scholarly journals LIN28 selectively modulates a subclass of let-7 microRNAs

2017 ◽  
Author(s):  
Dmytro Ustianenko ◽  
Hua-Sheng Chiu ◽  
Sebastien M. Weyn-Vanhentenryck ◽  
Pavel Sumazin ◽  
Chaolin Zhang
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Class I ◽  
Single Nucleotide ◽  
Potential Implication ◽  
Disease States ◽  
Resolution Mapping ◽  
Cold Shock Domain ◽  
Nucleotide Resolution

AbstractLIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remains poorly understood, because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD)—which binds a GGAG-like element in the precursor—and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif. This motif partitions the let-7 family into Class I precursors with both CSD and ZKD binding sites and Class II precursors with ZKD but no CSD binding sites. LIN28 in vivo recognition—and subsequent 3′ uridylation and degradation—of Class I precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the effects of the LIN28 activation with potential implication in development and cancer.

scholarly journals Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution

RNA Biology ◽  
2017 ◽  
Vol 14 (12) ◽  
pp. 1756-1765 ◽  
Author(s):  
Elizabeth Ransey ◽  
Anders Björkbom ◽  
Victor S. Lelyveld ◽  
Przemyslaw Biecek ◽  
Lorena Pantano ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Binding Sites ◽  
Rna Binding ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution ◽  
Rna Binding Sites

scholarly journals Profiling the binding sites of RNA-binding protein by LACE-seq

2021 ◽  
Author(s):  
Ruibao Su ◽  
Di Wang ◽  
Changchang Cao ◽  
Yuanchao Xue
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Transcription Termination ◽  
Early Embryo ◽  
Linear Amplification ◽  
Single Nucleotide ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Abstract RNA-binding proteins (RBPs) directly interact with various RNAs in living cells to regulate their processing, translation, and stability. Identifying the precise binding sites of RBPs is critical for appreciating their physiological or pathological roles in germline and early embryo development. Current methods typically need millions of cells to map RBP binding positions, which prevents us from appreciating the crucial role of RBPs in early development. Here, we present the LACE-seq method for unbiased mapping of RBP-binding sites at single-nucleotide resolution in fewer cells or even single oocytes. LACE-seq depends on RBP-mediated reverse transcription termination, and linear amplification of the cDNA ends for deep sequencing. To further promote its application, we describe a step-by-step protocol about how to construct a successful LACE-seq library.

scholarly journals Modeling RNA-binding protein specificity in vivo by precisely registering protein-RNA crosslink sites

2018 ◽  
Author(s):  
Huijuan Feng ◽  
Suying Bao ◽  
Sebastien M. Weyn-Vanhentenryck ◽  
Aziz Khan ◽  
Justin Wong ◽  
...  
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Specificity ◽  
Computational Method ◽  
Sr Protein ◽  
Genome Wide ◽  
Sequence Elements ◽  
Nucleotide Resolution

AbstractRNA-binding proteins (RBPs) regulate post-transcriptional gene expression by recognizing short and degenerate sequence elements in their target transcripts. Despite the expanding list of RBPs with in vivo binding sites mapped genomewide using crosslinking and immunoprecipitation (CLIP), defining precise RBP binding specificity remains challenging. We previously demonstrated that the exact protein-RNA crosslink sites can be mapped using CLIP data at single-nucleotide resolution and observed that crosslinking frequently occurs at specific positions in RBP motifs. Here we have developed a computational method, named mCross, to jointly model RBP binding specificity while precisely registering the crosslinking position in motif sites. We applied mCross to 112 RBPs using ENCODE eCLIP data and validated the reliability of the resulting motifs by genome-wide analysis of allelic binding sites also detected by CLIP. We found that the prototypical SR protein SRSF1 recognizes GGA clusters to regulate splicing in a much larger repertoire of transcripts than previously appreciated.

