RNA and gene regulation

Selenocysteine tRNA and selenocysteine decoding

Selenocysteine decoding is the process by which tRNA charged with selenocysteine reads selected UGA stop codons, directed by an mRNA structure called the SECIS element.

SELEX

SELEX (Systematic Evolution of Ligands by EXponential enrichment) is an in vitro selection method, reported in 1990, that isolates aptamers binding a chosen target molecule.

Seq-Well is a single-cell RNA sequencing method that traps individual cells in subnanoliter wells with barcoded mRNA-capture beads, introduced in Nature Methods in 2017, profiling thousands of cells for under $1 per cell.

Sex-lethal splicing factor

Sex-lethal (Sxl) is the master switch gene of Drosophila sex determination and dosage compensation, encoding a female-specific RNA binding protein that controls splicing of transformer and its own transcript and represses msl-2 translation.

Shapiro Senapathy algorithm

Shapiro Senapathy algorithm: a 1987 position weight matrix method for scoring eukaryotic splice sites, the basis of SpliceSiteFinder and related splice prediction tools.

Short hairpin RNA

Short hairpin RNA (shRNA) is an artificial stem-loop RNA expressed from DNA vectors, processed by Dicer into ~21-nt siRNA that loads RISC for long-term gene knockdown, unlike transient synthetic siRNA.

Sigma-E factor negative regulatory protein RseA

RseA (regulator of sigma E) is the inner membrane anti-sigma factor of Escherichia coli that sequesters sigma-E (RpoE); envelope stress triggers DegS, RseP, and ClpXP proteolysis of RseA, freeing sigma-E to transcribe envelope stress genes.

Signal transduction response regulator, phosphate regulon transcriptional regulatory protein PhoB

PhoB is the cytoplasmic response regulator of the PhoR/PhoB two-component system in Escherichia coli; phosphorylation by PhoR under phosphate starvation activates dimerization, Pho box DNA binding, and transcription of the phosphate regulon.

Silencer (genetics)

Silencer (genetics): a cis-acting, position- and orientation-independent DNA element bound by repressors to reduce transcription, exemplified by the REST-bound RE1; 2.8 million candidate silencers are enriched in disease variants.

SILVA ribosomal RNA database

SILVA is a curated, regularly updated database of aligned 16S/18S (SSU) and 23S/28S (LSU) rRNA sequences for Bacteria, Archaea, and Eukarya, hosted by DSMZ; release 144 (2026) holds 905,628 SSU Ref NR99 sequences and ships DADA2, Kraken2, MEGAN, and Qiime2 classifiers.

Single-cell ATAC-seq

Single-cell ATAC-seq (scATAC-seq) is a genomics assay that measures chromatin accessibility genome-wide in individual cells, first reported in 2015 and used to identify cell types and infer transcription-factor activity.

Single-cell ChIP-seq

Single-cell ChIP-seq is a family of genomics methods that profiles histone modifications or transcription factor binding in individual cells, first reported as Drop-ChIP in 2015.

Single-nucleus RNA sequencing

Single-nucleus RNA sequencing (snRNA-seq) is a transcriptomics method that profiles gene expression in individual nuclei rather than whole cells, first demonstrated in 2013 and now applied to frozen brain, kidney, heart, and tumor samples.

Site-directed RNA editing

Site-directed RNA editing uses engineered enzymes or guide RNAs to alter individual RNA bases without changing the genome, offering transient, repeatable therapies now in early clinical trials.

SLAM-seq

SLAM-seq is a metabolic RNA labeling method, reported in 2017, that measures transcript-specific RNA synthesis and decay by detecting 4-thiouridine incorporation as T-to-C conversions in sequencing data.

SLBP

SLBP (stem-loop binding protein, HBP, gene 7884) is a metazoan RNA-binding protein that binds the 26-nt stem-loop at the 3' end of replication-dependent histone mRNAs, enabling U7 snRNP-dependent 3' end processing, export, translation, and cell cycle-regulated degradation.

