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Article ; Online ; Conference proceedings: Chromatin remodeling and genome stability.

Barkess, Gráinne

2006 Volume 7, Issue 6, Page(s) 319

Abstract: A report on the 12th Tenovus Scotland Symposium 'Stability and Regulation of Genes and Genomes', Glasgow UK, 6-7 April 2006. ...

Abstract	A report on the 12th Tenovus Scotland Symposium 'Stability and Regulation of Genes and Genomes', Glasgow UK, 6-7 April 2006.
MeSH term(s)	Animals ; Chromatin Assembly and Disassembly ; Epigenesis, Genetic ; Genome, Archaeal ; Genome, Fungal ; Genomic Instability ; Humans ; Mutation
Language	English
Publishing date	2006
Publishing country	England
Document type	Congresses
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/gb-2006-7-6-319
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Article ; Online: Chromatin insulator elements: establishing barriers to set heterochromatin boundaries.

Barkess, Gráinne / West, Adam G

Epigenomics

2012 Volume 4, Issue 1, Page(s) 67–80

Abstract: Epigenomic profiling has revealed that substantial portions of genomes in higher eukaryotes are organized into extensive domains of transcriptionally repressive chromatin. The boundaries of repressive chromatin domains can be fixed by DNA elements known ... ...

Abstract	Epigenomic profiling has revealed that substantial portions of genomes in higher eukaryotes are organized into extensive domains of transcriptionally repressive chromatin. The boundaries of repressive chromatin domains can be fixed by DNA elements known as barrier insulators, to both shield neighboring gene expression and to maintain the integrity of chromosomal silencing. Here, we examine the current progress in identifying vertebrate barrier elements and their binding factors. We overview the design of the reporter assays used to define enhancer-blocking and barrier insulators. We look at the mechanisms vertebrate barrier proteins, such as USF1 and VEZF1, employ to counteract Polycomb- and heterochromatin-associated repression. We also undertake a critical analysis of whether CTCF could also act as a barrier protein. There is good evidence that barrier elements in vertebrates can form repressive chromatin domain boundaries. Future studies will determine whether barriers are frequently used to define repressive domain boundaries in vertebrates.
MeSH term(s)	Animals ; CCCTC-Binding Factor ; Chromatin/genetics ; Chromatin/metabolism ; Epigenomics ; Heterochromatin/genetics ; Heterochromatin/metabolism ; Histones/metabolism ; Humans ; Insulator Elements/genetics ; Polycomb-Group Proteins ; Repressor Proteins/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Upstream Stimulatory Factors/genetics ; Upstream Stimulatory Factors/metabolism
Chemical Substances	CCCTC-Binding Factor ; CTCF protein, human ; Chromatin ; Heterochromatin ; Histones ; Polycomb-Group Proteins ; Repressor Proteins ; Transcription Factors ; Upstream Stimulatory Factors
Language	English
Publishing date	2012-02-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2537199-X
ISSN	1750-192X ; 1750-1911
ISSN (online)	1750-192X
ISSN	1750-1911
DOI	10.2217/epi.11.112
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Article: Chromatin looping and the probability of transcription.

Li, Qiliang / Barkess, Gráinne / Qian, Hong

Trends in genetics : TIG

2006 Volume 22, Issue 4, Page(s) 197–202

Abstract: Recent studies of several multigene clusters have shown that gene activation by a remote enhancer is associated with chromatin loop formation. It is not fully understood how a chromatin loop forms in a nucleus or how it is involved in gene regulation. In ...

