49 results match your criteria centered intergenic

The CADM1 tumor suppressor gene is a major candidate gene in MDS with deletion of the long arm of chromosome 11.

Blood Adv 2021 Oct 12. Epub 2021 Oct 12.

Belgian Cancer Registry, Brussels, Belgium.

Myelodysplastic syndromes (MDS) represent a heterogeneous group of clonal hematopoietic stem-cell disorders characterized by ineffective hematopoiesis leading to peripheral cytopenias and in a substantial proportion of cases to acute myeloid leukemia. The deletion of the long arm of chromosome 11, del(11q), is a rare but recurrent clonal event in MDS. Here, we detail the largest series of 113 cases of MDS and myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN) harboring a del(11q) analyzed at clinical, cytological, cytogenetic and molecular levels. Read More

View Article and Full-Text PDF
October 2021

"Protein aggregates" contain RNA and DNA, entrapped by misfolded proteins but largely rescued by slowing translational elongation.

Aging Cell 2021 05 31;20(5):e13326. Epub 2021 Mar 31.

Central Arkansas Veterans Healthcare System, Little Rock, AR, USA.

All neurodegenerative diseases feature aggregates, which usually contain disease-specific diagnostic proteins; non-protein constituents, however, have rarely been explored. Aggregates from SY5Y-APP neuroblastoma, a cell model of familial Alzheimer's disease, were crosslinked and sequences of linked peptides identified. We constructed a normalized "contactome" comprising 11 subnetworks, centered on 24 high-connectivity hubs. Read More

View Article and Full-Text PDF

Novel Alzheimer Disease Risk Loci and Pathways in African American Individuals Using the African Genome Resources Panel: A Meta-analysis.

JAMA Neurol 2021 01;78(1):102-113

Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, New York.

Importance: Compared with non-Hispanic White individuals, African American individuals from the same community are approximately twice as likely to develop Alzheimer disease. Despite this disparity, the largest Alzheimer disease genome-wide association studies to date have been conducted in non-Hispanic White individuals. In the largest association analyses of Alzheimer disease in African American individuals, ABCA7, TREM2, and an intergenic locus at 5q35 were previously implicated. Read More

View Article and Full-Text PDF
January 2021

UNBRANCHED3 Expression and Inflorescence Development is Mediated by UNBRANCHED2 and the Distal Enhancer, KRN4, in Maize.

PLoS Genet 2020 04 24;16(4):e1008764. Epub 2020 Apr 24.

National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China.

Enhancers are cis-acting DNA segments with the ability to increase target gene expression. They show high sensitivity to DNase and contain specific DNA elements in an open chromatin state that allows the binding of transcription factors (TFs). While numerous enhancers are annotated in the maize genome, few have been characterized genetically. Read More

View Article and Full-Text PDF

Phylogeography of Begonia luzhaiensis suggests both natural and anthropogenic causes for the marked population genetic structure.

Bot Stud 2019 Sep 6;60(1):20. Epub 2019 Sep 6.

Research Museum and Herbarium (HAST), Biodiversity Research Center, Academia Sinica, Taipei, Taiwan.

Background: Sino-Vietnamese limestone karsts (SVLK) are a biodiversity hotspot rich in endemic plant species associated with caves and cave-like microhabitats. Based on phylogenetic studies of Begonia sect. Coelocentrum, a species-rich and characteristic SVLK clade, geographic isolation caused by extensive and continuous karstification was proposed as the major driving force triggering population diversification and geographic speciation. Read More

View Article and Full-Text PDF
September 2019

Bioinformatics analysis of the interactions among lncRNA, miRNA and mRNA expression, genetic mutations and epigenetic modifications in hepatocellular carcinoma.

Mol Med Rep 2019 Feb 5;19(2):1356-1364. Epub 2018 Dec 5.

Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China.

