scholarly journals Complex Genetic Interactions between Piwi and HP1a in the Repression of Transposable Elements and Tissue-Specific Genes in the Ovarian Germline

2021 ◽  
Vol 22 (24) ◽  
pp. 13430
Author(s):  
Artem A. Ilyin ◽  
Anastasia D. Stolyarenko ◽  
Nikolay Zenkin ◽  
Mikhail S. Klenov
Keyword(s):  
Transposable Elements ◽  
Rna Seq ◽  
Heterochromatin Protein ◽  
Protein Coding ◽  
Tissue Specific ◽  
Small Set ◽  
Similar Genetic Background ◽  
Genomic Regions ◽  
Pirna Pathway ◽  
Inappropriate Expression

Insertions of transposable elements (TEs) in eukaryotic genomes are usually associated with repressive chromatin, which spreads to neighbouring genomic sequences. In ovaries of Drosophila melanogaster, the Piwi-piRNA pathway plays a key role in the transcriptional silencing of TEs considered to be exerted mostly through the establishment of H3K9me3 histone marks recruiting Heterochromatin Protein 1a (HP1a). Here, using RNA-seq, we investigated the expression of TEs and the adjacent genomic regions upon Piwi and HP1a germline knockdowns sharing a similar genetic background. We found that the depletion of Piwi and HP1a led to the derepression of only partially overlapping TE sets. Several TEs were silenced predominantly by HP1a, whereas the upregulation of some other TEs was more pronounced upon Piwi knockdown and, surprisingly, was diminished upon a Piwi/HP1a double-knockdown. We revealed that HP1a loss influenced the expression of thousands of protein-coding genes mostly not adjacent to TE insertions and, in particular, downregulated a putative transcriptional factor required for TE activation. Nevertheless, our results indicate that Piwi and HP1a cooperatively exert repressive effects on the transcription of euchromatic loci flanking the insertions of some Piwi-regulated TEs. We suggest that this mechanism controls the silencing of a small set of TE-adjacent tissue-specific genes, preventing their inappropriate expression in ovaries.

scholarly journals Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Jinhang Zhu ◽  
Geng Chen ◽  
Sibo Zhu ◽  
Suqing Li ◽  
Zhuo Wen ◽  
...  
Keyword(s):  
Specific Protein ◽  
Human Tissues ◽  
Rna Seq ◽  
Protein Coding ◽  
Tissue Specific

scholarly journals Comprehensive Characterization of RNA Editing in Primary Gastric Adenocarcinoma through RNA-seq Data Analysis

2020 ◽  
Author(s):  
Javad Behroozi ◽  
Shirin Shahbazi ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Habibollah Mahmoodzadeh
Keyword(s):  
Gastric Cancer ◽  
Rna Editing ◽  
Gastric Adenocarcinoma ◽  
Cancer Progression ◽  
Variant Calling ◽  
Distinct Pattern ◽  
Rna Seq ◽  
Comprehensive Overview ◽  
Protein Coding ◽  
Genomic Regions

Abstract RNA editing is a post-transcriptional nucleotide modification in humans. Of the various types of RNA editing, the adenosine to inosine substitution is the most widespread in higher eukaryotes, which is mediated by ADAR family enzyme. Inosine is recognized by the biological machineries as guanosine, therefore, editing can potentially rendering substantial functional effects throughout the genome, depending on where it located. RNA editing could contribute to cancer by either exclusive editing of tumor suppressor/promoting genes or by introducing transcriptomic diversity to promote cancer progression. Here, we provided a comprehensive overview of the RNA editing sites in gastric adenocarcinoma and highlighted some of their possible contributions to gastric cancer. RNA-seq data corresponding to 8 gastric adenocarcinoma and their paired non-tumor counterparts were retrieved from GEO database. After pre-possessing and variant calling steps, a stringent filtering pipeline was employed to distinguish potential RNA editing sites from SNPs. The identified potential editing sites were annotated and compared with those in DARNED database. Totally, 12362 high-confidence adenosine to inosine RNA editing sites were detected across all samples. Of these, 12105 and 257 were known and novel editing events, respectively. These editing sites were unevenly distributed across genomic regions, nearly half of them were located in 3´UTR. Indeed, 4868, 3985 and 3509 editing sites were found to be common in both tissue, normal specific and cancer specific, respectively. Further analysis revealed significant number of differentially edited events among these sites, which were located in protein coding genes and microRNAs. Given the distinct pattern of RNA editing in gastric adenocarcinoma and adjacent normal tissue, edited sites have the potential to serve as biomarkers and therapeutic targets in gastric cancer diagnose, management and treatment.