Abstract	Recent studies of several multigene clusters have shown that gene activation by a remote enhancer is associated with chromatin loop formation. It is not fully understood how a chromatin loop forms in a nucleus or how it is involved in gene regulation. In this article, we propose that the major feature that determines loop formation is the flexibility of chromatin, and that this flexibility is modulated by histone acetylation (and other modifications). Thus, histone modifications will modulate distribution of the preferential looping site in chromatin, which, in turn, determines the probability of interaction between a remote enhancer and the cognate genes. This model can explain gene expression changes in the Hoxd gene cluster and the beta-globin locus.
MeSH term(s)	Acetylation ; Animals ; Chromatin/chemistry ; Chromatin/genetics ; Chromatin/metabolism ; Enhancer Elements, Genetic ; Gene Expression Regulation ; Globins/genetics ; Histones/metabolism ; Homeodomain Proteins/genetics ; Humans ; Locus Control Region ; Models, Genetic ; Multigene Family ; Probability ; Transcription, Genetic ; Transcriptional Activation
Chemical Substances	Chromatin ; Histones ; Homeodomain Proteins ; Globins (9004-22-2)
Language	English
Publishing date	2006-04
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	619240-3
ISSN	1362-4555 ; 0168-9525 ; 0168-9479
ISSN (online)	1362-4555
ISSN	0168-9525 ; 0168-9479
DOI	10.1016/j.tig.2006.02.004
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Article ; Online: The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene.

Barkess, Gráinne / Postnikov, Yuri / Campos, Chrisanne D / Mishra, Shivam / Mohan, Gokula / Verma, Sakshi / Bustin, Michael / West, Katherine L

The Biochemical journal

2012 Volume 442, Issue 3, Page(s) 495–505

Abstract: HMGNs are nucleosome-binding proteins that alter the pattern of histone modifications and modulate the binding of linker histones to chromatin. The HMGN3 family member exists as two splice forms, HMGN3a which is full-length and HMGN3b which lacks the C- ... ...

Abstract	HMGNs are nucleosome-binding proteins that alter the pattern of histone modifications and modulate the binding of linker histones to chromatin. The HMGN3 family member exists as two splice forms, HMGN3a which is full-length and HMGN3b which lacks the C-terminal RD (regulatory domain). In the present study, we have used the Glyt1 (glycine transporter 1) gene as a model system to investigate where HMGN proteins are bound across the locus in vivo, and to study how the two HMGN3 splice variants affect histone modifications and gene expression. We demonstrate that HMGN1, HMGN2, HMGN3a and HMGN3b are bound across the Glyt1 gene locus and surrounding regions, and are not enriched more highly at the promoter or putative enhancer. We conclude that the peaks of H3K4me3 (trimethylated Lys(4) of histone H3) and H3K9ac (acetylated Lys(9) of histone H3) at the active Glyt1a promoter do not play a major role in recruiting HMGN proteins. HMGN3a/b binding leads to increased H3K14 (Lys(14) of histone H3) acetylation and stimulates Glyt1a expression, but does not alter the levels of H3K4me3 or H3K9ac enrichment. Acetylation assays show that HMGN3a stimulates the ability of PCAF [p300/CREB (cAMP-response-element-binding protein)-binding protein-associated factor] to acetylate nucleosomal H3 in vitro, whereas HMGN3b does not. We propose a model where HMGN3a/b-stimulated H3K14 acetylation across the bodies of large genes such as Glyt1 can lead to more efficient transcription elongation and increased mRNA production.
MeSH term(s)	Acetylation ; Animals ; Binding Sites ; Cell Line ; Chromatin/metabolism ; Glycine Plasma Membrane Transport Proteins/genetics ; Glycine Plasma Membrane Transport Proteins/metabolism ; HMGN Proteins/genetics ; HMGN Proteins/metabolism ; Histones/genetics ; Histones/metabolism ; Mice ; Transfection
Chemical Substances	Chromatin ; Glycine Plasma Membrane Transport Proteins ; HMGN Proteins ; HMGN3 protein, mouse ; Histones ; Slc6a9 protein, mouse
Language	English
Publishing date	2012-01-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2969-5
ISSN	1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
ISSN (online)	1470-8728
ISSN	0006-2936 ; 0306-3275 ; 0264-6021
DOI	10.1042/BJ20111502
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Article: Non-coding transcripts far upstream of the epsilon-globin gene are distinctly expressed in human primary tissues and erythroleukemia cell lines.

