Available online at www.sciencedirect.
com
Exploring new roles for RNA-binding proteins in
epigenetic and gene regulation☆
Pedro Avila-Lopez 1,2 and Shannon M Lauberth 1,2,*
A significant portion of the human proteome comprises RNA-
binding proteins (RBPs) that play fundamental roles in
numerous biological processes. In the last decade, there has
been a staggering increase in RBP identification and
classification, which has fueled interest in the evolving roles of
RBPs and RBP-driven molecular mechanisms. Here, we focus
on recent insights into RBP-dependent regulation of the
epigenetic and transcriptional landscape. We describe
advances in methodologies that define the RNA-protein
interactome and machine-learning algorithms that are
streamlining RBP discovery and predicting new RNA-binding
regions. Finally, we present how RBP dysregulation leads to
alterations in tumor-promoting gene expression and discuss
the potential for targeting these RBPs for the development of
new cancer therapeutics.
Addresses
1
Simpson Querrey Institute for Epigenetics, Feinberg School of
Medicine, Northwestern University, Chicago, IL 60611, USA
2 than the well-known RNA-binding domains (RBDs)
Department of Biochemistry and Molecular Genetics, Feinberg School
of Medicine, Northwestern University, Chicago, IL 60611, USA
Corresponding author: Lauberth, Shannon M
(shannon.lauberth@northwestern.edu)
*
Twitter account: @LauberthLab
Current Opinion in Genetics & Development 2024, 84:102136
This review comes from a themed issue on Cancer Genomics
Edited by Shannon M. Lauberth and Ali Shilatifard
Available online xxxx
https://doi.org/10.1016/j.gde.2023.102136
0959–437X/© 2023 Published by Elsevier Ltd.
Introduction
Cumulative studies have raised the current census of
RNA-binding proteins (RBPs) encoded for by the
human genome to ∼2500 proteins [1–5]. The growing
number of RBPs has important implications for RNA
☆
Given the role as Guest Editor, Shannon M. Lauberth had no involvement in the peer review of the article and has no access to information
regarding its peer-review. Full responsibility for the editorial process of this article was delegated to Ali Shilatifard.
www.sciencedirect.com
]]
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metabolism as RBPs regulate the entire life cycle of
RNA. RBPs form functional interactions with RNA
during transcription, splicing, polyadenylation, sub­
cellular localization, translation, and decay [6]. Notably,
an increasingly supported paradigm is that RNAs reg­
ulate their own transcription by interacting and reg­
ulating sequence-specific DNA-binding transcription
factors (TFs) and chromatin-regulatory proteins [7–22].
TFs consist of two primary protein domains required to
regulate gene expression that include a DNA-binding
domain (DBD) that directs TF binding to cis-regulatory
elements and effector domains that facilitate TF inter­
actions with cofactors [23–25]. Similarly, epigenetic
regulators often engage with chromatin through reader
domains that facilitate recognition of specific histone
posttranslational modifications [26–28]. However, in­
creasing evidence finds that TFs and epigenetic reg­
ulators also bind RNA and often through domains other
that include the RNA recognition motif, K-homology
domain, double-strand RNA-binding domain, and zinc
finger domain [9,29–31]. Thus, the mechanisms under­
lying the recruitment/stabilization and functions of TFs
and chromatin regulators at specific genomic regions
require additional consideration for how RNA may be
involved. Also, since initial RBP annotations were lar­
gely based on the presence of conserved RBR domain
structure and function [30], the breadth of RBPs that
exist, particularly those devoid of typical RBRs, has not
yet been fully realized. The recent and significant ad­
vances in experimental technologies, including machine-
learning-based algorithms, promise to unveil new RBPs
and RBRs. Thus, a comprehensive identification of
RBPs and their functional consequences will provide
new insights into the regulation of gene expression
during normal development and disease and pro­
vides potential new targets for developing RBP-based
therapeutics.
Numerous reviews have detailed roles for RBPs in reg­
ulating posttranscriptional regulatory networks in normal
development and disease [32–37]. In this review, we
highlight recent technologies advancing the discovery of
diverse cellular RBPs and RBRs. We discuss the finding
that TFs and epigenetic regulators are among the
Current Opinion in Genetics & Development 2024, 84:102136
 2

Figure 1
Cancer Genomics

Current Opinion in Genetics & Development 2024, 84:102136

Current Opinion in Genetics and Development

Novel methodologies for investigating the RNA-binding capacity of RBPs. (a) UV cross-linking together with mass spectrometry-based profiling (RBR-ID) allows for the detection of RBPs and their
RBRs [43]. (b) Deep-learning models (HydRA, RNApred, catRAPID, RBPPred, and TriPepSVM) are proving effective in predicting noncanonical RBPs and RBRs [46–50]. (c) The KIN-CLIP approach
reveals the kinetics of RBP binding to RNA at endogenous gene loci [51]. (d) Split-pool recognition of interaction by tag extension (RNA & DNA SPRITE) enables simultaneous mapping of RNA–RNA,
RNA–DNA, and DNA–DNA contacts to comprehensively map RNA and DNA spatial organization [53]. Abbreviations: UV, ultraviolet; 4-SU, 4-thiouridine; PPI, protein–protein interactions; AI, artificial
intelligence.

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growing list of RBPs and that RNA functions should be
considered when defining mechanisms underlying
chromatin and gene regulation. Finally, we discuss im­
plications for RBPs in the dysregulation of gene ex­
pression in cancer and the recent exploratory efforts for
identifying molecules that probe RBP functions and
exhibit potential as novel cancer therapeutics.
Identification of RNA-binding proteins that
interface with chromatin and transcriptional
control
Cataloging additional RBPs across different tissues, de­
velopmental stages, and disease states is an important but
also challenging effort. In Figure 1, we highlight a few
recent methods that have streamlined RBP identification
and characterization. RBP identification has largely
stemmed from proteomic profiling analyses following affi­
nity purification of polyadenylated RNAs [2,38–41] and
noncoding RNAs [42–44] and by employing organic phase-
separation-based methods [3,45]. RBR identification tools,
including RNA-binding region identification (RBR-ID)
(Figure 1a), have defined RBRs with great precision using
mass spectrometric detection of RNA-cross-linked peptide
mass shifts following photoactivatable ribonucleoside-spe­
cific UVA cross-linking with 4-thiouridine [7,43]. RBR
mapping provides a powerful platform for prioritizing RBR
mutant design for exploring the functional significance of
RBP–RNA interactions. RBR-ID also recently provided
the unexpected realization that approximately half of the
TFs identified in the dataset bind RNA and in­
clude GATA1, GATA2, and RUNX1, MYC, and MAX [7].
