scholarly journals Widespread localisation of long noncoding RNAs to ribosomes: Distinguishing features and evidence for regulatory roles.

2015 ◽  
Author(s):  
Juna Carlevaro-Fita ◽  
Anisa Rahim ◽  
Roderic Guigo ◽  
Leah Vardy ◽  
Rory Johnson
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Cell Types ◽  
Long Noncoding Rnas ◽  
Open Reading Frames ◽  
Translation Machinery ◽  
Evolutionary Selection ◽  
Regulatory Interactions ◽  
Distinguishing Features ◽  
Reading Frames

The function of long noncoding RNAs (lncRNAs) depends on their location within the cell. While most studies to date have concentrated on their nuclear roles in transcriptional regulation, evidence is mounting that lncRNA also have cytoplasmic roles. Here we comprehensively map the cytoplasmic and ribosomal lncRNA population in a human cell. Three-quarters (74%) of lncRNAs are detected in the cytoplasm, the majority of which (62%) preferentially cofractionate with polyribosomes. Ribosomal lncRNA are highly expressed across tissues, under purifying evolutionary selection, and have cytoplasmic-to-nuclear ratios comparable to mRNAs and consistent across cell types. LncRNAs may be classified into three groups by their ribosomal interaction: non-ribosomal cytoplasmic lncRNAs, and those associated with either heavy or light polysomes. A number of mRNA-like features destin lncRNA for light polysomes, including capping and 5′UTR length, but not cryptic open reading frames or polyadenylation. Surprisingly, exonic retroviral sequences antagonise recruitment. In contrast, it appears that lncRNAs are recruited to heavy polysomes through basepairing to mRNAs. Finally, we show that the translation machinery actively degrades lncRNA. We propose that light polysomal lncRNAs are translationally engaged, while heavy polysomal lncRNAs are recruited indirectly. These findings point to extensive and reciprocal regulatory interactions between lncRNA and the translation machinery.

scholarly journals When Long Noncoding Becomes Protein Coding

2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Corrine Corrina R. Hartford ◽  
Ashish Lal
Keyword(s):  
Cell Division ◽  
Cell Signaling ◽  
Transcription Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Open Reading Frames ◽  
Protein Coding ◽  
Small Proteins ◽  
Coding Potential ◽  
Reading Frames

ABSTRACT Recent advancements in genetic and proteomic technologies have revealed that more of the genome encodes proteins than originally thought possible. Specifically, some putative long noncoding RNAs (lncRNAs) have been misannotated as noncoding. Numerous lncRNAs have been found to contain short open reading frames (sORFs) which have been overlooked because of their small size. Many of these sORFs encode small proteins or micropeptides with fundamental biological importance. These micropeptides can aid in diverse processes, including cell division, transcription regulation, and cell signaling. Here we discuss strategies for establishing the coding potential of putative lncRNAs and describe various functions of known micropeptides.

scholarly journals SARS-CoV-2 Transgressing LncRNAs Uncovers the Known Unknowns

2021 ◽  
Author(s):  
Nidhi Shukla ◽  
Anchita Prasad ◽  
Uma Kanga ◽  
Renuka Suravajhala ◽  
Vinod Kumar Nigam ◽  
...  
Keyword(s):  
Viral Infection ◽  
Noncoding Rnas ◽  
Viral Proteins ◽  
Viral Pathogenesis ◽  
Long Noncoding Rnas ◽  
Open Reading Frames ◽  
Regulatory Role ◽  
Disease Pathogenesis ◽  
Known Unknowns ◽  
Reading Frames

SARS-CoV-2 harbors many known unknown regions in the form of hypothetical open reading frames (ORFs). While the mechanisms underlying the disease pathogenesis are not clearly understood, molecules such as long noncoding RNAs (lncRNAs) play a key regulatory role in the viral pathogenesis from endocytosis. We asked whether or not the lncRNAs in the host are associated with the viral proteins and argue that lncRNA-mRNA molecules related to viral infection may regulate SARS-CoV-2 pathogenesis. Towards the end of the perspective, we provide challenges and insights into investigating these transgression pathways.

