Abstract:
:We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and doxorubicin-induced apoptosis, while this deletion also aggravated the invasive potential of MDA-MB-231 cells. However, the mechanistic relationship of the seemingly opposite contribution of BMAL1 deletion to carcinogenesis process is not known at genome-wide level. In this study, an RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways after treating BMAL1 knockout (KO) or wild-type (WT) MDA-MB-231 cells with cisplatin and doxorubicin to initiate apoptosis. Gene set enrichment analysis with the DEGs demonstrated that enrichment in multiple genes/pathways contributes to sensitization to cisplatin- or doxorubicin-induced apoptosis in BMAL1-dependent manner. Additionally, our DEG analysis suggested that non-coding transcript RNA (such as lncRNA and processed pseudogenes) may have role in cisplatin- or doxorubicin-induced apoptosis. Protein-protein interaction network obtained from common DEGs in cisplatin and doxorubicin treatments revealed that GSK3β, NACC1, and EGFR are the principal genes regulating the response of the KO cells. Moreover, the analysis of DEGs among untreated BMAL1 KO and WT cells revealed that epithelial-mesenchymal transition genes are up-regulated in KO cells. As a negative control, we have also analyzed the DEGs following treatment with an endoplasmic reticulum (ER) stress-inducing agent, tunicamycin, which was affected by BMAL1 deletion minimally. Collectively, the present study suggests that BMAL1 regulates many genes/pathways of which the alteration in BMAL1 KO cells may shed light on pleotropic phenotype observed.
journal_name
Funct Integr Genomicsjournal_title
Functional & integrative genomicsauthors
Emisoglu-Kulahli H,Gul S,Morgil H,Ozcan O,Aygenli F,Selvi S,Kavakli IH,Ozturk Ndoi
10.1007/s10142-020-00757-6subject
Has Abstractpub_date
2021-01-01 00:00:00pages
1-16issue
1eissn
1438-793Xissn
1438-7948pii
10.1007/s10142-020-00757-6journal_volume
21pub_type
杂志文章abstract::The oomycete pathogen Plasmopara viticola (Berk. et Curt.) Berl. et de Toni is the causing agent of the destructive downy mildew disease in grapevine. Despite the advances towards elucidation of grapevine resistance mechanisms to downy mildew, increased knowledge of the biological and genetic components of the pathosy...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-012-0261-8
更新日期:2012-06-01 00:00:00
abstract::Although the economic value of wheat flour is determined by the complement of gluten proteins, these proteins have been challenging to study because of the complexity of the major protein groups and the tremendous sequence diversity among wheat cultivars. The completion of a high-quality wheat genome sequence from the...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-019-00694-z
更新日期:2020-01-01 00:00:00
abstract::Gene order is largely collinear in the small-grained cereals, a feature which has proved helpful in both marker development and positional cloning. The accuracy of a virtual gene order map ("genome zipper") for barley (Hordeum vulgare), developed by combining a genetic map of this species with a large number of gene l...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-013-0327-2
更新日期:2013-08-01 00:00:00
abstract::EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs ((SSR)ESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl scrip...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-004-0128-8
更新日期:2005-04-01 00:00:00
abstract::Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multi...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-016-0530-z
更新日期:2017-01-01 00:00:00
abstract::Nuclear genomes of human, animals, and plants are organized into subunits called chromosomes. When isolated into aqueous suspension, mitotic chromosomes can be classified using flow cytometry according to light scatter and fluorescence parameters. Chromosomes of interest can be purified by flow sorting if they can be ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-012-0293-0
更新日期:2012-08-01 00:00:00
abstract::Late blight is a serious economic threat to potato crop, sometimes leading to complete crop loss. The resistance in potato to late blight can be qualitative or quantitative in nature. Qualitative resistance is not durable. Though quantitative resistance is durable, the breeding is challenging due to polygenic inherita...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-013-0358-8
更新日期:2014-06-01 00:00:00