This finding supports an emerging paradigm that the role
of RNA should be considered when defining gene-reg­
ulatory mechanisms. Increasing developments in machine-
learning technologies are also proving powerful in ex­
pediting progress toward RBP identification by increasing
the predictive power of proteome-wide RNA-binding ca­
pacity. One such example is the hybrid ensemble classifier
for RBPs (HydRA) (Figure 1b) [46]. HydRA is a novel
machine-learning-based algorithm that integrates deep-
learning algorithms, such as convolutional neural network,
transformer, and support vector machines to predict RBPs
and RBRs [46]. HydRA predictions have revealed 1487
previously unclassified human RBPs and 76 new RBRs
[46]. Other examples of RBP classification tools that are
dependent on machine-learning models that utilize protein
sequence information include RNApred [47], catRAPID
signature [48], RNA-binding protein predictor (RBPPred)
[49], and TriPepSVM [50]. Taken together, these various
technological advances are supporting the growing interest
in understanding how RNA alters the functions of an in­
creasing number of RBPs.
Recent technological developments also make it feasible
to measure the kinetics of RBP binding to and dis­
sociation from their cellular RNAs. An example of such
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RNA binding proteins in cancer Avila-Lopez and Lauberth 3
an approach is the kinetic cross-linking and im­
munoprecipitation (KIN-CLIP) technique (Figure 1c)
[51]. KIN-CLIP is a time-resolved laser cross-linking
approach that involves using a pulsed femtosecond (fs)
UV laser that can rapidly photo-cross-link proteins to
RNA relative to the association and dissociation rate
constants for the RNA-protein interactions [51]. Thus,
the power of measuring RBP–RNA-binding kinetics
with KIN-CLIP is the ability to distinguish between the
effects of cross-linking and RBP–RNA interactions at
individual binding sites in cells [51]. Determining the
kinetic landscape of RBPs in cells provides important
information about RBP–RNA interactions at en­
dogenous RBP-binding sites under different cellular
conditions. Finally, imaging technologies are at the
forefront of advancing our understanding of the sub­
cellular distribution and localization patterns of RBPs.
For example, the RBP Image database is a resource that
provides microscopy imaging data and curated pattern
descriptions for the subcellular localization of hundreds
of RBPs [52]. Moreover, RNA & DNA SPRITE (RD-
SPRITE) (Figure 1d) provides comprehensive mapping
of the spatial organization of RNA and DNA in the
nucleus [53]. RD-SPRITE identifies higher-order RNA-
chromatin hubs through split-and-pool barcoding of all
DNA and RNA contained within cross-linked RNA,
DNA, and protein complexes. The DNA and RNA se­
quencing reads with identical barcodes are merged into a
cluster that enables identification of simultaneous asso­
ciations of DNA and RNA molecules. This approach has
provided functional insights into the role that RNA in­
cluding low-abundance RNA molecules play in reg­
ulating the diffusion of other RNAs and proteins into
three-dimensional (3D) structures [53]. Taken together,
these various resources are available for guiding func­
tional investigations that will undeniably advance our
understanding of how RNA through RBP interactions
regulates gene control in normal development and
human diseases including cancer.
RNA-binding proteins functions associated
with epigenetic and transcriptional regulation
While TFs and epigenetic regulators are among the
growing number of noncanonical RBPs, it remains to be
determined whether RNA regulates their chromatin and
gene-regulatory functions or leads to other functional
consequences. Here, we focus on current studies that
demonstrate the importance of RNA through RBP in­
teractions in contributing to multifaceted roles in reg­
ulating gene expression as highlighted in Figure 2.
Specifically, we discuss the role of RBP–RNA interac­
tions in regulating the following: (i) TF and epigenetic
regulator recruitment/stabilization on chromatin, (ii) re­
lease of paused RNA polymerase II (RNAPII) into
productive elongation, (iii) altering chromatin state and
accessibility, (iv) shaping 3D nuclear organization, and
Current Opinion in Genetics & Development 2024, 84:102136
4 Cancer Genomics

Figure 2

Current Opinion in Genetics and Development

Multifaceted roles of RBPs in gene regulation. (a) RNA fine-tunes gene expression by contributing to the recruitment/stabilization of TFs, RNAPII, and
chromatin regulators [7–11,14,18,20,21]. (b) RNA-dependent recruitment/stabilization of TFs and cofactors on chromatin facilitates the release of
paused RNAPII into productive elongation [11,17]. (c) RNA regulates epigenetic regulators binding chromatin, which in turn leads to changes in the
PTMs of histones and nucleosome remodeling [9,10,13,15,16,19,20,22,29,58]. (d) RNA interactions with CTCF inhibit CTCF binding to low-affinity
binding sites across the genome, which in turn alters the 3D organization of the genome and leads to alterations in the expression of genes involved in
development and differentiation [59–62]. (e) RNA concentrates RBPs in phase condensates to inhibit PUM proteins from leading to defects in mitosis
[65]. Abbreviations: CTD, C-terminal domain; me3, trimethylation.

(v) regulation of RBP activities through phase-separation
condensate formation.
An increasing number of studies have revealed that RNA
contributes to both transcriptional repression and activation
through the dynamic regulation of TF and cofactor chro­
matin engagement [7–11,14,18,20,21]. A recent study
found that TFs interact with RNA through RBDs that
resemble the HIV trans-activator of transcription (Tat)
arginine-rich motif (ARM) [7]. Specifically, the ARM-like
domains were found to be more highly enriched in TFs
relative to other proteins within the proteome and are lo­
cated adjacent to TF DBDs [7]. RNA-dependent recruit­
ment/stabilization of TFs and cofactors on chromatin
promotes activation through enhanced RNAPII recruit­
ment and/or activity. Specifically, several RBPs, including
FUS [17] and ribogenesis factor WDR43 [11], have been
shown through RNA interactions to facilitate release of

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paused RNAPII into productive elongation. Also, RNAs
have been shown to interface with chromatin reader do­
mains to augment their recruitment/stabilization on chro­
matin. For example, enhancer-derived RNAs (eRNAs)
directly bind to the tandem bromodomains (BDs) of bro­
modomain and extra-terminal motif (BET) protein BRD4,
which increases BRD4 and RNAPII recruitment to aug­
ment enhancer- and tumor-promoting gene activation [8].
