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Article ; Online: Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.

Boyle, Evan A / Her, Hsuan-Lin / Mueller, Jasmine R / Naritomi, Jack T / Nguyen, Grady G / Yeo, Gene W

Cell genomics

2023 Volume 3, Issue 6, Page(s) 100317

Abstract: Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we ... ...

Abstract	Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts unprocessed reads into annotated binding sites using an improved statistical framework. Compared with existing methods, Skipper on average calls 210%-320% more transcriptomic binding sites and sometimes >1,000% more sites, providing deeper insight into post-transcriptional gene regulation. Skipper also calls binding to annotated repetitive elements and identifies bound elements for 99% of enhanced CLIP experiments. We perform nine translation factor enhanced CLIPs and apply Skipper to learn determinants of translation factor occupancy, including transcript region, sequence, and subcellular localization. Furthermore, we observe depletion of genetic variation in occupied sites and nominate transcripts subject to selective constraint because of translation factor occupancy. Skipper offers fast, easy, customizable, and state-of-the-art analysis of CLIP-seq data.
Language	English
Publishing date	2023-05-04
Publishing country	United States
Document type	Journal Article
ISSN	2666-979X
ISSN (online)	2666-979X
DOI	10.1016/j.xgen.2023.100317
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Article ; Online: Crosstalk between CRISPR-Cas9 and the human transcriptome.

Smargon, Aaron A / Madrigal, Assael A / Yee, Brian A / Dong, Kevin D / Mueller, Jasmine R / Yeo, Gene W

Nature communications

2022 Volume 13, Issue 1, Page(s) 1125

Abstract: CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP ( ... ...

Abstract	CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems.
MeSH term(s)	CRISPR-Cas Systems/genetics ; Gene Editing ; Humans ; RNA Editing ; RNA, Guide, CRISPR-Cas Systems/metabolism ; Transcriptome
Chemical Substances	RNA, Guide, CRISPR-Cas Systems
Language	English
Publishing date	2022-03-02
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28719-5
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Article ; Online: Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

Medina-Munoz, Hugo C / Kofman, Eric / Jagannatha, Pratibha / Boyle, Evan A / Yu, Tao / Jones, Krysten L / Mueller, Jasmine R / Lykins, Grace D / Doudna, Andrew T / Park, Samuel S / Blue, Steven M / Ranzau, Brodie L / Kohli, Rahul M / Komor, Alexis C / Yeo, Gene W

Nature communications

2024 Volume 15, Issue 1, Page(s) 875

Abstract: RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated ... ...

Abstract	RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
MeSH term(s)	RNA/metabolism ; Binding Sites/genetics ; RNA-Binding Proteins/metabolism ; RNA Processing, Post-Transcriptional
Chemical Substances	RNA (63231-63-0) ; RNA-Binding Proteins
Language	English
Publishing date	2024-01-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-45009-4
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Article: Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.

bioRxiv : the preprint server for biology

2023

Abstract	RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize fusions of RNA base-editors (rBEs) to RBPs to circumvent the limitations of immunoprecipitation (CLIP)-based methods that require enzymatic digestion and large amounts of input material. To broaden the repertoire of rBEs suitable for editing-based RBP-RNA interaction studies, we have devised experimental and computational assays in a framework called PRINTER (protein-RNA interaction-based triaging of enzymes that edit RNA) to assess over thirty A-to-I and C-to-U rBEs, allowing us to identify rBEs that expand the characterization of binding patterns for both sequence-specific and broad-binding RBPs. We also propose specific rBEs suitable for dual-RBP applications. We show that the choice between single or multiple rBEs to fuse with a given RBP or pair of RBPs hinges on the editing biases of the rBEs and the binding preferences of the RBPs themselves. We believe our study streamlines and enhances the selection of rBEs for the next generation of RBP-RNA target discovery.
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.25.558915
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Article ; Online: Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq.

Blue, Steven M / Yee, Brian A / Pratt, Gabriel A / Mueller, Jasmine R / Park, Samuel S / Shishkin, Alexander A / Starner, Anne C / Van Nostrand, Eric L / Yeo, Gene W

Nature protocols

2022 Volume 17, Issue 5, Page(s) 1223–1265

Abstract: Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a ... ...

Abstract	Discovery of interaction sites between RNA-binding proteins (RBPs) and their RNA targets plays a critical role in enabling our understanding of how these RBPs control RNA processing and regulation. Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP/RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size-matched input controls, the single-end enhanced CLIP (seCLIP) protocol allows for the profiling of these interactions with high resolution, efficiency and scalability. Here, we present a step-by-step guide to the seCLIP method, detailing critical steps and offering insights regarding troubleshooting and expected results while carrying out the ~4-d protocol. Furthermore, we describe a comprehensive bioinformatics pipeline that offers users the tools necessary to process two replicate datasets and identify reproducible and significant peaks for an RBP of interest in ~2 d.
MeSH term(s)	Binding Sites ; High-Throughput Nucleotide Sequencing/methods ; Immunoprecipitation ; Protein Binding ; RNA/genetics ; RNA-Binding Proteins/metabolism ; Transcriptome
Chemical Substances	RNA-Binding Proteins ; RNA (63231-63-0)
Language	English
Publishing date	2022-03-23
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2244966-8
ISSN	1750-2799 ; 1754-2189
ISSN (online)	1750-2799
ISSN	1754-2189
DOI	10.1038/s41596-022-00680-z
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Article ; Online: MECP2-related pathways are dysregulated in a cortical organoid model of myotonic dystrophy.