scholarly journals Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients

2018 ◽  
Vol 78 (15) ◽  
pp. 4411-4423 ◽  
Author(s):  
Lei Wang ◽  
Sara J. Felts ◽  
Virginia P. Van Keulen ◽  
Adam D. Scheid ◽  
Matthew S. Block ◽  
...  
Keyword(s):  
Immune Cell ◽  
Noncoding Rnas ◽  
Cell Types ◽  
Long Noncoding Rnas ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Melanoma Patients

scholarly journals Characterization of CELO Virus Proteins That Modulate the pRb/E2F Pathway

1999 ◽  
Vol 73 (8) ◽  
pp. 6517-6525 ◽  
Author(s):  
Heike Lehrmann ◽  
Matt Cotten
Keyword(s):  
Cell Types ◽  
Open Reading Frames ◽  
Reporter System ◽  
Human Adenoviruses ◽  
Tumor Virus ◽  
Celo Virus ◽  
Reading Frames ◽  
Pocket Domain ◽  
Virus Proteins

ABSTRACT The avian adenovirus CELO can, like the human adenoviruses, transform several mammalian cell types, yet it lacks sequence homology with the transforming, early regions of human adenoviruses. In an attempt to identify how CELO virus activates the E2F-dependent gene expression important for S phase in the host cell, we have identified two CELO virus open reading frames that cooperate in activating an E2F-inducible reporter system. The encoded proteins, GAM-1 and Orf22, were both found to interact with the retinoblastoma protein (pRb), with Orf22 binding to the pocket domain of pRb, similar to other DNA tumor virus proteins, and GAM-1 interacting with pRb regions outside the pocket domain. The motif in Orf22 responsible for the pRb interaction is essential for Orf22-mediated E2F activation, yet it is remarkably unlike the E1A LxCxD and may represent a novel form of pRb-binding peptide.

scholarly journals A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli

mBio ◽  
2016 ◽  
Vol 7 (6) ◽  
Author(s):  
Adi Oron-Gottesman ◽  
Martina Sauert ◽  
Isabella Moll ◽  
Hanna Engelberg-Kulka
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Ribosomal Protein ◽  
Genetic Code ◽  
Open Reading Frames ◽  
Translation Machinery ◽  
E Coli ◽  
Universal Characteristic ◽  
Living Organisms ◽  
Reading Frames

ABSTRACT Escherichia coli mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress, the induced MazF generates a stress-induced translation machinery (STM), composed of MazF-processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here, we further characterized the STM system, finding that MazF cleaves only ACA sites located in the open reading frames of processed mRNAs, while out-of-frame ACAs are resistant. This in-frame ACA cleavage of MazF seems to depend on MazF binding to an extracellular-death-factor (EDF)-like element in ribosomal protein bS1 (bacterial S1), apparently causing MazF to be part of STM ribosomes. Furthermore, due to the in-frame MazF cleavage of ACAs under stress, a bias occurs in the reading of the genetic code causing the amino acid threonine to be encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. IMPORTANCE The genetic code is a universal characteristic of all living organisms. It defines the set of rules by which nucleotide triplets specify which amino acid will be incorporated into a protein. Our results represent the first existing report on a stress-induced bias in the reading of the genetic code. We found that in E. coli , under stress, the amino acid threonine is encoded only by its synonym codon ACC, ACU, or ACG, instead of by ACA. This is because under stress, MazF generates a stress-induced translation machinery (STM) in which MazF cleaves in-frame ACA sites of the processed mRNAs.

scholarly journals Full-length annotation with multi-strategy RNA-seq uncovers transcriptional regulation of lncRNAs in diploid cotton G. arboreum1

2020 ◽  
Author(s):  
Xiaomin Zheng ◽  
Yanjun Chen ◽  
Yifan Zhou ◽  
Danyang Li ◽  
Keke Shi ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Full Length ◽  
Rna Seq ◽  
Accurate Identification ◽  
Tissue Samples ◽  
Protein Coding ◽  
Diploid Cotton ◽  
Cap Analysis