Similarly, RNA interacts with the BDs of PBRM1, a sub­
unit of the PBAF chromatin remodeling complex, which
facilitates PBAF chromatin access and PBRM1-mediated
cell growth effects [14]. Another well-known example is
RNA interactions with polycomb-repressive complex 2
(PRC2), which has been shown to associate with numerous
primary messenger RNAs (mRNAs) and long noncoding
RNAs [54–57]. Yet, the mechanisms underlying RNA
regulation of PRC2 have remained disparate. For example,
RNA has been shown to enhance PRC2 chromatin
binding, increase deposition of H3K27me3, and drive re­
pression of specific genes involved in cardiomyocyte dif­
ferentiation [13,29]. On the flip side of the coin, PRC2 can
be removed from active chromatin by transferring from
chromatin to RNA upon transcriptional activation, which
prevents PRC2 deposition of H3K27me3 on genes
[9,10,13,15,16,19,20,22]. The role of RNA in competitively
inhibiting access to active gene loci to protect from tran­
scriptional repression has also been demonstrated for the
ATP-dependent nucleosome remodeler and transcriptional
inhibitor Mi-2/CHD4 [58]. In addition to RNA regulating
chromatin engagement, several studies have also unveiled
that RNA impacts the enzymatic activity of chromatin-
modifying enzymes [12,19]. For example, a recent struc­
tural study revealed that RNA inhibits PRC2 enzymatic
activity by facilitating PRC2 dimerization, which in turn
sequesters PRC2’s catalytic subunit [19]. In addition,
eRNAs have been shown to reduce CBP’s autoinhibition
by preventing CBP’s basic activation loop from blocking
CBP’s active site [12]. RNA has also been shown to shape
3D nuclear organization by modulating the genome-wide
binding profile of CCCTC-binding factor (CTCF) [59–62].
Specifically, RNA promotes CTCF self-association, which
in turn correlates with CTCF chromatin binding and DNA
loop formation [60,62]. Interestingly, RNA–CTCF inter­
actions lead to the formation of distinct classes of chro­
matin loops, which suggests an RNA-dependent
mechanism for establishing cell-specific CTCF loops [62].
In addition, the long noncoding RNA Jpx has been shown
to inhibit ectopic CTCF binding to chromatin, which can
otherwise lead to alterations in anchor site usage and a
downregulation of Jpx target gene loci [59].
RNA contributions to transcriptional regulation also in­
volve its role in regulating the formation of membrane­
less subcellular compartments, known as biomolecular
condensates that promote the regulation of biochemical
activities inside cells [53,63–67]. While RNAs and RBPs
can undergo cophase separation [68], only recently have
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RNA binding proteins in cancer Avila-Lopez and Lauberth 5
RNAs been shown to employ phase separation as a
means of controlling RBP activities. For example, RNAs
facilitate the sequestration of factors in condensates.
This sequestration function is demonstrated for the long
noncoding NORAD that maintains genomic stability by
sequestering PUMILIO (PUM) proteins in phase-sepa­
rated condensates to inhibit their roles that otherwise
lead to aberrant mitosis [65]. Another example includes
RNA interactions with the paraspeckle protein PSPC1
that induces formation of transcription condensates that
tightly control the phosphorylation and RNA-induced
release of RNAPII into productive elongation [69].
Thus, further consideration of how RNA impacts the
binding specificity, affinity, and nuclear organization of
TFs and cofactors will further our understanding of the
comprehensive mechanisms underlying gene regulation.
Emerging identification of RNA-binding
proteins involved in altering gene expression
in human cancers
Numerous RBPs have been shown to dysregulate post­
transcriptional events in cancer, which leads to rapid
changes in protein expression levels that promote cancer
cell growth and progression [32,70]. The increasing
identification of TFs that bind RNA suggests additional
opportunity for defining new gene-regulatory mechan­
isms important in cancer. Consistent with RBPs involved
in gene control impacting tumorigenesis is the im­
balance in RBP expression levels identified by publicly
available databases, including the Cancer Genome Atlas
(TCGA) and GTEx [71,72]. Among the differentially
expressed RBPs that contribute to altered chromatin and
gene control in cancer are the well-known epigenetic
and transcriptional regulators, including TET2 [73–75],
MYCN [76–78], MEL18 [79,80], NANOG [81–84],
BRD4 [8,85,86], and PRC2 [79,87]. While these factors
are known to play critical roles in tumorigenesis, their
relationship with RNAs has not been fully elucidated.
Thus, there is an imminent need for defining the re­
lative contributions of RNA in altering the epigenetic
and transcriptional functions of these and the numerous
other factors recently identified [7]. Such studies will
undeniably advance our understanding of the dysregu­
lation of tumor-promoting gene networks and the de­
velopment of new targets with therapeutic implications.
In addition to dysregulated RBP expression, RBPs are
also enriched for mutations in various cancer types [88].
An assessment of the mutational landscape of thousands
of RBPs across cancer genomes revealed that RBPs un­
dergo frequent frameshift and in-frame deletions and
missense and nonsense mutations [88]. Moreover, hun­
dreds of candidate driver RBPs associated with func­
tional mutations in cancer were identified using
OncodriveFM [89]. This approach computes the func­
tional impact of nonsynonymous mutations in genes
Current Opinion in Genetics & Development 2024, 84:102136
6 Cancer Genomics
across a list of tumor samples and their impact on protein
function as an indication of positive selection and de­
tection of candidate driver genes [89]. Taken together,
mutational analysis and the prediction of candidate dri­
vers is informing altered RBP functions in cancer [90]
and suggests the importance of defining mechanisms
underlying RNA-dependent functions of RBPs in cancer
initiation and progression. Consistent with mutations
altering RBP function are mutations in splicing factors,
SF3B1, U2AF1, and PCBP1, that are linked to sig­
nificant splicing defects associated with cancer pheno­
types in multiple cancer types [91]. Recently, an analysis
of publicly available databases, including ClinVar [92]
and HGMD [93] that archive somatic and germline
variants associated with cancer phenotypes, revealed
hundreds of pathogenic mutations localized to TF-ARM
RBRs [7]. The significance of the TF-ARM mutations
was examined through an evaluation of the R269C mu­
tation in the ARM domain of the estrogen receptor 1
(ESR1), which is a mutation identified in a subset of
patients with pancreatic cancer [94]. Interestingly, this
mutation localized to the ARM domain disrupts
ESR1–RNA interactions [7], which suggests that cancer-
associated mutations in the RBR regions of TFs can
disrupt RBP–RNA interactions. Similarly, the glyci­
ne–arginine-rich domain that serves as a conserved RBR
domain in RBPs has been shown to be associated with
several diseases including neurological diseases and
cancer [95,96]. Interestingly, chromatin reader BDs of
the BET family members, that serve as targets for
pharmacological agents, also dual purpose as readers of
histone PTMs and RNA [8]. Similar to the arginine-rich
domain in TFs, the BDs of all BET family members
consist of a basic amino acid patch that surrounds the
acetyl-binding pocket and supports interactions with
acetylated histones [97,98]. Thus, it is possible that
these positively charged patches may facilitate BD-RNA
interactions. Supporting this potential mechanism is the
finding that positively charged patches facilitate BRDT
BD1 [99] and BRG1 BD [100] interactions with DNA.
