Regulation of chloroplast translation: interactions of RNA elements, RNA-binding proteins and the plastid ribosome

Chloroplast gene expression is primarily controlled during the translation of plastid mRNAs into proteins, and genetic studies have identified cis-acting RNA elements and trans-acting protein factors required for chloroplast translation. Biochemical analysis has identified both general and specific mRNA-binding proteins as components of the regulation of chloroplast translation, and has revealed that chloroplast translation is related to bacterial translation but is more complex. Utilizing proteomic and bioinformatic analyses, we have identified the proteins that function in chloroplast translation, including a complete set of chloroplast ribosomal proteins, and homologues of the 70 S initiation, elongation and termination factors. These analyses show that the translational apparatus of chloroplasts is related to that of bacteria, but has adopted a number of eukaryotic mechanisms to facilitate and regulate chloroplast translation.

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Combinatorial recognition of clustered RNA elements by a multidomain RNA-binding protein, IMP3

10.1101/398008 ◽

2018 ◽

Cited By ~ 1

Author(s):

Tim Schneider ◽

Lee-Hsueh Hung ◽

Masood Aziz ◽

Anna Wilmen ◽

Stephanie Thaum ◽

...

Keyword(s):

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Binding Protein ◽

Rna Binding Protein ◽

Binding Domains ◽

Systematic Strategy ◽

Rna Elements ◽

Target Rna

AbstractHow multidomain RNA-binding proteins recognize their specific target sequences, based on a combinatorial code, represents a fundamental unsolved question and has not been studied systematically so far. Here we focus on a prototypical multidomain RNA-binding protein, IMP3 (also called IGF2BP3), which contains six RNA-binding domains (RBDs): four KH and two RRM domains. We have established an integrative systematic strategy, combining single-domain-resolved SELEX-seq, motif-spacing analyses, in vivo iCLIP, functional validation assays, and structural biology. This approach identifies the RNA-binding specificity and RNP topology of IMP3, involving all six RBDs and a cluster of up to five distinct and appropriately spaced CA-rich and GGC-core RNA elements, covering a >100 nucleotide-long target RNA region. Our generally applicable approach explains both specificity and flexibility of IMP3-RNA recognition, providing a paradigm for the function of multivalent interactions with multidomain RNA-binding proteins in gene regulation.

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Binding patterns of RNA-binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab055 ◽

2021 ◽

Vol 3 (3) ◽

Author(s):

Masahiro Onoguchi ◽

Chao Zeng ◽

Ayako Matsumaru ◽

Michiaki Hamada

Keyword(s):

Rna Splicing ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Noncoding Rnas ◽

Biological Processes ◽

Rna Sequences ◽

Rna Elements ◽

Long Interspersed Element ◽

Functional Rna

Abstract Recent reports have revealed that repeat-derived sequences embedded in introns or long noncoding RNAs (lncRNAs) are targets of RNA-binding proteins (RBPs) and contribute to biological processes such as RNA splicing or transcriptional regulation. These findings suggest that repeat-derived RNAs are important as scaffolds of RBPs and functional elements. However, the overall functional sequences of the repeat-derived RNAs are not fully understood. Here, we show the putative functional repeat-derived RNAs by analyzing the binding patterns of RBPs based on ENCODE eCLIP data. We mapped all eCLIP reads to repeat sequences and observed that 10.75 % and 7.04 % of reads on average were enriched (at least 2-fold over control) in the repeats in K562 and HepG2 cells, respectively. Using these data, we predicted functional RNA elements on the sense and antisense strands of long interspersed element 1 (LINE1) sequences. Furthermore, we found several new sets of RBPs on fragments derived from other transposable element (TE) families. Some of these fragments show specific and stable secondary structures and are found to be inserted into the introns of genes or lncRNAs. These results suggest that the repeat-derived RNA sequences are strong candidates for the functional RNA elements of endogenous noncoding RNAs.

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A Large-Scale Binding and Functional Map of Human RNA Binding Proteins

10.1101/179648 ◽

2017 ◽

Cited By ~ 49

Author(s):

Eric L Van Nostrand ◽

Peter Freese ◽

Gabriel A Pratt ◽

Xiaofeng Wang ◽

Xintao Wei ◽

...

