scholarly journals Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

2001 ◽  
Vol 11 (5) ◽  
pp. 677-684
Author(s):  
Yutaka Suzuki ◽  
Tatsuhiko Tsunoda ◽  
Jun Sese ◽  
Hirotoshi Taira ◽  
Junko Mizushima-Sugano ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Genomic Sequences ◽  
Cdna Libraries ◽  
Promoter Regions ◽  
Specific Expression ◽  
Link Type ◽  
Potential Promoter ◽  
E Boxes

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and theTM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos.AU098358–AU100608.]

Rice Functional Genomics by Transposon Mutagenesis

2002 ◽  
Vol 06 (24) ◽  
pp. 930-935 ◽  
Author(s):  
Chang-deok Han
Keyword(s):  
Tissue Culture ◽  
Transposable Elements ◽  
Functional Genomics ◽  
Large Scale ◽  
Expression Patterns ◽  
Transposon Mutagenesis ◽  
Transposon Tagging ◽  
Genomic Sequences ◽  
Knock Out ◽  
Genetic Cross

Transposable elements are powerful mutagens. Along with genomic sequences, knock-out phenotypes and expression patterns are important information to elucidate the function of genes. In this review, I propose a strategy to develop tranposant lines on a large scale by combining genetic cross and tissue culture of Ac and Ds lines. Based on the facts that Ds tends to be inactive in F2 or later generation and Ds becomes reactivated via tissue culture, a large scale of transposants can be produced by tissue culture of seeds carrying Ac and inactive Ds. In this review, I describe limitations and considerations in operating transposon tagging systems in rice. Also, I discuss the efficiency of our gene trap system and technical procedures to clone Ds flanking DNA.

scholarly journals DISRUPTION OF CPG ISLAND-MEDIATED CHROMATIN ARCHITECTURE AND TRANSCRIPTIONAL HOMEOSTASIS DURING AGING

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S208-S208
Author(s):  
Samuel Beck ◽  
Junyeong Lee
Keyword(s):  
Large Scale ◽  
Cpg Island ◽  
Expression Patterns ◽  
Cpg Islands ◽  
Nuclear Lamina ◽  
The Body ◽  
Chromatin Architecture ◽  
Age Related ◽  
Dna Elements ◽  
Computational Analyses

Abstract Aging causes the global disorganization of nuclear chromatin architecture. In a normal young nucleus, silent heterochromatin is associated with the nuclear lamina layer underlying nuclear envelope, thus spatially separated from euchromatin at the nuclear center. Notably, aging causes the disruption of nuclear lamina and the decondensation of associated heterochromatin. However, it is not clearly understood how these changes of chromatin architectures contribute to age-related diseases. Through large-scale computational analyses, we present that CpG islands (CGIs) give important clues to answering this question. CGIs are DNA elements with high Cytosine-phosphate-Guanine dinucleotide frequencies. In human, about 60% of total genes contain CGIs at their promoters (CGI+ genes) and are broadly expressed throughout the body. The other 40% of genes that do not have CGIs (CGI- genes) exhibit tissue-restricted expression patterns. Our results demonstrate that, in normal young nuclei, only CGI- genes can reside within lamina-associated heterochromatin when transcriptionally inactive, while CGI+ genes associate with nuclear central euchromatin even when they are repressed. In parallel, we show that age-associated heterochromatin decondensation can specifically de-repress tissue-specific CGI- genes leading to their uncontrolled expressions. Our results further demonstrate that global misregulation of CGI- genes increases the noise in gene transcription that, in turn, causes the loss of cellular identities during aging. Taken together, our study establishes critical implication of CGI-mediated chromatin architecture in age-associated degenerative changes and loss of tissue homeostasis.

