3D1058 Electrochemical regulation of gene expression profiles of Rhodopseudomonas, a photosynthesis bacterium(Photobiology:Photosynthesis,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

The epididymis is necessary for post-testicular sperm maturation. During their epididymal transit, spermatozoa gain ability for progressive movement and fertilization. The epididymis is composed of several segments that have distinct gene expression profiles that enable the establishment of the changing luminal environment required for sperm maturation. The epididymal gene expression is regulated by endocrine, lumicrine, and paracrine factors in a segment-specific manner. Thus, in addition to its importance for male fertility, the epididymis is a valuable model tissue for studying the regulation of gene expression. This review concentrates on recent advances in understanding the androgen, small RNA, and epigenetically mediated regulation of segment-specific gene expression in the epididymis.

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Integrated transcriptomics and epigenomics reveal chamber-specific and species-specific characteristics of human and mouse hearts

PLoS Biology ◽

10.1371/journal.pbio.3001229 ◽

2021 ◽

Vol 19 (5) ◽

pp. e3001229

Author(s):

Junpeng Gao ◽

Yuxuan Zheng ◽

Lin Li ◽

Minjie Lu ◽

Xiangjian Chen ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Human Heart ◽

Nucleosome Occupancy ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Gene Expression Profiles ◽

Chromatin Accessibility ◽

Gene Body Methylation ◽

Mammalian Heart

DNA methylation, chromatin accessibility, and gene expression represent different levels information in biological process, but a comprehensive multiomics analysis of the mammalian heart is lacking. Here, we applied nucleosome occupancy and methylome sequencing, which detected DNA methylation and chromatin accessibility simultaneously, as well as RNA-seq, for multiomics analysis of the 4 chambers of adult and fetal human hearts, and adult mouse hearts. Our results showed conserved region-specific patterns in the mammalian heart at transcriptome and DNA methylation level. Adult and fetal human hearts showed distinct features in DNA methylome, chromatin accessibility, and transcriptome. Novel long noncoding RNAs were identified in the human heart, and the gene expression profiles of major cardiovascular diseases associated genes were displayed. Furthermore, cross-species comparisons revealed human-specific and mouse-specific differentially expressed genes between the atria and ventricles. We also reported the relationship among multiomics and found there was a bell-shaped relationship between gene-body methylation and expression in the human heart. In general, our study provided comprehensive spatiotemporal and evolutionary insights into the regulation of gene expression in the heart.

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Identification of Target Genes for the Tumor Suppressor RIZ1 Using Gene Expression Profiling.

Blood ◽

10.1182/blood.v104.11.4351.4351 ◽

2004 ◽

Vol 104 (11) ◽

pp. 4351-4351

Author(s):

Wei-Feng Dong ◽

Naoto Takahashi ◽

Matthew N. Bainbridge ◽

Andrea R. Hull ◽

Stuart A. Scott ◽

...

Keyword(s):

Gene Expression ◽

Tumor Suppressor ◽

Gene Expression Profiling ◽

Cell Line ◽

Expression Profiling ◽

Target Genes ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Gene Expression Profiles ◽

Cmv Promoter

Abstract RIZ1 (PRDM2) is a tumor suppressor gene on 1p36 that frequently undergoes deletion, rearrangements, and loss of heterozygosity in a broad spectrum of tumors. RIZ1 is a member of the nuclear protein methyltransferase superfamily involved in chromatin remodeling. RIZ1 contains a ~130 amino acid conserved domain (PR or SET) that is important in chromatin-mediated regulation of gene expression and in the development of cancer. RIZ1 methylates Histone H3 on K9 and this activity may play a role in transcription repression as H3-K9 methylation is known to be associated with repression. Aberrant activities or mistargeting of chromatin modifying activities are proving to have unexpected links to cancer. We and others have shown that RIZ1 expression is down regulated in human leukemias and in the human erythroleukemia cell line K562. Expression of RIZ1 in K562 reduced proliferation, increased apoptosis, and promoted erythroid differentiation. To understand how RIZ1’s DNA binding, methyltransferase, and transcription repressor functions are related to its tumor suppressor activity it is necessary to characterize RIZ1 target genes. We used DNA microarrays to globally monitor how RIZ1 affects gene expression profiles. We constructed a K562 cell line with RIZ1 stably integrated under the control of a CMV promoter and analyzed the gene expression profiles of K652 and K562 + RIZ1 using a 42K Stanford human gene microarray. By comparing the gene expression profiles of these cell lines, we identified potential RIZ1 gene targets that are up and down regulated in the presence of RIZ1. In total, we identified 5 upregulated genes and 20 down regulated genes using significance analysis of microarrays (SAM) and standard deviation filter analysis of the gene expression data. RIZ1-mediated changes in gene expression profiling indicate that RIZ1 is potentially involved in the regulation and connection of the IGF-1 (IGF-1, IGFBP2) and integrin (LMS1) pathways, and in the activation of the TGF-β (SPARC) pathway. The genes perturbed by RIZ1 expression suggest that the tumor suppressor properties of RIZ1 arise from its control of proliferation, apoptosis and differentiation using these pathways. Finally, we observed an overrepresentation of the SP-1 transcription factor binding sites in genes that are upregulated in the absence of RIZ1. This correlates with the ability of RIZ1 to recognize SP1 sequences.

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Organism-wide single-cell transcriptomics of long-lived C. elegans daf-2-/- mutants reveals tissue-specific reprogramming of gene expression networks

10.1101/509992 ◽

2019 ◽

Author(s):

Jessica L. Preston ◽

Nicholas Stiffler ◽

Maggie Weitzman

Keyword(s):

Gene Expression ◽

Single Cell ◽

Expression Profiles ◽

Regulation Of Gene Expression ◽

Gene Expression Profiles ◽

Machine Learning Algorithms ◽

Wild Type ◽

Tissue Specific ◽

C Elegans ◽

Specific Regulation

AbstractA critical requirement for a systems-level understanding of complex biological processes such as aging is the ability to directly characterize interactions between cells and tissues within a multicellular organism. C. elegans nematodes harboring mutations in the insulin-like receptor daf-2 exhibit dramatically-increased lifespans. To identify tissue-specific biochemical mechanisms regulating aging plasticity, we single-cell sequenced 3’-mRNA libraries generated from seven populations of whole day-one adult wild-type and daf-2-/- worms using the 10x ChromiumV1™platform. The age-synchronized samples were bioinformatically merged into a single aligned dataset containing 40,000 age-synchronized wild-type and daf-2-/- cellular transcriptomes partitioned into 101 clusters, using unsupervised machine-learning algorithms to identify common cell types. Here we describe the basic features of the adult C. elegans single-cell transcriptome and summarize functional alterations observed in the gene expression profiles of long-lived daf-2-/- worms. Comprehensive methods and datasets are provided. This is the first study to directly quantify cell-specific differential gene expression between two age-synchronized, genetically-distinct populations of multicellular organisms. This novel approach answers fundamental questions regarding tissue-specific regulation of gene expression and helps to establish a foundation for a comprehensive C. elegans single-cell gene expression atlas.

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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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