Xiang, Ping / Fang, Xiangdong / Yin, Wenxuan / Barkess, Grainne / Li, Qiliang

Biochemical and biophysical research communications

2006 Volume 344, Issue 2, Page(s) 623–630

Abstract: Non-coding exons of epsilon-globin mRNA originating within the 236 kb upstream region of the epsilon-globin gene were identified in human primary tissues and K562 cells. One predominant type of upstream epsilon mRNA, which originated in the -76 kb region ...

Abstract	Non-coding exons of epsilon-globin mRNA originating within the 236 kb upstream region of the epsilon-globin gene were identified in human primary tissues and K562 cells. One predominant type of upstream epsilon mRNA, which originated in the -76 kb region 5' to the epsilon gene, was present in human primary tissues, whereas 11 other isoforms were identified in K562 cells. Fragment from the -76 kb region possessed promoter activity and a prominent DNase I hypersensitive site was formed in the region approximately 2 kb 5' to the -76 kb promoter in human fetal liver, but not in K562 cells. The promoter activity in the -236 kb region resided in a retrotransposon in K562 cells. A DNase I hypersensitive site was formed at the -236 kb promoter in K562 cells, but not in human fetal liver. We discussed these results in the context of intergenic transcription and chromatin opening in the beta-globin gene cluster.
MeSH term(s)	Cell Line, Tumor ; Gene Expression Regulation ; Globins/genetics ; Globins/metabolism ; Humans ; Leukemia, Erythroblastic, Acute/genetics ; Leukemia, Erythroblastic, Acute/metabolism ; Open Reading Frames/genetics ; Organ Specificity ; Tissue Distribution ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; Globins (9004-22-2)
Language	English
Publishing date	2006-06-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	205723-2
ISSN	0006-291X ; 0006-291X
ISSN (online)	0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2006.03.189
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Article: Histone acetylation at the human beta-globin locus changes with developmental age.

Yin, Wenxuan / Barkess, Gráinne / Fang, Xiangdong / Xiang, Ping / Cao, Hua / Stamatoyannopoulos, George / Li, Qiliang

Blood

2007 Volume 110, Issue 12, Page(s) 4101–4107

Abstract: To delineate the relationship between epigenetic modifications and hemoglobin switching, we compared the pattern of histone acetylation and pol II binding across the beta-globin locus at fetal and adult stages of human development. To make this ... ...

Abstract	To delineate the relationship between epigenetic modifications and hemoglobin switching, we compared the pattern of histone acetylation and pol II binding across the beta-globin locus at fetal and adult stages of human development. To make this comparison possible, we introduced an external control into experimental samples in chromatin immunoprecipitation (ChIP) assays. Using this common standard, we found that the locus control region (LCR) was acetylated to the same level at all stages, whereas acetylation levels at the individual gene regions correlated with the state of transcription. In the active genes, the promoters were less acetylated compared with the coding regions. Furthermore, all globin promoters were acetylated to a similar level irrespective of the state of transcription. However, after correction for the loss of nucleosomes, the level of acetylation per histone at the active gamma and beta promoters was 5- to 7-fold greater than that at the inactive epsilon promoter. Although the histone acetylation level within the LCR was developmentally stable, pol II binding in fetal erythroblasts was 2- to 3-fold greater than that in adult erythroblasts. These results demonstrate that dynamic changes in histone acetylation and pol II take place as the human beta-globin gene region undergoes its developmental switches.
MeSH term(s)	Acetylation ; Adult ; Aging/physiology ; Chromatin Immunoprecipitation ; DNA Polymerase II/metabolism ; Erythroblasts/cytology ; Erythroblasts/metabolism ; Fetus/cytology ; Fetus/metabolism ; Globins/biosynthesis ; Globins/genetics ; Histones/metabolism ; Humans ; Locus Control Region/physiology ; Nucleosomes/genetics ; Nucleosomes/metabolism ; Promoter Regions, Genetic/physiology ; Quantitative Trait Loci/physiology ; Transcription, Genetic/physiology
Chemical Substances	Histones ; Nucleosomes ; Globins (9004-22-2) ; DNA Polymerase II (EC 2.7.7.7)
Language	English
Publishing date	2007-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	80069-7
ISSN	1528-0020 ; 0006-4971
ISSN (online)	1528-0020
ISSN	0006-4971
DOI	10.1182/blood-2007-05-091256
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Article ; Online: Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells.

