Hybrid Mice Reveal Parent-of-Origin and Cis- and Trans-Regulatory Effects in the Retina

Plant small RNAs play important roles in transcriptional and posttranscriptional regulation, with ongoing work demonstrating their functions in diverse pathways. Their roles in defense responses are a topic of active investigation, particularly the rich set of micro (mi)RNAs that target disease resistance genes such as nucleotide binding/leucine-rich repeat (NB-LRR) genes. The miRNA–NB-LRR interactions result in the production of phased, secondary small interfering (phasi)RNAs, and phasiRNAs function in both cis and trans to propagate negative regulatory effects across additional members of the target gene family. Yet, while phasiRNAs have the capacity to trigger targeted decay of specific targets, both in cis and trans, their functional relevance in NB-LRR regulation remains largely a matter of speculation.

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Faculty Opinions recommendation of Mapping cis- and trans-regulatory effects across multiple tissues in twins.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.717955361.793465005 ◽

2012 ◽

Author(s):

Anne Kwitek ◽

John MC Ma

Keyword(s):

Regulatory Effects ◽

Cis And Trans

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Discovery of target genes and pathways of blood trait loci using pooled CRISPR screens and single cell RNA sequencing

10.1101/2021.04.07.438882 ◽

2021 ◽

Author(s):

John A Morris ◽

Zharko Daniloski ◽

Júlia Domingo ◽

Timothy Barry ◽

Marcello Ziosi ◽

...

Keyword(s):

Single Cell ◽

Complex Traits ◽

Target Genes ◽

Association Studies ◽

Massively Parallel ◽

Genome Wide Association Studies ◽

Trait Loci ◽

Regulatory Effects ◽

Cell Transcriptome ◽

Cis And Trans

The majority of variants associated with complex traits and common diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown regulatory effects in cis and trans. By leveraging biobank-scale GWAS data, massively parallel CRISPR screens and single cell transcriptome sequencing, we discovered target genes of noncoding variants for blood trait loci. The closest gene was often the target gene, but this was not always the case. We also identified trans-effects networks of noncoding variants when cis target genes encoded transcription factors, such as GFI1B and NFE2. We observed that GFI1B trans-target genes were enriched for GFI1B binding sites and fine-mapped GWAS variants, and expressed in human bone marrow progenitor cells, suggesting that GFI1B acts as a master regulator of blood traits. This platform will enable massively parallel assays to catalog the target genes of human noncoding variants in both cis and trans.

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Y recombination arrest and degeneration in the absence of sexual dimorphism

10.1101/2021.05.18.444606 ◽

2021 ◽

Author(s):

Thomas Lenormand ◽

Denis Roze

Keyword(s):

Sexual Dimorphism ◽

Dosage Compensation ◽

Chromosome Evolution ◽

Sex Chromosome ◽

Current Theory ◽

Whole Process ◽

Y Chromosomes ◽

Regulatory Effects ◽

Cis And Trans ◽

Y Chromosome Degeneration

Current theory proposes degenerated sex chromosomes evolve via three successive steps: recombination arrest, which links male-beneficial alleles to the Y chromosome; degeneration of these regions due to the inefficacy of natural selection in the absence of recombination; and lastly, the evolution of dosage compensation to correct the resulting low expression of X-linked genes in males. Here we investigate new models of sex chromosome evolution incorporating the coevolution of cis- and trans-regulators of gene expression. We show that the early emergence of dosage compensation favors the maintenance of Y-linked inversions by creating sex-antagonistic regulatory effects. This is followed by inversion degeneration caused by regulatory divergence between the X and Y chromosomes. In stark contrast to the current theory, the whole process occurs without any selective pressure related to sexual dimorphism.

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Cis and Trans Regulatory Effects Contribute to Natural Variation in Transcriptome of Drosophila melanogaster

Molecular Biology and Evolution ◽

10.1093/molbev/msm247 ◽

2007 ◽

Vol 25 (1) ◽

pp. 101-110 ◽

Cited By ~ 25

Author(s):

A. Genissel ◽

L. M. McIntyre ◽

M. L. Wayne ◽

S. V. Nuzhdin

Keyword(s):

Drosophila Melanogaster ◽

Natural Variation ◽

Regulatory Effects ◽

Cis And Trans

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The Role of Zinc in Thyroid Hormones Metabolism

International Journal for Vitamin and Nutrition Research ◽

10.1024/0300-9831/a000262 ◽

2019 ◽

Vol 89 (1-2) ◽

pp. 80-88 ◽

Cited By ~ 6

Author(s):

Juliana Soares Severo ◽

Jennifer Beatriz Silva Morais ◽

Taynáh Emannuelle Coelho de Freitas ◽

Ana Letícia Pereira Andrade ◽

Mayara Monte Feitosa ◽

...

Keyword(s):

Thyroid Hormones ◽

Scientific Evidence ◽

Thyroid Stimulating Hormone ◽

Zinc Transporters ◽

Serum Concentrations ◽

Metabolic Adaptations ◽

Serum T3 ◽

Regulatory Effects ◽

Shed Light

Abstract. Thyroid hormones play an important role in body homeostasis by facilitating metabolism of lipids and glucose, regulating metabolic adaptations, responding to changes in energy intake, and controlling thermogenesis. Proper metabolism and action of these hormones requires the participation of various nutrients. Among them is zinc, whose interaction with thyroid hormones is complex. It is known to regulate both the synthesis and mechanism of action of these hormones. In the present review, we aim to shed light on the regulatory effects of zinc on thyroid hormones. Scientific evidence shows that zinc plays a key role in the metabolism of thyroid hormones, specifically by regulating deiodinases enzymes activity, thyrotropin releasing hormone (TRH) and thyroid stimulating hormone (TSH) synthesis, as well as by modulating the structures of essential transcription factors involved in the synthesis of thyroid hormones. Serum concentrations of zinc also appear to influence the levels of serum T3, T4 and TSH. In addition, studies have shown that Zinc transporters (ZnTs) are present in the hypothalamus, pituitary and thyroid, but their functions remain unknown. Therefore, it is important to further investigate the roles of zinc in regulation of thyroid hormones metabolism, and their importance in the treatment of several diseases associated with thyroid gland dysfunction.

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