scholarly journals Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation

Biology ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 61 ◽  
Author(s):  
Carlos Herrera-Úbeda ◽  
Marta Marín-Barba ◽  
Enrique Navas-Pérez ◽  
Jan Gravemeyer ◽  
Beatriz Albuixech-Crespo ◽  
...  
Keyword(s):  
Evolutionary Rate ◽  
Sequence Similarity ◽  
Anterior Part ◽  
Expression Domain ◽  
Hox Cluster ◽  
Human Genomes ◽  
Bona Fide ◽  
Non Coding Rnas ◽  
Early Origin ◽  
Origin Of Chordates

Homologous long non-coding RNAs (lncRNAs) are elusive to identify by sequence similarity due to their fast-evolutionary rate. Here we develop LincOFinder, a pipeline that finds conserved intergenic lncRNAs (lincRNAs) between distant related species by means of microsynteny analyses. Using this tool, we have identified 16 bona fide homologous lincRNAs between the amphioxus and human genomes. We characterized and compared in amphioxus and Xenopus the expression domain of one of them, Hotairm1, located in the anterior part of the Hox cluster. In addition, we analyzed the function of this lincRNA in Xenopus, showing that its disruption produces a severe headless phenotype, most probably by interfering with the regulation of the Hox cluster. Our results strongly suggest that this lincRNA has probably been regulating the Hox cluster since the early origin of chordates. Our work pioneers the use of syntenic searches to identify non-coding genes over long evolutionary distances and helps to further understand lncRNA evolution.

A gene with sequence similarity to Drosophila engrailed is expressed during the development of the neural tube and vertebrae in the mouse

Development ◽  
1988 ◽  
Vol 104 (2) ◽  
pp. 305-316 ◽  
Author(s):  
D. Davidson ◽  
E. Graham ◽  
C. Sime ◽  
R. Hill
Keyword(s):  
In Situ Hybridization ◽  
Neural Tube ◽  
Mouse Embryo ◽  
Sequence Similarity ◽  
Anterior Part ◽  
Limb Bud ◽  
Tissue Type ◽  
Restricted Domains ◽  
Restricted Region

The mouse genes En-1 and En-2 display sequence similarity, in and around the homeobox region, to the engrailed family in Drosophila. This paper describes their pattern of expression in the 12.5-day mouse embryo as determined by in situ hybridization. En-2 is expressed in a subset of cells expressing En-1. Both genes are expressed in the developing midbrain and its junction with the hindbrain. In addition, En-1 is expressed in the floor of the hindbrain, a restricted ventrolateral segment of the neural tube throughout the trunk and anterior part of the tail, the dermatome of tail somites, the centrum and costal processes in developing vertebrae, a restricted region of facial mesenchyme and the limb-bud ectoderm. Supplementary studies of 9.5-day and 10.5-day embryos showed that the same pattern of expression pertained in the neural tube, but that expression in the somites is at first confined to the dermatome and later found at a low level in restricted sclerotomal regions. Both genes are expressed in restricted domains which do not cross tissue-type boundaries. In several instances, however, boundaries of expression lie within morphologically undifferentiated tissue. These results suggest that En-1 and En-2 may be involved in the establishment or maintenance of the spatial integrity of specific domains within developing tissues.

HOX cluster-embedded antisense long non-coding RNAs in lung cancer

2019 ◽  
Vol 450 ◽  
pp. 14-21 ◽  
Author(s):  
Lianlian Li ◽  
Yong Wang ◽  
Guoqiang Song ◽  
Xiaoyu Zhang ◽  
Shan Gao ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Hox Cluster ◽  
Non Coding Rnas

scholarly journals Circulating exosome‐derived bona fide long non‐coding RNAs predicting the occurrence and metastasis of hepatocellular carcinoma

2019 ◽  
Vol 24 (2) ◽  
pp. 1311-1318 ◽  
Author(s):  
Yunjie Lu ◽  
Yunfei Duan ◽  
Qinghua Xu ◽  
Li Zhang ◽  
Weibo Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Bona Fide ◽  
Non Coding Rnas