With the growing number of RBPs and RBRs, further
mechanistic studies that directly manipulate the RBR
are needed to discern the direct (causal) functions of
RNA–RBP interactions in the dysregulation of gene
expression networks in various cancers.
RNA-binding proteins as therapeutic targets
for cancer
There is a growing interest in generating chemical
probes, small-molecule ligands that can inform RBP
function and enable the discovery of pharmacological
agents. Chemical probe design and development
have benefited from robust methodologies, including
activity-based protein profiling (ABPP). ABPP utilizes
small activity-based probes designed to bind or modify
Current Opinion in Genetics & Development 2024, 84:102136
enzyme-active sites to directly examine enzyme func­
tion within complex proteomes [101,102]. In addition,
proteomic platforms that integrate size-exclusion chro­
matography and high-throughput screening of electro­
philic compound libraries have accelerated the discovery
of small molecules that can impact protein complexes in
human cells [103]. Importantly, these analyses have re­
sulted in identifying effective chemical probes that
target protein domains extending well beyond enzyme-
active sites [103]. An example of small compounds co-
opting RBPs that regulate gene expression is the recent
finding that compounds engaging RBP NONO suppress
pro-tumorigenic transcriptional networks and impair
cancer cell proliferation [104]. This finding, together
with the growing number of RBPs in the cell, suggests
that advances in chemical proteomics will undeniably
aid in the design of effective chemical probes targeting
RBPs. Moreover, RNA and RBP contributions to phase
separation that in turn impacts RBP functions may also
inform the design of prospective therapeutics. Con­
sistent is the finding that numerous transcriptional reg­
ulators have been linked to the dysregulation of phase
separation, including UTX [105], MLL4 [106], WASP
[107], AKAP95 [108], and TAZ [109]. Also consistent is
the growing evidence that condensate dysregulation is
linked to pathogenic mutations that map to condensate-
promoting protein features including protein in­
trinsically disordered regions (IDRs) [110]. With IDRs
contributing to the arrangement of RNA-binding mod­
ules within an RBP, which impacts RNA-binding affinity
and specificity, targeting molecular condensates formed
by aberrant RBP–RNA interactions for removal may
leverage new cancer treatments [111,112].
In conclusion, while a growing number of chromatin-
and transcription-regulatory proteins have been de­
monstrated to bind RNA, the functional implications
remain largely unexplored. This calls for future studies
focused on examining the functional relationships be­
tween RBPs and their RNAs and the mechanisms that
ensue because these RNA interactions are formed. The
link between RBPs and gene control is consistent with
entering a new era of gene regulation that will largely
comprise exploring and highlighting new roles for RBPs
and to assess the actions of RBPs in cancer. Moreover,
the identified nexus between dysregulated RBP pro­
duction and function promises to elicit new therapeutic
targets for the tuning of gene expression programs that
shift disease-related networks.
Data
No data were used for the research described in the ar­
ticle.
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Declaration of Competing Interest
The authors declare that they have no known competing
financial interests or personal relationships that could
have appeared to influence the work reported in this
paper.
Acknowledgements
Research in the Lauberth lab is supported by a Grant from the NIH/
National Institute of General Medical Sciences (R35 GM128900), the
Robert H. Lurie Comprehensive Cancer Center, and Harold E Eisenberg
Foundation.
References and recommended reading
Papers of particular interest, published within the period of review, have
been highlighted as:
•• of special interest
•• of outstanding interest
1. Baltz AG, Munschauer M, Schwanhausser B, Vasile A, Murakawa
Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M,
et al.: The mRNA-bound proteome and its global occupancy
profile on protein-coding transcripts. Mol Cell 2012,
46:674-690.
2. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM,
Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, et al.:
Insights into RNA biology from an atlas of mammalian mRNA-
binding proteins. Cell 2012, 149:1393-1406.
3. Queiroz RML, Smith T, Villanueva E, Marti-Solano M, Monti M,
Pizzinga M, Mirea DM, Ramakrishna M, Harvey RF, Dezi V, et al.:
Comprehensive identification of RNA-protein interactions in
any organism using orthogonal organic phase separation
(OOPS). Nat Biotechnol 2019, 37:169-178.
4. Trendel J, Schwarzl T, Horos R, Prakash A, Bateman A, Hentze
MW, Krijgsveld J: The human RNA-binding proteome and its
dynamics during translational arrest. Cell 2019, 176:391-403
e319.
5. Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D,
Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M,
et al.: Purification of cross-linked RNA-protein complexes by
phenol-toluol extraction. Nat Commun 2019, 10:990.
6. Hentze MW, Castello A, Schwarzl T, Preiss T: A brave new world
of RNA-binding proteins. Nat Rev Mol Cell Biol 2018,
19:327-341.
7. Oksuz O, Henninger JE, Warneford-Thomson R, Zheng MM, Erb
•• H, Vancura A, Overholt KJ, Hawken SW, Banani SF, Lauman R,
et al.: Transcription factors interact with RNA to regulate
genes, e13, Mol Cell 2023, 83:2449-2463, https://doi.org/10.
1016/j.molcel.2023.06.012 Epub 2023 Jul 3.
n this study, the authors utilize an RNA-protein crosslinking assay (RBR-
ID) for high-resolution mapping of RBPs and RNA binding regions. The
proteomic analyses performed in this study revealed that many se­
quence-specific TFs bind RNA. The TF RNA binding interface was
mapped to a non-canonical RNA binding region referred to as an ARM
that is highly conserved and was shown by the authors to be required for
TF function during embryonic development. Moreover, the authors re­
vealed that TF-RNA interactions are important for increasing TF binding
to DNA, which in turn contributes to fine-tuning gene regulation.
8. Rahnamoun H, Lee J, Sun Z, Lu H, Ramsey KM, Komives EA,
Lauberth SM: RNAs interact with BRD4 to promote enhanced
chromatin engagement and transcription activation. Nat
Struct Mol Biol 2018, 25:687-697.
9. Beltran M, Tavares M, Justin N, Khandelwal G, Ambrose J, Foster
BM, Worlock KB, Tvardovskiy A, Kunzelmann S, Herrero J, et al.:
G-tract RNA removes Polycomb repressive complex 2 from
genes. Nat Struct Mol Biol 2019, 26:899-909.
10. Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K,
Fisher CL, Sibley CR, Foster BM, Bartke T, et al.: The interaction
www.sciencedirect.com
RNA binding proteins in cancer Avila-Lopez and Lauberth 7
of PRC2 with RNA or chromatin is mutually antagonistic.
Genome Res 2016, 26:896-907.