The present study aimed to investigate the regulatory networks involving long noncoding RNA (lncRNA), microRNA (miRNA), mRNA, genetic mutations and epigenetic modifications in hepatocellular carcinoma (HCC) by analyzing datasets from The Cancer Genome Atlas (TCGA) database. TCGA was mined, and miRNAs, lncRNAs and mRNAs that were differentially expressed in HCC were identified using R software. A gene regulatory network was constructed using Cytoscape software. Read More

View Article and Full-Text PDF
February 2019

Insights into the genetics of blood pressure in black South African individuals: the Birth to Twenty cohort.

BMC Med Genomics 2018 01 17;11(1). Epub 2018 Jan 17.

School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, Johannesburg, South Africa.

Background: Cardiovascular diseases (CVDs) are the leading cause of non-communicable disease deaths globally, with hypertension being a major risk factor contributing to CVDs. Blood pressure is a heritable trait, with relatively few genetic studies having been performed in Africans. This study aimed to identify genetic variants associated with variance in systolic (SBP) and diastolic (DBP) blood pressure in black South Africans. Read More

View Article and Full-Text PDF
January 2018

Genome-wide DNase hypersensitivity, and occupancy of RUNX2 and CTCF reveal a highly dynamic gene regulome during MC3T3 pre-osteoblast differentiation.

PLoS One 2017 27;12(11):e0188056. Epub 2017 Nov 27.

Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont, United States of America.

The ability to discover regulatory sequences that control bone-related genes during development has been greatly improved by massively parallel sequencing methodologies. To expand our understanding of cis-regulatory regions critical to the control of gene expression during osteoblastogenesis, we probed the presence of open chromatin states across the osteoblast genome using global DNase hypersensitivity (DHS) mapping. Our profiling of MC3T3 mouse pre-osteoblasts during differentiation has identified more than 224,000 unique DHS sites. Read More

View Article and Full-Text PDF
December 2017

CRISPR/Cas9-Mediated Scanning for Regulatory Elements Required for HPRT1 Expression via Thousands of Large, Programmed Genomic Deletions.

Am J Hum Genet 2017 Aug 14;101(2):192-205. Epub 2017 Jul 14.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA. Electronic address:

The extent to which non-coding mutations contribute to Mendelian disease is a major unknown in human genetics. Relatedly, the vast majority of candidate regulatory elements have yet to be functionally validated. Here, we describe a CRISPR-based system that uses pairs of guide RNAs (gRNAs) to program thousands of kilobase-scale deletions that deeply scan across a targeted region in a tiling fashion ("ScanDel"). Read More

View Article and Full-Text PDF

Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data.

Front Neurol 2016 18;7:168. Epub 2016 Oct 18.

Center for Computational Science, University of Miami Miller School of Medicine , Miami, FL , USA.

Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Read More

View Article and Full-Text PDF
October 2016

Major and minor crRNA annealing sites facilitate low stringency DNA protospacer binding prior to Type I-A CRISPR-Cas interference in Sulfolobus.

RNA Biol 2016 Nov 12;13(11):1166-1173. Epub 2016 Sep 12.

a Archaea Centre, Department of Biology , Copenhagen University , Copenhagen N , Denmark.

The stringency of crRNA-protospacer DNA base pair matching required for effective CRISPR-Cas interference is relatively low in crenarchaeal Sulfolobus species in contrast to that required in some bacteria. To understand its biological significance we studied crRNA-protospacer interactions in Sulfolobus islandicus REY15A which carries multiple, and functionally diverse, interference complexes. A range of mismatches were introduced into a vector-borne protospacer that was identical to spacer 1 of CRISPR locus 2, with a cognate CCN PAM sequence. Read More

View Article and Full-Text PDF
November 2016

Pulling the sting out of nettle systematics - A comprehensive phylogeny of the genus Urtica L. (Urticaceae).

Mol Phylogenet Evol 2016 09 19;102:9-19. Epub 2016 May 19.

