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cis regulatory element

Alain Pacis, Florence Mailhot-Léonard, Ludovic Tailleux, Haley E Randolph, Vania Yotova, Anne Dumaine, Jean-Christophe Grenier, Luis B Barreiro
DNA methylation is considered to be a relatively stable epigenetic mark. However, a growing body of evidence indicates that DNA methylation levels can change rapidly; for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells with Mycobacterium tuberculosis We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements...
March 18, 2019: Proceedings of the National Academy of Sciences of the United States of America
Anastasia Y Glagoleva, Nikita V Ivanisenko, Elena K Khlestkina
BACKGROUND: Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoids; it is involved in biosynthesis of all classes of flavonoid compounds. Nevertheless, the Chs gene family in bread wheat (Triticum aestivum L.) has been not characterized yet. The aim of the current study was to investigate structural and functional organization of the Chs genes and evolution of this gene family in bread wheat and relative species...
March 18, 2019: BMC Genetics
Neus Roca-Ayats, Núria Martínez-Gil, Mónica Cozar, Marina Gerousi, Natàlia Garcia-Giralt, Diana Ovejero, Leonardo Mellibovsky, Xavier Nogués, Adolfo Díez-Pérez, Daniel Grinberg, Susanna Balcells
Genome-wide association studies (GWAS) have repeatedly identified genetic variants associated with bone mineral density (BMD) and osteoporotic fracture in non-coding regions of C7ORF76, a poorly studied gene of unknown function. The aim of the present study was to elucidate the causality and molecular mechanisms underlying the association. We re-sequenced the genomic region in two extreme BMD groups from the BARCOS cohort of postmenopausal women to search for functionally relevant variants. Eight selected variants were tested for association in the complete cohort and 2 of them (rs4342521 and rs10085588) were found significantly associated with lumbar spine BMD and nominally associated with osteoporotic fracture...
March 13, 2019: Bone
Yuan Lin, Fanli Meng, Chao Fang, Bo Zhu, Jiming Jiang
Background: Enhancers are one of the most important classes of cis -regulatory elements (CREs) and play key roles in regulation of transcription in higher eukaryotes. Enhancers are difficult to identify because they lack positional constraints relative to their cognate genes. Excitingly, several recent studies showed that plant enhancers can be predicted based on their distinct features associated with open chromatin. However, experimental validation is necessary to confirm the predicted enhancer function...
2019: Plant Methods
Chringma Sherpa, Patrick E H Jackson, Laurie R Gray, Kathryn Anastos, Stuart F J Le Grice, Marie-Louise Hammarskjold, David Rekosh
The HIV-1 Rev Response Element (RRE) is a cis -acting RNA element characterized by multiple stem-loops. Binding and multimerization of the HIV Rev protein on the RRE promotes nucleocytoplasmic export of incompletely spliced mRNAs, an essential step in HIV replication. Most of our understanding of the Rev-RRE regulatory axis comes from studies of lab-adapted HIV clones. However, in human infection, HIV evolves rapidly and mechanistic studies of naturally occurring Rev and RRE sequences are essential to understanding this system...
March 13, 2019: Journal of Virology
Zhuo Zhou, Keith E Giles, Gary Felsenfeld
We have identified regulatory mechanisms in which an RNA transcript forms a DNA duplex·RNA triple helix with a gene or one of its regulatory elements, suggesting potential auto-regulatory mechanisms in vivo. We describe an interaction at the human β-globin locus, in which an RNA segment embedded in the second intron of the β-globin gene forms a DNA·RNA triplex with the HS2 sequence within the β-globin locus control region, a major regulator of globin expression. We show in human K562 cells that the triplex is stable in vivo...
March 13, 2019: Proceedings of the National Academy of Sciences of the United States of America
Verena Thormann, Laura V Glaser, Maika C Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H Meijsing
The glucocorticoid receptor (GR), a hormone-activated transcription factor, binds to a myriad of genomic binding sites yet seems to regulate a much smaller number of genes. Genome-wide analysis of GR binding and gene regulation has shown that the likelihood of GR-dependent regulation increases with decreased distance of its binding to the transcriptional start site of a gene. To test if we can adopt this knowledge to expand the repertoire of GR target genes, we used CRISPR/Cas-mediated homology-directed repair to add a single GR-binding site directly upstream of the transcriptional start site of each of four genes...