11. Bi X, Xu Y, Li T, Li X, Li W, Shao W, Wang K, Zhan G, Wu Z, Liu W,
et al.: RNA targets ribogenesis factor WDR43 to chromatin for
transcription and pluripotency control. Mol Cell 2019,
75:102-116 e109.
12. Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R,
Berger SL: RNA binding to CBP stimulates histone acetylation
and transcription. Cell 2017, 168:135-149 e122.
13. Cifuentes-Rojas C, Hernandez AJ, Sarma K, Lee JT: Regulatory
interactions between RNA and polycomb repressive complex
2. Mol Cell 2014, 55:171-185.
14. De Silva SM, Dhiman A, Sood S, Mercedes KF, Simmons WJ,
Henen MA, Vogeli B, Dykhuizen EC, Musselman CA: PBRM1
bromodomains associate with RNA to facilitate chromatin
association. Nucleic Acids Res 2023, 51:3631-3649.
15. Kaneko S, Son J, Bonasio R, Shen SS, Reinberg D: Nascent RNA
interaction keeps PRC2 activity poised and in check. Genes
Dev 2014, 28:1983-1988.
16. Kaneko S, Son J, Shen SS, Reinberg D, Bonasio R: PRC2 binds
active promoters and contacts nascent RNAs in embryonic
stem cells. Nat Struct Mol Biol 2013, 20:1258-1264.
17. Schwartz JC, Ebmeier CC, Podell ER, Heimiller J, Taatjes DJ,
Cech TR: FUS binds the CTD of RNA polymerase II and
regulates its phosphorylation at Ser2. Genes Dev 2012,
26:2690-2695.
18. Sigova AA, Abraham BJ, Ji X, Molinie B, Hannett NM, Guo YE,
Jangi M, Giallourakis CC, Sharp PA, Young RA: Transcription
factor trapping by RNA in gene regulatory elements. Science
2015, 350:978-981.
19. Song J, Gooding AR, Hemphill WO, Love BD, Robertson A, Yao L,
Zon LI, North TE, Kasinath V, Cech TR: Structural basis for
inactivation of PRC2 by G-quadruplex RNA. Science 2023,
381:1331-1337.
20. Wang X, Paucek RD, Gooding AR, Brown ZZ, Ge EJ, Muir TW,
Cech TR: Molecular analysis of PRC2 recruitment to DNA in
chromatin and its inhibition by RNA. Nat Struct Mol Biol 2017,
24:1028-1038.
21. Wei C, Xiao R, Chen L, Cui H, Zhou Y, Xue Y, Hu J, Zhou B,
Tsutsui T, Qiu J, et al.: RBFox2 binds nascent RNA to globally
regulate polycomb complex 2 targeting in mammalian
genomes. Mol Cell 2016, 62:982.
22. Zhang Q, McKenzie NJ, Warneford-Thomson R, Gail EH, Flanigan
SF, Owen BM, Lauman R, Levina V, Garcia BA, Schittenhelm RB,
et al.: RNA exploits an exposed regulatory site to inhibit the
enzymatic activity of PRC2. Nat Struct Mol Biol 2019,
26:237-247.
23. Frankel AD, Kim PS: Modular structure of transcription factors:
implications for gene regulation. Cell 1991, 65:717-719.
24. Lambert SA, Jolma A, Campitelli LF, Das PK, Yin Y, Albu M, Chen
X, Taipale J, Hughes TR, Weirauch MT: The human transcription
factors. Cell 2018, 172:650-665.
25. Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM:
A census of human transcription factors: function, expression
and evolution. Nat Rev Genet 2009, 10:252-263.
26. Vann KR, Klein BJ, Kutateladze TG: Mechanistic similarities in
recognition of histone tails and DNA by epigenetic readers.
Curr Opin Struct Biol 2021, 71:1-6.
27. Musselman CA, Lalonde ME, Cote J, Kutateladze TG: Perceiving
the epigenetic landscape through histone readers. Nat Struct
Mol Biol 2012, 19:1218-1227.
28. Andrews FH, Strahl BD, Kutateladze TG: Insights into newly
discovered marks and readers of epigenetic information. Nat
Chem Biol 2016, 12:662-668.
29. Long Y, Hwang T, Gooding AR, Goodrich KJ, Rinn JL, Cech TR:
RNA is essential for PRC2 chromatin occupancy and function
in human pluripotent stem cells. Nat Genet 2020, 52:931-938.
Current Opinion in Genetics & Development 2024, 84:102136
8 Cancer Genomics
30. Lunde BM, Moore C, Varani G: RNA-binding proteins: modular
design for efficient function. Nat Rev Mol Cell Biol 2007,
8:479-490.
31. Maris C, Dominguez C, Allain FH: The RNA recognition motif, a
plastic RNA-binding platform to regulate post-transcriptional
gene expression. FEBS J 2005, 272:2118-2131.
32. Pereira B, Billaud M, Almeida R: RNA-binding proteins in
cancer: old players and new actors. Trends Cancer 2017,
3:506-528.
33. Choi PS, Thomas-Tikhonenko A: RNA-binding proteins of
COSMIC importance in cancer. J Clin Investig (18) 2021,
131:e151627.
34. Shi DL, Cheng XN, Saquet A, Grifone R: Emerging roles of RNA-
binding proteins in inner ear hair cell development and
regeneration. Int J Mol Sci (20) 2022, 23:12393.
35. Corley M, Burns MC, Yeo GW: How RNA-binding proteins
interact with RNA: molecules and mechanisms. Mol Cell 2020,
78:9-29.
36. Gebauer F, Schwarzl T, Valcarcel J, Hentze MW: RNA-binding
proteins in human genetic disease. Nat Rev Genet 2021,
22:185-198.
37. Nussbacher JK, Tabet R, Yeo GW, Lagier-Tourenne C:
Disruption of RNA metabolism in neurological diseases and
emerging therapeutic interventions. Neuron 2019,
102:294-320.
38. Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K,
Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, et al.: The
RNA-binding proteomes from yeast to man harbour
conserved enigmRBPs. Nat Commun 2015, 6:10127.
39. Conrad T, Albrecht AS, de Melo Costa VR, Sauer S, Meierhofer D,
Orom UA: Serial interactome capture of the human cell
nucleus. Nat Commun 2016, 7:11212.
40. Kwon SC, Yi H, Eichelbaum K, Fohr S, Fischer B, You KT, Castello
A, Krijgsveld J, Hentze MW, Kim VN: The RNA-binding protein
repertoire of embryonic stem cells. Nat Struct Mol Biol 2013,
20:1122-1130.
41. Perez-Perri JI, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M,
Brosig A, Hentze MW: Discovery of RNA-binding proteins and
characterization of their dynamic responses by enhanced
RNA interactome capture. Nat Commun 2018, 9:4408.
42. Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y,
Pulido-Quetglas C, et al.: Capturing the interactome of newly
transcribed RNA. Nat Methods 2018, 15:213-220.
43. He C, Sidoli S, Warneford-Thomson R, Tatomer DC, Wilusz JE,
Garcia BA, Bonasio R: High-resolution mapping of RNA-
binding regions in the nuclear proteome of embryonic stem
cells. Mol Cell 2016, 64:416-430.
44. Huang R, Han M, Meng L, Chen X: Capture and identification of
RNA-binding proteins by using click Chemistry-assisted RNA-
interactome Capture (CARIC) strategy. J Vis Exp 2018, 140,
https://doi.org/10.3791/58580 e58580.
45. Caudron-Herger M, Wassmer E, Nasa I, Schultz AS, Seiler J,
Kettenbach AN, Diederichs S: Identification, quantification and
bioinformatic analysis of RNA-dependent proteins by RNase
treatment and density gradient ultracentrifugation using
R-DeeP. Nat Protoc 2020, 15:1338-1370.
46. Jin W, Brannan KW, Kapeli K, Park SS, Tan HQ, Gosztyla ML,
• Mujumdar M, Ahdout J, Henroid B, Rothamel K, et al.: HydRA:
deep-learning models for predicting RNA-binding capacity
from protein interaction association context and protein
sequence. Mol Cell 2023, 83:2595-2611 e2511.
In this study, the authors demonstrate the power of implementing a ma­
chine-learning-based algorithm referred to as hybrid ensemble classifier
(HydRA). By incorporating both intermolecular protein context and se­
quence-level information, this algorithm guides predictions of unexpected
RBPs and the regions that are involved in RBP-RNA interactions.
47. Kumar M, Gromiha MM, Raghava GP: SVM based prediction of
RNA-binding proteins using binding residues and
evolutionary information. J Mol Recognit 2011, 24:303-313.
Current Opinion in Genetics & Development 2024, 84:102136
48. Livi CM, Klus P, Delli Ponti R, Tartaglia GG: catRAPID signature:
identification of ribonucleoproteins and RNA-binding regions.
Bioinformatics 2016, 32:773-775.
49. Zhang X, Liu S: RBPPred: predicting RNA-binding proteins
from sequence using SVM. Bioinformatics 2017, 33:854-862.
50. Bressin A, Schulte-Sasse R, Figini D, Urdaneta EC, Beckmann
BM, Marsico A: TriPepSVM: de novo prediction of RNA-binding
proteins based on short amino acid motifs. Nucleic Acids Res
2019, 47:4406-4417.
51. Sharma D, Zagore LL, Brister MM, Ye X, Crespo-Hernandez CE,
Licatalosi DD, Jankowsky E: The kinetic landscape of an RNA-
binding protein in cells. Nature 2021, 591:152-156.
52. Benoit Bouvrette LP, Wang X, Boulais J, Kong J, Syed EU, Blue
SM, Zhan L, Olson S, Stanton R, Wei X, et al.: RBP Image
Database: a resource for the systematic characterization of
the subcellular distribution properties of human RNA binding
proteins. Nucleic Acids Res 2023, 51:D1549-D1557.
53. Quinodoz SA, Jachowicz JW, Bhat P, Ollikainen N, Banerjee AK,
• Goronzy IN, Blanco MR, Chovanec P, Chow A, Markaki Y, et al.:
RNA promotes the formation of spatial compartments in the
nucleus. Cell 2021, 184:5775-5790 e5730.
Importantly, this study provides new insights into RNA involvement in
the formation of molecular condensates. The authors describe an im­
proved method that they refer to as RNA & DNA SPRITE (RD-SPRITE),
which enables the simultaneous mapping of RNA-RNA, RNA-DNA, and
DNA-DNA contacts in the cell. Using this powerful methodology, the
authors unveil that nascent RNA, even that which is produced at low
levels can drive and organize functional compartments comprised of
regulatory factors within the nucleus to regulate gene expression.
54. Yan J, Dutta B, Hee YT, Chng WJ: Towards understanding of
PRC2 binding to RNA. RNA Biol 2019, 16:176-184.
55. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song
JJ, Kingston RE, Borowsky M, Lee JT: Genome-wide
identification of polycomb-associated RNAs by RIP-seq. Mol
Cell 2010, 40:939-953.
56. Davidovich C, Zheng L, Goodrich KJ, Cech TR: Promiscuous
RNA binding by Polycomb repressive complex 2. Nat Struct
Mol Biol 2013, 20:1250-1257.
57. Rosenberg M, Blum R, Kesner B, Aeby E, Garant JM, Szanto A,
Lee JT: Motif-driven interactions between RNA and PRC2 are
rheostats that regulate transcription elongation. Nat Struct
Mol Biol 2021, 28:103-117.
58. Ullah I, Tholken C, Zhong Y, John M, Rossbach O, Lenz J,
Gossringer M, Nist A, Albert L, Stiewe T, et al.: RNA inhibits dMi-
2/CHD4 chromatin binding and nucleosome remodeling. Cell
Rep 2022, 39:110895.
59. Oh HJ, Aguilar R, Kesner B, Lee HG, Kriz AJ, Chu HP, Lee JT: Jpx
• RNA regulates CTCF anchor site selection and formation of
chromosome loops. Cell 2021, 184:6157-6173 e6124.
This study provides new functional insights into a chromatin archi­
tectural role for the Jpx RNA that has been classically known for its role
in controlling X-inactivation. The authors report that the Jpx RNA reg­
ulates CTCF binding on a global scale by releasing CTCF from DNA at
low-affinity CTCF binding sites. This regulation of CTCF by Jpx has
important implications for the displacement of chromosome loops and
the formation of new loops that are associated with the downregulation
of genes involved in development and differentiation.
60. Saldana-Meyer R, Rodriguez-Hernaez J, Escobar T, Nishana M,
Jacome-Lopez K, Nora EP, Bruneau BG, Tsirigos A, Furlan-
Magaril M, Skok J, et al.: RNA interactions are essential for
CTCF-mediated genome organization. Mol Cell 2019,
76:412-422 e415.
61. Saldana-Meyer R, Gonzalez-Buendia E, Guerrero G, Narendra V,
Bonasio R, Recillas-Targa F, Reinberg D: CTCF regulates the
human p53 gene through direct interaction with its natural
antisense transcript, Wrap53. Genes Dev 2014, 28:723-734.
62. Hansen AS, Hsieh TS, Cattoglio C, Pustova I, Saldana-Meyer R,
Reinberg D, Darzacq X, Tjian R: Distinct classes of chromatin
loops revealed by deletion of an RNA-binding region in CTCF.