Jiwaji, Meesbah / Sandison, Mairi E / Reboud, Julien / Stevenson, Ross / Daly, Rónán / Barkess, Gráinne / Faulds, Karen / Kolch, Walter / Graham, Duncan / Girolami, Mark A / Cooper, Jonathan M / Pitt, Andrew R

PloS one

2014 Volume 9, Issue 6, Page(s) e99458

Abstract: Introduction: Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of ... ...

Abstract	Introduction: Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell. Methods: In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis. Findings: We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles. Conclusions: The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein.
MeSH term(s)	DNA, Single-Stranded/pharmacology ; Gene Knockdown Techniques/methods ; Gold ; HeLa Cells ; Humans ; Metal Nanoparticles/chemistry ; Metal Nanoparticles/ultrastructure ; Metallothionein/genetics ; Metallothionein/metabolism ; Oligonucleotides, Antisense/pharmacology ; RNA, Messenger/analysis ; RNA, Small Interfering/pharmacology ; Transfection
Chemical Substances	DNA, Single-Stranded ; MT2A protein, human ; Oligonucleotides, Antisense ; RNA, Messenger ; RNA, Small Interfering ; Gold (7440-57-5) ; Metallothionein (9038-94-2)
Language	English
Publishing date	2014-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0099458
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Article ; Online: Quantification of functionalised gold nanoparticle-targeted knockdown of gene expression in HeLa cells.

Meesbah Jiwaji / Mairi E Sandison / Julien Reboud / Ross Stevenson / Rónán Daly / Gráinne Barkess / Karen Faulds / Walter Kolch / Duncan Graham / Mark A Girolami / Jonathan M Cooper / Andrew R Pitt

PLoS ONE, Vol 9, Iss 6, p e

2014 Volume 99458

Abstract: Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide ... ...

Abstract	Gene therapy continues to grow as an important area of research, primarily because of its potential in the treatment of disease. One significant area where there is a need for better understanding is in improving the efficiency of oligonucleotide delivery to the cell and indeed, following delivery, the characterization of the effects on the cell.In this report, we compare different transfection reagents as delivery vehicles for gold nanoparticles functionalized with DNA oligonucleotides, and quantify their relative transfection efficiencies. The inhibitory properties of small interfering RNA (siRNA), single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA) sequences targeted to human metallothionein hMT-IIa are also quantified in HeLa cells. Techniques used in this study include fluorescence and confocal microscopy, qPCR and Western analysis.We show that the use of transfection reagents does significantly increase nanoparticle transfection efficiencies. Furthermore, siRNA, ssRNA and ssDNA sequences all have comparable inhibitory properties to ssDNA sequences immobilized onto gold nanoparticles. We also show that functionalized gold nanoparticles can co-localize with autophagosomes and illustrate other factors that can affect data collection and interpretation when performing studies with functionalized nanoparticles.The desired outcome for biological knockdown studies is the efficient reduction of a specific target; which we demonstrate by using ssDNA inhibitory sequences targeted to human metallothionein IIa gene transcripts that result in the knockdown of both the mRNA transcript and the target protein.
Keywords	Medicine ; R ; Science ; Q
Subject code	612 ; 500
Language	English
Publishing date	2014-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article: Transcriptional potentials of the beta-like globin genes at different developmental stages in transgenic mice and hemoglobin switching.

Li, Qiliang / Han, Hemei / Ye, Xin / Stafford, Mary / Barkess, Grainne / Stamatoyannopoulos, George

Blood cells, molecules & diseases

2004 Volume 33, Issue 3, Page(s) 318–325

Abstract: Developmental-stage-specific regulation and physiological levels of expression of the globin genes can be recaptured in transgenic mice carrying a YAC/BAC- or cosmid-based construct. By contrast, proper developmental regulation and high-level expression ... ...

