Advances in CLIP Technologies for Studies of Protein-RNA Interactions.

Abstract:

:RNA binding proteins (RBPs) regulate all aspects in the life cycle of RNA molecules. To elucidate the elements that guide RNA specificity, regulatory mechanisms, and functions of RBPs, methods that identify direct endogenous protein-RNA interactions are particularly valuable. UV crosslinking and immunoprecipitation (CLIP) purifies short RNA fragments that crosslink to a specific protein and then identifies these fragments by sequencing. When combined with high-throughput sequencing, CLIP can produce transcriptome-wide maps of RNA crosslink sites. The protocol is comprised of several dozen biochemical steps, and improvements made over the last 15 years have increased its resolution, sensitivity, and convenience. Adaptations of CLIP are also emerging in the epitranscriptomic field to map the positions of RNA modifications accurately. Here, we describe the rationale for each step in the protocol and discuss the impact of variations to help users determine the most suitable option.

journal_name

Mol Cell

journal_title

Molecular cell

authors

Lee FCY,Ule J

doi

10.1016/j.molcel.2018.01.005

subject

Has Abstract

pub_date

2018-02-01 00:00:00

pages

354-369

issue

3

eissn

1097-2765

issn

1097-4164

pii

S1097-2765(18)30005-4

journal_volume

69

pub_type

杂志文章,评审
  • Robust Ordering of Anaphase Events by Adaptive Thresholds and Competing Degradation Pathways.

    abstract::The splitting of chromosomes in anaphase and their delivery into the daughter cells needs to be accurately executed to maintain genome stability. Chromosome splitting requires the degradation of securin, whereas the distribution of the chromosomes into the daughter cells requires the degradation of cyclin B. We show t...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2015.09.022

    authors: Kamenz J,Mihaljev T,Kubis A,Legewie S,Hauf S

    更新日期:2015-11-05 00:00:00

  • Transient DNA Occupancy of the SMC Interarm Space in Prokaryotic Condensin.

    abstract::Multi-subunit SMC ATPases control chromosome superstructure and DNA topology, presumably by DNA translocation and loop extrusion. Chromosomal DNA is entrapped within the tripartite SMCkleisin ring. Juxtaposed SMC heads ("J heads") or engaged SMC heads ("E heads") split the SMCkleisin ring into "S" and "K" sub-compartm...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2019.05.001

    authors: Vazquez Nunez R,Ruiz Avila LB,Gruber S

    更新日期:2019-07-25 00:00:00

  • Modular RNA heats up.

    abstract::In this issue of Molecular Cell, Mariner et al. (2008) demonstrate that Alu RNA from a human SINE represses RNA polymerase II transcription during heat shock. This noncoding RNA is the first example of a "protein-like" transcription factor with a distinct modular architecture. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2008.02.001

    authors: Shamovsky I,Nudler E

    更新日期:2008-02-29 00:00:00

  • The three-dimensional structure of the autoproteolytic, nuclear pore-targeting domain of the human nucleoporin Nup98.

    abstract::Nup98 is a component of the nuclear pore that plays its primary role in the export of RNAs. Nup98 is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-ter...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(02)00589-0

    authors: Hodel AE,Hodel MR,Griffis ER,Hennig KA,Ratner GA,Xu S,Powers MA

    更新日期:2002-08-01 00:00:00

  • Nuclear myosin VI enhances RNA polymerase II-dependent transcription.

    abstract::Myosin VI is the only myosin that moves toward the minus end of actin filaments, suggesting a unique biological function. Here, we show that myosin VI is present in the nucleus of mammalian cells where it colocalizes with newly transcribed mRNA and with RNA polymerase II (RNAPII) and is detected in the RNAPII complex....

