U.S. flag

An official website of the United States government

Dot gov

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Https

Secure .gov websites use HTTPS
A lock ( ) or https:// means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.

PubAg

Main content area

You searched for: Journal name Genomics Remove constraint Journal name: Genomics Publication year rev 7978-2022 Remove constraint Publication year rev: 7978-2022 Source 2022 v.114 no.3 Remove constraint Source: 2022 v.114 no.3
Start Over

Search

48  Search Results

« Previous | 1 - 20 of 48 |
Number of results to display per page

Search Results

1. An informatics approach to distinguish RNA modifications in nanopore direct RNA sequencing

Author:
Soundhar Ramasamy; Shubham Mishra; Surbhi Sharma; Sangamithirai Subramanian Parimalam; Thangavel Vaijayanthi; Yoto Fujita; Basavaraj Kovi; Hiroshi Sugiyama; Ganesh N. Pandian
Source:
Genomics 2022 v.114 no.3 pp. 110372
ISSN:
0888-7543
Subject:
chromatography; data collection; gene expression; genomics; humans; mass spectrometry; models; nanopores; ribosomal RNA; yeasts
Abstract:
... Modifications in RNA can influence their structure, function, and stability and play essential roles in gene expression and regulation. Methods to detect RNA modifications rely on biophysical techniques such as chromatography or mass spectrometry, which are low throughput, or on high throughput short-read sequencing techniques based on selectively reactive chemical probes. Recent studies have util ...
DOI:
10.1016/j.ygeno.2022.110372

2. Bone marrow mesenchymal stem cells-derived exosomal microRNA-16-5p restrains epithelial-mesenchymal transition in breast cancer cells via EPHA1/NF-κB signaling axis

Author:
Yuan Zhang; Xiaofeng Lai; Qingfang Yue; Fei Cao; Yue Zhang; Yang Sun; Jun Tian; Yizhao Lu; Li He; Jun Bai; Yifang Wei
Source:
Genomics 2022 v.114 no.3 pp. 110341
ISSN:
0888-7543
Subject:
bone marrow; breast neoplasms; carcinogenesis; exosomes; gene overexpression; genomics; mice; xenotransplantation
Abstract:
... This study intends to conquer the mystery of microRNA-16-5p/erythropoietin-producing hepatocellular A1/nuclear factor-κB signaling (miR-16-5p/EPHA1/NF-κB signaling) in breast cancer. Expression of miR-16-5p, EPHA1 and NF-κB signaling-related proteins were detected. Gene overexpression or silencing was used to examine the biological roles of bone marrow mesenchymal stem cells (BMSCs)-derived exo-mi ...
DOI:
10.1016/j.ygeno.2022.110341

3. Combined GWAS and QTL mapping revealed candidate genes and SNP network controlling recovery and tolerance traits associated with drought tolerance in seedling winter wheat

Author:
Ahmed Sallam; Shamseldeen Eltaher; Ahmad M. Alqudah; Vikas Belamkar; P. Stephen Baenziger
Source:
Genomics 2022 v.114 no.3 pp. 110358
ISSN:
0888-7543
Subject:
chromosomes; drought tolerance; genes; genomics; seedlings; winter wheat
Abstract:
... To date, very little research on drought tolerance has been conducted at the seedling stage in winter wheat. In this study, two types of traits, namely tolerance and recovery traits, associated with drought tolerance were scored in biparental mapping population (BPP) and association mapping population (A-set). The results of this study revealed no or weak significant correlation between the two ty ...
DOI:
10.1016/j.ygeno.2022.110358

4. Cross-talk between enhancers, structural elements and activating transcription factors maintains the 3D architecture and expression of the CFTR gene