Expression Trapping: Identification of Novel Genes Expressed in Hematopoietic and Endothelial Lineages by Gene Trapping in ES Cells

Blood ◽  
1998 ◽  
Vol 92 (12) ◽  
pp. 4622-4631 ◽  
Author(s):  
William L. Stanford ◽  
Georgina Caruana ◽  
Katherine A. Vallis ◽  
Maneesha Inamdar ◽  
Michihiro Hidaka ◽  
...  
Keyword(s):  
Large Scale ◽  
Es Cells ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Gene Trap ◽  
Novel Genes ◽  
Specific Expression ◽  
Blood Island

Abstract We have developed a large-scale, expression-based gene trap strategy to perform genome-wide functional analysis of the murine hematopoietic and vascular systems. Using two different gene trap vectors, we have isolated embryonic stem (ES) cell clones containing lacZreporter gene insertions in genes expressed in blood island and vascular cells, muscle, stromal cells, and unknown cell types. Of 79 clones demonstrating specific expression patterns, 49% and 16% were preferentially expressed in blood islands and/or the vasculature, respectively. The majority of ES clones that expressedlacZ in blood islands also expressed lacZ upon differentiation into hematopoietic cells on OP9 stromal layers. Importantly, the in vivo expression of the lacZ fusion products accurately recapitulated the observed in vitro expression patterns. Expression and sequence analysis of representative clones suggest that this approach will be useful for identifying and mutating novel genes expressed in the developing hematopoietic and vascular systems.

Expression Trapping: Identification of Novel Genes Expressed in Hematopoietic and Endothelial Lineages by Gene Trapping in ES Cells

Blood ◽  
1998 ◽  
Vol 92 (12) ◽  
pp. 4622-4631 ◽  
Author(s):  
William L. Stanford ◽  
Georgina Caruana ◽  
Katherine A. Vallis ◽  
Maneesha Inamdar ◽  
Michihiro Hidaka ◽  
...  
Keyword(s):  
Large Scale ◽  
Es Cells ◽  
Expression Patterns ◽  
Embryonic Stem ◽  
Gene Trap ◽  
Novel Genes ◽  
Specific Expression ◽  
Blood Island

We have developed a large-scale, expression-based gene trap strategy to perform genome-wide functional analysis of the murine hematopoietic and vascular systems. Using two different gene trap vectors, we have isolated embryonic stem (ES) cell clones containing lacZreporter gene insertions in genes expressed in blood island and vascular cells, muscle, stromal cells, and unknown cell types. Of 79 clones demonstrating specific expression patterns, 49% and 16% were preferentially expressed in blood islands and/or the vasculature, respectively. The majority of ES clones that expressedlacZ in blood islands also expressed lacZ upon differentiation into hematopoietic cells on OP9 stromal layers. Importantly, the in vivo expression of the lacZ fusion products accurately recapitulated the observed in vitro expression patterns. Expression and sequence analysis of representative clones suggest that this approach will be useful for identifying and mutating novel genes expressed in the developing hematopoietic and vascular systems.

scholarly journals Detection of Alu Exonization Events in Human Frontal Cortex From RNA-Seq Data

2021 ◽  
Vol 8 ◽  
Author(s):  
Liliana Florea ◽  
Lindsay Payer ◽  
Corina Antonescu ◽  
Guangyu Yang ◽  
Kathleen Burns
Keyword(s):  
Frontal Cortex ◽  
Large Scale ◽  
Reference Genome ◽  
Expression Patterns ◽  
Data Sets ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Specific Expression ◽  
Human Frontal Cortex ◽  
Alternatively Spliced

Alu exonization events functionally diversify the transcriptome, creating alternative mRNA isoforms and accounting for an estimated 5% of the alternatively spliced (skipped) exons in the human genome. We developed computational methods, implemented into a software called Alubaster, for detecting incorporation of Alu sequences in mRNA transcripts from large scale RNA-seq data sets. The approach detects Alu sequences derived from both fixed and polymorphic Alu elements, including Alu insertions missing from the reference genome. We applied our methods to 117 GTEx human frontal cortex samples to build and characterize a collection of Alu-containing mRNAs. In particular, we detected and characterized Alu exonizations occurring at 870 fixed Alu loci, of which 237 were novel, as well as hundreds of putative events involving Alu elements that are polymorphic variants or rare alleles not present in the reference genome. These methods and annotations represent a unique and valuable resource that can be used to understand the characteristics of Alu-containing mRNAs and their tissue-specific expression patterns.

