C/D box sRNA, CRISPR RNA and tRNA processing in an archaeon with a minimal fragmented genome

2013 ◽  
Vol 41 (1) ◽  
pp. 411-415 ◽  
Author(s):  
Hagen Richter ◽  
Sabine Mohr ◽  
Lennart Randau
Keyword(s):  
Rna Processing ◽  
Sequencing Data ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Single Organism ◽  
A Genome ◽  
Processing Pathways ◽  
Trna Half ◽  
Nanoarchaeum Equitans

The analysis of deep sequencing data allows for a genome-wide overview of all the small RNA molecules (the ‘sRNome’) that are present in a single organism. In the present paper, we review the processing of CRISPR (clustered regularly interspaced short palindromic repeats) RNA, C/D box sRNA (small non-coding RNA) and tRNA in Nanoarchaeum equitans. The minimal and fragmented genome of this tiny archaeon permits a sequencing depth that enables the identification of processing intermediates in the study of RNA processing pathways. These intermediates include circular C/D box sRNA molecules and tRNA half precursors.

scholarly journals Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Liping Guan ◽  
Ke Cao ◽  
Yong Li ◽  
Jian Guo ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Relationship ◽  
Dna Markers ◽  
High Throughput Sequencing ◽  
Prunus Persica ◽  
Genetic Research ◽  
Diploid Species ◽  
Sequencing Data ◽  
Relationship Analysis ◽  
Genome Wide ◽  
A Genome

Abstract Background Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited. Results In this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions. Conclusions The results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

scholarly journals Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

2019 ◽  
Vol 116 (12) ◽  
pp. 5653-5658 ◽  
Author(s):  
Lin Shao ◽  
Feng Xing ◽  
Conghao Xu ◽  
Qinghua Zhang ◽  
Jian Che ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Molecular Mechanisms ◽  
Sequencing Data ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Parental Allele ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Allele Specific

Utilization of heterosis has greatly increased the productivity of many crops worldwide. Although tremendous progress has been made in characterizing the genetic basis of heterosis using genomic technologies, molecular mechanisms underlying the genetic components are much less understood. Allele-specific expression (ASE), or imbalance between the expression levels of two parental alleles in the hybrid, has been suggested as a mechanism of heterosis. Here, we performed a genome-wide analysis of ASE by comparing the read ratios of the parental alleles in RNA-sequencing data of an elite rice hybrid and its parents using three tissues from plants grown under four conditions. The analysis identified a total of 3,270 genes showing ASE (ASEGs) in various ways, which can be classified into two patterns: consistent ASEGs such that the ASE was biased toward one parental allele in all tissues/conditions, and inconsistent ASEGs such that ASE was found in some but not all tissues/conditions, including direction-shifting ASEGs in which the ASE was biased toward one parental allele in some tissues/conditions while toward the other parental allele in other tissues/conditions. The results suggested that these patterns may have distinct implications in the genetic basis of heterosis: The consistent ASEGs may cause partial to full dominance effects on the traits that they regulate, and direction-shifting ASEGs may cause overdominance. We also showed that ASEGs were significantly enriched in genomic regions that were differentially selected during rice breeding. These ASEGs provide an index of the genes for future pursuit of the genetic and molecular mechanism of heterosis.

Genome-wide computational prediction and experimental validation of quinoa (Chenopodium quinoa) microRNAs

2019 ◽  
Vol 99 (5) ◽  
pp. 666-675 ◽  
Author(s):  
Ashutosh Sharma ◽  
Paola Isabel Angulo Bejerano ◽  
Irais Castillo Maldonado ◽  
Marcos de Donato Capote ◽  
Alfredo Madariaga-Navarrete ◽  
...  
Keyword(s):  
Experimental Validation ◽  
Protein Quality ◽  
Chenopodium Quinoa ◽  
Computational Prediction ◽  
Transcriptional Gene Silencing ◽  
Rt Pcr ◽  
Rna Molecules ◽  
Post Transcriptional Gene Silencing ◽  
Non Coding Rna ◽  
Genome Wide