In Silico Interaction of HOX Cluster‐Embedded MicroRNAs and Long Non‐Coding RNAs in Oral Cancer

2021 ◽  
Author(s):  
Kanaka Sai Ram Padam ◽  
Dhanraj Salur Basavarajappa ◽  
U Sangeetha Shenoy ◽  
Sanjiban Chakrabarty ◽  
Shama Prasada Kabekkodu ◽  
...  
Keyword(s):  
Oral Cancer ◽  
In Silico ◽  
Hox Cluster ◽  
Non Coding Rnas

scholarly journals Dynamic Expression of Long Non-Coding RNAs Throughout Parasite Sexual and Neural Maturation in Schistosoma Japonicum

2020 ◽  
Vol 6 (2) ◽  
pp. 15 ◽  
Author(s):  
Lucas Maciel ◽  
David Morales-Vicente ◽  
Sergio Verjovski-Almeida
Keyword(s):  
Schistosoma Japonicum ◽  
Sexual Maturation ◽  
System Development ◽  
Sequence Similarity ◽  
Nervous System Development ◽  
Rna Seq ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Synteny Conservation ◽  
Non Coding Rnas

Schistosoma japonicum is a flatworm that causes schistosomiasis, a neglected tropical disease. S. japonicum RNA-Seq analyses has been previously reported in the literature on females and males obtained during sexual maturation from 14 to 28 days post-infection in mouse, resulting in the identification of protein-coding genes and pathways, whose expression levels were related to sexual development. However, this work did not include an analysis of long non-coding RNAs (lncRNAs). Here, we applied a pipeline to identify and annotate lncRNAs in 66 S. japonicum RNA-Seq publicly available libraries, from different life-cycle stages. We also performed co-expression analyses to find stage-specific lncRNAs possibly related to sexual maturation. We identified 12,291 S. japonicum expressed lncRNAs. Sequence similarity search and synteny conservation indicated that some 14% of S. japonicum intergenic lncRNAs have synteny conservation with S. mansoni intergenic lncRNAs. Co-expression analyses showed that lncRNAs and protein-coding genes in S. japonicum males and females have a dynamic co-expression throughout sexual maturation, showing differential expression between the sexes; the protein-coding genes were related to the nervous system development, lipid and drug metabolism, and overall parasite survival. Co-expression pattern suggests that lncRNAs possibly regulate these processes or are regulated by the same activation program as that of protein-coding genes.

scholarly journals Specific Features of RNA Polymerases I and III: Structure and Assembly

2021 ◽  
Vol 8 ◽  
Author(s):  
Tomasz W. Turowski ◽  
Magdalena Boguta
Keyword(s):  
Ribosomal Rna ◽  
Untranslated Region ◽  
Protein Complexes ◽  
Rna Polymerase I ◽  
Initiation Factors ◽  
Cytoplasmic Ribosome ◽  
Functional Equivalent ◽  
Bona Fide ◽  
Non Coding Rnas ◽  
Polymerase I

RNA polymerase I (RNAPI) and RNAPIII are multi-heterogenic protein complexes that specialize in the transcription of highly abundant non-coding RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA). In terms of subunit number and structure, RNAPI and RNAPIII are more complex than RNAPII that synthesizes thousands of different mRNAs. Specific subunits of the yeast RNAPI and RNAPIII form associated subcomplexes that are related to parts of the RNAPII initiation factors. Prior to their delivery to the nucleus where they function, RNAP complexes are assembled at least partially in the cytoplasm. Yeast RNAPI and RNAPIII share heterodimer Rpc40-Rpc19, a functional equivalent to the αα homodimer which initiates assembly of prokaryotic RNAP. In the process of yeast RNAPI and RNAPIII biogenesis, Rpc40 and Rpc19 form the assembly platform together with two small, bona fide eukaryotic subunits, Rpb10 and Rpb12. We propose that this assembly platform is co-translationally seeded while the Rpb10 subunit is synthesized by cytoplasmic ribosome machinery. The translation of Rpb10 is stimulated by Rbs1 protein, which binds to the 3′-untranslated region of RPB10 mRNA and hypothetically brings together Rpc19 and Rpc40 subunits to form the αα-like heterodimer. We suggest that such a co-translational mechanism is involved in the assembly of RNAPI and RNAPIII complexes.