Keyword(s):

Large Scale ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Large Set ◽

Functional Elements ◽

Dna Elements ◽

Cleavage And Polyadenylation ◽

Rna Elements ◽

And Function

Genomes encompass all the information necessary to specify the development and function of an organism. In addition to genes, genomes also contain a myriad of functional elements that control various steps in gene expression. A major class of these elements function only when transcribed into RNA as they serve as the binding sites for RNA binding proteins (RBPs), which act to control post-transcriptional processes including splicing, cleavage and polyadenylation, RNA editing, RNA localization, stability, and translation. Despite the importance of these functional RNA elements encoded in the genome, they have been much less studied than genes and DNA elements. Here, we describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. These data expand the catalog of functional elements encoded in the human genome by addition of a large set of elements that function at the RNA level through interaction with RBPs.

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A large-scale binding and functional map of human RNA-binding proteins

Nature ◽

10.1038/s41586-020-2077-3 ◽

2020 ◽

Vol 583 (7818) ◽

pp. 711-719 ◽

Cited By ~ 26

Author(s):

Eric L. Van Nostrand ◽

Peter Freese ◽

Gabriel A. Pratt ◽

Xiaofeng Wang ◽

Xintao Wei ◽

...

Keyword(s):

Human Genome ◽

Binding Sites ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Regulatory Elements ◽

Phase Iii ◽

Large Set ◽

Data Set ◽

Rna Elements

AbstractMany proteins regulate the expression of genes by binding to specific regions encoded in the genome1. Here we introduce a new data set of RNA elements in the human genome that are recognized by RNA-binding proteins (RBPs), generated as part of the Encyclopedia of DNA Elements (ENCODE) project phase III. This class of regulatory elements functions only when transcribed into RNA, as they serve as the binding sites for RBPs that control post-transcriptional processes such as splicing, cleavage and polyadenylation, and the editing, localization, stability and translation of mRNAs. We describe the mapping and characterization of RNA elements recognized by a large collection of human RBPs in K562 and HepG2 cells. Integrative analyses using five assays identify RBP binding sites on RNA and chromatin in vivo, the in vitro binding preferences of RBPs, the function of RBP binding sites and the subcellular localization of RBPs, producing 1,223 replicated data sets for 356 RBPs. We describe the spectrum of RBP binding throughout the transcriptome and the connections between these interactions and various aspects of RNA biology, including RNA stability, splicing regulation and RNA localization. These data expand the catalogue of functional elements encoded in the human genome by the addition of a large set of elements that function at the RNA level by interacting with RBPs.

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Binding patterns of RNA binding proteins to repeat-derived RNA sequences reveal putative functional RNA elements

10.1101/2021.06.03.446901 ◽

2021 ◽

Author(s):

Masahiro Onoguchi ◽

Chao Zeng ◽

Ayako Matsumaru ◽

Michiaki Hamada

Keyword(s):

Rna Splicing ◽

Binding Proteins ◽

Rna Binding ◽

Rna Binding Proteins ◽

Noncoding Rnas ◽

Biological Processes ◽

Rna Sequences ◽

Rna Elements ◽

Long Interspersed Element ◽

Functional Rna

Recent reports have revealed that repeat-derived sequences embedded in introns or long noncoding RNAs (lncRNAs) are targets of RNA binding proteins (RBPs) and contribute to biological processes such as RNA splicing or transcriptional regulation. These findings suggest that repeat-derived RNAs are important as scaffolds of RBPs and functional elements. However, the overall functional sequences of the repeat-derived RNAs are not fully understood. Here, we show the putative functional repeat-derived RNAs by analyzing the binding patterns of RBPs based on ENCODE eCLIP data. We mapped all eCLIP reads to repeat sequences and observed that 10.75 % and 7.04 % of reads on average were enriched (at least 2-fold over control) in the repeats in K562 and HepG2 cells, respectively. Using these data, we predicted functional RNA elements on the sense and antisense strands of long interspersed element 1 (LINE1) sequences. Furthermore, we found several new sets of RBPs on fragments derived from other transposable element (TE) families. Some of these fragments show specific and stable secondary structures and are found to be inserted into the introns of genes or lncRNAs. These results suggest that the repeat-derived RNA sequences are strong candidates for the functional RNA elements of endogenous noncoding RNAs.

Download Full-text