

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James E. Graham and coauthors. 2017. Cell 169, 1201–1213.e17.

doi.org/10.1016/j.cell.2017.05.041

pmc.ncbi.nlm.nih.gov/articles/PMC5548433/

Regulated eukaryotic DNA replication origin firing with purified proteins by Joseph T. P. Yeeles and others (2015)

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Joseph T. P. Yeeles and coauthors. 2015. Nature 519, 431–435.

doi.org/10.1038/nature14285

www.nature.com/articles/nature14285

Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing by Dirk Remus and others (2009)

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Dirk Remus and coauthors. 2009. Cell 139, 719–730.

doi.org/10.1016/j.cell.2009.10.015

pubmed.ncbi.nlm.nih.gov/19896182/

Activation of GCN2 by the ribosomal P-stalk by Alison J. Inglis and others (2019)

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Original research by Alison J. Inglis and colleagues.

doi.org/10.1073/pnas.1813352116

pmc.ncbi.nlm.nih.gov/articles/PMC6421407/

Epigenetic inheritance uncoupled from sequence-specific recruitment by Kaushik Ragunathan and others (2015)

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Original research by Kaushik Ragunathan and colleagues.

doi.org/10.1126/science.1258699

pmc.ncbi.nlm.nih.gov/articles/PMC4385470/

Ribosome-dependent activation of stringent control by Alan Brown and others (2016)

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Original research by Alan Brown and colleagues.

doi.org/10.1038/nature17675

pmc.ncbi.nlm.nih.gov/articles/PMC4900451/

Sestrin2 is a leucine sensor for the mTORC1 pathway by Rachel L. Wolfson and others (2016)

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Original research by Rachel L. Wolfson and colleagues.

doi.org/10.1126/science.aab2674

pmc.ncbi.nlm.nih.gov/articles/PMC4698017/

Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells by Krishna M. Vattem and Ronald C. Wek (2004)

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Original research by Krishna M. Vattem and Ronald C. Wek.

doi.org/10.1073/pnas.0400541101

pmc.ncbi.nlm.nih.gov/articles/PMC509193/

Regulated translation initiation controls stress-induced gene expression in mammalian cells by Heather P. Harding and others (2000)

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Original research by Heather P. Harding and colleagues.

doi.org/10.1016/S1097-2765(00)00108-8

pubmed.ncbi.nlm.nih.gov/11106749/

Translational control through differential ribosome pausing during amino acid limitation in mammalian cells by Alicia M. Darnell and others (2018)

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Original research by Alicia M. Darnell and colleagues.

doi.org/10.1016/j.molcel.2018.06.041

pmc.ncbi.nlm.nih.gov/articles/PMC6516488/

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