Slide-seq

Slide-seq is a spatial transcriptomics method, introduced at the Broad Institute in 2019, that transfers RNA from tissue sections onto DNA-barcoded 10 µm beads so gene expression is measured with position preserved.

Sm and LSm protein families

The Sm and LSm protein families, also called Sm and Sm-like proteins, are RNA-binding protein families that form seven-membered rings central to RNA splicing and decay.

Sm-like protein Lsm1

Lsm1 (LSM1, CaSm) is a Sm-like protein forming the cytoplasmic Lsm1-7 heptameric ring that binds deadenylated mRNA 3' ends, protects them, and activates decapping in 5'-to-3' mRNA decay, distinct from the nuclear Lsm2-8 splicing complex.

Small Cajal body-specific RNA

Small Cajal body-specific RNAs (scaRNAs, SCARNA genes) are non-coding guide RNAs in Cajal bodies that direct 2'-O-methylation and pseudouridylation of spliceosomal snRNAs; at least 24 human scaRNAs exist, with CAB-box or GU-repeat localization signals.

Small interfering RNA

Small interfering RNA (siRNA), the ~19–30 bp duplex of RNA interference, guides Argonaute/RISC to cleave matching mRNA; discovered via Fire and Mello's 2006 Nobel work, with patisiran the first FDA-approved siRNA drug (2018).

Small nuclear ribonucleoprotein G

SNRPG (Sm-G, small nuclear ribonucleoprotein G) is a human 2p13.3 gene encoding an 8.5 kDa Sm core protein of the U1, U2, U4, and U5 snRNPs and the minor U12 spliceosome, assembled by the SMN complex, with reported roles in cancer.

Small nuclear RNA

Small nuclear RNA (snRNA; U1-U6, U11, U12, U4atac, U6atac): 100-300-nucleotide nuclear RNAs forming the catalytic core of major and minor spliceosomes that remove introns from pre-mRNA.

Small nucleolar RNA host gene 1

SNHG1 (small nucleolar RNA host gene 1; UHG, U22HG, LINC00057) is a human lncRNA gene at 11q12.3 hosting eight SNORD snoRNAs, upregulated in many cancers and a proposed prognostic biomarker.

Small nucleolar RNA SNORD115

SNORD115 (HBII-52) is a paternally expressed cluster of about 47 orphan C/D box snoRNA genes at the imprinted 15q11-q13 Prader-Willi locus, with an 18-nt complementarity to HTR2C exon Vb and a modifying interaction with SNORD116.

Small nucleolar RNA SNORD116

SNORD116 (HBII-85) is an orphan box C/D snoRNA cluster in the paternally imprinted SNHG14 host gene at 15q11-q13; its loss causes Prader-Willi syndrome, and mouse deletion produces hyperphagia and growth deficiency.

Small nucleolar RNA U3

U3 snoRNA (SNORD3A) is the first-discovered, most abundant box C/D small nucleolar RNA, ubiquitous in eukaryotes; it guides pre-rRNA cleavage at A0/A1/A2 for 18S rRNA, forms the SSU processome with fibrillarin and Utp proteins, and has mitotic and antiviral roles.

Small ribosomal subunit protein uS3m, fungi

Small ribosomal subunit protein uS3m, called Var1 in yeast, is the mitochondrially encoded small-subunit mitoribosomal protein of fungi and plants. It forms the mRNA entry channel with uS4 and uS5, has ~30% asparagine from AT-rich mtDNA, and is lost in the yeast CTG clade.

Small RNA sequencing

Small RNA sequencing (sRNA-seq, small RNA-seq) profiles short RNAs such as miRNAs (18-23 nt), piRNAs, and tRNA fragments by ligating 3' and 5' adapters, reverse transcribing, PCR amplifying, and size-selecting libraries; adapter ligation bias is its main challenge.