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2006.07.005

    authors: Vreugde S,Ferrai C,Miluzio A,Hauben E,Marchisio PC,Crippa MP,Bussi M,Biffo S

    更新日期:2006-09-01 00:00:00

  • Cap-assisted internal initiation of translation of histone H4.

    abstract::In eukaryotes, a crucial step of translation initiation is the binding of the multifactor complex eIF4F to the 5' end of the mRNA, a prerequisite to recruitment of the activated small ribosomal 43S particle. Histone H4 mRNAs have short 5'UTRs, which do not conform to the conventional scanning-initiation model. Here we...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2010.12.019

    authors: Martin F,Barends S,Jaeger S,Schaeffer L,Prongidi-Fix L,Eriani G

    更新日期:2011-01-21 00:00:00

  • Signaling from across the way: transactivation of VEGF receptors by HSPGs.

    abstract::Heparan sulfate proteoglycans (HSPGs) influence the signaling of many growth factors, and recent work shows that they can promote VEGF signaling in trans from the surface of an adjacent cell. This mode of signaling also alters the activation state and internalization of VEGF receptors. ...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2006.05.004

    authors: Selleck SB

    更新日期:2006-05-19 00:00:00

  • The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules.

    abstract::Stress granules are mRNA-protein assemblies formed from nontranslating mRNAs. Stress granules are important in the stress response and may contribute to some degenerative diseases. Here, we describe the stress granule transcriptome of yeast and mammalian cells through RNA-sequencing (RNA-seq) analysis of purified stre...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2017.10.015

    authors: Khong A,Matheny T,Jain S,Mitchell SF,Wheeler JR,Parker R

    更新日期:2017-11-16 00:00:00

  • Proteasome active sites allosterically regulate each other, suggesting a cyclical bite-chew mechanism for protein breakdown.

    abstract::In eukaryotes, the 20S proteasome contains two chymotrypsin-like, two trypsin-like, and two active sites shown here to have caspase-like specificity. We report that certain sites allosterically regulate each other's activities. Substrates of a chymotrypsin-like site stimulate dramatically the caspase-like activity and...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80341-x

    authors: Kisselev AF,Akopian TN,Castillo V,Goldberg AL

    更新日期:1999-09-01 00:00:00

  • Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease.

    abstract::Deubiquitinating enzymes (DUBs) recognize and cleave linkage-specific polyubiquitin (polyUb) chains, but mechanisms underlying specificity remain elusive in many cases. The severe acute respiratory syndrome (SARS) coronavirus papain-like protease (PLpro) is a DUB that cleaves ISG15, a two-domain Ub-like protein, and L...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2016.04.016

    authors: Békés M,van der Heden van Noort GJ,Ekkebus R,Ovaa H,Huang TT,Lima CD

    更新日期:2016-05-19 00:00:00

  • The three Rs of transcription: recruit, retain, and recycle.

    abstract::The dynamic protein interactions required for transcription are functionally important yet poorly understood; in this issue of Molecular Cell, Zobeck et al. (2010) resolve the sequential recruitment and selective recycling of transcription factors at an actively transcribing locus in Drosophila. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2010.12.010

    authors: Motta-Mena LB,Partch CL,Gardner KH

    更新日期:2010-12-22 00:00:00

  • The response regulator BvgA and RNA polymerase alpha subunit C-terminal domain bind simultaneously to different faces of the same segment of promoter DNA.

    abstract::Examination of the binding of FeBABE-conjugated BvgA to the fha promoter of Bordetella pertussis has revealed that three dimers, formed by head-to-head association of monomers, bind one face of the DNA helix from the inverted-heptad primary binding site to the -35 region. The orientation of BvgA monomers within the di...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00007-8

    authors: Boucher PE,Maris AE,Yang MS,Stibitz S

    更新日期:2003-01-01 00:00:00

  • Mechanism of homology recognition in DNA recombination from dual-molecule experiments.

    abstract::In E. coli homologous recombination, a filament of RecA protein formed on DNA searches and pairs a homologous sequence within a second DNA molecule with remarkable speed and fidelity. Here, we directly probe the strength of the two-molecule interactions involved in homology search and recognition using dual-molecule m...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.03.029

    authors: De Vlaminck I,van Loenhout MT,Zweifel L,den Blanken J,Hooning K,Hage S,Kerssemakers J,Dekker C

    更新日期:2012-06-08 00:00:00

  • HATs off to PIC assembly.

    abstract::There are many regulated steps in the assembly of a transcription preinitiation complex (PIC). In this issue of Molecular Cell, Black et. al. (2006) reveal a catalytic switch mechanism in which autoacetylation of the HAT p300 triggers its dissociation from a promoter in a manner that is coupled to TFIID association. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章,评审

    doi:10.1016/j.molcel.2006.08.022

    authors: Pugh BF

    更新日期:2006-09-15 00:00:00

  • Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes.

