scholarly journals Structure and variability of human chromosome ends.

1990 ◽  
Vol 10 (2) ◽  
pp. 518-527 ◽  
Author(s):  
T de Lange ◽  
L Shiue ◽  
R M Myers ◽  
D R Cox ◽  
S L Naylor ◽  
...  
Keyword(s):  
De Novo ◽  
Hybrid Cell ◽  
Somatic Cells ◽  
Terminal Segment ◽  
Human Chromosomes ◽  
Primary Tumors ◽  
Length Polymorphisms ◽  
Subtelomeric Repeat ◽  
Flanking Sequences ◽  
Flanking Regions

Mammalian telomeres are thought to be composed of a tandem array of TTAGGG repeats. To further define the type and arrangement of sequences at the ends of human chromosomes, we developed a direct cloning strategy for telomere-associated DNA. The method involves a telomere enrichment procedure based on the relative lack of restriction endonuclease cutting sites near the ends of human chromosomes. Nineteen (TTAGGG)n-bearing plasmids were isolated, two of which contain additional human sequences proximal to the telomeric repeats. These telomere-flanking sequences detect BAL 31-sensitive loci and thus are located close to chromosome ends. One of the flanking regions is part of a subtelomeric repeat that is present at 10 to 25% of the chromosome ends in the human genome. This sequence is not conserved in rodent DNA and therefore should be a helpful tool for physical characterization of human chromosomes in human-rodent hybrid cell lines; some of the chromosomes that may be analyzed in this manner have been identified, i.e., 7, 16, 17, and 21. The minimal size of the subtelomeric repeat is 4 kilobases (kb); it shows a high frequency of restriction fragment length polymorphisms and undergoes extensive de novo methylation in somatic cells. Distal to the subtelomeric repeat, the chromosomes terminate in a long region (up to 14 kb) that may be entirely composed of TTAGGG repeats. This terminal segment is unusually variable. Although sperm telomeres are 10 to 14 kb long, telomeres in somatic cells are several kilobase pairs shorter and very heterogeneous in length. Additional telomere reduction occurs in primary tumors, indicating that somatic telomeres are unstable and may continuously lose sequences from their termini.

Structure and variability of human chromosome ends

1990 ◽  
Vol 10 (2) ◽  
pp. 518-527
Author(s):  
T de Lange ◽  
L Shiue ◽  
R M Myers ◽  
D R Cox ◽  
S L Naylor ◽  
...  
Keyword(s):  
De Novo ◽  
Hybrid Cell ◽  
Somatic Cells ◽  
Terminal Segment ◽  
Human Chromosomes ◽  
Primary Tumors ◽  
Length Polymorphisms ◽  
Subtelomeric Repeat ◽  
Flanking Sequences ◽  
Flanking Regions

Mammalian telomeres are thought to be composed of a tandem array of TTAGGG repeats. To further define the type and arrangement of sequences at the ends of human chromosomes, we developed a direct cloning strategy for telomere-associated DNA. The method involves a telomere enrichment procedure based on the relative lack of restriction endonuclease cutting sites near the ends of human chromosomes. Nineteen (TTAGGG)n-bearing plasmids were isolated, two of which contain additional human sequences proximal to the telomeric repeats. These telomere-flanking sequences detect BAL 31-sensitive loci and thus are located close to chromosome ends. One of the flanking regions is part of a subtelomeric repeat that is present at 10 to 25% of the chromosome ends in the human genome. This sequence is not conserved in rodent DNA and therefore should be a helpful tool for physical characterization of human chromosomes in human-rodent hybrid cell lines; some of the chromosomes that may be analyzed in this manner have been identified, i.e., 7, 16, 17, and 21. The minimal size of the subtelomeric repeat is 4 kilobases (kb); it shows a high frequency of restriction fragment length polymorphisms and undergoes extensive de novo methylation in somatic cells. Distal to the subtelomeric repeat, the chromosomes terminate in a long region (up to 14 kb) that may be entirely composed of TTAGGG repeats. This terminal segment is unusually variable. Although sperm telomeres are 10 to 14 kb long, telomeres in somatic cells are several kilobase pairs shorter and very heterogeneous in length. Additional telomere reduction occurs in primary tumors, indicating that somatic telomeres are unstable and may continuously lose sequences from their termini.