Abstract	Developmental-stage-specific regulation and physiological levels of expression of the globin genes can be recaptured in transgenic mice carrying a YAC/BAC- or cosmid-based construct. By contrast, proper developmental regulation and high-level expression cannot be achieved coordinately in transgenic mice carrying a more manipulated construct, such as a plasmid-based globin gene construct. These differences provide us an opportunity to define the requirements for a developmentally regulated, high-level expression of the globin genes in vivo. To achieve this, as a first step, we studied maximum transcriptional potentials of the beta-globin genes at various stages of development. microLCR-enhanced expression of the epsilon-, gamma-, and beta-globin genes driven by their minimal promoters was estimated and compared with that in betaYAC transgenic mice. Quantitative measurements of steady state mRNA levels of the epsilon-, gamma-, and beta-globin genes showed that the microLCR was able to enhance expression of each beta-like globin gene to levels similar to those in the betaYAC mice. Moreover, transcriptional potentials of each globin gene were unchanged during the entire course of development. These observations indicate that the highest level of expression of the globin genes can be achieved in both embryonic and definitive erythropoiesis regardless of developmental specificity of the genes. This finding implies that transcription suppression is the major mechanism of the developmental specificity of the expression of the beta-like globin genes.
MeSH term(s)	Animals ; Erythropoiesis/genetics ; Erythropoiesis/physiology ; Gene Expression Regulation/genetics ; Gene Expression Regulation/physiology ; Genes, Switch/genetics ; Hemoglobins/biosynthesis ; Hemoglobins/genetics ; Locus Control Region/genetics ; Mice ; Mice, Transgenic ; Promoter Regions, Genetic ; Transcription, Genetic ; Transgenes/genetics
Chemical Substances	Hemoglobins
Language	English
Publishing date	2004-11
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	1237083-6
ISSN	1096-0961 ; 1079-9796
ISSN (online)	1096-0961
ISSN	1079-9796
DOI	10.1016/j.bcmd.2004.06.005
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Article ; Online: Unique reporter-based sensor platforms to monitor signalling in cells.

Jiwaji, Meesbah / Daly, Rónán / Gibriel, Abdullah / Barkess, Gráinne / McLean, Pauline / Yang, Jingli / Pansare, Kshama / Cumming, Sarah / McLauchlan, Alisha / Kamola, Piotr J / Bhutta, Musab S / West, Adam G / West, Katherine L / Kolch, Walter / Girolami, Mark A / Pitt, Andrew R

PloS one

2012 Volume 7, Issue 11, Page(s) e50521

Abstract: Introduction: In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell ... ...

Abstract	Introduction: In recent years much progress has been made in the development of tools for systems biology to study the levels of mRNA and protein, and their interactions within cells. However, few multiplexed methodologies are available to study cell signalling directly at the transcription factor level. Methods: Here we describe a sensitive, plasmid-based RNA reporter methodology to study transcription factor activation in mammalian cells, and apply this technology to profiling 60 transcription factors in parallel. The methodology uses two robust and easily accessible detection platforms; quantitative real-time PCR for quantitative analysis and DNA microarrays for parallel, higher throughput analysis. Findings: We test the specificity of the detection platforms with ten inducers and independently validate the transcription factor activation. Conclusions: We report a methodology for the multiplexed study of transcription factor activation in mammalian cells that is direct and not theoretically limited by the number of available reporters.
MeSH term(s)	Blotting, Western ; Cadmium Chloride/pharmacology ; Cell Line ; Colforsin/pharmacology ; Dexamethasone/pharmacology ; Humans ; Oligonucleotide Array Sequence Analysis ; Plasmids/genetics ; Real-Time Polymerase Chain Reaction ; Systems Biology/methods ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Transcription Factors ; Colforsin (1F7A44V6OU) ; Dexamethasone (7S5I7G3JQL) ; Cadmium Chloride (J6K4F9V3BA)
Language	English
Publishing date	2012-11-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0050521
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