scholarly journals New N-Acetyltransferase Fold in the Structure and Mechanism of the Phosphonate Biosynthetic Enzyme FrbF

2011 ◽  
Vol 286 (41) ◽  
pp. 36132-36141 ◽  
Author(s):  
Brian Bae ◽  
Ryan E. Cobb ◽  
Matthew A. DeSieno ◽  
Huimin Zhao ◽  
Satish K. Nair
Keyword(s):  
Crystal Structure ◽  
Sequence Similarity ◽  
Active Site Residues ◽  
Putative Active Site ◽  
Bona Fide ◽  
Acetyl Transfer ◽  
Derivatives Of ◽  
Molecular Framework ◽  
Acyl Derivatives ◽  
Significant Attention

The enzyme FrbF from Streptomyces rubellomurinus has attracted significant attention due to its role in the biosynthesis of the antimalarial phosphonate FR-900098. The enzyme catalyzes acetyl transfer onto the hydroxamate of the FR-900098 precursors cytidine 5′-monophosphate-3-aminopropylphosphonate and cytidine 5′-monophosphate-N-hydroxy-3-aminopropylphosphonate. Despite the established function as a bona fide N-acetyltransferase, FrbF shows no sequence similarity to any member of the GCN5-like N-acetyltransferase (GNAT) superfamily. Here, we present the 2.0 Å resolution crystal structure of FrbF in complex with acetyl-CoA, which demonstrates a unique architecture that is distinct from those of canonical GNAT-like acetyltransferases. We also utilized the co-crystal structure to guide structure-function studies that identified the roles of putative active site residues in the acetyltransferase mechanism. The combined biochemical and structural analyses of FrbF provide insights into this previously uncharacterized family of N-acetyltransferases and also provide a molecular framework toward the production of novel N-acyl derivatives of FR-900098.

scholarly journals The Transcribed-Ultra Conserved Regions: Novel Non-Coding RNA Players in Neuroblastoma Progression

2019 ◽  
Vol 5 (2) ◽  
pp. 39
Author(s):  
Nithya Mudgapalli ◽  
Brianna P. Shaw ◽  
Srinivas Chava ◽  
Kishore B. Challagundla
Keyword(s):  
Gene Copy Number ◽  
Therapy Resistance ◽  
Gene Copy ◽  
Chemotherapy Response ◽  
Conserved Regions ◽  
Oncogenic Pathways ◽  
Non Coding Rna ◽  
Human Genomes ◽  
Health And Disease ◽  
Non Coding Rnas

The Transcribed-Ultra Conserved Regions (T-UCRs) are a class of novel non-coding RNAs that arise from the dark matter of the genome. T-UCRs are highly conserved between mouse, rat, and human genomes, which might indicate a definitive role for these elements in health and disease. The growing body of evidence suggests that T-UCRs contribute to oncogenic pathways. Neuroblastoma is a type of childhood cancer that is challenging to treat. The role of non-coding RNAs in the pathogenesis of neuroblastoma, in particular for cancer development, progression, and therapy resistance, has been documented. Exosmic non-coding RNAs are also involved in shaping the biology of the tumor microenvironment in neuroblastoma. In recent years, the involvement of T-UCRs in a wide variety of pathways in neuroblastoma has been discovered. Here, we present an overview of the involvement of T-UCRs in various cellular pathways, such as DNA damage response, proliferation, chemotherapy response, MYCN (v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)) amplification, gene copy number, and immune response, as well as correlate it to patient survival in neuroblastoma.

scholarly journals Cloning of somatolactin alpha and beta cDNAs in zebrafish and phylogenetic analysis of two distinct somatolactin subtypes in fish