Author:
Shiyi Yin; Monali NandyMazumdar; Alekh Paranjapye; Ann Harris
Source:
Genomics 2022 v.114 no.3 pp. 110350
ISSN:
0888-7543
Subject:
CRISPR-Cas systems; chromatin; cystic fibrosis transmembrane conductance regulator; gene expression; genes; genome-wide association study; genomics; loci
Abstract:
... Robust protocols to examine 3D chromatin structure have greatly advanced knowledge of gene regulatory mechanisms. Here we focus on the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which provides a paradigm for validating models of gene regulation built upon genome-wide analysis. We examine the mechanisms by which multiple cis-regulatory elements (CREs) at the CFTR gene coordina ...
DOI:
10.1016/j.ygeno.2022.110350

5. Human umbilical cord mesenchymal stem cell-derived extracellular vesicles loaded with miR-223 ameliorate myocardial infarction through P53/S100A9 axis

Author:
Mei Yang; Mingmei Liao; Ruijie Liu; Qi Zhang; Sai Zhang; Yi He; Jin Jin; Pengfei Zhang; Lin Zhou
Source:
Genomics 2022 v.114 no.3 pp. 110319
ISSN:
0888-7543
Subject:
angiogenesis; cardiomyocytes; fibrosis; genes; genomics; humans; inflammation; mesenchymal stromal cells; myocardial infarction; rats; therapeutics; umbilical cord
Abstract:
... Mesenchymal stem cell (MSC)-derived extracellular vesicles (EVs) have been proposed as a promising strategy for myocardial infarction (MI). This study aims to explore the mechanism of human umbilical cord MSCs (hucMSCs)-derived EVs loaded with miR-223 on MI. Inflammation, cell biological functions, and fibrosis in vitro were measured. Furthermore, MI rat models were established to verify the role ...
DOI:
10.1016/j.ygeno.2022.110319

6. Identification of the accessible chromatin regions in six tissues in the soybean

Author:
Mingkun Huang; Ling Zhang; Limeng Zhou; Wai-Shing Yung; Zhili Wang; Zhixia Xiao; Qianwen Wang; Xin Wang; Man-Wah Li; Hon-Ming Lam
Source:
Genomics 2022 v.114 no.3 pp. 110364
ISSN:
0888-7543
Subject:
chromatin; chromatin immunoprecipitation; flower buds; flowers; genes; genomics; leaf buds; sequence analysis; soybeans; transcription factors
Abstract:
... Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hen ...
DOI:
10.1016/j.ygeno.2022.110364

7. Impaired CD4+ T cell differentiation in HIV-1 infected patients receiving early anti-retroviral therapy

Author:
Stefan Petkov; Francesca Chiodi
Source:
Genomics 2022 v.114 no.3 pp. 110367
ISSN:
0888-7543
Subject:
CD4-positive T-lymphocytes; GATA transcription factors; antiretroviral agents; cell differentiation; gene expression regulation; genomics; memory; therapeutics; transcription (genetics); transcriptome
Abstract:
... Differentiation of CD4+ T naïve (TN) into central memory (TCM) cells involves extensive molecular processes. We compared the transcriptomes of CD4+ TN and TCM cells from HIV-1 infected patients receiving early anti-retroviral therapy (ART; EA; n = 13) and controls (n = 15). Comparison of protein coding genes between TCM and TN revealed 533 and 82 differentially expressed genes (DEGs) in controls a ...
DOI:
10.1016/j.ygeno.2022.110367

8. Methods for predicting single-cell miRNA in breast cancer

Author:
Chengkui Zhao; Qi Cheng; Weixin Xie; Jiayu Xu; Siwen Xu; Ying Wang; Weixing Feng
Source:
Genomics 2022 v.114 no.3 pp. 110353
ISSN:
0888-7543
Subject:
apoptosis; breast neoplasms; cell proliferation; data collection; genes; genomics; microRNA; sequence analysis
Abstract:
... It has been demonstrated that miRNAs are involved in many biological processes including cell proliferation and differentiation, apoptosis, and stress responses. Although single-cell RNA sequencing technology is prevailing nowadays, it still remains challenging in quantifying miRNA at the single-cell level. Herein, we present the computational methods to infer the single-cell miRNA expression leve ...
DOI:
10.1016/j.ygeno.2022.110353