CpG islands in genes showing tissue-specific expression

1990 ◽  
Vol 326 (1235) ◽  
pp. 207-215 ◽  
Keyword(s):  
Gene Expression ◽  
Cpg Islands ◽  
Housekeeping Genes ◽  
Tissue Expression ◽  
Proximal Promoter ◽  
Cell Type ◽  
Promoter Regions ◽  
Specific Expression ◽  
Tissue Specific ◽  
Single Cell Type

Patterns of DNA methylation at GpG dinucleotides and their relations with gene expression are complex. Methylation-free CpG clusters, so-called HTF islands, are most often associated with the promoter regions of housekeeping genes, whereas genes expressed in a single-cell type are usually deficient in these sequences. However, in the human carbonic anhydrase (CA) gene family, both the ubiquitously expressed CAII and the muscle specific CAIII appear to have such CpG islands although erythrocyte-specific CAI does not. The CAII island is quantitatively more CpG rich than that of CAIII, with a CpG :GpC ratio of 0.94 compared with 0.82 for CAIII. Estimation of CpG:GpC ratios in the proximal-promoter regions of 44 vertebrate genes suggest that 40% of genes with tissue-specific or limited tissue distribution may show methylation-free CpG clusters in their promoter regions. In many cases the CpG:GpC ratio is less than that found in housekeeping genes and this may reflect variation in the interaction of CpG clusters with regulatory factors that define different patterns of tissue expression.

scholarly journals Expression profiling of antisense transcripts on DNA arrays

2007 ◽  
Vol 28 (3) ◽  
pp. 294-300 ◽  
Author(s):  
Andreas Werner ◽  
Gabriele Schmutzler ◽  
Mark Carlile ◽  
Colin G. Miles ◽  
Heiko Peters
Keyword(s):  
Large Scale ◽  
Expression Patterns ◽  
Distribution Patterns ◽  
Mouse Kidney ◽  
Dna Arrays ◽  
Antisense Transcripts ◽  
Specific Expression ◽  
Tissue Specific ◽  
Antisense Rnas ◽  
Specific Distribution

The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor antisense transcription in mouse kidney and brain. We took advantage of the reversely annotated oligonucleotides on the U74 mouse genome array from Affymetrix that hybridize to NATs overlapping with the sense transcript in the area of the probe set. In RNA samples from mouse kidney and brain, 11.9% and 10.1%, respectively, of 5,652 potential NATs returned positive and about half of the antisense RNAs were detected in both tissues, which was similar to the fraction of sense transcripts expressed in both tissues. Notably, we found that the majority of NATs are related to the sense transcriptome since corresponding sense transcripts were detected for 92.5% (kidney) and 74.5% (brain) of the detected antisense RNAs. Antisense RNA transcription was confirmed by real-time PCR and included additional RNA samples from heart, thymus, and liver. The randomly selected transcripts showed tissue specific expression patterns and varying sense/antisense ratios. The results indicate that antisense transcriptomes are tissue specific, and although pairing of sense/antisense transcripts are known to result in rapid degradation, our data provide proof of principle that the sensitivity of commercial DNA arrays is sufficient to assess NATs in total RNA of whole organs.

scholarly journals A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila

PLoS Genetics ◽  
2021 ◽  
Vol 17 (6) ◽  
pp. e1009613
Author(s):  
Clara Poupault ◽  
Diane Choi ◽  
Khanh Lam-Kamath ◽  
Deepshe Dewett ◽  
Ansa Razzaq ◽  
...  
Keyword(s):  
Promoter Region ◽  
Core Promoter ◽  
Expression Patterns ◽  
Core Promoter Region ◽  
Promoter Regions ◽  
Specific Expression ◽  
General Activation ◽  
Different Color ◽  
Photoreceptor Neurons ◽  
Distal Promoter