    abstract::Nucleosome loss from a promoter region has recently been described as a potential mechanism for transcriptional regulation. We investigated whether H3/H4 histone chaperones mediate the loss of nucleosomes from the promoter of the yeast PHO5 gene during transcriptional activation. We found that antisilencing function 1...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2004.05.016

    authors: Adkins MW,Howar SR,Tyler JK

    更新日期:2004-06-04 00:00:00

  • The APC/C subunit Mnd2/Apc15 promotes Cdc20 autoubiquitination and spindle assembly checkpoint inactivation.

    abstract::The fidelity of chromosome segregation depends on the spindle assembly checkpoint (SAC). In the presence of unattached kinetochores, anaphase is delayed when three SAC components (Mad2, Mad3/BubR1, and Bub3) inhibit Cdc20, the activating subunit of the anaphase-promoting complex (APC/C). We analyzed the role of Cdc20 ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2012.07.031

    authors: Foster SA,Morgan DO

    更新日期:2012-09-28 00:00:00

  • Adaptation in CRISPR-Cas Systems.

    abstract::Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins constitute an adaptive immune system in prokaryotes. The system preserves memories of prior infections by integrating short segments of foreign DNA, termed spacers, into the CRISPR array in a process termed adaptati...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2016.01.030

    authors: Sternberg SH,Richter H,Charpentier E,Qimron U

    更新日期:2016-03-17 00:00:00

  • Cdh1 is a HECT of an activator.

    abstract::Cdh1 is a well-established activator of APC/C, a RING-type ubiquitin ligase. In this issue of Molecular Cell, Wan et al. (2011) report an APC/C-independent role of Cdh1 during development as an activator for Smurf1, a HECT-type ubiquitin ligase. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2011.11.012

    authors: Jia L,Yu H

    更新日期:2011-12-09 00:00:00

  • Sam68 is required for both NF-κB activation and apoptosis signaling by the TNF receptor.

    abstract::The RNA-binding protein Sam68 is implicated in various cellular processes including RNA metabolism, apoptosis, and signal transduction. Here we identify a role of Sam68 in TNF-induced NF-κB activation and apoptosis. We found that Sam68 is recruited to the TNF receptor, and its deficiency dramatically reduces RIP recru...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2011.05.007

    authors: Ramakrishnan P,Baltimore D

    更新日期:2011-07-22 00:00:00

  • Oligomeric initiator protein-mediated DNA looping negatively regulates plasmid replication in vitro by preventing origin melting.

    abstract::Although DNA looping between the initiator binding sites (iterons) of the replication origin (ori) of a plasmid and the iterons located in a cis-acting control sequence called inc has been postulated to promote negative control of plasmid DNA replication, not only was definitive evidence for such looping lacking, but ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.10.037

    authors: Zzaman S,Bastia D

    更新日期:2005-12-22 00:00:00

  • A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im.

    abstract::Human cleavage factor I(m) (CFI(m)) is a heterodimeric RNA binding protein complex that functions at an early step in the assembly of the pre-mRNA 3' processing complex. In this report we show that CFI(m) can stimulate both cleavage and poly(A) addition, and can act to suppress poly(A) site cleavage in a sequence-depe...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(03)00453-2

    authors: Brown KM,Gilmartin GM

    更新日期:2003-12-01 00:00:00

  • Gene-Specific Control of tRNA Expression by RNA Polymerase II.

    abstract::Increasing evidence suggests that tRNA levels are dynamically and specifically regulated in response to internal and external cues to modulate the cellular translational program. However, the molecular players and the mechanisms regulating the gene-specific expression of tRNAs are still unknown. Using an inducible aux...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2020.03.023

    authors: Gerber A,Ito K,Chu CS,Roeder RG

    更新日期:2020-05-21 00:00:00

  • New functions for Y family polymerases.

    abstract::The Y family of DNA polymerases plays crucial roles in carrying out translesion synthesis past damaged bases in DNA. Several recent papers suggest that they might have other roles as well in gene conversion, in nucleotide excision repair (NER), and in DNA replication under stressed conditions. ...