9. Multiple types of noncoding RNA are involved in potential modulation of PTTG1's expression and function in breast cancer

Author:
Linhang Mei
Source:
Genomics 2022 v.114 no.3 pp. 110352
ISSN:
0888-7543
Subject:
breast neoplasms; genes; genomics; microRNA; morbidity; non-coding RNA; transforming growth factor beta
Abstract:
... Breast cancer is a malignant type with morbidity ranking the first of women globally. As widely acknowledged, there exist close links between ncRNA-mRNA axis and breast cancer. In this study, we first overviewed expression and prognostic values of pituitary tumor transforming gene (PTTGs) in breast cancer. Next, two binding miRNAs (miR-186-5p and miR-655-3p) of PTTG1 in breast cancer were identifi ...
DOI:
10.1016/j.ygeno.2022.110352

10. Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro

Author:
Morten Seirup; Srikumar Sengupta; Scott Swanson; Brian E. McIntosh; Mike Collins; Li-Fang Chu; Zhang Cheng; David U. Gorkin; Bret Duffin; Jennifer M. Bolin; Cara Argus; Ron Stewart; James A. Thomson
Source:
Genomics 2022 v.114 no.3 pp. 110330
ISSN:
0888-7543
Subject:
albumins; biochemical pathways; chromatin; drugs; gene expression; genes; genomics; hepatocytes; hepatotoxicity; liver; pharmaceutical industry; sequence analysis
Abstract:
... Primary hepatocytes are widely used in the pharmaceutical industry to screen drug candidates for hepatotoxicity, but hepatocytes quickly dedifferentiate and lose their mature metabolic function in culture. Attempts have been made to better recapitulate the in vivo liver environment in culture, but the full spectrum of signals required to maintain hepatocyte function ex vivo remains elusive. To elu ...
DOI:
10.1016/j.ygeno.2022.110330

11. Sequencing and de novo transcriptome assembly for discovering regulators of gene expression in Jack (Artocarpus heterophyllus)

Author:
Kishor U. Tribhuvan; Devendra K. Singh; Bhubaneshwar Pradhan; Sujit K. Bishi; Avinash Pandey; Sudhir Kumar; Jyotika Bhati; Dwijesh C. Mishra; Antra Das; T.R. Sharma; A. Pattanayak; Binay K. Singh
Source:
Genomics 2022 v.114 no.3 pp. 110356
ISSN:
0888-7543
Subject:
Artocarpus heterophyllus; fruit trees; gene expression; genomics; microRNA; transcriptome; unigenes
Abstract:
... Jack (Artocarpus heterophyllus) is a multipurpose fruit-tree species with minimal genomic resources. The study reports developing comprehensive transcriptome data containing 80,411 unigenes with an N50 value of 1265 bp. We predicted 64,215 CDSs from the unigenes and annotated and functionally categorized them into the biological process (23,230), molecular function (27,149), and cellular component ...
DOI:
10.1016/j.ygeno.2022.110356

12. Single cell study of cellular diversity and mutual communication in chronic heart failure and drug repositioning

Author:
Jingjing Wan; Zhen Zhang; Saisai Tian; Si Huang; Huizi Jin; Xia Liu; Weidong Zhang
Source:
Genomics 2022 v.114 no.3 pp. 110322
ISSN:
0888-7543
Subject:
RNA; blood vessels; cell communication; collagen; fibroblasts; fibrosis; genomics; heart failure; histones; landscapes; morphogenesis; therapeutics
Abstract:
... Non-cardiomyocytes (non-CMs) play an important role in the process of cardiac remodeling of chronic heart failure. The mechanism of non-CMs transit and interact with each other remains largely unknown. Here, we try to characterize the cellular landscape of non-CMs in mice with chronic heart failure by using single-cell RNA sequencing (scRNA-seq) and provide potential therapeutic hunts. Cellular an ...
DOI:
10.1016/j.ygeno.2022.110322