AbstractLong noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. High-throughput and accurate identification of lncRNAs is still lacking in plants. To build an accurate atlas of lncRNA in cotton, we combined Isoform-sequencing (Iso-seq), strand-specific RNA-seq (ssRNA-seq), cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA (PULL) to integrate multi-omics data. A total of 9240 lncRNAs from 21 tissue samples of the diploid cotton Gossypium arboreum were identified. We revealed that alternative usage of transcription start site (TSS) and transcription end site (TES) of lncRNAs occurs pervasively during plant growth and responses to stress. We identified the lncRNAs which co-expressed or be linked to the protein coding genes (PCGs) or GWAS studied SNPs associated with ovule and fiber development. We also mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing (ChIRP-seq) and validated the trans transcriptional regulation of lnc-Ga13g0352 via virus induced gene suppression (VIGS) assay. These findings provide valuable research resources for plant community and broaden our understandings of biogenesis and regulation function of plant lncRNAs.One sentence summaryThe full-length annotation and transcriptional regulation of long noncoding RNAs in cotton.

scholarly journals When Long Noncoding RNAs Meet Genome Editing in Pluripotent Stem Cells

2017 ◽  
Vol 2017 ◽  
pp. 1-13
Author(s):  
Fuquan Chen ◽  
Jiaojiao Ji ◽  
Jian Shen ◽  
Xinyi Lu
Keyword(s):  
Stem Cells ◽  
Transcriptional Regulation ◽  
Genome Editing ◽  
Pluripotent Stem Cells ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Past

Most of the human genome can be transcribed into RNAs, but only a minority of these regions produce protein-coding mRNAs whereas the remaining regions are transcribed into noncoding RNAs. Long noncoding RNAs (lncRNAs) were known for their influential regulatory roles in multiple biological processes such as imprinting, dosage compensation, transcriptional regulation, and splicing. The physiological functions of protein-coding genes have been extensively characterized through genome editing in pluripotent stem cells (PSCs) in the past 30 years; however, the study of lncRNAs with genome editing technologies only came into attentions in recent years. Here, we summarize recent advancements in dissecting the roles of lncRNAs with genome editing technologies in PSCs and highlight potential genome editing tools useful for examining the functions of lncRNAs in PSCs.

scholarly journals Aquaporin AQP11 in the testis: molecular identity and association with the processing of residual cytoplasm of elongated spermatids

Reproduction ◽  
2010 ◽  
Vol 139 (1) ◽  
pp. 209-216 ◽  
Author(s):  
C H Yeung ◽  
T G Cooper
Keyword(s):  
Cell Types ◽  
Open Reading Frames ◽  
Molecular Forms ◽  
Reading Frame ◽  
Pcr Products ◽  
Mrna And Protein Expression ◽  
Intracellular Organelles ◽  
Residual Bodies ◽  
Reading Frames

AQP11 is one of the latest aquaporin (AQP) family members found, which differs from the other AQPs by its intracellular localisation and unusual water pore nucleotides with unclear function. Despite the highest mRNA expression among organs having been reported in the testis, the testicular molecule has not been studied in detail. Immunohistochemistry of rat adult testis localised AQP11 to the elongated spermatids (ES) and no other cell types except residual bodies inside Sertoli cells. It was absent from early ES at least until stage 13, and after a first diffuse appearance in the caudal cytoplasm became concentrated in intracellular organelles by stage 17, was strongest in vesicles in the anterior cytoplasm at the final ES stages and appeared in residual bodies. Staining was detected on the distal quarter of the sperm tail only immediately before spermiation. A similar localisation was found in the mouse and developmental profiles for both the open reading frame mRNA and protein expression in 8–50 dpp testis pinpointed its first appearance coinciding with late stage ES. Sequencing of PCR products of testicular Aqp11 containing the open reading frames confirmed a full match with GenBank databases for rat, mouse and human. Western blotting revealed two or more molecular forms with the 26/27 kDa species dominating in the rat/mouse testis and the 33/34 kDa form selectively allocated to the spermatozoa. In view of intracellular vacuolation leading to polycystic kidney in Aqp11-null mice, a possible role of testicular AQP11 in the recycling of surplus cytoplasmic components of the ES and sustaining Sertoli cell capacity in the support of spermatogenesis was discussed.

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