Gene expression phylogenies and ancestral transcriptome reconstruction resolves major transitions in the origins of pregnancy

Structural and physiological changes in the female reproductive system underlie the origins of pregnancy in multiple vertebrate lineages. In mammals, for example, the glandular portion of the lower reproductive tract has transformed into a structure specialized for supporting fetal development. These specializations range from relatively simple maternal provisioning in egg-laying monotremes to an elaborate suite of traits that support intimate maternal-fetal interactions in Eutherians. Among these traits are the maternal decidua and fetal component of the placenta, but there is considerable uncertainty about how these structures evolved. We identified the origins of pregnancy utilizing ancestral transcriptome reconstruction to infer functional evolution of the maternal-fetal interface. Remarkably, we found that maternal gene expression profiles are correlated with degree of placental invasion. These results indicate that an epitheliochorial-like placenta evolved early in the mammalian stem-lineage and that the ancestor of Eutherians had a hemochorial placenta, and suggest maternal control of placental invasiveness. Collectively, these data resolve major transitions in the evolution of pregnancy and indicate that ancestral transcriptome reconstruction can be used to study the function of ancestral cell, tissue, and organ systems.

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Combining Nearest Neighbor Classifiers Versus Cross-Validation Selection

Statistical Applications in Genetics and Molecular Biology ◽

10.2202/1544-6115.1054 ◽

2004 ◽

Vol 3 (1) ◽

pp. 1-19 ◽

Cited By ~ 8

Author(s):

Minhui Paik ◽

Yuhong Yang

Keyword(s):

Gene Expression ◽

Cross Validation ◽

Nearest Neighbor ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Data Sets ◽

Weighting Method ◽

Considerable Uncertainty ◽

Combined Classifier ◽

Nearest Neighbor Classifiers

Various discriminant methods have been applied for classification of tumors based on gene expression profiles, among which the nearest neighbor (NN) method has been reported to perform relatively well. Usually cross-validation (CV) is used to select the neighbor size as well as the number of variables for the NN method. However, CV can perform poorly when there is considerable uncertainty in choosing the best candidate classifier. As an alternative to selecting a single “winner," we propose a weighting method to combine the multiple NN rules. Four gene expression data sets are used to compare its performance with CV methods. The results show that when the CV selection is unstable, the combined classifier performs much better.

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piRNAs as Modulators of Disease Pathogenesis

International Journal of Molecular Sciences ◽

10.3390/ijms22052373 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2373

Author(s):

Kayla J. Rayford ◽

Ayorinde Cooley ◽

Jelonia T. Rumph ◽

Ashutosh Arun ◽

Girish Rachakonda ◽

...

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Gene Expression Profiles ◽

Regulatory Elements ◽

The Body ◽

Small Interfering Rnas ◽

Disease Pathogenesis ◽

The Past ◽

Organ Systems

Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and translation, sncRNAs are becoming vital to many cellular processes. Within the past decade, a novel class of sncRNAs called PIWI-interacting RNAs (piRNAs) have been implicated in various diseases, and understanding their complete function is of vital importance. Historically, piRNAs have been shown to be indispensable in germline integrity and stem cell development. Accumulating research evidence continue to reveal the many arms of piRNA function. Although piRNA function and biogenesis has been extensively studied in Drosophila, it is thought that they play similar roles in vertebrate species, including humans. Compounding evidence suggests that piRNAs encompass a wider functional range than small interfering RNAs (siRNAs) and microRNAs (miRNAs), which have been studied more in terms of cellular homeostasis and disease. This review aims to summarize contemporary knowledge regarding biogenesis, and homeostatic function of piRNAs and their emerging roles in the development of pathologies related to cardiomyopathies, cancer, and infectious diseases.

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