13. Transcriptome analysis in the spleen of Northern Snakehead (Channa argus) challenged with Nocardia seriolae

Author:
Jian Teng; Yan Zhao; Qing Lei Meng; Shu Ren Zhu; Hong Ju Chen; Liang Yi Xue; Xiang Shan Ji
Source:
Genomics 2022 v.114 no.3 pp. 110357
ISSN:
0888-7543
Subject:
Channa argus; Nocardia seriolae; aquaculture industry; bacterial infections; fish; gene expression regulation; genes; genomics; immune response; pathogenicity; protein-protein interactions; spleen; transcriptomics; China
Abstract:
... Northern snakehead (Channa argus) is an indigenous fish species and is one of popularly cultured snakeheads in China and other Asian countries. Unfortunately, Nocardia seriolae infections have caused considerable losses in the snakehead aquaculture industry. However, the infectivity and the immune response induced by N. seriolae in snakehead are unclear. In order to better understand the immune re ...
DOI:
10.1016/j.ygeno.2022.110357

14. Transcriptome and DNA methylome provide insights into the molecular regulation of drought stress in sea buckthorn

Author:
Zhongrui Lyu; Guoyun Zhang; Yating Song; Songfeng Diao; Caiyun He; Jianguo Zhang
Source:
Genomics 2022 v.114 no.3 pp. 110345
ISSN:
0888-7543
Subject:
DNA; DNA methylation; DNA methyltransferase; Hippophae rhamnoides; drought; drought tolerance; epigenetics; genomics; microRNA; transcription (genetics); transcriptome; transcriptomics; trees; water stress
Abstract:
... Sea buckthorn is a typical drought-resistant tree species. However, there is a general lack of understanding of the pattern of DNA methylation linked with sea buckthorn responses to drought, and its relationship with drought tolerance mechanisms. In this study, we performed whole-transcriptome RNA sequencing and methylome sequencing in response to drought stress to explore differentially expressed ...
DOI:
10.1016/j.ygeno.2022.110345

15. Transcriptome and metabolome profiling unveil the accumulation of flavonoids in Dendrobium officinale

Author:
Yingdan Yuan; Jiajia Zuo; Hanyue Zhang; Mengting Zu; Maoyun Yu; Sian Liu
Source:
Genomics 2022 v.114 no.3 pp. 110324
ISSN:
0888-7543
Subject:
Dendrobium officinale; data collection; flavonols; genomics; herbal medicines; mass spectrometry; metabolome; metabolomics; secondary metabolites; sequence analysis; transcriptome; transcriptomics; China
Abstract:
... Dendrobium officinale is a Chinese herbal medicine with a long history of use in China. Flavonoids are known to be an important secondary metabolite in Dendrobium officinale, but very little is known about their molecular regulation mechanism in D. officinale. In this study, we collected one to four years old D. officinale stems for the purpose of RNA-sequencing and mass spectrometry data collecti ...
DOI:
10.1016/j.ygeno.2022.110324

16. miR-10b-5p-mediated upregulation of PIEZO1 predicts poor prognosis and links to purine metabolism in breast cancer

Author:
Xu Chen; Jing Chen
Source:
Genomics 2022 v.114 no.3 pp. 110351
ISSN:
0888-7543
Subject:
biomarkers; breast neoplasms; computer simulation; genomics; humans; metabolism; neoplasm cells; prognosis; therapeutics
Abstract:
... Increasing evidence has reported the critical roles of PIEZO1 in organism. However, the knowledge of PIEZO1 in human cancers is still inadequate. In silico analyses and experimental validation were performed to analyze PIEZO1's expression, prognostic values and potential upstream/downstream mechanism in breast cancer. PIEZO1 was significantly overexpressed in human breast cancer cell lines and tis ...
DOI:
10.1016/j.ygeno.2022.110351