MicroRNAs (miRNAs) are highly conserved, endogenous, short (21–24 nucleotides), non-coding RNA molecules that play significant roles in post-transcriptional gene silencing by directing target mRNA cleavage or translational inhibition. Nonetheless, highly nutritious “super grain” quinoa (Chenopodium quinoa) is an extreme abiotic stress tolerant Andean seed crop of many potential uses, with outstanding protein quality and a load of vitamins, minerals, as well as flavonoid antioxidants. In this study, applying genome-wide in silico approaches (referring to the recently published quinoa genome) and following a set of stringent filtering measures, a total of 22 potentially conserved microRNAs belonging to 18 families were characterized from quinoa and 11 randomly selected putative microRNAs (cqu-miR160a, cqu-miR162a, cqu-miR164a, cqu-miR166b, cqu-miR167a, cqu-miR172a, cqu-miR319a, cqu-miR390a, cqu-miR393a, cqu-miR394a, and cqu-miR398b) were validated successfully by RT-PCR. Using the psRNATarget tool, a sum of 59 potential miRNA targets, mostly transcription factors, were identified that are involved in biosynthesis, metabolic processes, and signal transduction. Among the detected targets, six target transcripts (F-Box proteins, TCP, MYB, WD protein, NAC, and CSD) were reported to have specific roles in both flavonoids biosynthesis and stress response signaling in some plants. To the best of our knowledge, this is the first report of quinoa microRNAs and their targets.

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

Next generation sequencing allows deeper analysis and understanding of genomes and transcriptomes including aspects to fertility

2011 ◽  
Vol 23 (1) ◽  
pp. 75 ◽  
Author(s):  
Thomas Werner
Keyword(s):  
Next Generation Sequencing ◽  
Transcriptional Control ◽  
Target Genes ◽  
De Novo ◽  
Alternative Promoters ◽  
Next Generation ◽  
Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Generation Sequencing

Reproduction and fertility are controlled by specific events naturally linked to oocytes, testes and early embryonal tissues. A significant part of these events involves gene expression, especially transcriptional control and alternative transcription (alternative promoters and alternative splicing). While methods to analyse such events for carefully predetermined target genes are well established, until recently no methodology existed to extend such analyses into a genome-wide de novo discovery process. With the arrival of next generation sequencing (NGS) it becomes possible to attempt genome-wide discovery in genomic sequences as well as whole transcriptomes at a single nucleotide level. This does not only allow identification of the primary changes (e.g. alternative transcripts) but also helps to elucidate the regulatory context that leads to the induction of transcriptional changes. This review discusses the basics of the new technological and scientific concepts arising from NGS, prominent differences from microarray-based approaches and several aspects of its application to reproduction and fertility research. These concepts will then be illustrated in an application example of NGS sequencing data analysis involving postimplantation endometrium tissue from cows.

scholarly journals TCF7L2 lncRNA: a link between bipolar disorder and body mass index through glucocorticoid signaling

2021 ◽  
Author(s):  
Duan Liu ◽  
Thanh Thanh Le Nguyen ◽  
Huanyao Gao ◽  
Huaizhi Huang ◽  
Daniel C. Kim ◽  
...  
Keyword(s):  
Body Mass Index ◽  
Bipolar Disorder ◽  
Body Mass ◽  
Genome Wide Association Study ◽  
Induced Pluripotent Stem Cell ◽  
Sequencing Data ◽  
Peripheral Tissues ◽  
Genome Wide ◽  
A Genome ◽  
Trait Locus