abstract::MicroRNAs (miRNAs) are small RNAs (sRNAs) that regulate gene expression in development and adaptive responses to the environment. The early days in the sRNA field was one of the most exciting and promising moments in modern biology, attracting large investments to the understanding of the underlining mechanisms and th...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-016-0513-0
更新日期:2017-05-01 00:00:00
abstract::MicroRNAs, small regulatory molecules with significant impacts on the transcriptional network of all living organisms, have been the focus of several studies conducted mostly on modern wheat cultivars. In this study, we investigated miRNA repertoires of modern durum wheat and its wild relatives, with differing degrees...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0453-0
更新日期:2015-09-01 00:00:00
abstract::Culex pipiens mosquitoes are important disease vectors inhabiting temperate zones, worldwide. The seasonal reduction in temperature and photoperiod accompanying late summer and early fall prompts female mosquitoes to enter diapause, a stage of developmental arrest and physiological conditioning that enhances survival ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0432-5
更新日期:2015-07-01 00:00:00
abstract::The aim of this study was to examine the effect of abscisic acid (ABA), sucrose, and auxin on grape fruit development and to assess the mechanism of these three factors on the grape fruit ripening process. Different concentrations of ABA, sucrose, and auxin were used to treat the grape fruit, and the ripening-related ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-017-0546-z
更新日期:2017-07-01 00:00:00
abstract::The ubiquitous cell membrane proteins called aquaporins are now firmly established as channel proteins that control the specific transport of water molecules across cell membranes in all living organisms. The aquaporins are thus likely to be of fundamental significance to all facets of plant growth and development aff...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-007-0049-4
更新日期:2007-10-01 00:00:00
abstract::The proneness of diseases and susceptibility towards drugs vary from person to person. At present, there is a strong demand for the personalization of drugs. The genetic signature behind proneness of the disease has been studied through a comprehensive 'octopodial approach'. All the genetic variants included in the ap...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-017-0559-7
更新日期:2017-07-01 00:00:00
abstract::GDSL-type esterase/lipase (GELP) is mainly characterized by a conserved GDSL domain at N terminus, and is widely found in all living species, both prokaryotes and eukaryotes. GELP gene family consists of a wide range of members playing important roles in plant physiological processes, such as development, stress respo...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-018-0620-1
更新日期:2018-11-01 00:00:00
abstract::GRAS domain genes are a group of important plant-specific transcription factors that have been reported to be involved in plant development. In order to know the roles of GRAS genes in grapevine, a widely cultivated fruit crop, the study on grapevine GRAS (VvGRAS) was carried out, and from which, 43 were identified fr...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-016-0479-y
更新日期:2016-07-01 00:00:00
abstract::The assembly of a 1.3-Mb size region of the wheat genome has provided the opportunity to study a recent nuclear mitochondrial DNA insertion (NUMT). In the present study, we have studied two bacterial artificial chromosomes (BACs) and characterized a 52-kb NUMT segment from the tetraploid and hexaploid wheat BAC librar...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-011-0237-0
更新日期:2011-12-01 00:00:00
abstract::The ever-rising population of the twenty-first century together with the prevailing challenges, such as deteriorating quality of arable land and water, has placed a big challenge for plant breeders to satisfy human needs for food under erratic weather patterns. Rice, wheat, and maize are the major staple crops consume...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-019-00684-1
更新日期:2019-09-01 00:00:00
abstract::Genomic structural variation is an important and abundant source of genetic and phenotypic variation. We previously reported an initial analysis of copy number variations (CNVs) in Angus cattle selected for resistance or susceptibility to gastrointestinal nematodes. In this study, we performed a large-scale analysis o...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-011-0252-1
更新日期:2012-03-01 00:00:00
abstract::Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In thi...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-015-0437-0
更新日期:2015-07-01 00:00:00