17. A chromosome-level genome of the kuruma shrimp (Marsupenaeus japonicus) provides insights into its evolution and cold-resistance mechanism

Author:
Xianyun Ren; Jianjian Lv; Meng Liu; Qiong Wang; Huixin Shao; Ping Liu; Jian Li
Source:
Genomics 2022 v.114 no.3 pp. 110373
ISSN:
0888-7543
Subject:
Marsupenaeus japonicus; chromosomes; cold stress; cold tolerance; genome assembly; genomics; marine crustaceans; shrimp; temperature; transcriptome
Abstract:
... Marsupenaeus japonicus is an important marine crustacean species. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for genome-assisted breeding. Consequently, we determined the chromosome-level genome of M. japonicus. Here we determine the chromosome-level genome assembly for M. japonicus with a total of 665.19 ...
DOI:
10.1016/j.ygeno.2022.110373

18. A comprehensive meta-analysis of non-coding polymorphisms associated with precancerous lesions and cervical cancer

Author:
Agneesh Pratim Das; Sandeep Saini; Subhash M. Agarwal
Source:
Genomics 2022 v.114 no.3 pp. 110323
ISSN:
0888-7543
Subject:
T-lymphocytes; alleles; carcinogenesis; case-control studies; cervix; cytotoxicity; databases; genomics; heterozygosity; homozygosity; interferons; interleukin-10; interleukin-6; meta-analysis; metalloproteinases; odds ratio; risk; uterine cervical neoplasms
Abstract:
... To study the risk of polymorphisms present in the non-coding regions of genes related with cervical cancer. The PubMed database was extensively searched using text-mining techniques to identify literature containing the association of single nucleotide polymorphisms and cervical cancer. Case-control studies published till June 2020 were considered for the meta-analysis if they fulfilled the select ...
DOI:
10.1016/j.ygeno.2022.110323

19. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities

Author:
Julie Demars; Yann Labrune; Nathalie Iannuccelli; Alice Deshayes; Sophie Leroux; Hélène Gilbert; Patrick Aymard; Florence Benitez; Juliette Riquet
Source:
Genomics 2022 v.114 no.3 pp. 110361
ISSN:
0888-7543
Subject:
chocolate; color; copy number variation; cream; epistasis; experimental design; genomics; genotyping; melanogenesis; phenotype; pigmentation; pseudogenes; rabbits; single nucleotide polymorphism arrays
Abstract:
... Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high ...
DOI:
10.1016/j.ygeno.2022.110361

20. Assembly of a hybrid mangrove, Bruguiera hainesii, and its two ancestral contributors, Bruguiera cylindrica and Bruguiera gymnorhiza

Author:
Jeremy R. Shearman; Chaiwat Naktang; Chutima Sonthirod; Wasitthee Kongkachana; Sonicha U-thoomporn; Nukoon Jomchai; Chatree Maknual; Suchart Yamprasai; Waratthaya Promchoo; Panthita Ruang-areerate; Wirulda Pootakham; Sithichoke Tangphatsornruang
Source:
Genomics 2022 v.114 no.3 pp. 110382
ISSN:
0888-7543
Subject:
Bayesian theory; Bruguiera gymnorhiza; chromosomes; fish; genome; genomics; phylogeny
Abstract:
... Mangroves are plants that live in tropical and subtropical coastal regions of the world, they are adapted to high salt environments and cyclic tidal flooding. Mangroves play important ecological roles, including acting as breeding grounds for many fish species and to prevent coastal erosion. The genomes of three mangrove species, Bruguiera gymnorhiza, Bruguiera cylindrica, and a hybrid of the two, ...
DOI:
10.1016/j.ygeno.2022.110382