scholarly journals An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Frédéric Jehl ◽  
Kévin Muret ◽  
Maria Bernard ◽  
Morgane Boutin ◽  
Laetitia Lagoutte ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Biological Processes ◽  
Rna Seq ◽  
Protein Coding ◽  
Tissue Specific ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Immune Tissues ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.

GSD_1.0 (canFam4): A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

2020 ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cell Receptor ◽  
Chromosome Length ◽  
Domestic Dog ◽  
Gene Products ◽  
Cancer Genes ◽  
Rna Seq ◽  
Protein Coding ◽  
Leukocyte Antigen ◽  
Genomic Regions

Abstract We present GSD_1.0, a novel high-quality domestic dog reference genome with chromosome length scaffolds and gap number reduced 41-fold, from 23,836 to 585. Annotation with novel and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of closed gaps harboured previously hidden functional elements, including promoters, genes and miRNAs. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leukocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. The sequencing of 27 dogs from 19 breeds with linked read technology uncovered 22.1 million SNPs, indels and larger structural variants. Intersection with protein coding genes showed that 1.4% could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

scholarly journals The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 918
Author(s):  
Dareen Almojil ◽  
Yann Bourgeois ◽  
Marcin Falis ◽  
Imtiyaz Hariyani ◽  
Justin Wilcox ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Regulatory Networks ◽  
Biological Processes ◽  
Structural Rearrangements ◽  
Protein Coding ◽  
Vast Number ◽  
Haploid Genome Size ◽  
Genomic Regions ◽  
The Impact ◽  
Host Genes

Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase in genomic data, as well as progress in genome annotation and molecular biology techniques, have revealed the vast number of ways mobile elements have impacted the evolution of eukaryotes. In addition to being the main cause of difference in haploid genome size, TEs have affected the overall organization of genomes by accumulating preferentially in some genomic regions, by causing structural rearrangements or by modifying the recombination rate. Although the vast majority of insertions is neutral or deleterious, TEs have been an important source of evolutionary novelties and have played a determinant role in the evolution of fundamental biological processes. TEs have been recruited in the regulation of host genes and are implicated in the evolution of regulatory networks. They have also served as a source of protein-coding sequences or even entire genes. The impact of TEs on eukaryotic evolution is only now being fully appreciated and the role they may play in a number of biological processes, such as speciation and adaptation, remains to be deciphered.

scholarly journals A novel canine reference genome resolves genomic architecture and uncovers transcript complexity

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cell Receptor ◽  
Chromosome Length ◽  
Domestic Dog ◽  
Gene Products ◽  
Cancer Genes ◽  
Rna Seq ◽  
Structural Variants ◽  
Protein Coding ◽  
Genomic Regions

AbstractWe present GSD_1.0, a high-quality domestic dog reference genome with chromosome length scaffolds and contiguity increased 55-fold over CanFam3.1. Annotation with generated and existing long and short read RNA-seq, miRNA-seq and ATAC-seq, revealed that 32.1% of lifted over CanFam3.1 gaps harboured previously hidden functional elements, including promoters, genes and miRNAs in GSD_1.0. A catalogue of canine “dark” regions was made to facilitate mapping rescue. Alignment in these regions is difficult, but we demonstrate that they harbour trait-associated variation. Key genomic regions were completed, including the Dog Leucocyte Antigen (DLA), T Cell Receptor (TCR) and 366 COSMIC cancer genes. 10x linked-read sequencing of 27 dogs (19 breeds) uncovered 22.1 million SNPs, indels and larger structural variants. Subsequent intersection with protein coding genes showed that 1.4% of these could directly influence gene products, and so provide a source of normal or aberrant phenotypic modifications.

