Functional characterization of KlHEM13, a hypoxic gene of Kluyveromyces lactis

2005 ◽  
Vol 51 (3) ◽  
pp. 241-249 ◽  
Author(s):  
Moisés Blanco ◽  
Manuel Becerra ◽  
M Isabel González-Siso ◽  
M Esperanza Cerdán
Keyword(s):  
Kluyveromyces Lactis ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Heme Biosynthesis ◽  
Coproporphyrinogen Oxidase

The KlHEM13 gene of Kluyveromyces lactis encoding the coproporphyrinogen oxidase (EC 1.3.3.3), an oxygen-requiring enzyme that catalyzes the sixth step of heme biosynthesis, was cloned and functionally characterized. The coding and upstream regions of KlHEM13 were analyzed and the putative cis regulatory elements were discussed in relation to the mechanisms of regulation of this hypoxic gene in K. lactis.Key words: coproporphyrinogen oxidase (CPO), HEM13, hypoxic genes, Kluyveromyces lactis.

Abstract 050: Fine-mapping and Bioinformatics Characterization of QT Interval Loci in African Americans: The Population Architecture Using Genomics and Epidemiology (PAGE) Study

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
Christy L Avery ◽  
Praveen Sethupathy ◽  
Steven Buyske ◽  
Q. C He ◽  
Dan Y Lin ◽  
...  
Keyword(s):  
African American ◽  
African Americans ◽  
Fine Mapping ◽  
Qt Interval ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
European Ancestry ◽  
Functional Evaluation ◽  
Human Cardiomyocytes

The QT interval (QT) is a heritable trait and its prolongation is an established risk factor for ventricular tachyarrhythmia and sudden cardiac death. Most genetic studies of QT have examined populations of European ancestry, although the increased genetic diversity in populations of African descent provides opportunity for fine-mapping, which can help narrow association signals and identify candidates for functional characterization. We examined whether eleven previously identified QT loci comprising 6,681 variants on the Illumina Metabochip array were associated with QT in 7,516 African American participants from the Atherosclerosis Risk in Communities study and Women’s Health Initiative clinical trial. Among associated loci, we used conditional analyses and queried bioinformatics databases to identify and functionally categorize signals. We identified nine of the eleven QT loci in African American populations ( P <0.0045 under an additive genetic model adjusting for ancestry and demographic characteristics: NOS1AP, ATP1B1, SCN5A, SLC35F1, KCNH2, KCNQ1, LITAF, NDRG4, and RFFL ). We also identified two independent secondary signals in NOS1AP and ATP1B1 ( P < 7.4x10 −6 ). Conditional analyses adjusting for published loci in European populations demonstrated that eight of these eleven SNPs (nine primary; two secondary) were independent of previously reported SNPs. We then performed the first bioinformatics-based functional characterization of QT loci using the eleven primary and secondary variants and SNPs in strong LD (r 2 > 0.5) among these African American participants. Only the SCN5A locus included a non-synonymous coding variant (rs1805124, H558R, r 2 = 0.7 with primary SNP rs9871385, P = 4.7x10 −4 ). The remaining ten loci harbored variants located exclusively within non-coding regions. Specifically, three contained SNPs within candidate long-range regulatory elements in human cardiomyocytes, five were in or near annotated promoter regions, and the remaining two were in un-annotated, but highly conserved non-coding elements. Several of the QT risk alleles at these SNPs significantly alter the predicted binding affinity for transcription factors, such as TBX5 and AhR, which have been previously implicated in cardiac formation and function. In summary, the findings provide compelling evidence that the same genes influence variation in QT across global populations and that additional, independent signals exist in African Americans. Moreover, of those SNPs identified as strong candidates for functional evaluation, the majority implicate gene regulatory dysfunction in QT prolongation.

scholarly journals Functional characterization of Lilium lancifolium cold-responsive Zinc Finger Homeodomain (ZFHD) gene in abscisic acid and osmotic stress tolerance

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11508
Author(s):  
Yubing Yong ◽  
Yue Zhang ◽  
Yingmin Lyu
Keyword(s):  
Abscisic Acid ◽  
Transgenic Plants ◽  
Zinc Finger ◽  
Promoter Region ◽  
Salt Water ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Response Analysis ◽  
Lilium Lancifolium

Background. We have previously performed an analysis of the cold-responsive transcriptome in the mature leaves of tiger lily (Lilium lancifolium) by gene co-expression network identification. The results has revealed that a ZFHD gene, notated as encoding zinc finger homeodomain protein, may play an essential regulating role in tiger lily response to cold stress. Methods. A further investigation of the ZFHD gene (termed as LlZFHD4) responding to osmotic stresses, including cold, salt, water stresses, and abscisic acid (ABA) was performed in this study. Based on the transcriptome sequences, the coding region and 5′ promoter region of LlZFHD4 were cloned from mature tiger lily leaves. Stress response analysis was performed under continuous 4 °C, NaCl, PEG, and ABA treatments. Functional characterization of LlZFHD4 was conducted in transgenic Arabidopsis, tobacco, and yeast. Results. LlZFHD4 encodes a nuclear-localized protein consisting of 180 amino acids. The N-terminal region of LlZFHD4 has transcriptional activation activity in yeast. The 4 °C, NaCl, PEG, and ABA treatments induced the expression of LlZFHD4. Several stress- or hormone-responsive cis-acting regulatory elements (T-Box, BoxI. and ARF) and binding sites of transcription factors (MYC, DRE and W-box) were found in the core promoter region (789 bp) of LlZFHD4. Also, the GUS gene driven by LlZFHD4 promoter was up-regulated by cold, NaCl, water stresses, and ABA in Arabidopsis. Overexpression of LlZFHD4 improved cold and drought tolerance in transgenic Arabidopsis; higher survival rate and better osmotic adjustment capacity were observed in LlZFHD4 transgenic plants compared to wild type (WT) plants under 4 °C and PEG conditions. However, LlZFHD4 transgenic plants were less tolerant to salinity and more hypersensitive to ABA compared to WT plants. The transcript levels of stress- and ABA-responsive genes were much more up-regulated in LlZFHD4 transgenic Arabidopsis than WT. These results indicate LlZFHD4 is involved in ABA signaling pathway and plays a crucial role in regulating the response of tiger lily to cold, salt and water stresses.