Nees-Institut für Biodiversität der Pflanzen, Rheinische Friedrich-Wilhelms-Universität, Meckenheimer Allee 170, D-53115 Bonn, Germany. Electronic address:

The genus Urtica L. is subcosmopolitan, found on all continents (except Antarctica) and most extratropical islands and ranges from Alaska to Patagonia, Spitzbergen to the Cape and Camtschatka to the subantarctic islands. However, throughout its geographical range morphologically nearly indistinguishable species are found alongside morphologically quite disparate species, with the overall diversity of morphological characters extremely limited. Read More

View Article and Full-Text PDF
September 2016

Dynamic reprogramming of DNA methylation in SETD2-deregulated renal cell carcinoma.

Oncotarget 2016 Jan;7(2):1927-46

Department of Molecular Pharmacology and Experimental Therapeutics and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, MN, USA.

Clear cell renal cell carcinomas (ccRCCs) harbor frequent mutations in epigenetic modifiers including SETD2, the H3K36me3 writer. We profiled DNA methylation (5mC) across the genome in cell line-based models of SETD2 inactivation and SETD2 mutant primary tumors because 5mC has been linked to H3K36me3 and is therapeutically targetable. SETD2 depleted cell line models (long-term and acute) exhibited a DNA hypermethylation phenotype coinciding with ectopic gains in H3K36me3 centered across intergenic regions adjacent to low expressing genes, which became upregulated upon dysregulation of the epigenome. Read More

View Article and Full-Text PDF
January 2016

The Ino80 complex prevents invasion of euchromatin into silent chromatin.

Genes Dev 2015 Feb;29(4):350-5

Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA;

Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Read More

View Article and Full-Text PDF
February 2015

Non-coding RNA: what is functional and what is junk?

Front Genet 2015 26;6. Epub 2015 Jan 26.

Department of Biochemistry, University of Toronto Toronto, ON, Canada.

The genomes of large multicellular eukaryotes are mostly comprised of non-protein coding DNA. Although there has been much agreement that a small fraction of these genomes has important biological functions, there has been much debate as to whether the rest contributes to development and/or homeostasis. Much of the speculation has centered on the genomic regions that are transcribed into RNA at some low level. Read More

View Article and Full-Text PDF
February 2015

BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

BMC Bioinformatics 2014 Jul 3;15:233. Epub 2014 Jul 3.

Department of Biological Sciences, Hunter College, The City University of New York, 10065 New York, NY, USA.

Background: The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. Read More

View Article and Full-Text PDF

RNA sequencing of the exercise transcriptome in equine athletes.

PLoS One 2013 31;8(12):e83504. Epub 2013 Dec 31.

Department of Pathology, Diagnostic and Veterinary Clinic - Sport Horse Research Centre, University of Perugia, Perugia, Italy.

The horse is an optimal model organism for studying the genomic response to exercise-induced stress, due to its natural aptitude for athletic performance and the relative homogeneity of its genetic and environmental backgrounds. Here, we applied RNA-sequencing analysis through the use of SOLiD technology in an experimental framework centered on exercise-induced stress during endurance races in equine athletes. We monitored the transcriptional landscape by comparing gene expression levels between animals at rest and after competition. Read More

View Article and Full-Text PDF

Analyses of RANK and RANKL in the post-GWAS context: functional evidence of vitamin D stimulation through a RANKL distal region.

J Bone Miner Res 2013 Dec;28(12):2550-60

URFOA, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques), Red Temática de Investigación Cooperativa en Envejecimiento y Fragilidad (RETICEF), Barcelona, Spain.

Over the past decade, many genome-wide association studies (GWAs) and meta-analyses have identified genes and regions involved in osteoporotic phenotypes. Nevertheless, the large majority of these results were not tested at any functional level. GWA-associated single-nucleotide polymorphisms (SNPs) near candidate genes such as RANK and RANKL suggest that these SNPs and/or other variants nearby may be involved in bone phenotype determination. Read More

View Article and Full-Text PDF
December 2013

Homologous chromosomes move and rapidly initiate contact at the sites of double-strand breaks in genes in G₀-phase human cells.

