RNA and gene regulation

Cytidine-to-uridine RNA editing

Cytidine-to-uridine RNA editing, also called C-to-U or cytosine-to-uracil editing, is RNA deamination catalyzed by APOBEC1 with cofactors A1CF and RBM47, first seen on apolipoprotein B mRNA in 1987, widespread in plant organelles, and now engineered into programmable editors like RESCUE and RECODE.

Cytoplasmic mRNA localization

Cytoplasmic mRNA localization is the directed transport of messenger RNA to specific cytoplasmic sites, using zipcodes, RNA-binding proteins, and molecular motors, from bacteria to neurons.

Cytoplasmic polyadenylation element

Cytoplasmic polyadenylation element (CPE), UUUUA(1-2)U motif in mRNA 3'UTRs, also called CPE; bound by CPEB1-4 proteins, present in 20-30% of vertebrate genes, controls poly(A) tail length and translation in oocytes, neurons, and cancer.

DDX3X

DDX3X (DEAD-box helicase 3 X-linked) is an X-linked ATP-dependent RNA helicase gene at Xp11.4 with a Y-linked paralog DDX3Y. Mutations cause DDX3X syndrome, up to 3% of intellectual disability in females, and DDX3X acts mainly as a tumour suppressor in cancer.

De novo transcriptome assembly

De novo transcriptome assembly is a bioinformatics method that reconstructs transcript sequences directly from RNA sequencing reads without a reference genome, using tools such as Trinity.

DEAD-box and DExH helicases in pre-mRNA splicing

DEAD-box and DExH (DEAH-box) helicases are ATP-driven RNA helicases that the spliceosome uses to rearrange its protein and RNA architecture at nearly every step of pre-mRNA splicing.

DEAD-box helicases in translation initiation

DEAD-box helicases in translation initiation are ATP-dependent RNA helicases, principally eIF4A, Ded1/DDX3, and DHX29, that unwind secondary structure in mRNA 5′ UTRs so the 43S preinitiation complex can scan to the start codon.

Deadenylation

Deadenylation is the enzymatic shortening of the poly(A) tail of eukaryotic messenger RNAs, the first and rate-limiting step in mRNA decay, carried out mainly by the PAN2-PAN3 and CCR4-NOT complexes.

DEAH-box RNA helicases

DEAH-box RNA helicases are ATP-dependent enzymes that translocate along single-stranded RNA in the 3'→5' direction, remodeling RNA-protein complexes; the spliceosomal members Prp2, Prp16, Prp22, and Prp43 drive late stages of pre-mRNA splicing.

Decapping complex

Decapping complex: the Dcp1-Dcp2 holoenzyme (with Lsm1-7, Pat1, Edc1-3, EDC4) that removes the mRNA 5' cap, committing transcripts to 5'-3' decay by Xrn1; distinct from scavenger DCPS and DXO enzymes.

Degradome sequencing

Degradome sequencing, also known as PARE or GMUCT, is a high-throughput sequencing method that maps RNA decay fragments to identify microRNA-directed mRNA cleavage sites genome-wide, most informatively in plants.

Deleted in esophageal cancer 1

DELEC1 (deleted in esophageal cancer 1, formerly DEC1, alias CTS9) is a human long non-coding RNA gene at 9q33.1, a candidate tumor suppressor with reduced expression in esophageal squamous cell carcinoma; distinct from DLEC1 at 3p22.3.

Demethylation

Demethylation is the removal of methyl groups from compounds, especially DNA demethylation of 5-methylcytosine via passive replication dilution or active TET-mediated oxidation, deamination, and base excision repair pathways.

Di19

Di19 (drought-induced 19) is a family of plant Cys2/His2 zinc-finger transcription factors with two atypical zinc-finger domains, conserved in angiosperms, regulating drought, salt, cold responses, flowering, and development.

DIAPH1

DIAPH1 (diaphanous-related formin 1, mDia1), a Rho-effector formin gene on 5q31; causes DFNA1 deafness, and gain-of-function R1213 variants cause macrothrombocytopenia with hearing loss, while biallelic loss causes neurodevelopmental syndrome.

Dicer

Dicer (DICER1, chromosome 14q32.13) is the RNase III enzyme that cleaves pre-miRNAs and dsRNA into 21-23 nt miRNAs and siRNAs; germline variants cause DICER1 tumor predisposition with goiter, lung cysts, and rare tumors.

Differential display

Differential display, also called DD-PCR or DDRT-PCR, is a PCR-based method for comparing mRNA populations between samples and isolating differentially expressed genes, introduced in 1992.

Differential methylation analysis

Differential methylation analysis is a bioinformatics method that compares DNA methylation levels between sample groups, identifying differentially methylated CpG sites and regions in EWAS and cancer studies.

Digital spatial profiling

Digital spatial profiling (DSP) is a spatial omics method that quantifies dozens to thousands of proteins or transcripts in selected regions of tissue sections, commercialized as GeoMx and reported in 2020.

Dim1 family

about 20 words: Dim1 family, or Dim1, is a conserved, thioredoxin-like protein family. It functions as a U5 snRNP component and 18S rRNA dimethyltransferase in essential eukaryotic cell functions.

Direct RNA sequencing

Direct RNA sequencing, also known as direct RNA-seq, is a nanopore method that reads native RNA molecules single-file through a protein pore, detecting modifications like m6A.

DNA methylation

DNA methylation (5-methylcytosine) is an epigenetic mark on cytosine, mostly at CpG sites, written by DNMT1/3 enzymes, erased by TET proteins, silencing promoters, and used in cancer biomarkers and epigenetic aging clocks.

DNA methylation array

A DNA methylation array, or methylation array, is a microarray that measures methylation at hundreds of thousands of CpG sites, used widely in cancer research.

DNA-binding domain

DNA-binding domain (DBD): protein domain recognizing specific DNA sequences, used by transcription factors. Key families: helix-turn-helix/homeodomain, Cys2His2 zinc finger (3% of human genes), winged helix; ~60 amino acids average.

DNase-Seq

DNase-Seq is a sequencing method that maps DNase I hypersensitive sites, the nucleosome-depleted open chromatin regions where regulatory DNA is accessible, across a genome, combining DNase I footprinting with next-generation sequencing.

DNMT2 and tRNA m5C methylation

DNMT2, officially named TRDMT1 in humans, is an enzyme that adds a methyl group to cytosine 38 in the anticodon loop of specific transfer RNAs.

Domain X

Domain X (IPR024937; Pfam PF01348 Intron_maturas2) is the conserved maturase domain of group II intron-encoded proteins, following an RT domain, promoting RNA splicing; plant MatK and MatR retain it while their RT and endonuclease domains are degenerate.

Downregulation and upregulation

Downregulation and upregulation describe decreased or increased expression of a gene product or receptor. They occur at transcriptional, post-transcriptional, translational, and epigenetic levels, and for GPCRs reflect changes in total receptor number.

DroNc-seq

DroNc-seq is a droplet-based single-nucleus RNA sequencing method that profiles gene expression in thousands of nuclei from frozen or archived tissue, such as post-mortem human brain.