A Genome-Wide Investigation of Expression Characteristics of Natural Antisense Transcripts in Liver and Muscle Samples of Pigs

Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the plus or minus strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here, we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript, and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was nonrandom across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, which suggests that they are a fundamental component of gene regulation.

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Cell-specific cis-natural antisense transcripts (cis-NATs) in the sperm and the pollen vegetative cells of Arabidopsis thaliana

F1000Research ◽

10.12688/f1000research.13311.1 ◽

2018 ◽

Vol 7 ◽

pp. 93

Author(s):

Peng Qin ◽

Ann E. Loraine ◽

Sheila McCormick

Keyword(s):

Gene Expression ◽

Vegetative Cell ◽

Cell Types ◽

Antisense Transcripts ◽

Vegetative Cells ◽

Natural Antisense Transcripts ◽

Protein Coding ◽

Regulate Gene Expression ◽

Genome Wide ◽

Gene Models

Background: cis-NATs (cis-natural antisense transcripts) are transcribed from opposite strands of adjacent genes and have been shown to regulate gene expression by generating small RNAs from the overlapping region. cis-NATs are important for plant development and resistance to pathogens and stress. Several genome-wide investigations identified a number of cis-NAT pairs, but these investigations predicted cis-NATS using expression data from bulk samples that included lots of cell types. Some cis-NAT pairs identified from those investigations might not be functional, because both transcripts of cis-NAT pairs need to be co-expressed in the same cell. Pollen only contains two cell types, two sperm and one vegetative cell, which makes cell-specific investigation of cis-NATs possible. Methods: We investigated potential protein-coding cis-NATs in pollen and sperm using pollen RNA-seq data and TAIR10 gene models using the Integrated Genome Browser. We then used sperm microarray data and sRNAs in sperm and pollen to determine possibly functional cis-NATs in the sperm or vegetative cell, respectively. Results: We identified 1471 potential protein-coding cis-NAT pairs, including 131 novel pairs that were not present in TAIR10 gene models. In pollen, 872 possibly functional pairs were identified. 72 and 56 pairs were potentially functional in sperm and vegetative cells, respectively. sRNAs were detected at 794 genes, belonging to 739 pairs. Conclusion: These potential candidates in sperm and the vegetative cell are tools for understanding gene expression mechanisms in pollen.

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Natural antisense transcripts of MIR398 genes suppress microR398 processing and attenuate plant thermotolerance

Nature Communications ◽

10.1038/s41467-020-19186-x ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Yajie Li ◽

Xiaorong Li ◽

Jun Yang ◽

Yuke He

Keyword(s):

Genetic Manipulation ◽

Biological Processes ◽

Sequencing Data ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Genome Wide ◽

Eukaryotic Gene Expression ◽

Eukaryotic Gene ◽

Regulatory Loop ◽

Antisense Genes

Abstract MicroRNAs (miRNAs) and natural antisense transcripts (NATs) control many biological processes and have been broadly applied for genetic manipulation of eukaryotic gene expression. Still unclear, however, are whether and how NATs regulate miRNA production. Here, we report that the cis-NATs of MIR398 genes repress the processing of their pri-miRNAs. Through genome-wide analysis of RNA sequencing data, we identify cis-NATs of MIRNA genes in Arabidopsis and Brassica. In Arabidopsis, MIR398b and MIR398c are coexpressed in vascular tissues with their antisense genes NAT398b and NAT398c, respectively. Knock down of NAT398b and NAT398c promotes miR398 processing, resulting in stronger plant thermotolerance owing to silencing of miR398-targeted genes; in contrast, their overexpression activates NAT398b and NAT398c, causing poorer thermotolerance due to the upregulation of miR398-targeted genes. Unexpectedly, overexpression of MIR398b and MIR398c activates NAT398b and NAT398c. Taken together, these results suggest that NAT398b/c repress miR398 biogenesis and attenuate plant thermotolerance via a regulatory loop.

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A Genome-Wide Epstein-Barr Virus Polyadenylation Map and Its Antisense RNA to EBNA

Journal of Virology ◽

10.1128/jvi.01593-18 ◽

2018 ◽

Vol 93 (2) ◽

Cited By ~ 3

Author(s):

Vladimir Majerciak ◽

Wenjing Yang ◽

Jing Zheng ◽

Jun Zhu ◽

Zhi-Ming Zheng

Keyword(s):

Cell Lines ◽

Epstein Barr Virus ◽

Lytic Infection ◽

Viral Gene ◽

Human Pathogen ◽

Antisense Transcripts ◽

Barr Virus ◽

Genome Wide ◽

A Genome ◽

Epstein Barr

ABSTRACTEpstein-Barr virus (EBV) is a ubiquitous human pathogen associated with Burkitt's lymphoma and nasopharyngeal carcinoma. Although the EBV genome harbors more than a hundred genes, a full transcription map with EBV polyadenylation profiles remains unknown. To elucidate the 3′ ends of all EBV transcripts genome-wide, we performed the first comprehensive analysis of viral polyadenylation sites (pA sites) using our previously reported polyadenylation sequencing (PA-seq) technology. We identified that EBV utilizes a total of 62 pA sites in JSC-1, 60 in Raji, and 53 in Akata cells for the expression of EBV genes from both plus and minus DNA strands; 42 of these pA sites are commonly used in all three cell lines. The majority of identified pA sites were mapped to the intergenic regions downstream of previously annotated EBV open reading frames (ORFs) and viral promoters. pA sites lacking an association with any known EBV genes were also identified, mostly for the minus DNA strand within the EBNA locus, a major locus responsible for maintenance of viral latency and cell transformation. The expression of these novel antisense transcripts to EBNA were verified by 3′ rapid amplification of cDNA ends (RACE) and Northern blot analyses in several EBV-positive (EBV+) cell lines. In contrast to EBNA RNA expressed during latency, expression of EBNA-antisense transcripts, which is restricted in latent cells, can be significantly induced by viral lytic infection, suggesting potential regulation of viral gene expression by EBNA-antisense transcription during lytic EBV infection. Our data provide the first evidence that EBV has an unrecognized mechanism that regulates EBV reactivation from latency.IMPORTANCEEpstein-Barr virus represents an important human pathogen with an etiological role in the development of several cancers. By elucidation of a genome-wide polyadenylation landscape of EBV in JSC-1, Raji, and Akata cells, we have redefined the EBV transcriptome and mapped individual polymerase II (Pol II) transcripts of viral genes to each one of the mapped pA sites at single-nucleotide resolution as well as the depth of expression. By unveiling a new class of viral lytic RNA transcripts antisense to latent EBNAs, we provide a novel mechanism of how EBV might control the expression of viral latent genes and lytic infection. Thus, this report takes another step closer to understanding EBV gene structure and expression and paves a new path for antiviral approaches.

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