April 2019: Life Science Alliance
Yoon-Ha Jang, Yi-Seul Park, Jung-Soo Nam, Yeji Yang, Ji-Eun Lee, Kwang-Hee Lee, Minho Kang, Alex Chialastri, Hohsuk Noh, Jungwon Park, Jin Seok Lee, Kwang-Il Lim
Controlling the interactions between cells and viruses is critical for treating infected patients, preventing viral infections, and improving virus-based therapeutics. Chemical methods using small molecules and biological methods using proteins and nucleic acids are employed for achieving this control, albeit with limitations. We found, for the first time, that retroviral DNA integration patterns in the human genome, the result of complicated interactions between cells and viruses, can be engineered by adapting cells to the defined nanotopography of silica bead monolayers...
March 13, 2019: Nanoscale
Linbo Wang, Hong Ma, Juan Lin
Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches...
2019: Frontiers in Plant Science
Ritu Batra, Priyanka Agarwal, Sandhya Tyagi, Dinesh Kumar Saini, Vikas Kumar, Anuj Kumar, Sanjay Kumar, Harindra Singh Balyan, Renu Pandey, Pushpendra Kumar Gupta
In plants, the enzyme CCD8 (carotenoid cleavage dioxygenase 8) is involved in the synthesis of an important hormone, strigolactone, and therefore, plays an important role in controlling growth and development. Using cDNA and protein sequence derived from the gene ZmCCD8 from maize, we identified putative orthologs of the gene encoding CCD8 in six other monocots and eight dicots; the sequence similarity ranged from 52-75.9% at the gene level and 60.9-93.7% at the protein level. The average length of the gene was ~3...
2019: PloS One
Piyapat Pin-On, Chatchawit Aporntewan, Jirattha Siriluksana, Narumol Bhummaphan, Pithi Chanvorachote, Apiwat Mutirangura
Epigenetic regulatory changes alter the gene regulation function of DNA repeat elements in cancer and consequently promote malignant phenotypes. Some short tandem repeat sequences, distributed throughout the human genome, can play a role as cis-regulatory elements of the genes. Distributions of tandem long (≥10) and short (<10) A-T repeats in the genome are different depending on gene functions. Long repeats are more commonly found in housekeeping genes and may regulate genes in harmonious fashion. Mononucleotide A-repeats around transcription start sites interact with Argonaute proteins (AGOs) to regulate gene expression...
March 8, 2019: Gene
Xiaoyu Weng, John T Lovell, Scott L Schwartz, Changde Cheng, Taslima Haque, Li Zhang, Samsad Razzaque, Thomas E Juenger
Photoperiod is a key environmental cue affecting flowering and biomass traits in plants. Key components of the photoperiodic flowering pathway have been identified in many species, but surprisingly few studies have globally examined the diurnal rhythm of gene expression with changes in day-length. Using a cost-effective 3'-Tag RNA sequencing strategy, we characterize 9,010 photoperiod responsive genes with strict statistical testing across a diurnal time series in the C4 perennial grass, Panicum hallii. We show that the vast majority of photoperiod responses are driven by complex interactions between day-length and sampling periods...
March 7, 2019: Plant, Cell & Environment
Olof S Dallner, Jill M Marinis, Yi-Hsueh Lu, Kivanc Birsoy, Emory Werner, Gulya Fayzikhodjaeva, Brian D Dill, Henrik Molina, Arden Moscati, Zoltán Kutalik, Pedro Marques-Vidal, Tuomas O Kilpeläinen, Niels Grarup, Allan Linneberg, Yinxin Zhang, Roger Vaughan, Ruth J F Loos, Mitchell A Lazar, Jeffrey M Friedman
Quantitative changes in leptin concentration lead to alterations in food intake and body weight, but the regulatory mechanisms that control leptin gene expression are poorly understood. Here we report that fat-specific and quantitative leptin expression is controlled by redundant cis elements and trans factors interacting with the proximal promoter together with a long noncoding RNA (lncOb). Diet-induced obese mice lacking lncOb show increased fat mass with reduced plasma leptin levels and lose weight after leptin treatment, whereas control mice do not...