scholarly journals Assexon: Assembling Exon Using Gene Capture Data

2019 ◽  
Vol 15 ◽  
pp. 117693431987479 ◽  
Author(s):  
Hao Yuan ◽  
Calder Atta ◽  
Luke Tornabene ◽  
Chenhong Li
Keyword(s):  
De Novo ◽  
Phylogenetic Signal ◽  
Read Depth ◽  
Model Organisms ◽  
Coding Regions ◽  
Exon Capture ◽  
Flanking Sequences ◽  
Phylogenetic Divergence ◽  
Lepisosteus Oculatus ◽  
Flanking Regions

Exon capture across species has been one of the most broadly applied approaches to acquire multi-locus data in phylogenomic studies of non-model organisms. Methods for assembling loci from short-read sequences (eg, Illumina platforms) that rely on mapping reads to a reference genome may not be suitable for studies comprising species across a wide phylogenetic spectrum; thus, de novo assembling methods are more generally applied. Current approaches for assembling targeted exons from short reads are not particularly optimized as they cannot (1) assemble loci with low read depth, (2) handle large files efficiently, and (3) reliably address issues with paralogs. Thus, we present Assexon: a streamlined pipeline that de novo assembles targeted exons and their flanking sequences from raw reads. We tested our method using reads from Lepisosteus osseus (4.37 Gb) and Boleophthalmus pectinirostris (2.43 Gb), which are captured using baits that were designed based on genome sequence of Lepisosteus oculatus and Oreochromis niloticus, respectively. We compared performance of Assexon to PHYLUCE and HybPiper, which are commonly used pipelines to assemble ultra-conserved element (UCE) and Hyb-seq data. A custom exon capture analysis pipeline (CP) developed by Yuan et al was compared as well. Assexon accurately assembled more than 3400 to 3800 (20%-28%) loci than PHYLUCE and more than 1900 to 2300 (8%-14%) loci than HybPiper across different levels of phylogenetic divergence. Assexon ran at least twice as fast as PHYLUCE and HybPiper. Number of loci assembled using CP was comparable with Assexon in both tests, while Assexon ran at least 7 times faster than CP. In addition, some steps of CP require the user’s interaction and are not fully automated, and this user time was not counted in our calculation. Both Assexon and CP retrieved no paralogs in the testing runs, but PHYLUCE and Hybpiper did. In conclusion, Assexon is a tool for accurate and efficient assembling of large read sets from exon capture experiments. Furthermore, Assexon includes scripts to filter poorly aligned coding regions and flanking regions, calculate summary statistics of loci, and select loci with reliable phylogenetic signal. Assexon is available at https://github.com/yhadevol/Assexon .

scholarly journals De Novo SNP Discovery and Genotyping of Iranian Pimpinella Species Using ddRAD Sequencing

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1342
Author(s):  
Shaghayegh Mehravi ◽  
Gholam Ali Ranjbar ◽  
Ghader Mirzaghaderi ◽  
Anita Alice Severn-Ellis ◽  
Armin Scheben ◽  
...  
Keyword(s):  
De Novo ◽  
Genetic Relationships ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Genomic Resources ◽  
High Quality Snps ◽  
The Family ◽  
Double Digestion ◽  
Flanking Sequences ◽  
Downstream Analysis

The species of Pimpinella, one of the largest genera of the family Apiaceae, are traditionally cultivated for medicinal purposes. In this study, high-throughput double digest restriction-site associated DNA sequencing technology (ddRAD-seq) was used to identify single nucleotide polymorphisms (SNPs) in eight Pimpinella species from Iran. After double-digestion with the enzymes HpyCH4IV and HinfI, a total of 334,702,966 paired-end reads were de novo assembled into 1,270,791 loci with an average of 28.8 reads per locus. After stringent filtering, 2440 high-quality SNPs were identified for downstream analysis. Analysis of genetic relationships and population structure, based on these retained SNPs, indicated the presence of three major groups. Gene ontology and pathway analysis were determined by using comparison SNP-associated flanking sequences with a public non-redundant database. Due to the lack of genomic resources in this genus, our present study is the first report to provide high-quality SNPs in Pimpinella based on a de novo analysis pipeline using ddRAD-seq. This data will enhance the molecular knowledge of the genus Pimpinella and will provide an important source of information for breeders and the research community to enhance breeding programs and support the management of Pimpinella genomic resources.

