scholarly journals A Genome-Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

2017 ◽  
Vol 8 ◽  
Author(s):  
Xie Fuli ◽  
Zhao Wenlong ◽  
Wang Xiao ◽  
Zhang Jing ◽  
Hao Baohai ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Small Rnas ◽  
Mesorhizobium Huakuii ◽  
Genome Wide ◽  
A Genome

scholarly journals A genome-wide identification and comparative analysis of the lentil MLO genes

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0194945 ◽  
Author(s):  
Carlos Polanco ◽  
Luis E. Sáenz de Miera ◽  
Kirstin Bett ◽  
Marcelino Pérez de la Vega
Keyword(s):  
Comparative Analysis ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Approach to Discovery of Small RNAs Involved in Regulation of Virulence in Vibrio cholerae

2011 ◽  
Vol 7 (7) ◽  
pp. e1002126 ◽  
Author(s):  
Evan S. Bradley ◽  
Kip Bodi ◽  
Ayman M. Ismail ◽  
Andrew Camilli
Keyword(s):  
Vibrio Cholerae ◽  
Small Rnas ◽  
Genome Wide ◽  
A Genome

A genome-wide sequence-independent comparative analysis of insertion–deletion polymorphisms in multiple Mycobacterium tuberculosis strains

2006 ◽  
Vol 157 (3) ◽  
pp. 282-290 ◽  
Author(s):  
Tatyana Azhikina ◽  
Nikolay Gvozdevsky ◽  
Anna Botvinnik ◽  
Alexey Fushan ◽  
Igor Shemyakin ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Comparative Analysis ◽  
Genome Wide ◽  
A Genome

The top skin-associated genes: a comparative analysis of human and mouse skin transcriptomes

2014 ◽  
Vol 395 (6) ◽  
pp. 577-591 ◽  
Author(s):  
Peter Arne Gerber ◽  
Bettina Alexandra Buhren ◽  
Holger Schrumpf ◽  
Bernhard Homey ◽  
Albert Zlotnik ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Human Skin ◽  
Current Knowledge ◽  
Mouse Skin ◽  
Published Data ◽  
Healthy Human ◽  
Genome Wide ◽  
A Genome ◽  
Human And Mouse

Abstract The mouse represents a key model system for the study of the physiology and biochemistry of skin. Comparison of skin between mouse and human is critical for interpretation and application of data from mouse experiments to human disease. Here, we review the current knowledge on structure and immunology of mouse and human skin. Moreover, we present a systematic comparison of human and mouse skin transcriptomes. To this end, we have recently used a genome-wide database of human gene expression to identify genes highly expressed in skin, with no, or limited expression elsewhere – human skin-associated genes (hSAGs). Analysis of our set of hSAGs allowed us to generate a comprehensive molecular characterization of healthy human skin. Here, we used a similar database to generate a list of mouse skin-associated genes (mSAGs). A comparative analysis between the top human (n=666) and mouse (n=873) skin-associated genes (SAGs) revealed a total of only 30.2% identity between the two lists. The majority of shared genes encode proteins that participate in structural and barrier functions. Analysis of the top functional annotation terms revealed an overlap for morphogenesis, cell adhesion, structure, and signal transduction. The results of this analysis, discussed in the context of published data, illustrate the diversity between the molecular make up of skin of both species and grants a probable explanation, why results generated in murine in vivo models often fail to translate into the human.

scholarly journals Processed Small RNAs in Archaea and BHB Elements

2015 ◽  
Vol 1 (1) ◽  
pp. 18 ◽  
Author(s):  
Sarah Juliane Berkemer ◽  
Christian Höner zu Siederdissen ◽  
Fabian Amman ◽  
Axel Wintsche ◽  
Sebastian Will ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Small Rnas ◽  
Pattern Search ◽  
Search Methods ◽  
Genome Wide ◽  
Archaeal Species ◽  
A Genome ◽  
Pattern Search Methods ◽  
Genome Wide Survey ◽  
Common Sequence

Bulge-helix-bulge (BHB) elements guide the enzymatic splicing machinery that in Archaea excises introns from tRNAs, rRNAs from their primary precursor, and accounts for the assembly of piece-wise encoded tRNAs. This processing pathway renders the intronic sequences as circularized RNA species. Although archaeal transcriptomes harbor a large number of circular small RNAs, it remains unknown whether most or all of them are produced through BHB-dependent splicing. We therefore conduct a genome-wide survey of BHB elements of a phylogenetically diverse set of archaeal species and complement this approach by searching for BHB-like structures in the vicinity of circularized transcripts. We find that besides tRNA introns, the majority of box C/D snoRNAs is associated with BHB elements. Not all circularized sRNAs, however, can be explained by BHB elements, suggesting that there is at least one other mechanism of RNA circularization at work in Archaea. Pattern search methods were unable, however, to identify common sequence and/or secondary structure features that could be characteristic for such a mechanism.