Color vision in Drosophila melanogaster is based on the expression of five different color-sensing Rhodopsin proteins in distinct subtypes of photoreceptor neurons. Promoter regions of less than 300 base pairs are sufficient to reproduce the unique, photoreceptor subtype-specific rhodopsin expression patterns. The underlying cis-regulatory logic remains poorly understood, but it has been proposed that the rhodopsin promoters have a bipartite structure: the distal promoter region directs the highly restricted expression in a specific photoreceptor subtype, while the proximal core promoter region provides general activation in all photoreceptors. Here, we investigate whether the rhodopsin promoters exhibit a strict specialization of their distal (subtype specificity) and proximal (general activation) promoter regions, or if both promoter regions contribute to generating the photoreceptor subtype-specific expression pattern. To distinguish between these two models, we analyze the expression patterns of a set of hybrid promoters that combine the distal promoter region of one rhodopsin with the proximal core promoter region of another rhodopsin. We find that the function of the proximal core promoter regions extends beyond providing general activation: these regions play a previously underappreciated role in generating the non-overlapping expression patterns of the different rhodopsins. Therefore, cis-regulatory motifs in both the distal and the proximal core promoter regions recruit transcription factors that generate the unique rhodopsin patterns in a combinatorial manner. We compare this combinatorial regulatory logic to the regulatory logic of olfactory receptor genes and discuss potential implications for the evolution of rhodopsins.

scholarly journals Assessing the Gene Regulatory Landscape in 1,188 Human Tumors

2017 ◽  
Author(s):  
C Calabrese ◽  
K Lehmann ◽  
L Urban ◽  
F Liu ◽  
S Erkek ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Large Scale ◽  
Human Cancer ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Whole Genome ◽  
Somatic Variation ◽  
Specific Expression ◽  
Large Scale Assessment

AbstractCancer is characterised by somatic genetic variation, but the effect of the majority of non-coding somatic variants and the interface with the germline genome are still unknown. We analysed the whole genome and RNA-Seq data from 1,188 human cancer patients as provided by the Pan-cancer Analysis of Whole Genomes (PCAWG) project to map cis expression quantitative trait loci of somatic and germline variation and to uncover the causes of allele-specific expression patterns in human cancers. The availability of the first large-scale dataset with both whole genome and gene expression data enabled us to uncover the effects of the non-coding variation on cancer. In addition to confirming known regulatory effects, we identified novel associations between somatic variation and expression dysregulation, in particular in distal regulatory elements. Finally, we uncovered links between somatic mutational signatures and gene expression changes, including TERT and LMO2, and we explained the inherited risk factors in APOBEC-related mutational processes. This work represents the first large-scale assessment of the effects of both germline and somatic genetic variation on gene expression in cancer and creates a valuable resource cataloguing these effects.

Expression analysis of seed-specific genes in four angiosperm species with an emphasis on the unconserved expression patterns of homologous genes

2013 ◽  
Vol 23 (4) ◽  
pp. 223-231 ◽  
Author(s):  
Lichao Ma ◽  
Yanrong Wang ◽  
Wenxian Liu ◽  
Zhipeng Liu
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Homologous Gene ◽  
Promoter Regions ◽  
Specific Expression ◽  
Seed Formation ◽  
Control Seed ◽  
Homologous Genes ◽  
Expression Of Genes ◽  
Angiosperm Species

AbstractMedicago truncatula, soybean (Glycine max), Arabidopsis thaliana and rice (Oryza sativa) all belong to the core angiosperm group of plants. Seed-specific genes are important for seed formation and development in these angiosperms. The identification of genes specifically expressed in angiosperm seeds and the comparison of the expression patterns of homologous genes among different angiosperm species can provide novel insights into the functions of genes that control seed development and the evolution of angiosperms. We downloaded the sequences and expression data from the relevant databases, and the seed-specific expression of genes was identified with cut-offs of a gene expression level ratio ≥ 5 and a Z-score ≥ 6. The genes were analysed using local BLAST software with an E-value ≤ 1.0E − 505. A total of 605, 581, 778 and 722 genes showed specific expression in the seeds of Medicago, soybean, Arabidopsis and rice, respectively. Additionally, we compared the expression patterns of seed-specific genes from each species with their homologues in the other three species, and found that the degree of variation in the expression patterns of homologous genes was low among closely related species but higher among more distantly related ones. The discrepancy between the homologous gene expression patterns may be caused by the different characteristics of the cis-elements in the promoter regions of the homologous genes.

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