Distal regulatory elements from the mouse metallothionein locus stimulate gene expression in transgenic mice

1993 ◽  
Vol 13 (9) ◽  
pp. 5266-5275
Author(s):  
R D Palmiter ◽  
E P Sandgren ◽  
D M Koeller ◽  
R L Brinster
Keyword(s):  
Transgenic Mice ◽  
Regulatory Elements ◽  
High Level Expression ◽  
Hypersensitive Sites ◽  
Enhanced Expression ◽  
Rat Growth ◽  
Flanking Sequences ◽  
High Level ◽  
Distal Regulatory Elements ◽  
Flanking Regions

DNA regions of 10 and 7 kb that flank the mouse metallothionein II (MT-II) and MT-I genes, respectively, were combined with a minimally marked MT-I (MT-I*) gene and tested in transgenic mice. This construct resulted in (i) position-independent expression of MT-I* mRNA and copy number-dependent expression, (ii) levels of hepatic MT-I mRNA per cell per transgene that were about half that derived from endogenous MT-I genes, (iii) appropriate regulation by metals and hormones, and (iv) tissue distribution of transgene mRNA that resembled that of endogenous MT-I mRNA. These features were not observed when MT-I* was tested without the flanking regions. These MT-I flanking sequences also improved the expression of rat growth hormone reporter genes, with or without introns, that were under the control of the MT-I promoter. Moreover, they enhanced expression from two of four heterologous promoters/enhancers that were tested. Deletion analysis indicated that regions known to have DNase I-hypersensitive sites were necessary but not sufficient for high-level expression. These data suggest that the DNA regions flanking the mouse MT-I and MT-II genes have functions like the locus control regions described for other genes.

Use of brain radiotherapy as part of first course of treatment for NSCLC with de novo brain metastasis.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 9118-9118
Author(s):  
Rafael Arteta-Bulos ◽  
Nadeem Bilani ◽  
Leah Elson ◽  
Elizabeth Blessing Elimimian ◽  
Diana Saravia ◽  
...  
Keyword(s):  
Brain Metastasis ◽  
De Novo ◽  
Local Therapy ◽  
Insurance Status ◽  
Primary Tumors ◽  
Brain Radiotherapy ◽  
Facility Type ◽  
Brain Radiation ◽  
To Receive ◽  
N Staging

9118 Background: Loco-regional management of brain metastases from non-small cell lung cancer (NSCLC) are surgery and/or brain radiotherapy, either whole brain (WBRT) or stereotactic (SRS). We used a national registry to evaluate trends in the use of brain radiotherapy as part of the first course of management in patients diagnosed with de novo brain metastasis. Methods: We retrospectively analyzed the National Cancer Database (NCDB) to identify patients with NSCLC and de novo brain metastasis diagnosed from 2004-2016. We described the socio-demographic and clinical characteristics of this population, then used chi-squared testing to evaluate for an association between these variables and the use of brain radiotherapy (either SRS or WBRT). Significant variables (p < 0.05) were included in a multiple logistic regression model. Results: Of n = 41,454 patients with NSCLC and de novo brain metastasis, n = 27,949 (67.4%) received either SRS or WBRT as part of their first course of treatment, while n = 13,505 (32.6%) did not receive primary brain radiation. Of those that did not receive radiation: n = 9,927 (73.5%) were < 70 years old while n = 3,578 (26.5%) were ≥70. N = 11,081 (82.7%) were White, n = 1,550 (11.6%) were Black and n = 768 (5.7%) were Asian. Variables significantly associated with the use of primary brain radiotherapy at the multivariate level were: treatment facility type (p = 0.004), tumor histology (p < 0.001), clinical T-staging (p < 0.001), and clinical N-staging (p < 0.001). Age, sex, race, comorbidity, grade, insurance status, and setting (metro vs. rural vs. urban) were not significantly associated with the use of radiotherapy. Compared to patients treated at community cancer programs (CPs), those treated at comprehensive community CPs (OR 1.152, 95% CI 1.027-1.291, p = 0.015) and academic CPs (OR 1.242, 95% CI 1.104-1.398, p < 0.001) were more likely to receive primary brain radiotherapy. Patients with squamous NSCLC were less likely (OR 0.680, 95% CI 0.619-0.747, p < 0.001) to receive brain radiotherapy compared to those with adenocarcinoma. Finally, patients with advanced T-staging (p < 0.001) and N-staging (p < 0.001) were less likely (OR < 1) to receive brain radiotherapy as part of the first course of treatment. Conclusions: While insurance status and setting were not significantly associated with the use of brain radiotherapy, facility type was. Further research is needed to evaluate whether this is a true disparity in medical practice, or the differences can be explained by characteristics of the patient population undocumented by the NCDB (e.g. severity of brain metastasis). Additionally, patients with larger primary tumors were less likely to receive brain radiation as part of the first course of treatment, which may reflect the need for local therapy prior to treating metastatic sites.