Mol Cell 2019, 76:395-411 e313.
www.sciencedirect.com

63. Weber AP: SC: evidence for and against liquid-liquid phase
separation in the nucleus. Noncoding RNA (4) 2019, 5:50.
64. Pandya-Jones A, Markaki Y, Serizay J, Chitiashvili T, Mancia Leon
WR, Damianov A, Chronis C, Papp B, Chen CK, McKee R, et al.: A
protein assembly mediates Xist localization and gene
silencing. Nature 2020, 587:145-151.
65. Elguindy MM, Mendell JT: NORAD-induced Pumilio phase
separation is required for genome stability. Nature 2021,
595:303-308.
66. Nair SJ, Yang L, Meluzzi D, Oh S, Yang F, Friedman MJ, Wang S,
•• Suter T, Alshareedah I, Gamliel A, et al.: Phase separation of
ligand-activated enhancers licenses cooperative
chromosomal enhancer assembly. Nat Struct Mol Biol 2019,
26:193-203.
Here, the authors provide one of the first lines of evidence that RNAs
drive phase separation to facilitate regulatory control over RBP activ­
ities. By focusing on lncRNA NORAD that is activated by DNA damage,
the authors reveal mechanistic insights into NORAD regulation of
Pumilio RBPs, PUM1, and PUM2 in maintaining genome stability.
Specifically, the authors reveal that NORAD effectively competes with
other cellular RNAs for interactions with PUM proteins by forming bio­
molecular condensates. This RNA-dependent mechanism sequesters
and inhibits PUM proteins, which has important implications for genome
maintenance.
67. Markaki Y, Chong JG, Wang Y, Jacobson EC, Luong C, Tan SYX,
Jachowicz JW, Strehle M, Maestrini D, Banerjee AK, et al.: Xist
nucleates local protein gradients to propagate silencing
across the X chromosome. Cell 2021, 184:6212.
68. Lin Y, Protter DS, Rosen MK, Parker R: Formation and
maturation of phase-separated liquid droplets by RNA-
binding proteins. Mol Cell 2015, 60:208-219.
69. Shao W, Bi X, Pan Y, Gao B, Wu J, Yin Y, Liu Z, Peng M, Zhang W,
Jiang X, et al.: Phase separation of RNA-binding protein
promotes polymerase binding and transcription. Nat Chem
Biol 2022, 18:70-80.
70. Kang D, Lee Y, Lee JS: RNA-binding proteins in cancer:
functional and therapeutic perspectives. Cancers (9) 2020,
12:2699.
71. Chang K, Creighton CJ, Davis C, Donehower L, Drummond J,
Wheeler D, Ally A, Balasundaram M, Birol I, Butterfield YSN, et al.:
The cancer genome Atlas Pan-Cancer analysis project. Nat
Genet 2013, 45:1113-1120.
72. Consortium GT: The Genotype-Tissue Expression (GTEx)
project. Nat Genet 2013, 45:580-585.
73. Bensberg M, Rundquist O, Selimovic A, Lagerwall C, Benson M,
Gustafsson M, Vogt H, Lentini A, Nestor CE: TET2 as a tumor
suppressor and therapeutic target in T-cell acute
lymphoblastic leukemia. Proc Natl Acad Sci USA (34) 2021,
118:e2110758118.
74. Lio CJ, Yuita H, Rao A: Dysregulation of the TET family of
epigenetic regulators in lymphoid and myeloid malignancies.
Blood 2019, 134:1487-1497.
75. Wang L, Ozark PA, Smith ER, Zhao Z, Marshall SA, Rendleman
EJ, Piunti A, Ryan C, Whelan AL, Helmin KA, et al.: TET2
coactivates gene expression through demethylation of
enhancers. Sci Adv 2018, 4:eaau6986.
76. Huang M, Weiss WA: Neuroblastoma and MYCN. Cold Spring
Harb Perspect Med 2013, 3:a014415.
77. Rickman DS, Schulte JH, Eilers M: The expanding world of N-
MYC-driven tumors. Cancer Discov 2018, 8:150-163.
78. Liu R, Shi P, Wang Z, Yuan C, Cui H: Molecular mechanisms of
MYCN dysregulation in cancers. Front Oncol 2020, 10:625332.
79. Parreno V, Martinez AM, Cavalli G: Mechanisms of Polycomb
group protein function in cancer. Cell Res 2022, 32:231-253.
80. Piunti A, Shilatifard A: The roles of Polycomb repressive
complexes in mammalian development and cancer. Nat Rev
Mol Cell Biol 2021, 22:326-345.
www.sciencedirect.com
RNA binding proteins in cancer Avila-Lopez and Lauberth 9
81. Gong S, Li Q, Jeter CR, Fan Q, Tang DG, Liu B: Regulation of
NANOG in cancer cells. Mol Carcinog 2015, 54:679-687.
82. Jeter CR, Badeaux M, Choy G, Chandra D, Patrawala L, Liu C,
Calhoun-Davis T, Zaehres H, Daley GQ, Tang DG: Functional
evidence that the self-renewal gene NANOG regulates human
tumor development. Stem Cells 2009, 27:993-1005.
83. Lin T, Ding YQ, Li JM: Overexpression of Nanog protein is
associated with poor prognosis in gastric adenocarcinoma.
Med Oncol 2012, 29:878-885.
84. Meng HM, Zheng P, Wang XY, Liu C, Sui HM, Wu SJ, Zhou J,
Ding YQ, Li J: Over-expression of Nanog predicts tumor
progression and poor prognosis in colorectal cancer. Cancer
Biol Ther 2010, 9:295-302.
85. Du Z, Song X, Yan F, Wang J, Zhao Y, Liu S: Genome-wide
transcriptional analysis of BRD4-regulated genes and
pathways in human glioma U251 cells. Int J Oncol 2018,
52:1415-1426.
86. French CA: Small-molecule targeting of BET proteins in
cancer. Adv Cancer Res 2016, 131:21-58.
87. Laugesen A, Hojfeldt JW, Helin K: Role of the Polycomb
Repressive Complex 2 (PRC2) in transcriptional regulation
and cancer. Cold Spring Harb Perspect Med (9) 2016, 6:a026575.
88. Neelamraju Y, Gonzalez-Perez A, Bhat-Nakshatri P, Nakshatri H,
Janga SC: Mutational landscape of RNA-binding proteins in
human cancers. RNA Biol 2018, 15:115-129.
89. Gonzalez-Perez A, Lopez-Bigas N: Functional impact bias
reveals cancer drivers. Nucleic Acids Res 2012, 40:e169.
90. Castello A, Fischer B, Hentze MW, Preiss T: RNA-binding
proteins in Mendelian disease. Trends Genet 2013, 29:318-327.
91. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M,
Zhang Q, McMichael JF, Wyczalkowski MA, et al.: Mutational
landscape and significance across 12 major cancer types.