March 6, 2019: Nature Medicine
Claudio Stasolla, Shuanglong Huang, Robert D Hill, Abir U Igamberdiev
Plant growth and development rely on the orchestration of cell proliferation, differentiation, and ultimately death. After varying rounds of divisions, cells respond to positional cues by acquiring a specific fate and embarking onto distinct developmental pathways which might differ significantly from those of adjacent cells exposed to diverse cues. Differential cell behaviour is most apparent in response to stress, when some cells might be more vulnerable than others to the same stress condition. This appears to be the case for stem cells which show abnormal features of differentiation and ultimately signs of deterioration at the onset of specific types of stress such as hypoxia and water deficit...
March 6, 2019: Journal of Experimental Botany
Adwaita Prasad Parida, Amrapali Sharma, Arun Kumar Sharma
DNA methylation is an important epigenetic modification that governs transcriptional regulation. The methylation mark is read by a special class of proteins called methyl-CpG-binding domain proteins. The role of DNA methylation has been found in X-chromosome inactivation, genomic imprinting, transposon silencing, and self-incompatibility. Recently, remodeling of global DNA methylation was demonstrated in Arabidopsis during low phosphate availability. The present study reports that AtMBD4 gene of Arabidopsis negatively regulates phosphate starvation...
March 2019: Journal of Biosciences
Zhenhui Zhong, Lianyu Lin, Meilian Chen, Lili Lin, Xiaofeng Chen, Yahong Lin, Xi Chen, Zonghua Wang, Justice Norvienyeku, Huakun Zheng
BACKGROUND: Rice (Oryza sativa L.) is one of the most important crops that serves as staple food for ~ 50% of the human population worldwide. Some important agronomic traits that allow rice to cope with numerous abiotic and biotic stresses have been selected and fixed during domestication. Knowledge on how expression divergence of genes gradually contributes to phenotypic differentiation in response to biotic stress and their contribution to rice population speciation is still limited...
March 1, 2019: Rice
Arne C Lekven, Craig J Lilie, Holly C Gibbs, David G Green, Avantika Singh, Alvin T Yeh
One of the earliest patterning events in the vertebrate neural plate is the specification of mes/r1, the territory comprising the prospective mesencephalon and the first hindbrain rhombomere. Within mes/r1, an interface of gene expression defines the midbrain-hindbrain boundary (MHB), a lineage restriction that separates the mesencephalon and rhombencephalon. wnt1 is critical to mes/r1 development and functions within the MHB as a component of the MHB gene regulatory network (GRN). Despite its importance to these critical and early steps of vertebrate neurogenesis, little is known about the factors responsible for wnt1 transcriptional regulation...
March 1, 2019: Development Genes and Evolution
Tahmid Mehdi, Swneke D Bailey, Paul Guilhamon, Mathieu Lupien
MOTIVATION: The 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals. RESULTS: C3D accurately predicts 32...
March 1, 2019: Bioinformatics
Melissa Ranjit, Masaki Hirano, Kosuke Aoki, Yusuke Okuno, Fumiharu Ohka, Akane Yamamichi, Akira Kato, Sachi Maeda, Kazuya Motomura, Keitaro Matsuo, Atsushi Enomoto, Yasushi Ino, Tomoki Todo, Masahide Takahashi, Toshihiko Wakabayashi, Takuya Kato, Atsushi Natsume
RET finger protein (RFP) forms a complex with histone deacetylase 1, resulting in aberrant deacetylation of H3K27ac and dysregulation of cis-regulatory elements. We evaluated the modulatory effects of RFP knockdown on cis-regulatory elements, gene expression, and chemosensitivity to temozolomide both in glioblastoma cells and in an intracranial glioblastoma model. The combination of RFP knockdown and temozolomide treatment markedly suppressed the glioblastoma cell growth due to oxidative stress and aberrant cell cycle and increased survival time in mice with glioblastoma...
February 26, 2019: Cell Reports
Yumeng Cai, Jing Yan, Qike Li, Zhefang Deng, Shaoli Liu, Jiang Lu, Yali Zhang
The whole promoter regions of SUTs in Vitis were firstly isolated. SUTs are involved in the adaptation to biotic and abiotic stresses. The vulnerability of Vitis vinifera to abiotic and biotic stresses limits its yields. In contrast, Vitis amurensis displays resistance to environmental stresses, such as microbial pathogens, low temperatures, and drought. Sucrose transporters (SUTs) are important regulators for plant growth and stress tolerance; however, the role that SUTs play in stress resistance in V. amurensis is not known...
February 26, 2019: Plant Molecular Biology
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