Mechanisms of long noncoding RNA function in development and disease

doi:10.1007/S00018-016-2174-5

REVIEW

Mechanisms of long noncoding RNA function in development

and disease

Sandra U. Schmitz

1

•

Phillip Grote

2

•

Bernhard G. Herrmann

1,3

Received: 1 February 2016 / Revised: 23 February 2016 / Accepted: 1 March 2016 / Published online: 23 March 2016

Ó The Author(s) 2016. This article is published with open access at Springerlink.com

Abstract Since decades it has been known that non-

protein-coding RNAs have important cellular functions.

Deep sequencing recently facilitated the discovery of

thousands of novel transcripts, now classiﬁed as long non-

coding RNAs (lncRNAs), in many vertebrate and

invertebrate species. LncRNAs are involved in a wide range

of cellular mechanisms, from almost all aspec ts of gene

expression to protein translation and stability. Recent

ﬁndings implicate lncRNAs as key players of cellular dif-

ferentiation, cell lineage choice, organogenesis and tissue

homeostasis. Moreover, lncRNAs are involved in patho-

logical conditions such as cancer and cardiovascular

disease, and therefore provide novel biomarkers and phar-

maceutical targets. Here we discuss examples illustrating

the versatility of lncRNAs in gene control, development and

differentiation, as well as in human disease.

Keywords LncRNA  Differentiation 

Cardiovascular disease  Cancer  Gene regulation 

Chromatin  Epigenetics  Genome organization

Introduction

It has long been known that several classes of non-protein-

coding RNA molecules exert important cellular funct ions.

For instance, ribosomal RNAs (rRNAs) are essential ele-

ments of the translation machinery and small nuclear

RNAs (snRNAs) are required for splicing of nascent RNA

transcripts. Also, various classes of small (around 20–30

nucleotides) noncoding RNAs such as micro (mi)RNAs,

small inhibitory (si)RNAs or PIWI intera cting (pi)RNAs

are well known as gene silencers. With the recent advent of

massive parallel sequencing techniques, however, it has

been observed that a tremendously high portion, approxi-

mately 70 %, of the genome is transcribed in various

contexts and cell types [

1, 2]. A large proportion of these

newly detected RNA transcripts are structurally indistin-

guishable from protein-coding and processed messenger

RNAs (mRNAs). They tend to be expressed at a very low

level and have little to no protein-coding potential. This

subclass of noncoding transcripts of variable length and

function is collectively referred to as long noncoding

RNAs (lncRNAs).

A plethora of biological tissues, organs, pathological

samples and cultured cells have been analyzed for non-

coding RNA expression, and it is clear that these molecules

are omnipresent. Apparently, deﬁning noncoding RNA

function has proven more challenging than detecting them,

as the number of reports showing comprehensive func-

tional data is far smaller than those describing their

identiﬁcation in various contexts. The ﬂexib ility of RNA

transcripts and their ability to fold into complex 3D-con-

formations enables them to form speciﬁc interactions with

proteins. They can interact with RNA or DNA molecules

via base pairing, even with double-stranded DNA, and

form networks with DNA, protein complexes and RNA

& Sandra U. Schmitz

sschmitz@molgen.mpg.de

& Bernhard G. Herrmann

herrmann@molgen.mpg.de

1

Department of Developmental Genetics, Max Planck Institute

for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin,

Germany

2

Institute of Cardiovascular Regeneration, Center for

Molecular Medicine, Goethe University, Theodor-Stern-Kai

7, 60590 Frankfurt, Germany

3

Institute for Medical Genetics, Campus Benjamin Franklin,

Charite-University Medicine Berlin, Hindenburgdamm 30,

12203 Berlin, Germany

Cell. Mol. Life Sci. (2016) 73:2491–2509

DOI 10.1007/s00018-016-2174-5

Cellular and Molecular Life Sciences

123

molecules, illustrating their large pote ntial as an important

player with many biological functions. In this review, we

will discuss mechanisms of lncRNA functions with a focus

on their role in developm ent and disease (Table

1).

Molecular and genetic structure of LncRNAs

Like mRNAs, lncRNAs are transcr ibed by Polymerase II,

mostly 5

0

-capped, polyadenylated and spliced, though on

average they contain a lower number of exons than

mRNAs and their expression level assessed across different

tissues is lower [

3, 4]. There are various algorithms cal-

culating the coding probability based on the length of a

potential open reading frame (ORF), the similarity of such

an ORF to known protein-coding genes, frequency of in-

frame nucleotide hexamers or other empirical sequence

features [

5]. In general, RNA transcripts containing short

(\100 nt) non-conserved ORFs, which have no homology

to known peptide sequences and do not match to peptides

identiﬁed in mass spectrometry screens are considered

noncoding [

6]. Interestingly, the majority of lncRNAs are

associated with ribosomes [

7, 8], though they d o not show

the characteristic release of ribosomes [

9] or the typical

3-nucleotide phasing corresponding to codons of an ORF

[

10, 11]. However, in rare instances, functional

oligopeptides have been found to be translated from puta-

tive lncRNAs [

12–14].