Cell Cycle 2013 Feb 31;12(4):547-52. Epub 2013 Jan 31.

Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA, USA.

We recently reported that homologous chromosomes make contact at the sites of double-strand breaks (DSBs) induced by ionizing radiation (IR) and the restriction endonuclease I-PpoI in G₀/G₁-phase somatic human cells. The contact involves short segments of homologous chromosomes and is centered on a DSB that occurs in a gene; contact does not occur at a DSB in intergenic DNA. Contact between homologous chromosomes is abrogated by inhibition of transcription and requires the kinase activity of ATM, but not DNA-PK. Read More

View Article and Full-Text PDF
February 2013

Homologous chromosomes make contact at the sites of double-strand breaks in genes in somatic G0/G1-phase human cells.

Proc Natl Acad Sci U S A 2012 Jun 29;109(24):9454-9. Epub 2012 May 29.

Department of Pathology and Laboratory Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA.

Double-strand DNA breaks (DSBs) are continuously induced in cells by endogenously generated free radicals and exogenous genotoxic agents such as ionizing radiation. DSBs activate the kinase activity in sensor proteins such as ATM and DNA-PK, initiating a complex DNA damage response that coordinates various DNA repair pathways to restore genomic integrity. In this study, we report the unexpected finding that homologous chromosomes contact each other at the sites of DSBs induced by either radiation or the endonuclease I-PpoI in human somatic cells. Read More

View Article and Full-Text PDF

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Cell 2012 Jan;148(1-2):84-98

Genome Institute of Singapore, Singapore 138672, Republic of Singapore.

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Read More

View Article and Full-Text PDF
January 2012

Cooperative regulation of the Vibrio vulnificus nan gene cluster by NanR protein, cAMP receptor protein, and N-acetylmannosamine 6-phosphate.

J Biol Chem 2011 Nov 28;286(47):40889-99. Epub 2011 Sep 28.

National Research Laboratory of Molecular Microbiology and Toxicology, Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea.

The nan cluster of Vibrio vulnificus, a food-borne pathogen, consists of two divergently transcribed operons, nanT(PSL)AR and nanEK nagA, required for transport and catabolism of N-acetylneuraminic acid (Neu5Ac). A mutation of nanR abolished the extensive lag phase observed for the bacteria growing on Neu5Ac and increased transcription of nanT(P) and nanE, suggesting that NanR is a transcriptional repressor of both nan operons. Intracellular accumulation of Neu5Ac was dependent on the carbon source, implying that the nan operons are also subject to catabolite repression. Read More

View Article and Full-Text PDF
November 2011

Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens.

Proc Natl Acad Sci U S A 2011 Feb 7;108(7):3035-40. Epub 2011 Feb 7.

Fishberg Department of Neuroscience, Mount Sinai School of Medicine, New York, NY 10029, USA.

Repeated cocaine exposure induces persistent alterations in genome-wide transcriptional regulatory networks, chromatin remodeling activity and, ultimately, gene expression profiles in the brain's reward circuitry. Virtually all previous investigations have centered on drug-mediated effects occurring throughout active euchromatic regions of the genome, with very little known concerning the impact of cocaine exposure on the regulation and maintenance of heterochromatin in adult brain. Here, we report that cocaine dramatically and dynamically alters heterochromatic histone H3 lysine 9 trimethylation (H3K9me3) in the nucleus accumbens (NAc), a key brain reward region. Read More

View Article and Full-Text PDF
February 2011

Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.

Mycologia 2010 Mar-Apr;102(2):291-304

Area de Biodiversidad y Conservación, Universidad Rey Juan Carlos, C/ Tulipán s/n, 28933 Móstoles, Madrid, Spain.