Nature 2013, 502:333-339.
92. Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla
S, Gu B, Hart J, Hoffman D, Jang W, et al.: ClinVar: improving
access to variant interpretations and supporting evidence.
Nucleic Acids Res 2018, 46:D1062-D1067.
93. Stenson PD, Mort M, Ball EV, Chapman M, Evans K, Azevedo L,
Hayden M, Heywood S, Millar DS, Phillips AD, et al.: The Human
Gene Mutation Database (HGMD((R))): optimizing its use in a
clinical diagnostic or research setting. Hum Genet 2020,
139:1197-1207.
94. Boldes T, Merenbakh-Lamin K, Journo S, Shachar E, Lipson D,
Yeheskel A, Pasmanik-Chor M, Rubinek T, Wolf I: R269C variant
of ESR1: high prevalence and differential function in a subset
of pancreatic cancers. BMC Cancer 2020, 20:531.
95. Doron-Mandel E, Koppel I, Abraham O, Rishal I, Smith TP,
Buchanan CN, Sahoo PK, Kadlec J, Oses-Prieto JA, Kawaguchi
R, et al.: The glycine arginine-rich domain of the RNA-binding
protein nucleolin regulates its subcellular localization. EMBO
J 2021, 40:e107158.
96. Jarvelin AI, Noerenberg M, Davis I, Castello A: The new (dis)
order in RNA regulation. Cell Commun Signal 2016, 14:9.
97. Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP,
Barsyte-Lovejoy D, Felletar I, Volkmer R, Muller S, Pawson T,
et al.: Histone recognition and large-scale structural analysis
of the human bromodomain family. Cell 2012, 149:214-231.
98. Fujisawa T, Filippakopoulos P: Functions of bromodomain-
containing proteins and their roles in homeostasis and
cancer. Nat Rev Mol Cell Biol 2017, 18:246-262.
99. Miller TC, Simon B, Rybin V, Grotsch H, Curtet S, Khochbin S,
Carlomagno T, Muller CW: A bromodomain-DNA interaction
facilitates acetylation-dependent bivalent nucleosome
recognition by the BET protein BRDT. Nat Commun 2016,
7:13855.
100. Morrison EA, Sanchez JC, Ronan JL, Farrell DP, Varzavand K,
Johnson JK, Gu BX, Crabtree GR, Musselman CA: DNA binding
Current Opinion in Genetics & Development 2024, 84:102136
10 Cancer Genomics
drives the association of BRG1/hBRM bromodomains with
nucleosomes. Nat Commun 2017, 8:16080.
101. Liu Y, Patricelli MP, Cravatt BF: Activity-based protein profiling:
the serine hydrolases. Proc Natl Acad Sci USA 1999,
96:14694-14699.
102. Speers AE, Cravatt BF: Activity-Based Protein Profiling (ABPP)
and Click Chemistry (CC)-ABPP by MudPIT mass
spectrometry. Curr Protoc Chem Biol 2009, 1:29-41.
103. Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL,
• DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR,
et al.: Proteomic discovery of chemical probes that perturb
protein complexes in human cells. Mol Cell 2023,
83:1725-1742 e1712.
In this study, the authors describe a novel screening platform used for the
discovery of chemical probes with therapeutic relevance. The functional
screen that is described in their study is focused on disrupting native
protein complexes. Specifically, through a combination of size exclusion
chromatography and cysteine-directed ABPP, the authors reveal the ef­
fects of electrophilic compounds on altering native protein complexes. This
function-based screening platform has great potential for expanding the
types of proteins that can be targeted and will undeniably aid in the dis­
covery of new chemical probes for the ‘ undruggable ’ proteome.
104. Kathman SG, Koo SJ, Lindsey GL, Her HL, Blue SM, Li H, Jaensch
•• S, Remsberg JR, Ahn K, Yeo GW, et al.: Remodeling oncogenic
transcriptomes by small molecules targeting NONO. Nat
Chem Biol 2023, 19:825-836.
This study performed activity-based profiling analysis of a collection of
electrophilic compounds that resulted in the identification of effective com­
pounds that suppress the expression of oncogenic TF, androgen receptor.
The target of the AR-inhibiting compounds was identified as the RBP,
NONO. Further mechanistic insights revealed that the NONO ligands lead to
alterations in the transcriptome of cancer cells by stabilizing NONO-mRNA
interactions that lead to aberrant accumulation of NONO in perinuclear
bodies.
Current Opinion in Genetics & Development 2024, 84:102136
105. Shi B, Li W, Song Y, Wang Z, Ju R, Ulman A, Hu J, Palomba F,
Zhao Y, Le JP, et al.: UTX condensation underlies its tumour-
suppressive activity. Nature 2021, 597:726-731.
106. Fasciani A, D’Annunzio S, Poli V, Fagnocchi L, Beyes S, Michelatti
D, Corazza F, Antonelli L, Gregoretti F, Oliva G, et al.: MLL4-
associated condensates counterbalance Polycomb-mediated
nuclear mechanical stress in Kabuki syndrome. Nat Genet
2020, 52:1397-1411.
107. Yuan B, Zhou X, Suzuki K, Ramos-Mandujano G, Wang M,
Tehseen M, Cortes-Medina LV, Moresco JJ, Dunn S, Hernandez-
Benitez R, et al.: Wiskott-Aldrich syndrome protein forms
nuclear condensates and regulates alternative splicing. Nat
Commun 2022, 13:3646.
108. Li W, Hu J, Shi B, Palomba F, Digman MA, Gratton E, Jiang H:
Biophysical properties of AKAP95 protein condensates regulate
splicing and tumorigenesis. Nat Cell Biol 2020, 22:960-972.
109. Lu Y, Wu T, Gutman O, Lu H, Zhou Q, Henis YI, Luo K: Phase
separation of TAZ compartmentalizes the transcription
machinery to promote gene expression. Nat Cell Biol 2020,
22:453-464.
110. Banani SF, Afeyan LK, Hawken SW, Henninger JE, Dall’Agnese A,
Clark VE, Platt JM, Oksuz O, Hannett NM, Sagi I, et al.: Genetic
variation associated with condensate dysregulation in
disease. Dev Cell 2022, 57:1776-1788 e1778.
111. Chandra B, Michmerhuizen NL, Shirnekhi HK, Tripathi S, Pioso
BJ, Baggett DW, Mitrea DM, Iacobucci I, White MR, Chen J, et al.:
Phase separation mediates NUP98 fusion oncoprotein
leukemic transformation. Cancer Discov 2022, 12:1152-1169.
112. Boija A, Klein IA, Young RA: Biomolecular condensates and
cancer. Cancer Cell 2021, 39:174-192.
www.sciencedirect.com