scholarly journals FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

2019 ◽  
Vol 47 (19) ◽  
pp. e113-e113 ◽  
Author(s):  
Jean-Michel Carter ◽  
Warren Emmett ◽  
Igor Rdl Mozos ◽  
Annika Kotter ◽  
Mark Helm ◽  
...  
Keyword(s):  
Mapping Method ◽  
Single Nucleotide ◽  
Genome Wide ◽  
A Genome ◽  
Target Sites ◽  
Reliable Detection ◽  
Resolution Mapping ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Abstract Methyl-5-uridine (m5U) is one the most abundant non-canonical bases present in cellular RNA, and in yeast is found at position U54 of tRNAs where modification is catalysed by the methyltransferase Trm2. Although the mammalian enzymes that catalyse m5U formation are yet to be identified via experimental evidence, based on sequence homology to Trm2, two candidates currently exist, TRMT2A and TRMT2B. Here we developed a genome-wide single-nucleotide resolution mapping method, Fluorouracil-Induced-Catalytic-Crosslinking-Sequencing (FICC-Seq), in order to identify the relevant enzymatic targets. We demonstrate that TRMT2A is responsible for the majority of m5U present in human RNA, and that it commonly targets U54 of cytosolic tRNAs. By comparison to current methods, we show that FICC-Seq is a particularly robust method for accurate and reliable detection of relevant enzymatic target sites. Our associated finding of extensive irreversible TRMT2A-tRNA crosslinking in vivo following 5-Fluorouracil exposure is also intriguing, as it suggests a tangible mechanism for a previously suspected RNA-dependent route of Fluorouracil-mediated cytotoxicity.

scholarly journals An improved iCLIP protocol

2021 ◽  
Author(s):  
Flora C. Y. Lee ◽  
Anob M. Chakrabarti ◽  
Heike Hänel ◽  
Elisa Monzón-Casanova ◽  
Martina Hallegger ◽  
...  
Keyword(s):  
Cdna Library ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Library Preparation ◽  
Powerful Technique ◽  
Uv Crosslinking ◽  
Nucleotide Resolution ◽  
Cdna Library Preparation

AbstractCrosslinking and Immunoprecipitation (CLIP) is a powerful technique to obtain transcriptome-wide maps of in vivo protein-RNA interactions, which are important to understand the post-transcriptional mechanisms mediated by RNA binding proteins (RBPs). Many variant CLIP protocols have been developed to improve the efficiency and convenience of cDNA library preparation. Here we describe an improved individual nucleotide resolution CLIP protocol (iiCLIP), which can be completed within 4 days from UV crosslinking to libraries for sequencing. For benchmarking, we directly compared PTBP1 iiCLIP libraries with the iCLIP2 protocol produced under standardised conditions, and with public eCLIP and iCLIP PTBP1 data. We visualised enriched motifs surrounding the identified crosslink positions and RNA maps of these crosslinks around the alternative exons regulated by PTBP1. Notably, motif enrichment was higher in iiCLIP and iCLIP2 in comparison to public eCLIP and iCLIP, and we show how this impacts the specificity of RNA maps. In conclusion, iiCLIP is technically convenient and efficient, and enables production of highly specific datasets for identifying RBP binding sites.

scholarly journals Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

2015 ◽  
Vol 12 (8) ◽  
pp. 767-772 ◽  
Author(s):  
Bastian Linder ◽  
Anya V Grozhik ◽  
Anthony O Olarerin-George ◽  
Cem Meydan ◽  
Christopher E Mason ◽  
...  
Keyword(s):  
Single Nucleotide ◽  
Resolution Mapping ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

scholarly journals Mapping of In Vivo RNA-Binding Sites by Ultraviolet (UV)-Cross-Linking Immunoprecipitation (CLIP)

2018 ◽  
Vol 2018 (12) ◽  
pp. pdb.top097931 ◽  
Author(s):  
Jennifer C. Darnell ◽  
Aldo Mele ◽  
Ka Ying Sharon Hung ◽  
Robert B. Darnell
Keyword(s):  
Binding Sites ◽  
Rna Binding ◽  
Cross Linking ◽  
Rna Binding Sites

scholarly journals SSMART: Sequence-structure motif identification for RNA-binding proteins

2018 ◽  
Author(s):  
Alina Munteanu ◽  
Neelanjan Mukherjee ◽  
Uwe Ohler
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Sequence Motif ◽  
Primary Sequence ◽  
Sequence Structure ◽  
Rna Targets

AbstractMotivationRNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized.ResultsWe developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is able to recover both sequence and structure motifs implanted into 3‘UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP.AvailabilitySSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/[email protected]

Sign in / Sign up

Export Citation Format

Share Document