scholarly journals Stress Resets Transgenerational Small RNA Inheritance

2019 ◽  
Author(s):  
Leah Houri-Ze’evi ◽  
Guy Teichman ◽  
Hila Gingold ◽  
Oded Rechavi
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Memory Trace ◽  
Mapk Pathway ◽  
Transgenerational Inheritance ◽  
Cultivation Conditions ◽  
C Elegans ◽  
Genome Wide ◽  
A Genome ◽  
Basic Concepts

AbstractTransgenerational inheritance of small RNAs is challenging basic concepts of heredity and achieving control over such responses is of great interest. InC. elegansnematodes, small RNAs are transmitted across generations to establish a transgenerational memory trace of ancestral environments and distinguish self from non-self genes. Inheritance of small RNAs is regulated by dedicated machinery and carryover of aberrant heritable small RNA responses was shown to be maladaptive and to induce sterility. Here we show that various types of stress (starvation, high temperatures, and high osmolarity) but not non-stressful changes in cultivation conditions, lead to resetting of small RNA inheritance. We found that stress leads to a genome-wide reduction in heritable small RNA levels and that mutants defective in different stress pathways exhibit irregular RNAi inheritance dynamics. Moreover, we discovered that resetting of heritable RNAi is orchestrated by MAPK pathway factors, the transcription factor SKN-1, and the MET-2 methyltransferase. Termination of small RNA inheritance, and the fact that this process depends on stress, could protect from run-on of environment-irrelevant heritable gene regulation.

scholarly journals A small RNA pathway mediates global allelic dosage in endosperm

2017 ◽  
Author(s):  
Robert M. Erdmann ◽  
P.R. V. Satyaki ◽  
Maja Klosinska ◽  
Mary Gehring
Keyword(s):  
Small Rna ◽  
Small Rnas ◽  
Inverse Relationship ◽  
Paternal Genome ◽  
Pol Iv ◽  
Genome Wide ◽  
A Genome ◽  
Normal Seed ◽  
Wide Scale ◽  
Parent Of Origin

SummaryBalance between maternal and paternal genomes within the triploid endosperm is necessary for normal seed development. The majority of genes in Arabidopsis endosperm are expressed in a 2:1 maternal:paternal ratio, reflecting endosperm genomic DNA content. Here we find that the 2:1 transcriptional ratio is not, unexpectedly, a passive default but is actively regulated. We describe an inverse relationship between the parent-of-origin of small RNAs and mRNAs in endosperm on a genome-wide scale. Disruption of the Pol IV small RNA pathway causes the entire transcriptome to become more maternally biased. Furthermore, paternal inheritance of a RNA Pol IV mutation is sufficient to rescue seed abortion caused by excess paternal genome dosage. These results indicate that maintenance of the maternal:paternal transcriptome ratio in endosperm is an active process and reveal a function for RNA Pol IV in mediating the global transcriptional balance between maternally and paternally inherited genomes in endosperm.

scholarly journals Comparative analysis of transposable elements provides insights into genome evolution in the genus Camelus

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Mohanad A. Ibrahim ◽  
Badr M. Al-Shomrani ◽  
Mathew Simenc ◽  
Sultan N. Alharbi ◽  
Fahad H. Alqahtani ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Transposable Elements ◽  
Genome Evolution ◽  
De Novo ◽  
Endogenous Retroviruses ◽  
Similar Proportion ◽  
Copy Numbers ◽  
Genome Wide ◽  
Vicugna Pacos ◽  
A Genome

Abstract Background Transposable elements (TEs) are common features in eukaryotic genomes that are known to affect genome evolution critically and to play roles in gene regulation. Vertebrate genomes are dominated by TEs, which can reach copy numbers in the hundreds of thousands. To date, details regarding the presence and characteristics of TEs in camelid genomes have not been made available. Results We conducted a genome-wide comparative analysis of camelid TEs, focusing on the identification of TEs and elucidation of transposition histories in four species: Camelus dromedarius, C. bactrianus, C. ferus, and Vicugna pacos. Our TE library was created using both de novo structure-based and homology-based searching strategies (https://github.com/kacst-bioinfo-lab/TE_ideintification_pipeline). Annotation results indicated a similar proportion of each genomes comprising TEs (35–36%). Class I LTR retrotransposons comprised 16–20% of genomes, and mostly consisted of the endogenous retroviruses (ERVs) groups ERVL, ERVL-MaLR, ERV_classI, and ERV_classII. Non-LTR elements comprised about 12% of genomes and consisted of SINEs (MIRs) and the LINE superfamilies LINE1, LINE2, L3/CR1, and RTE clades. Least represented were the Class II DNA transposons (2%), consisting of hAT-Charlie, TcMar-Tigger, and Helitron elements and comprising about 1–2% of each genome. Conclusions The findings of the present study revealed that the distribution of transposable elements across camelid genomes is approximately similar. This investigation presents a characterization of TE content in four camelid to contribute to developing a better understanding of camelid genome architecture and evolution.

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