Classification and Functions of Long Non-coding RNAs (lncRNAs) – Key Vocabulary

A collection of vocabulary flashcards covering essential terms, classes, mechanisms, and exemplar molecules related to the classification and functions of long non-coding RNAs as presented in the lecture article.

Long non-coding RNA (lncRNA)

A non-protein-coding RNA transcript longer than ~200 nucleotides that can act as a regulatory molecule in many cellular processes.

lincRNA (Long Intergenic ncRNA)

An lncRNA transcribed from an intergenic region that does not overlap protein-coding genes.

Intronic lncRNA

An lncRNA transcribed entirely from an intron of a protein-coding gene.

Sense lncRNA

An lncRNA transcribed from the same (sense) strand as an overlapping protein-coding gene.

Antisense lncRNA

An lncRNA transcribed from the antisense strand of a protein-coding gene, partly or wholly overlapping that gene.

Cis-acting lncRNA

An lncRNA that regulates transcription of genes located nearby on the same chromosome.

Trans-acting lncRNA

An lncRNA that regulates genes located at distant loci or on other chromosomes.

Transcriptional interference

A regulatory mechanism in which an lncRNA transcript blocks formation of the pre-initiation complex or transcription factor binding at a promoter.

Chromatin modification by lncRNA

Recruitment of chromatin-remodelling complexes (e.g., PRC2, Rpd3S HDAC) by an lncRNA to alter histone marks and gene expression.

Polycomb Repressive Complex 2 (PRC2)

A histone-methyltransferase complex (H3K27me3) often guided to loci by lncRNAs such as Xist or HOTAIR for transcriptional silencing.

Rpd3S HDAC complex

A histone deacetylase complex that can be recruited by lncRNAs (e.g., GAL10-ncRNA) to reduce histone acetylation and repress genes.

K4-K36 domain

A chromatin signature with H3K4me3 at the 5′ end and H3K36me3 across the body of a gene, characteristic of actively transcribed lincRNAs and mRNAs.

Enhancer RNA (eRNA)

An lncRNA transcribed from an enhancer that positively regulates expression of nearby genes.

Competing endogenous RNA (ceRNA)

An RNA (often lncRNA) that sequesters microRNAs, thereby relieving repression of other microRNA targets.

Splicing regulation by lncRNA

Modulation of pre-mRNA splicing through lncRNA binding to splicing factors or to the pre-mRNA itself.

Translational control by lncRNA

Regulation of mRNA translation via lncRNA interaction with initiation factors or ribosomes (e.g., BC1, BC200).

Natural antisense inhibitor

An antisense lncRNA that forms an RNA duplex with a sense mRNA, leading to its degradation or altered processing.

Small interfering RNA (siRNA) pathway

A gene-silencing mechanism that can be influenced by lncRNAs (e.g., rncs-1 modulating Dicer activity).

Signal archetype (lncRNA)

lncRNA acting as a molecular indicator whose expression reflects cellular state or stimulus (e.g., Xist, COLDAIR).

Decoy archetype (lncRNA)

lncRNA that binds and sequesters proteins or microRNAs away from their natural targets (e.g., PANDA, PTENP1).

Guide archetype (lncRNA)

lncRNA that directs ribonucleoprotein complexes to specific genomic loci (e.g., HOTAIR guiding PRC2).

Scaffold archetype (lncRNA)

lncRNA serving as a structural platform to assemble multiple proteins into a functional complex (e.g., HOTAIR joining PRC2 and LSD1).

RNA–DNA hybrid

A duplex formed between an RNA strand and complementary DNA, used by some lncRNAs for locus targeting (e.g., DHFR upstream transcripts).

RNA–RNA pairing

Base-pair interaction between two RNA molecules, common in ceRNA networks and antisense regulation.

DHFR upstream transcripts

Cis-acting lncRNAs transcribed 5′ of the DHFR gene that block PIC formation via RNA–DNA triplexes.

SRG1 RNA

A yeast cis-lncRNA covering the SER3 promoter to inhibit transcription factor binding and silence SER3.

Xist

A 19-kb nuclear lncRNA that coats the inactive X chromosome and recruits PRC2 for chromosome-wide silencing.

HOTAIR

A 2.2-kb lncRNA from the HOXC locus that guides PRC2 and LSD1 to distant genes (e.g., HOXD) for chromatin repression.

HOTTIP

A 3.8-kb lncRNA at the 5′ end of the HOXA cluster that recruits MLL complexes to maintain active chromatin.

lincRNA-p21

A p53-induced lincRNA that represses transcription of multiple genes by recruiting repressive complexes.

7SK RNA

A 330-nt nuclear lncRNA serving as a scaffold in 7SK snRNP to inhibit P-TEFb and pause transcription elongation.

B2 SINE RNA

A stress-induced lncRNA that binds RNA polymerase II to globally repress transcription during heat shock.

BC1 / BC200 RNAs

Neuron-enriched cytoplasmic lncRNAs that bind eIF4A and PABP to block assembly of the translation initiation complex.

Malat1

A 7-kb nuclear-retained lncRNA that modulates distribution and phosphorylation of SR splicing factors, affecting alternative splicing.

Zeb2NAT

An antisense lncRNA that prevents splicing of a retained intron in Zeb2 mRNA, enabling its translation during EMT.

Khalil et al. 2009 finding

Discovery that many human lincRNAs physically associate with chromatin-modifying complexes, underscoring regulatory roles.

NONCODE database

A comprehensive repository (v3.0) of experimentally supported lncRNAs from multiple species.

GENCODE lncRNA catalog

Manually curated annotation of human lncRNAs including genomic features and conservation data.

Length-based lncRNA groups

Proposed sub-classes: small (200–950 nt), medium (950–4,800 nt), and large (>4,800 nt) lncRNAs, differing in species distribution.

K4-K36 conserved domain

Actively transcribed regions of lincRNAs conserved between species (~70% human–mouse overlap), indicating functional constraint.

ceRNA hypothesis

Concept that transcripts (coding or non-coding) communicate by competing for shared microRNAs, forming post-transcriptional networks.

Enhancer-associated lncRNAs (ncRNA-a)

lncRNAs such as ncRNA-a1 transcribed from active enhancers that boost expression of neighboring genes.