2004 ◽  
Vol 182 (3) ◽  
pp. 509-518 ◽  
Author(s):  
Y Zhu ◽  
JW Stiller ◽  
MP Shaner ◽  
A Baldini ◽  
JL Scemama ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Sequence Similarity ◽  
Anterior Part ◽  
Phylogenetic Analyses ◽  
Pars Intermedia ◽  
Pituitary Hormone ◽  
High Sequence Identity ◽  
Trace Back ◽  
Typical Range ◽  
Teleost Genome

Somatolactin (SL) is a pituitary hormone belonging to the growth hormone/prolactin superfamily, with recognizable homologues in all fish taxa examined to date. Although sequences from most fish share reasonably high sequence identity, several more highly divergent SLs have been reported. Goldfish SL and a second SL protein found in rainbow trout (rtSLP) are remarkably different from each other and also dissimilar to other SLs. It has been unclear whether rtSLP is a recent paralogue restricted to rainbow trout, or reflects a more ancient duplication of the SL gene, and whether it is related to the goldfish sequence. Here we report the cloning of two different zebrafish SL cDNAs, which share only 57.5% nucleotide and 47.7% deduced amino acid identities. One copy, designated zebrafish SLalpha (zfSLalpha), displays a typical range of sequence similarity to most other SLs. The other copy, zebrafish SLbeta (zfSLbeta), shows low identity to most other SLs; surprisingly, it is most similar to the divergent SL sequence from goldfish. The mRNAs of zfSLalpha and zfSLbeta were expressed specifically in two distinct regions of the pars intermedia in zebrafish. Cells expressing zfSLalpha are located at the posterior pars intermedia, bordering the neurohypophysis, whereas zfSLbeta is expressed in the anterior part of the pars intermedia, bordering the pars distalis. Phylogenetic analyses indicate that zfSLbeta, goldfish SL and rtSLP all belong to the SL hormone family; however, along with the genes from eel and catfish, these divergent sequences form a group that is clearly distinct from all other SLs. These results suggest the presence of two distinct SL families, SLalpha and SLbeta, which may trace back to a teleost genome duplication prior to divergence of the cyprinids and salmonids.

scholarly journals Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuanda Lv ◽  
Fengqin Hu ◽  
Yongfeng Zhou ◽  
Feilong Wu ◽  
Brandon S. Gaut
Keyword(s):  
Abiotic Stress ◽  
Stress Response ◽  
Transposable Elements ◽  
Rna Sequencing ◽  
Sequence Similarity ◽  
Long Terminal Repeat Retrotransposons ◽  
Differentially Expressed ◽  
Abiotic Stress Response ◽  
Total Rna ◽  
Non Coding Rnas

Abstract Background Several studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic stress response. However, our understanding of the complement, function and origin of lncRNAs – and especially transposon derived lncRNAs (TE-lncRNAs) - in response to abiotic stress is still in its infancy. Results We utilized a dataset of 127 RNA sequencing samples that included total RNA datasets and PacBio fl-cDNA data to discover lncRNAs in maize. Overall, we identified 23,309 candidate lncRNAs from polyA+ and total RNA samples, with a strong discovery bias within total RNA. The majority (65%) of the 23,309 lncRNAs had sequence similarity to transposable elements (TEs). Most had similarity to long-terminal-repeat retrotransposons from the Copia and Gypsy superfamilies, reflecting a high proportion of these elements in the genome. However, DNA transposons were enriched for lncRNAs relative to their genomic representation by ~ 2-fold. By assessing the fraction of lncRNAs that respond to abiotic stresses like heat, cold, salt and drought, we identified 1077 differentially expressed lncRNA transcripts, including 509 TE-lncRNAs. In general, the expression of these lncRNAs was significantly correlated with their nearest gene. By inferring co-expression networks across our large dataset, we found that 39 lncRNAs are as major hubs in co-expression networks that respond to abiotic stress, and 18 appear to be derived from TEs. Conclusions Our results show that lncRNAs are enriched in total RNA samples, that most (65%) are derived from TEs, that at least 1077 are differentially expressed during abiotic stress, and that 39 are hubs in co-expression networks, including a small number that are evolutionary conserved. These results suggest that lncRNAs, including TE-lncRNAs, may play key regulatory roles in moderating abiotic responses.

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