Morelli, Kathryn H / Jin, Wenhao / Shathe, Shashank / Madrigal, Assael A / Jones, Krysten L / Schwartz, Joshua L / Bridges, Tristan / Mueller, Jasmine R / Shankar, Archana / Chaim, Isaac A / Day, John W / Yeo, Gene W

Science translational medicine

2022 Volume 14, Issue 651, Page(s) eabn2375

Abstract: Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase ( ...

Abstract	Myotonic dystrophy type 1 (DM1) is a multisystem, autosomal-dominant inherited disorder caused by CTG microsatellite repeat expansions (MREs) in the 3' untranslated region of the dystrophia myotonica-protein kinase (
MeSH term(s)	Adult ; CELF Proteins/genetics ; CELF Proteins/metabolism ; Humans ; Methyl-CpG-Binding Protein 2/genetics ; Methyl-CpG-Binding Protein 2/metabolism ; Myotonic Dystrophy/genetics ; Myotonic Dystrophy/metabolism ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Organoids/metabolism ; RNA Splicing ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Trinucleotide Repeat Expansion
Chemical Substances	CELF Proteins ; CELF2 protein, human ; MECP2 protein, human ; Methyl-CpG-Binding Protein 2 ; Nerve Tissue Proteins ; RNA-Binding Proteins
Language	English
Publishing date	2022-06-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.abn2375
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Article ; Online: RANK ligand converts the NCoR/HDAC3 co-repressor to a PGC1β- and RNA-dependent co-activator of osteoclast gene expression.

Abe, Yohei / Kofman, Eric R / Almeida, Maria / Ouyang, Zhengyu / Ponte, Filipa / Mueller, Jasmine R / Cruz-Becerra, Grisel / Sakai, Mashito / Prohaska, Thomas A / Spann, Nathanael J / Resende-Coelho, Ana / Seidman, Jason S / Stender, Joshua D / Taylor, Havilah / Fan, Weiwei / Link, Verena M / Cobo, Isidoro / Schlachetzki, Johannes C M / Hamakubo, Takao /

Jepsen, Kristen / Sakai, Juro / Downes, Michael / Evans, Ronald M / Yeo, Gene W / Kadonaga, James T / Manolagas, Stavros C / Rosenfeld, Michael G / Glass, Christopher K

Molecular cell

2023 Volume 83, Issue 19, Page(s) 3421–3437.e11

Abstract: The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of ... ...

Abstract	The nuclear receptor co-repressor (NCoR) complex mediates transcriptional repression dependent on histone deacetylation by histone deacetylase 3 (HDAC3) as a component of the complex. Unexpectedly, we found that signaling by the receptor activator of nuclear factor κB (RANK) converts the NCoR/HDAC3 co-repressor complex to a co-activator of AP-1 and NF-κB target genes that are required for mouse osteoclast differentiation. Accordingly, the dominant function of NCoR/HDAC3 complexes in response to RANK signaling is to activate, rather than repress, gene expression. Mechanistically, RANK signaling promotes RNA-dependent interaction of the transcriptional co-activator PGC1β with the NCoR/HDAC3 complex, resulting in the activation of PGC1β and inhibition of HDAC3 activity for acetylated histone H3. Non-coding RNAs Dancr and Rnu12, which are associated with altered human bone homeostasis, promote NCoR/HDAC3 complex assembly and are necessary for RANKL-induced osteoclast differentiation in vitro. These findings may be prototypic for signal-dependent functions of NCoR in other biological contexts.
MeSH term(s)	Humans ; Mice ; Animals ; Co-Repressor Proteins/genetics ; RNA ; Osteoclasts/metabolism ; RANK Ligand/genetics ; Nuclear Receptor Co-Repressor 1/genetics ; Nuclear Receptor Co-Repressor 1/metabolism ; Gene Expression
Chemical Substances	Co-Repressor Proteins ; histone deacetylase 3 (EC 3.5.1.98) ; RNA (63231-63-0) ; RANK Ligand ; Nuclear Receptor Co-Repressor 1
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.08.029
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Article ; Online: Principles of RNA processing from analysis of enhanced CLIP maps for 150 RNA binding proteins.

Van Nostrand, Eric L / Pratt, Gabriel A / Yee, Brian A / Wheeler, Emily C / Blue, Steven M / Mueller, Jasmine / Park, Samuel S / Garcia, Keri E / Gelboin-Burkhart, Chelsea / Nguyen, Thai B / Rabano, Ines / Stanton, Rebecca / Sundararaman, Balaji / Wang, Ruth / Fu, Xiang-Dong / Graveley, Brenton R / Yeo, Gene W

Genome biology

2020 Volume 21, Issue 1, Page(s) 90

Abstract: Background: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but ... ...