The current classification of what used to be called Catapyrenium comprises eight genera belonging to distinct lineages in the Verrucariaceae. Previous phylogenetic studies have shown that the redefined genus Catapyrenium (Catapyrenium s. str. Read More

View Article and Full-Text PDF

Upstream curved sequences in E. coli are related to the regulation of transcription initiation.

Comput Biol Chem 2009 Aug 7;33(4):275-82. Epub 2009 Jul 7.

Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 31905, Israel.

The advancement in Escherichia coli genome research has made the information regarding transcription start sites of many genes available. A study relying on the availability of transcription start locations was performed. The first question addressed was what an average DNA curvature profile upstream of genes would look like when these genes are aligned by transcription start sites in comparison to alignment by translation start sites. Read More

View Article and Full-Text PDF

Interspliced transcription chimeras: neglected pathological mechanism infiltrating gene accession queries?

J Biomed Inform 2009 Apr 13;42(2):382-9. Epub 2008 Nov 13.

Institute of Medical Technology, University of Tampere, Finland.

Over half of the DNA of mammalian genomes is transcribed, and one of the emerging enigmas in the field of RNA research is intergenic splicing or transcription induced chimerism. We argue that fused low-copy-number transcripts constitute neglected pathological mechanism akin to copy number variation, due to loss of stoichiometric subunit ratios in protein complexes. An obstacle for transcriptomics meta-analysis of published microarrays is the traditional nomenclature of merged transcript neighbors under same accession codes. Read More

View Article and Full-Text PDF

Triatominae-Trypanosoma cruzi/T. rangeli: Vector-parasite interactions.

Acta Trop 2009 May-Jun;110(2-3):137-47. Epub 2008 Oct 15.

Universidad del Tolima, Barrio Santa Helena, Ibagué, Colombia.

Of the currently known 140 species in the family Reduviidae, subfamily Triatominae, those which are most important as vectors of the aetiologic agent of Chagas disease, Trypanosoma cruzi, belong to the tribes Triatomini and Rhodniini. The latter not only transmit T. cruzi but also Trypanosoma rangeli, which is considered apathogenic for the mammalian host but can be pathogenic for the vectors. Read More

View Article and Full-Text PDF

CoGemiR: a comparative genomics microRNA database.

BMC Genomics 2008 Oct 6;9:457. Epub 2008 Oct 6.

TIGEM Telethon Institute of Genetics and Medicine, Via Pietro Castellino 111, 80131 Naples Italy.

Background: MicroRNAs are small highly conserved non-coding RNAs which play an important role in regulating gene expression by binding the 3'UTR of target mRNAs. The majority of microRNAs are localized within other transcriptional units (host genes) and are co-expressed with them, which strongly suggests that microRNAs and corresponding host genes use the same promoter and other expression control elements. The remaining fraction of microRNAs is intergenic and is endowed with an independent regulatory region. Read More

View Article and Full-Text PDF
October 2008

Phenotype-defining functions of multiple non-coding RNA pathways.

Cell Cycle 2008 Jun 19;7(11):1630-9. Epub 2008 Mar 19.

Translational and Functional Genomics Laboratory, Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York 12208, USA.

One of the surprising revelations of the initial stage of the ENCODE project was the conclusion that more than 90% of human genome is transcribed. A major component of this vast transcriptional output is represented by highly heterogeneous families of transcripts defined as short non-coding RNAs (sncRNAs) with no or limited protein-coding potentials. Here we carried out the sequence homolog profiling of the 2301 human sncRNAs with confirmed sequence identities [including 943 transintrons; 235 expressed distal intergenic sequences (EDIS); and 1005 piRNAs] as well as >1000 hypothetical transcripts derived from allelic variants of human SNP sequences with strong associations to human diseases or linkages to phenotypes established in genome-wide association studies. Read More

View Article and Full-Text PDF