scholarly journals A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

2020 ◽  
Author(s):  
Chao Wang ◽  
Ola Wallerman ◽  
Maja-Louise Arendt ◽  
Elisabeth Sundström ◽  
Åsa Karlsson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Cancer Genes ◽  
Rna Seq ◽  
Structural Variants ◽  
Functional Elements ◽  
High Quality ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Long Read ◽  
Genomic Regions

AbstractHere we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large proportion of these harboured previously hidden elements, including genes, promoters and miRNAs. Short-read dark regions were detected, and genomic regions completed, including the DLA, TCR and 366 cancer genes. 10x sequencing of 27 dogs uncovered a total of 22.1 million SNPs, Indels and larger structural variants (SVs). 1.4% overlap with protein coding genes and could provide a source of normal or aberrant phenotypic modifications.

scholarly journals Reprogramming mRNA Expression in Response to Defect in RNA Polymerase III Assembly in the Yeast Saccharomyces cerevisiae

2021 ◽  
Vol 22 (14) ◽  
pp. 7298
Author(s):  
Izabela Rudzińska ◽  
Małgorzata Cieśla ◽  
Tomasz W. Turowski ◽  
Alicja Armatowska ◽  
Ewa Leśniewska ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Ribosome Biogenesis ◽  
Rna Polymerase Iii ◽  
Mrna Levels ◽  
Rna Seq ◽  
Yeast Saccharomyces Cerevisiae ◽  
Protein Coding ◽  
General Transcription Factor ◽  
Pol I ◽  
Pol Iii

The coordinated transcription of the genome is the fundamental mechanism in molecular biology. Transcription in eukaryotes is carried out by three main RNA polymerases: Pol I, II, and III. One basic problem is how a decrease in tRNA levels, by downregulating Pol III efficiency, influences the expression pattern of protein-coding genes. The purpose of this study was to determine the mRNA levels in the yeast mutant rpc128-1007 and its overdose suppressors, RBS1 and PRT1. The rpc128-1007 mutant prevents assembly of the Pol III complex and functionally mimics similar mutations in human Pol III, which cause hypomyelinating leukodystrophies. We applied RNAseq followed by the hierarchical clustering of our complete RNA-seq transcriptome and functional analysis of genes from the clusters. mRNA upregulation in rpc128-1007 cells was generally stronger than downregulation. The observed induction of mRNA expression was mostly indirect and resulted from the derepression of general transcription factor Gcn4, differently modulated by suppressor genes. rpc128-1007 mutation, regardless of the presence of suppressors, also resulted in a weak increase in the expression of ribosome biogenesis genes. mRNA genes that were downregulated by the reduction of Pol III assembly comprise the proteasome complex. In summary, our results provide the regulatory links affected by Pol III assembly that contribute differently to cellular fitness.

scholarly journals SAUTE: sequence assembly using target enrichment

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexandre Souvorov ◽  
Richa Agarwala
Keyword(s):  
De Bruijn Graph ◽  
Challenging Problem ◽  
Target Enrichment ◽  
Rna Seq ◽  
Sequencing Technology ◽  
Insert Size ◽  
Systematic Biases ◽  
Target Sequences ◽  
Genomic Regions ◽  
Higher Sensitivity

Abstract Background Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions. Results To facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose SAUTE and SAUTE_PROT assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for SAUTE and SAUTE_PROT, respectively. Conclusions For RNA-seq, comparisons with Trinity, rnaSPAdes, SPAligner, and SPAdes assembly of reads aligned to target proteins by DIAMOND show that SAUTE_PROT finds more coding sequences that translate to benchmark proteins. Using AMRFinderPlus calls, we find SAUTE has higher sensitivity and precision than SPAdes, plasmidSPAdes, SPAligner, and SPAdes assembly of reads aligned to target regions by HISAT2. It also has better sensitivity than SKESA but worse precision.

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