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SMART-seq
SMART-seq is a plate-based single-cell RNA sequencing method that uses template-switching reverse transcription to build full-length cDNA libraries from individual cells, first reported in 2012 and refined as Smart-seq2 in 2013.
SMART-seq2
SMART-seq2 is a plate-based single-cell RNA sequencing method that converts one cell's RNA into a full-length cDNA library, reported by Simone Picelli and colleagues in 2013.
SMN complex and snRNP assembly
SMN complex and snRNP assembly: the survival of motor neuron (SMN) protein complex with Gemins 2–8 and Unrip chaperones assembly of heptameric Sm cores onto snRNAs; its deficiency causes spinal muscular atrophy.
snoRNA guide–target mapping
snoRNA guide–target mapping is the set of rules and experimental methods connecting each RNA methylation or pseudouridylation site to the snoRNA guide that specifies it, using fixed geometry rather than sequence alone.
snoRNAs and scaRNAs in disease
Small nucleolar RNAs (snoRNAs) and small Cajal-body RNAs (scaRNAs) are non-coding RNAs whose defects cause diseases including Prader-Willi syndrome, Labrune syndrome, dyskeratosis congenita, cancer, and neuropsychiatric disorders.
snoRNP core proteins and assembly factors
snoRNP core proteins and assembly factors: the four core proteins of box C/D (fibrillarin, NOP56, NOP58, 15.5K) and box H/ACA (dyskerin, NHP2, NOP10, GAR1) snoRNPs, plus chaperones SHQ1, NAF1, NUFIP1, and HSP90/R2TP that assemble them.
snRNP Assembly
snRNP assembly (snRNP biogenesis, snurpogenesis): construction of spliceosomal U1, U2, U4, U5, U6 snRNPs from snRNAs and Sm/LSm proteins, driven by the PRMT5 and SMN complexes; SMN defects cause spinal muscular atrophy.
Sof1-like protein
Sof1-like protein (IPR007287, Pfam PF04158) is a conserved eukaryotic protein domain named after yeast SOF1, an essential nucleolar U3 snoRNA-associated factor required for 40S ribosomal subunit biogenesis; orthologs include human DCAF13, distinct from mouse sperm SOF1.
SOX gene family
SOX gene family (SRY-related HMG box): about 20 human genes encoding HMG-box transcription factors discovered in 1990 via Sry; they bind the DNA minor groove, act with partner factors, and drive development, stem cell identity, and disease.
SOX9
SOX9 (SRY-box transcription factor 9) is a chromosome 17 transcription factor essential for cartilage development and testis determination; mutations cause campomelic dysplasia with XY sex reversal.
Spatial transcriptomics
Spatial transcriptomics is a family of molecular biology methods that maps gene expression across intact tissue while recording each transcript's position, introduced by Patrik Ståhl in 2016.
SPI1
SPI1, also called PU.1 or the Spi-1 proto-oncogene, is a human gene on chromosome 11p11.2 encoding an ETS transcription factor that regulates blood cell development and is linked to leukemia.
Splice site mutation
Splice site mutation: a DNA change disrupting spliceosome recognition of exon-intron boundaries (GT donor, AG acceptor dinucleotides), causing exon skipping, intron retention, or cryptic site use; a major cause of genetic disease, targetable by splice-switching antisense oligonucleotides.
Splice site prediction
Splice site prediction is the computational identification of splice donor and acceptor sites in DNA or RNA, using machine-learning models to support gene annotation and variant interpretation.
Splice-site recognition and consensus sequences
Splice-site recognition is how the spliceosome locates the short motifs marking where an intron begins and ends; in mammals, consensus sequences are too loose to specify splicing alone.
Spliceosome
Spliceosome: nuclear RNA-protein machine (U1, U2, U4, U5, U6 snRNPs plus ~150 proteins) that removes introns from pre-mRNA via two transesterifications; a parallel minor spliceosome (U11, U12, U4atac, U6atac, shared U5) splices ~0.5% of introns.
Spliceosome assembly pathway
The spliceosome assembly pathway is the ordered sequence of complexes through which the spliceosome forms on pre-mRNA, spanning at least 10 states from E to the intron-lariat spliceosome.
Splicing analysis methods and resources
Splicing analysis methods and resources are the computational tools for detecting and quantifying alternative splicing in RNA-seq, spanning event-level callers like rMATS and long-read isoform tools like IsoQuant.
Splicing factor U2AF
U2AF (U2AF65/U2AF35 heterodimer, U2AF2/U2AF1) is the essential splicing factor that binds the polypyrimidine tract and 3' splice site AG to define 3' splice sites and recruit U2 snRNP.
Squamosa promoter-binding protein
Squamosa promoter-binding protein (SBP/SPL) is a plant-specific transcription factor family defined by a ~76-amino-acid SBP DNA-binding domain with two zinc fingers, first found in Antirrhinum majus, regulating flowering, phase change, fruit development, and copper homeostasis, largely via miR156.
SR1 RNA (Bacillus)
SR1 is a 205-nt dual-function small RNA of Bacillus subtilis: it base-pairs with ahrC mRNA to inhibit arginine catabolism gene translation and encodes the peptide SR1P, which stabilizes gapA mRNA via GapA.
SREBF2
SREBF2 (SREBP-2, bHLHd2), human gene at 22q13.2, encodes a bHLH-Zip transcription factor regulating cholesterol synthesis and uptake genes via SCAP/INSIG sterol sensing, with intronic miR-33a; central to statin action and linked to SREBF2-related developmental disease.
SRSF1
SRSF1, also called ASF/SF2 or SRp30a, is the founding human SR splicing factor: a 248-aa RRM/RS-domain protein binding exonic splicing enhancers, regulated by SRPK1/CLK1 phosphorylation, with roles in mRNA export, translation, and cancer.
SRSF3
SRSF3 (SRp20, SFRS3), the smallest of the 12 human SR splicing factors, is a 164-aa RNA-binding protein on chromosome 6p21.31 that regulates splicing, export, and translation, is essential for development, and is dysregulated in cancer.
STARR-seq
STARR-seq (self-transcribing active regulatory region sequencing) is a massively parallel reporter assay, reported in 2013, that directly and quantitatively measures enhancer activity for millions of genomic DNA fragments at once.
STAT3
STAT3 (signal transducer and activator of transcription 3, APRF) is a chromosome 17q21.1 transcription factor activated by JAK-mediated Y705 phosphorylation; central to immunity and a validated but clinically unapproved cancer drug target.
Staufen (protein)
Staufen (Stau1/Stau2) is a family of double-stranded RNA-binding proteins, first found in Drosophila localizing bicoid and oskar mRNAs, that transport and regulate mRNAs in dendrites, control synaptic plasticity, and modify neurodegeneration via mTOR and autophagy.
Staufen proteins
Staufen proteins are a conserved family of double-stranded RNA-binding proteins, first identified in Drosophila, that localize mRNAs and, in mammals, direct bound transcripts into Staufen-mediated decay.
Staufen-mediated decay
Staufen-mediated decay (SMD), or STAU1-mediated mRNA decay, is a mammalian mRNA degradation pathway triggered when Staufen1 or Staufen2 binds double-stranded RNA sites in 3'-UTRs and recruits UPF1, competing with nonsense-mediated mRNA decay and regulating differentiation.
Stress-responsive small RNAs in bacteria
Stress-responsive small RNAs are short bacterial non-coding RNAs, typically 50 to 200 nucleotides long, that base-pair with target messenger RNAs to repress or activate them during stresses.