AbstractBipolar disorder (BD) and obesity are highly comorbid. We previously performed a genome-wide association study (GWAS) for BD risk accounting for the effect of body mass index (BMI), which identified a genome-wide significant single-nucleotide polymorphism (SNP) in the gene encoding the transcription factor 7 like 2 (TCF7L2). However, the molecular function of TCF7L2 in the central nervous system (CNS) and its possible role in the BD and BMI interaction remained unclear. In the present study, we demonstrated by studying human induced pluripotent stem cell (hiPSC)-derived astrocytes, cells that highly express TCF7L2 in the CNS, that the BD-BMI GWAS risk SNP is associated with glucocorticoid-dependent repression of the expression of a previously uncharacterized TCF7L2 transcript variant. That transcript is a long non-coding RNA (lncRNA-TCF7L2) that is highly expressed in the CNS but not in peripheral tissues such as the liver and pancreas that are involved in metabolism. In astrocytes, knockdown of the lncRNA-TCF7L2 resulted in decreased expression of the parent gene, TCF7L2, as well as alterations in the expression of a series of genes involved in insulin signaling and diabetes. We also studied the function of TCF7L2 in hiPSC-derived astrocytes by integrating RNA sequencing data after TCF7L2 knockdown with TCF7L2 chromatin-immunoprecipitation sequencing (ChIP-seq) data. Those studies showed that TCF7L2 directly regulated a series of BD risk genes. In summary, these results support the existence of a CNS-based mechanism underlying BD-BMI genetic risk, a mechanism based on a glucocorticoid-dependent expression quantitative trait locus that regulates the expression of a novel TCF7L2 non-coding transcript.

scholarly journals Hda1C restricts the transcription initiation frequency to limit divergent non-coding RNA transcription

2021 ◽  
Author(s):  
Uthra Gowthaman ◽  
Maxim Ivanov ◽  
Isabel Schwarz ◽  
Heta P. Patel ◽  
Niels A. Müller ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Histone Deacetylation ◽  
Gene Promoters ◽  
Genetic Screens ◽  
Fluorescence Measurements ◽  
Non Coding Rna ◽  
Genome Wide ◽  
A Genome ◽  
Initiation Frequency

ABSTRACTNucleosome-depleted regions (NDRs) at gene promoters support initiation of RNA Polymerase II transcription. Interestingly, transcription often initiates in both directions, resulting in an mRNA, and a divergent non-coding (DNC) transcript with an unclear purpose. Here, we characterized the genetic architecture and molecular mechanism of DNC transcription in budding yeast. We identified the Hda1 histone deacetylase complex (Hda1C) as a repressor of DNC in high-throughput reverse genetic screens based on quantitative single-cell fluorescence measurements. Nascent transcription profiling showed a genome-wide role of Hda1C in DNC repression. Live-cell imaging of transcription revealed that Hda1C reduced the frequency of DNC transcription. Hda1C contributed to decreased acetylation of histone H3 in DNC regions, supporting DNC repression by histone deacetylation. Our data support the interpretation that DNC results as a consequence of the NDR-based architecture of eukaryotic promoters, but that it is governed by locus-specific repression to maintain genome fidelity.

scholarly journals Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1606
Author(s):  
Shuai Zhang ◽  
Ruixue Wang ◽  
Cheng Huang ◽  
Ludan Zhang ◽  
Lin Sun
Keyword(s):  
Gene Expression ◽  
Sex Chromosome ◽  
Global Gene Expression ◽  
Regulatory Genes ◽  
Dosage Effect ◽  
Macromolecular Complex ◽  
Sequencing Data ◽  
Genome Wide ◽  
A Genome ◽  
Modulation Of Gene Expression

Aneuploidy, which disrupts the genetic balance due to partial genome dosage changes, is usually more detrimental than euploidy variation. To investigate the modulation of gene expression in aneuploidy, we analyzed the transcriptome sequencing data of autosomal and sex chromosome trisomy in Drosophila. The results showed that most genes on the varied chromosome (cis) present dosage compensation, while the remainder of the genome (trans) produce widespread inverse dosage effects. Some altered functions and pathways were identified as the common characteristics of aneuploidy, and several possible regulatory genes were screened for an inverse dosage effect. Furthermore, we demonstrated that dosage changes of inverse regulator Inr-a/pcf11 can produce a genome-wide inverse dosage effect. All these findings suggest that the mechanism of genomic imbalance is related to the changes in the stoichiometric relationships of macromolecular complex members that affect the overall function. These studies may deepen the understanding of gene expression regulatory mechanisms.

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