scholarly journals Structure of the SAD mutation and the location of control sites at silent mating type genes in Saccharomyces cerevisiae.

1984 ◽  
Vol 4 (7) ◽  
pp. 1278-1285 ◽  
Author(s):  
J Hicks ◽  
J Strathern ◽  
A Klar ◽  
S Ismail ◽  
J Broach
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Control Site ◽  
Left Hand ◽  
Low Level ◽  
Flanking Sequences ◽  
Mating Type Genes ◽  
Weak Expression ◽  
The Right ◽  
Flanking Regions

The SAD mutation, an extra mating type cassette, has been shown to arise from an unequal mitotic crossover between the MAT and HMR loci, resulting in the formation of a hybrid cassette and a duplication of the MAT-HMR interval. The SAD cassette contains the "a" information and left-hand flanking regions from the parental HMRa cassette and the right-hand flanking sequences of the parental MAT cassette. This arrangement of flanking sequences causes a leaky but reproducible mating phenotype correlated with a low-level expression of the cassette as measured by RNA blotting. This weak expression is attributed to the loss of one flanking control site normally present at the silent HM storage loci.

scholarly journals Recovery of non-reference sequences missing from the human reference genome

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Ran Li ◽  
Xiaomeng Tian ◽  
Peng Yang ◽  
Yingzhi Fan ◽  
Ming Li ◽  
...  
Keyword(s):  
Human Genome ◽  
Tandem Repeats ◽  
Reference Genome ◽  
De Novo ◽  
Precise Location ◽  
Protein Coding ◽  
Human Reference Genome ◽  
Mhc Haplotype ◽  
Reference Sequences ◽  
Flanking Regions

Abstract Background The non-reference sequences (NRS) represent structure variations in human genome with potential functional significance. However, besides the known insertions, it is currently unknown whether other types of structure variations with NRS exist. Results Here, we compared 31 human de novo assemblies with the current reference genome to identify the NRS and their location. We resolved the precise location of 6113 NRS adding up to 12.8 Mb. Besides 1571 insertions, we detected 3041 alternate alleles, which were defined as having less than 90% (or none) identity with the reference alleles. These alternate alleles overlapped with 1143 protein-coding genes including a putative novel MHC haplotype. Further, we demonstrated that the alternate alleles and their flanking regions had high content of tandem repeats, indicating that their origin was associated with tandem repeats. Conclusions Our study detected a large number of NRS including many alternate alleles which are previously uncharacterized. We suggested that the origin of alternate alleles was associated with tandem repeats. Our results enriched the spectrum of genetic variations in human genome.

scholarly journals Microtubule Cytoskeleton Remodeling by Acentriolar Microtubule-organizing Centers at the Entry and Exit from Mitosis in Drosophila Somatic Cells

2009 ◽  
Vol 20 (11) ◽  
pp. 2796-2808 ◽  
Author(s):  
Sara Moutinho-Pereira ◽  
Alain Debec ◽  
Helder Maiato
Keyword(s):  
Cell Cycle ◽  
Mitotic Spindle ◽  
De Novo ◽  
Animal Cell ◽  
Somatic Cells ◽  
Spindle Assembly ◽  
Entry And Exit ◽  
Down Regulation ◽  
Microtubule Organizing Centers ◽  
Cytoskeleton Remodeling