Deep-sequencing experiments revealed many examples

of genes producing both protein-coding and noncoding

transcripts by alternative splicing. Howeve r, so far , only

very few reports demonstrate a functional role for both the

noncoding RNA(s) and the protein(s) encoded by tran-

scripts derived from the same gene [

15, 16 ]. It is tempting

to speculate that such dual usage of transcr ipts is more

frequent than anticipated.

RNA molecules have the potential to form highly

structured macromolecules by folding into double-stranded

stems, single-stranded loops and bulges, which again can

fold further into three-dimensional structures, allowing for

the potential formation of complex shapes. So far, the

structure of only a few RNAs has been experimentally

determined using a combination of chemical assays, and by

determining the accessibility of base-paired or single-

stranded RNA by various RNases [

17, 18]. However, these

methods still have the limitation that they can only reveal

the secondary, but not the tertiary (3D) structure. In addi-

tion, computational predictions are only beginning to

provide reliable results, but program learni ng from exper-

imental data might improve the predictions and more

closely mirror experimental observations. This process is

miRNA

intergenic

overlapping - antisense

divergent (pancRNA)

unidirectional - bidirectional

enhancer RNAs

intronic

miRNA host gene

overlapping - sense

protein coding gene

noncoding gene

convergent

;;

A

B

C

D

E

F

G

Fig. 1 Classiﬁcation of lncRNAs according to their position relative

to neighboring gene(s). a Divergently transcribed lncRNA originating

from the same promoter region as the adjacent (usually protein

coding) gene, but from the opposite strand; b convergently tran-

scribed genes encoded on opposite strands and facing each other;

c intergenic (or intervening) lncRNA (or lincRNA) located distant

from other genes (usually [10 kb); d examples for various cases of

lncRNAs overlapping with other genes on the same or the opposite

strand; e enhancer RNAs expressed as uni- or bidirectional tran-

scripts; f LncRNA transcribed from an intron of another gene;

g lncRNA hosting a miRNA. Noncoding genes are shown in green,

protein-coding genes in orange

2492 S. U. Schmitz et al.

123

accelerated by recently developed techniques combined

with high-throughput sequencing, such as SHAPE-MaP

and icSHAPE [

19, 20 ].

The similarity between mRNA-encoding and lncRNA

genes is furthermore reﬂected by the chromatin signatures at

the genomic regions from where they are transcribed. Their

a

b

c

d

e

Eviction of proteins from chromatin

Stabilizing looping and recruitment

of transcriptional regulators

Counteracting loop formation

Recruitment of proteins

Scaffolding of proteins

Sequestering of proteins

or miRNAs

Alternative splicing

Stabilizing of mRNAs

f

g

h

xxx

x

Enhancer

x

Enhancer off

x

Enhancer on

Fig. 2 Schematic representation of cellular mechanisms involving

lncRNAs. a LncRNA transcripts evicting proteins from chromatin;

here, pancRNAs prevent DNMT from methylating DNA in their

promoter region, thereby ensuring mRNA transcription. b LncRNAs

recruiting the Mediator complex to an enhancer region, stabilizing

loop formation and transcription of the associated gene. c LncRNAs

transcribed from an enhancer region interfering with enhancer-

promoter contact, thereby inhibiting transcription of the protein-

coding gene. d LncRNA recruiting proteins, such as chromatin-

modifying complexes to speciﬁc target sites in the genome, e.g. via

DNA-RNA triplex formation. e LncRNA acting as scaffold linking

different proteins required for concerted action. f LncRNA binding

and sequestering proteins to prevent or attenuate their action, e.g.

binding to mRNAs (left); circRNA sequestering miRNAs to prevent

their binding to mRNAs (right). g Example of a lncRNA changing the

splicing pattern by binding to a primary RNA transcript. h LncRNA

stabilizing a mRNA by recruiting proteins such as STAU1, thereby

preventing degradation

Mechanisms of long noncoding RNA function in development and disease 2493

123

Table 1 List of lncRNAs and their main features mentioned in this review

Name Genomic

Mechanisms of long noncoding RNA function in development and disease

Citations

New insights into the mechanisms of epithelial–mesenchymal transition and implications for cancer

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

Multi-omics approaches to disease.

LncRNADisease 2.0: an updated database of long non-coding RNA-associated diseases.

NONCODEV5: a comprehensive annotation database for long non-coding RNAs.

References

An integrated encyclopedia of DNA elements in the human genome

An integrated encyclopedia of DNA elements in the human genome.

Circular RNAs are a large class of animal RNAs with regulatory potency

Natural RNA circles function as efficient microRNA sponges

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

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