The regulatory elements of PLZF gene are not conserved as reveled by molecular cloning and functional characterization of PLZF gene promoter of Clarias batrachus

Gene Reports ◽  
2019 ◽  
Vol 16 ◽  
pp. 100402
Author(s):  
Swapnarani Nayak ◽  
Lipika Patnaik ◽  
Meenati Manjari Soren ◽  
V. Chakrapani ◽  
Shibani Dutta Mohapatra ◽  
...  
Keyword(s):  
Molecular Cloning ◽  
Functional Characterization ◽  
Gene Promoter ◽  
Regulatory Elements ◽  
Clarias Batrachus

Identification and functional characterization of regulatory elements of the glutamine synthetase gene from rat liver

1993 ◽  
Vol 213 (3) ◽  
pp. 1067-1073 ◽  
Author(s):  
Joachim FAHRNER ◽  
Wil T. LABRUYERE ◽  
Christine GAUNITZ ◽  
Antoon F. M. MOORMAN ◽  
Rolf GEBHARDT ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Rat Liver ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Glutamine Synthetase Gene

scholarly journals funMotifs: Tissue-specific transcription factor motifs

2019 ◽  
Author(s):  
Husen M. Umer ◽  
Karolina Smolinska-Garbulowska ◽  
Nour-al-dain Marzouka ◽  
Zeeshan Khaliq ◽  
Claes Wadelius ◽  
...  
Keyword(s):  
Large Scale ◽  
Tissue Specificity ◽  
Functional Characterization ◽  
Regulatory Elements ◽  
Web Based ◽  
Tissue Specific ◽  
Functional Variants ◽  
Genome Wide ◽  
Reporter Assays

ABSTRACTTranscription factors (TF) regulate gene expression by binding to specific sequences known as motifs. A bottleneck in our knowledge of gene regulation is the lack of functional characterization of TF motifs, which is mainly due to the large number of predicted TF motifs, and tissue specificity of TF binding. We built a framework to identify tissue-specific functional motifs (funMotifs) across the genome based on thousands of annotation tracks obtained from large-scale genomics projects including ENCODE, RoadMap Epigenomics and FANTOM. The annotations were weighted using a logistic regression model trained on regulatory elements obtained from massively parallel reporter assays. Overall, genome-wide predicted motifs of 519 TFs were characterized across fifteen tissue types. funMotifs summarizes the weighted annotations into a functional activity score for each of the predicted motifs. funMotifs enabled us to measure tissue specificity of different TFs and to identify candidate functional variants in TF motifs from the 1000 genomes project, the GTEx project, the GWAS catalogue, and in 2,515 cancer samples from the Pan-cancer analysis of whole genome sequences (PCAWG) cohort. To enable researchers annotate genomic variants or regions of interest, we have implemented a command-line pipeline and a web-based interface that can publicly be accessed on: http://bioinf.icm.uu.se/funmotifs.

scholarly journals Functional characterization of the cis-regulatory elements of the rat ribophorin I gene

1995 ◽  
Vol 23 (3) ◽  
pp. 313-319 ◽  
Author(s):  
Ayyappan K. Rajasekaran ◽  
Zhongmin Zhou ◽  
Kulkarni Prakash ◽  
Gokul Das ◽  
Gert Kreibich
Keyword(s):  
Functional Characterization ◽  
Regulatory Elements ◽  
I Gene

Functional characterization of KIHEM13, a hypoxic gene of Kluyveromyces lactis

2005 ◽  
Vol 51 (5) ◽  
pp. 431-431 ◽  
Author(s):  
Moisés Blanco ◽  
Manuel Becerra ◽  
M Isabel González-Siso ◽  
M Esperanza Cerdán
Keyword(s):  
Kluyveromyces Lactis ◽  
Functional Characterization

scholarly journals How to find genomic regions relevant for gene regulation

2021 ◽  
Vol 33 (2) ◽  
pp. 157-165
Author(s):  
Xuanzong Guo ◽  
Uwe Ohler ◽  
Ferah Yildirim
Keyword(s):  
Functional Characterization ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
High Throughput Analysis ◽  
Protein Coding ◽  
Coding Regions ◽  
The Past ◽  
Genomic Regions ◽  
Regulatory Functions

Abstract Genetic variants associated with human diseases are often located outside the protein coding regions of the genome. Identification and functional characterization of the regulatory elements in the non-coding genome is therefore of crucial importance for understanding the consequences of genetic variation and the mechanisms of disease. The past decade has seen rapid progress in high-throughput analysis and mapping of chromatin accessibility, looping, structure, and occupancy by transcription factors, as well as epigenetic modifications, all of which contribute to the proper execution of regulatory functions in the non-coding genome. Here, we review the current technologies for the definition and functional validation of non-coding regulatory regions in the genome.

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