abstract::Comparative genomic analysis is the cornerstone of in silico-based approaches to understanding biological systems and processes across cereal species, such as rice, wheat and barley, in order to identify genes of agronomic interest. The size of the genomic repositories is nearly doubling every year, and this has signi...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-004-0102-5
更新日期:2004-03-01 00:00:00
abstract::The Maize Gene Discovery Project (MGDP) is a 5-year NSF-funded plant genome initiative that began in 1998. The MGDP collaboration involves researchers at six universities from diverse disciplines with the common goal of discovering new maize genes and developing tools for the phenotypic characterization of maize mutan...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s10142-002-0078-y
更新日期:2003-03-01 00:00:00
abstract::Abiotic stress tolerance is a complex trait regulated by multiple genes and gene networks in plants. A range of abiotic stresses are known to limit rice productivity. Meta-transcriptomics has emerged as a powerful approach to decipher stress-associated molecular network in model crops. However, retaining specificity o...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,meta分析
doi:10.1007/s10142-019-00697-w
更新日期:2020-01-01 00:00:00
abstract::Stem blister canker, caused by Botryosphaeria dothidea, is becoming the most serious disease of poplar in China. The molecular basis of the poplar in response to stem blister canker is not well understood. To reveal the global transcriptional changes of poplar to infection by B. dothidea, Solexa paired-end sequencing ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-014-0379-y
更新日期:2014-09-01 00:00:00
abstract::Water temperature affects the survival, growth, immunity, reproduction, and productivity of farmed fish. The temperature beyond suitable range will disrupt the normal physiological activity. Common carp (Cyprinus carpio L.) is a representative eurythermic fish; they are able to sense and respond to changes in water te...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-018-0643-7
更新日期:2019-03-01 00:00:00
abstract::Intronless genes, a characteristic feature of prokaryotes, constitute a significant portion of the eukaryotic genomes. Our analysis revealed the presence of 11,109 (19.9%) and 5,846 (21.7%) intronless genes in rice and Arabidopsis genomes, respectively, belonging to different cellular role and gene ontology categories...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-007-0052-9
更新日期:2008-02-01 00:00:00
abstract::Drought is a major abiotic stress affecting crop productivity and quality. As a class of noncoding RNA, microRNA (miRNA) plays important roles in plant growth, development, and stress response. However, their response and roles in tomato drought stress is largely unknown. Here, by using high-throughput sequencing, we ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-017-0575-7
更新日期:2018-01-01 00:00:00
abstract::Fungal species are potential dye decomposers since these secrete spectra of extracellular enzymes involved in catabolism. However, cellular mechanisms underlying azo dye catalysis and detoxification are incompletely understood and obscure. A potential strain designated as Penicillium oxalicum SAR-3 demonstrated broad-...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-014-0405-0
更新日期:2014-12-01 00:00:00
abstract::In theory, gene therapy is a simple concept which holds great promise as a cure for disease. In practice, however, considerable obstacles have to be overcome, including problems with safe and efficient gene delivery and stable gene expression. This review gives an overview on the history of gene therapy and analyses s...
journal_title:Functional & integrative genomics
pub_type: 杂志文章,评审
doi:10.1007/s101420000011
更新日期:2000-09-01 00:00:00
abstract::A cDNA library containing approximately 5,000 clones from germinating barley embryos was constructed and used to examine the variation in gene expression patterns during the first 4 days postimbibition. The expression profiles of embryos (including scutellum) from 4 to 96 h postimbibition were compared to a reference ...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-005-0133-6
更新日期:2005-07-01 00:00:00
abstract::The symbiotic N(2)-fixing alpha-proteobacterium Sinorhizobium meliloti has three replicons: a circular chromosome (3.7 Mb) and two smaller replicons, pSymA (1.4 Mb) and pSymB (1.7 Mb). Sequence analysis has revealed that an essential gene is carried on pSymB, which brings into question whether pSymB should be consider...
journal_title:Functional & integrative genomics
pub_type: 杂志文章
doi:10.1007/s10142-002-0068-0
更新日期:2002-11-01 00:00:00