Abstract	Background: A critical step in uncovering rules of RNA processing is to study the in vivo regulatory networks of RNA binding proteins (RBPs). Crosslinking and immunoprecipitation (CLIP) methods enable mapping RBP targets transcriptome-wide, but methodological differences present challenges to large-scale analysis across datasets. The development of enhanced CLIP (eCLIP) enabled the mapping of targets for 150 RBPs in K562 and HepG2, creating a unique resource of RBP interactomes profiled with a standardized methodology in the same cell types. Results: Our analysis of 223 eCLIP datasets reveals a range of binding modalities, including highly resolved positioning around splicing signals and mRNA untranslated regions that associate with distinct RBP functions. Quantification of enrichment for repetitive and abundant multicopy elements reveals 70% of RBPs have enrichment for non-mRNA element classes, enables identification of novel ribosomal RNA processing factors and sites, and suggests that association with retrotransposable elements reflects multiple RBP mechanisms of action. Analysis of spliceosomal RBPs indicates that eCLIP resolves AQR association after intronic lariat formation, enabling identification of branch points with single-nucleotide resolution, and provides genome-wide validation for a branch point-based scanning model for 3' splice site recognition. Finally, we show that eCLIP peak co-occurrences across RBPs enable the discovery of novel co-interacting RBPs. Conclusions: This work reveals novel insights into RNA biology by integrated analysis of eCLIP profiling of 150 RBPs with distinct functions. Further, our quantification of both mRNA and other element association will enable further research to identify novel roles of RBPs in regulating RNA processing.
MeSH term(s)	Binding Sites ; Hep G2 Cells ; Humans ; Immunoprecipitation ; Introns ; K562 Cells ; RNA/metabolism ; RNA Processing, Post-Transcriptional ; RNA Splicing ; RNA, Ribosomal/metabolism ; RNA-Binding Proteins/metabolism ; Repetitive Sequences, Nucleic Acid ; Retroelements ; Spliceosomes/metabolism
Chemical Substances	RNA, Ribosomal ; RNA-Binding Proteins ; Retroelements ; RNA (63231-63-0)
Language	English
Publishing date	2020-04-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-020-01982-9
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Article: Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

Xiang, Joy S / Mueller, Jasmine R / Luo, En-Ching / Yee, Brian A / Schafer, Danielle / Schmok, Jonathan C / Tan, Frederick E / Rothamel, Katherine / McVicar, Rachael N / Kwong, Elizabeth M / Croker, Ben A / Jones, Krysten L / Her, Hsuan-Lin / Chen, Chun-Yuan / Vu, Anthony Q / Jin, Wenhao / Park, Samuel S / Le, Phuong / Brannan, Kristopher W /

Kofman, Eric R / Li, Yanhua / Tankka, Alexandra T / Dong, Kevin D / Song, Yan / Clark, Alex E / Carlin, Aaron F / Van Nostrand, Eric L / Leibel, Sandra L / Yeo, Gene W

Research square

2022

Abstract: The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation ...

Abstract	The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-1394331/v1
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Article: Discovery and functional interrogation of SARS-CoV-2 protein-RNA interactions.

Xiang, Joy S / Mueller, Jasmine R / Luo, En-Ching / Yee, Brian A / Schafer, Danielle / Schmok, Jonathan C / Tan, Frederick E / Rothamel, Katherine / McVicar, Rachael N / Kwong, Elizabeth M / Jones, Krysten L / Her, Hsuan-Lin / Chen, Chun-Yuan / Vu, Anthony Q / Jin, Wenhao / Park, Samuel S / Le, Phuong / Brannan, Kristopher W / Kofman, Eric R /

Li, Yanhua / Tankka, Alexandra T / Dong, Kevin D / Song, Yan / Carlin, Aaron F / Van Nostrand, Eric L / Leibel, Sandra L / Yeo, Gene W

bioRxiv : the preprint server for biology

2022

Abstract	The COVID-19 pandemic is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The betacoronvirus has a positive sense RNA genome which encodes for several RNA binding proteins. Here, we use enhanced crosslinking and immunoprecipitation to investigate SARS-CoV-2 protein interactions with viral and host RNAs in authentic virus-infected cells. SARS-CoV-2 proteins, NSP8, NSP12, and nucleocapsid display distinct preferences to specific regions in the RNA viral genome, providing evidence for their shared and separate roles in replication, transcription, and viral packaging. SARS-CoV-2 proteins expressed in human lung epithelial cells bind to 4773 unique host coding RNAs. Nine SARS-CoV-2 proteins upregulate target gene expression, including NSP12 and ORF9c, whose RNA substrates are associated with pathways in protein N-linked glycosylation ER processing and mitochondrial processes. Furthermore, siRNA knockdown of host genes targeted by viral proteins in human lung organoid cells identify potential antiviral host targets across different SARS-CoV-2 variants. Conversely, NSP9 inhibits host gene expression by blocking mRNA export and dampens cytokine productions, including interleukin-1α/β. Our viral protein-RNA interactome provides a catalog of potential therapeutic targets and offers insight into the etiology of COVID-19 as a safeguard against future pandemics.
Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.21.481223
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