scholarly journals RNA-Seq analysis reveals expression regulatory divergence of W-linked genes between two contrasting chicken breeds

2022 ◽  
Author(s):  
Hongchang Gu ◽  
Liang Wang ◽  
Xueze Lv ◽  
Weifang Yang ◽  
Yu Chen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sex Chromosomes ◽  
Phenotypic Diversity ◽  
Regulation Of Gene Expression ◽  
W Chromosome ◽  
White Leghorn ◽  
Complex Process ◽  
Chicken Breeds ◽  
Trans Regulation ◽  
Cis And Trans

Abstract The regulation of gene expression is a complex process involving organism function and phenotypic diversity, and is caused by cis- and trans- regulation. While prior studies identified the regulatory pattern of the autosome rewiring in hybrids, the role of gene regulation in W sex chromosomes is not clear due to their degradation and sex-limit expression. Here, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibited broad differences of gender-related traits, and assessed the expression of the genes on W chromosome to disentangle the contribution of cis- and trans-factors to expression divergence. We found that there was not appear to be an association between female fecundity and W chromosome gene expression, that 44% of expressed genes had divergent expression between breeds in both tissues, with only 17% of them showing greater expression in White Leghorn. We observed that the proportion of trans-acting genes in W chromosome was higher than cis-regulatory divergence. There were most parental divergence expression genes in muscle, also more heterosis compared with other two tissues. A strong dominant impact of Cornish alleles in brain, while obvious crosses-specific regulatory patterns appeared in liver. Taken together, this work describes the regulatory divergence of W-linked genes between two contrasting breeds and indicates sex chromosomes have a unique regulation and expression mechanism.

scholarly journals The Evolutionary Forces Shaping Cis- and Trans-Regulation of Gene Expression within a Population of Outcrossing Plants

2020 ◽  
Vol 37 (8) ◽  
pp. 2386-2393
Author(s):  
Emily B Josephs ◽  
Young Wha Lee ◽  
Corlett W Wood ◽  
Daniel J Schoen ◽  
Stephen I Wright ◽  
...  
Keyword(s):  
Gene Expression ◽  
Negative Selection ◽  
General Pattern ◽  
Regulation Of Gene Expression ◽  
Intermediate Frequency ◽  
Clear Understanding ◽  
Evolutionary Forces ◽  
In Trans ◽  
Trans Regulation ◽  
Cis And Trans

Abstract Understanding the persistence of genetic variation within populations has long been a goal of evolutionary biology. One promising route toward achieving this goal is using population genetic approaches to describe how selection acts on the loci associated with trait variation. Gene expression provides a model trait for addressing the challenge of the maintenance of variation because it can be measured genome-wide without information about how gene expression affects traits. Previous work has shown that loci affecting the expression of nearby genes (local or cis-eQTLs) are under negative selection, but we lack a clear understanding of the selective forces acting on variants that affect the expression of genes in trans. Here, we identify loci that affect gene expression in trans using genomic and transcriptomic data from one population of the obligately outcrossing plant, Capsella grandiflora. The allele frequencies of trans-eQTLs are consistent with stronger negative selection acting on trans-eQTLs than cis-eQTLs, and stronger negative selection acting on trans-eQTLs associated with the expression of multiple genes. However, despite this general pattern, we still observe the presence of a trans-eQTL at intermediate frequency that affects the expression of a large number of genes in the same coexpression module. Overall, our work highlights the different selective pressures shaping variation in cis- and trans-regulation.

scholarly journals Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits

2017 ◽  
Vol 100 (6) ◽  
pp. 985-986 ◽  
Author(s):  
Chen Yao ◽  
Roby Joehanes ◽  
Andrew D. Johnson ◽  
Tianxiao Huan ◽  
Chunyu Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Complex Traits ◽  
Regulation Of Gene Expression ◽  
Trans Regulation

scholarly journals Kangaroo gene mapping and sequencing: insights into mammalian genome evolution

2013 ◽  
Vol 61 (1) ◽  
pp. 4 ◽  
Author(s):  
Jennifer A. Marshall Graves
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Molecular Biology ◽  
Dna Sequence ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Regulation Of Gene Expression ◽  
Mammalian Genome ◽  
Epigenetic Silencing ◽  
Gene Arrangement