Cytoskeleton microtubules undergo a reversible metamorphosis as cells enter and exit mitosis to build a transient mitotic spindle required for chromosome segregation. Centrosomes play a dominant but dispensable role in microtubule (MT) organization throughout the animal cell cycle, supporting the existence of concurrent mechanisms that remain unclear. Here we investigated MT organization at the entry and exit from mitosis, after perturbation of centriole function in Drosophila S2 cells. We found that several MTs originate from acentriolar microtubule-organizing centers (aMTOCs) that contain γ-tubulin and require Centrosomin (Cnn) for normal architecture and function. During spindle assembly, aMTOCs associated with peripheral MTs are recruited to acentriolar spindle poles by an Ncd/dynein-dependent clustering mechanism to form rudimentary aster-like structures. At anaphase onset, down-regulation of CDK1 triggers massive formation of cytoplasmic MTs de novo, many of which nucleated directly from aMTOCs. CDK1 down-regulation at anaphase coordinates the activity of Msps/XMAP215 and the kinesin-13 KLP10A to favor net MT growth and stability from aMTOCs. Finally, we show that microtubule nucleation from aMTOCs also occurs in cells containing centrosomes. Our data reveal a new form of cell cycle–regulated MTOCs that contribute for MT cytoskeleton remodeling during mitotic spindle assembly/disassembly in animal somatic cells, independently of centrioles.

Are the survival benefits associated with primary resection in de novo metastatic colorectal cancer (mCRC) mediated by reversal of systemic inflammation?

2014 ◽  
Vol 32 (3_suppl) ◽  
pp. 464-464
Author(s):  
Phillip V. Tran ◽  
Mathu Samanthaby ◽  
Hui-li Wong ◽  
Jayesh Desai ◽  
Jeanne Tie ◽  
...  
Keyword(s):  
Systemic Inflammation ◽  
Primary Tumor ◽  
De Novo ◽  
Tumor Resection ◽  
Primary Resection ◽  
Primary Tumors ◽  
Axial Diameter ◽  
Neutrophil Lymphocyte Ratio ◽  
Metastatic Burden ◽  
Tumour Bulk

464 Background: Despite reported survival benefits for primary tumor resection in de novo mCRC, its use remains controversial, particularly as the biological explanation remains unclear. We explored whether reversal of systemic inflammation, a marker of a tumor-promoting immune response and poor prognosis, is associated with improved survival in pts undergoing primary resection. Methods: We identified pts who underwent primary resection for de novo mCRC from a prospective CRC database, excluding pts who had metastatectomy. Neutrophil-lymphocyte ratio (NLR) was used to represent systemic inflammation. Survival differences associated with reversal of systemic inflammation, as defined by NLR falling from an elevated level (> 5) at diagnosis to ≤ 5 postoperatively, were examined. Associations between falling NLR and primary tumor bulk (maximal length assessed by pathologist) as well as metastatic burden (maximal axial diameter of largest metastasis assessed by radiologist) were explored. Results: Baseline and postoperative NLR were examined in 156 pts with median age 69y and median overall survival (OS) 18.3 mo. Baseline NLR was elevated in 66 (42%) pts; primary resection resulted in falling NLR in 37 of these pts (56%). Compared to pts with persistent NLR >5, a falling NLR was significantly associated with improved OS (HR 0.53, p = 0.012). Falling NLR was also associated with larger primary tumors, although this was not significant (median length 55mm vs. 45mm, p = 0.059). In a preliminary analysis of 26 pts with retrievable radiology, falling NLR was associated with lower metastatic burden compared to an unchanged NLR (median diameter 29mm vs. 41mm, p = 0.046). Conclusions: Our data demonstrates improved OS in pts who have reversal of systemic inflammation following primary resection in de novo mCRC. The possible associations between reversed systemic inflammation with larger primary tumors or a lower metastatic burden suggest an immune mediated response to reduced tumour bulk as an explanation for the reported survival advantage associated with primary resection. If confirmed, this might define a subgroup of pts who might benefit most from primary resection.

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