    journal_title:Molecular cell

    pub_type: 杂志文章,评审

    doi:10.1016/j.molcel.2006.10.021

    authors: Lehmann AR

    更新日期:2006-11-17 00:00:00

  • A peptide signal for adapter protein-mediated degradation by the AAA+ protease ClpCP.

    abstract::ComS is an antiadaptor protein that binds to MecA, displacing the competence transcription factor ComK. This protects ComK from degradation by the ClpCP protease and turns on the switch leading to bistable gene expression. Here we identify the motifs on ComK and ComS that mediate binding to MecA, and we show that they...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2007.05.011

    authors: Prepiak P,Dubnau D

    更新日期:2007-06-08 00:00:00

  • Multisite Phosphorylation of S6K1 Directs a Kinase Phospho-code that Determines Substrate Selection.

    abstract::Multisite phosphorylation of kinases can induce on-off or graded regulation of catalytic activity; however, its influence on substrate specificity remains unclear. Here, we show that multisite phosphorylation of ribosomal protein S6 kinase 1 (S6K1) alters target selection. Agonist-inducible phosphorylation of glutamyl...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2018.11.017

    authors: Arif A,Jia J,Willard B,Li X,Fox PL

    更新日期:2019-02-07 00:00:00

  • METTL3 Gains R/W Access to the Epitranscriptome.

    abstract::Epitranscriptomic marks are dynamically placed on mRNA by "writer" or "eraser" enzymes, while "readers" modulate their function accordingly. Lin et al. (2016) now report that the N6-methyladenosine:RNA methyltransferase METTL3 is both a writer and a reader, directly enhancing mRNA translation. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2016.04.024

    authors: Schumann U,Shafik A,Preiss T

    更新日期:2016-05-05 00:00:00

  • Asymmetric segregation of PIE-1 in C. elegans is mediated by two complementary mechanisms that act through separate PIE-1 protein domains.

    abstract::The CCCH finger protein PIE-1 is a regulator of germ cell fate that segregates with the germ lineage in early embryos. At each asymmetric division, PIE-1 is inherited preferentially by the germline daughter and is excluded from the somatic daughter. We show that this asymmetry is regulated at the protein level by two ...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)00043-5

    authors: Reese KJ,Dunn MA,Waddle JA,Seydoux G

    更新日期:2000-08-01 00:00:00

  • Structural basis of Rho GTPase-mediated activation of the formin mDia1.

    abstract::Diaphanous-related formins (DRFs) regulate dynamics of unbranched actin filaments during cell contraction and cytokinesis. DRFs are autoinhibited through intramolecular binding of a Diaphanous autoinhibitory domain (DAD) to a conserved N-terminal regulatory element. Autoinhibition is relieved through binding of the GT...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/j.molcel.2005.04.002

    authors: Otomo T,Otomo C,Tomchick DR,Machius M,Rosen MK

    更新日期:2005-04-29 00:00:00

  • yTAFII61 has a general role in RNA polymerase II transcription and is required by Gcn4p to recruit the SAGA coactivator complex.

    abstract::We obtained a recessive insertion mutation in the gene encoding yeast TBP-associated factor yTAFII61/68 that impairs Gcn4p-independent and Gcn4p-activated HIS3 transcription. This mutation also reduces transcription of seven other class II genes, thus indicating a broad role for this yTAFII in RNA polymerase II transc...

    journal_title:Molecular cell

    pub_type: 杂志文章

    doi:10.1016/s1097-2765(00)80166-5

    authors: Natarajan K,Jackson BM,Rhee E,Hinnebusch AG

    更新日期:1998-11-01 00:00:00

  • Telomeres thrown for a loop.

    abstract::A remarkable paper from the de Lange lab (Wang et al., 2004) in a recent issue of Cell reveals that homologous recombination can result in the abrupt shortening of telomeres in a process that appears to involve reciprocal crossing over within the t-loop structure that protects chromosome ends. ...

    journal_title:Molecular cell

    pub_type: 评论,杂志文章

    doi:10.1016/j.molcel.2004.11.006

    authors: Haber JE

    更新日期:2004-11-19 00:00:00