The deep divergence of marsupials and eutherian mammals 160 million years ago provides genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. Following the pioneering work of Professor Desmond W. Cooper, emerging techniques in cytogenetics and molecular biology have been adapted to characterise the genomes of kangaroos and other marsupials. In particular, genetic and genomic work over four decades has shown that marsupial sex chromosomes differ significantly from the eutherian XY chromosome pair in their size, gene content and activity. These differences can be exploited to deduce how mammalian sex chromosomes, sex determination and epigenetic silencing evolved.

scholarly journals Mechanisms Regulating Abnormal Circular RNA Biogenesis in Cancer

Cancers ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 4185
Author(s):  
Ying Huang ◽  
Qubo Zhu
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Circular Rna ◽  
Regulatory Elements ◽  
Circular Rnas ◽  
Transcriptional Level ◽  
Closed Loops ◽  
Rna Biogenesis ◽  
Cis And Trans ◽  
Functional Mechanisms

Circular RNAs (circRNAs), which are a class of endogenous RNA with covalently closed loops, play important roles in epigenetic regulation of gene expression at both the transcriptional and post-transcriptional level. Accumulating evidence demonstrated that numerous circRNAs were abnormally expressed in tumors and their dysregulation was involved in the tumorigenesis and metastasis of cancer. Although the functional mechanisms of many circRNAs have been revealed, how circRNAs are dysregulated in cancer remains elusive. CircRNAs are generated by a “back-splicing” process, which is regulated by different cis-regulatory elements and trans-acting proteins. Therefore, how these cis and trans elements change during tumorigenesis and how they regulate the biogenesis of circRNAs in cancer are two questions that interest us. In this review, we summarized the pathways for the biogenesis of circRNAs; and then illustrated how circRNAs dysregulated in cancer by discussing the changes of cis-regulatory elements and trans-acting proteins that related to circRNA splicing and maturation in cancer.

scholarly journals Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Jukka-Pekka Verta ◽  
Felicity C Jones
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Gill Tissue ◽  
Regulatory Control ◽  
F1 Hybrids ◽  
Adaptive Divergence ◽  
Expression Divergence ◽  
Early Stages ◽  
Specific Regulation ◽  
Cis And Trans

Regulation of gene expression is thought to play a major role in adaptation, but the relative importance of cis- and trans- regulatory mechanisms in the early stages of adaptive divergence is unclear. Using RNAseq of threespine stickleback fish gill tissue from four independent marine-freshwater ecotype pairs and their F1 hybrids, we show that cis-acting (allele-specific) regulation consistently predominates gene expression divergence. Genes showing parallel marine-freshwater expression divergence are found near to adaptive genomic regions, show signatures of natural selection around their transcription start sites and are enriched for cis-regulatory control. For genes with parallel increased expression among freshwater fish, the quantitative degree of cis- and trans-regulation is also highly correlated across populations, suggesting a shared genetic basis. Compared to other forms of regulation, cis-regulation tends to show greater additivity and stability across different genetic and environmental contexts, making it a fertile substrate for the early stages of adaptive evolution.

scholarly journals Polymorphic Cis- and Trans-Regulation of Human Gene Expression

PLoS Biology ◽  
2010 ◽  
Vol 8 (9) ◽  
pp. e1000480 ◽  
Author(s):  
Vivian G. Cheung ◽  
Renuka R. Nayak ◽  
Isabel Xiaorong Wang ◽  
Susannah Elwyn ◽  
Sarah M. Cousins ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Gene ◽  
Human Gene Expression ◽  
Trans Regulation ◽  
Cis And Trans

scholarly journals Cis- and trans-regulation of luteovirus gene expression by the 3′ end of the viral genome

2015 ◽  
Vol 206 ◽  
pp. 37-45 ◽  
Author(s):  
W. Allen Miller ◽  
Jacquelyn Jackson ◽  
Ying Feng
Keyword(s):  
Gene Expression ◽  
Viral Genome ◽  
Trans Regulation ◽  
Cis And Trans

scholarly journals Landscape and evolution of cis- and trans-regulation in chicken genome between two contrasted breeds analyzed in three tissues at one day of age

2019 ◽  
Author(s):  
Qiong Wang ◽  
Yaxiong Jia ◽  
Yuan Wang ◽  
Zhihua Jiang ◽  
Xiang Zhou ◽  
...  
Keyword(s):  
Chicken Genome ◽  
Reproductive Traits ◽  
Purifying Selection ◽  
Population Divergence ◽  
White Leghorn ◽  
Specific Expression ◽  
Regulatory Variation ◽  
Allele Specific ◽  
Trans Regulation ◽  
Cis And Trans

Abstract Background Gene expression variation is an important mechanism underlying phenotypic variation, and can occur via cis- and trans-regulation. In order to understand the role of cis- and trans-regulatory variation on population divergence of chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, with major differences in size and reproductive traits, and used them to identify the degree of cis versus trans variation in brain, liver and muscle of both male and female samples at 1-day age. Results We provided a landscape about how the transcriptomes are regulated between two contrasted breeds by allele specific expression analysis. Our results showed that compared with the cis-regulated genes, trans-acted genes existed more extensively in the chicken genome. Furthermore, a widespread compensatory tendency exists in chicken genome. Most importantly, we found the evidence of stronger purifying selection for trans-regulatory variation than the cis-elements. Conclusions Our research performed the first study to describe the transcriptome regulation between White Leghorn and Cornish Game breeds and suggests that artificial selection associated with domestication in chicken may have more often acted on trans-regulatory variation.

scholarly journals Regulation of gene expression in cis and trans

2019 ◽  
Author(s):  
Πιβκο Παβελ
Keyword(s):  
Gene Expression ◽  
Regulation Of Gene Expression ◽  
Cis And Trans ◽  
In Cis

Η τρανς-ενεργοποίηση είναι το φαινόμενο όπου ένας μεταγραφικός ενισχυτής ενεργοποιεί έναν υποκινητή που βρίσκεται στο ομόλογο χρωμόσωμα. Έχει τεκμηριωθεί επαρκώς στη Drosophila όπου τα ομόλογα είναι στενά συνδεδεμένα στους περισσότερους, αν όχι όλοι, σωματικούς πυρήνες, αλλά είναι γνωστό ότι σπάνια εμφανίζονται και στα θηλαστικά. Επωφελήθηκα από τη θέση-κατευθυνόμενη διαγονιδίωση για να εισάγουμε κατασκευάσματα αναφοράς στον ίδιο γενετικό τόπο στην Drosophila και έχουν αξιολογήσει την ικανότητά τους να εμπλέκονται στη μεταμόσχευση ελέγχοντας πολλούς ετερόζυγους συνδυασμούς. Διαπιστώνω ότι η μετατόπιση απαιτεί την ύπαρξη ενός στοιχείου μονωτή και στις δύο ομόλογες. Ομοτυπικές δια-αλληλεπιδράσεις μεταξύ τεσσάρων διαφορετικών μονωτών μπορούν να υποστηρίξουν τη μετάδοση: ο μονωτήρας του τσιγγάνου (GI), Wari, Fab-8 και 1A2. Τα GI και Fab-8 είναι πιο αποτελεσματικά από το Wari ή το 1A2. Παρουσιάζω ότι με την παρουσία μονωτών, η μετατόπιση εμφανίζει τα χαρακτηριστικά που έχουν περιγραφεί προηγουμένως: απαιτεί ομόλογο ζεύγος, αλλά μπορεί να συμβεί σε οποιονδήποτε από αρκετούς τόπους στο γονιδίωμα. ένας μοναχικός ενισχυτής που έρχεται αντιμέτωπος με έναν ενισχυτή αναφοράς δεν επαρκεί για να οδηγήσει τη μεταγραφή. είναι ασθενέστερη από τη δράση του ίδιου ζεύγους ενισχυτή-προαγωγού στο cis και καταστέλλεται περαιτέρω από ανταγωνισμό cis-προαγωγέα. Αν και είναι απαραίτητο, η παρουσία ομοτυπιών μονωτών δεν επαρκεί για τη μεταμόσχευση. η θέση, ο αριθμός και ο προσανατολισμός τους. Μία μοναδική GI γειτονική προς αμφότερα τον ενισχυτή και τον προαγωγό είναι η βέλτιστη διαμόρφωση. Η ταυτότητα των ενισχυτών και των προαγωγέων στην περιοχή ενός ζεύγους μονωτήρων που αλληλεπιδρούν είναι επίσης σημαντική, ενδεικτική των πολύπλοκων αλληλεπιδράσεων ενισχυτή μονωτή-ενισχυτή.

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