Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes (Q24815416)

1

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Pragya Srivastava

2

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Sushanta Kumar Das Sutar

3

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Kaushal Kumar

4

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Dipayan Dasgupta

5

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Gajinder Pal Singh

6

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Vani Brahmachari

7

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Samir K Brahmachari

The nucleosome: from genomic organization to genomic regulation

8

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language of work or name

English

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publication date

2005

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published in

BMC Bioinformatics

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volume

6

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issue

1

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page(s)

126

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cites work

1 reference

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Orchestrated response: a symphony of transcription factors for gene control

7 April 2017

1 reference

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Heterochromatin and epigenetic control of gene expression

7 April 2017

1 reference

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Origin of a substantial fraction of human regulatory sequences from transposable elements

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

The 5'-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Chromatin higher order structure: opening up chromatin for transcription

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Compactness of human housekeeping genes: selection for economy or genomic design?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Improved recombinant gene expression in CHO cells using matrix attachment regions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Spatial organization of gene expression: the active chromatin hub.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Visualization of chromatin domains created by the gypsy insulator of Drosophila

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Human housekeeping genes are compact

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Clustering of housekeeping genes provides a unified model of gene order in the human genome

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Computer prediction of sites associated with various elements of the nuclear matrix

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Control of meiotic recombination and gene expression in yeast by a simple repetitive DNA sequence that excludes nucleosomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Mathematical model to predict regions of chromatin attachment to the nuclear matrix

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Simple repetitive sequences in the genome: structure and functional significance

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Dissection of the locus control function located on the chicken lysozyme gene domain in transgenic mice.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Transcriptional activation. Switched-on chromatin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Acceptor sites for retroviral integrations map near DNase I-hypersensitive sites in chromatin

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Functional analysis of a homopolymeric (dA-dT) element that provides nucleosomal access to yeast and mammalian transcription factors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

A Nuclear Matrix/Scaffold Attachment Region Co-localizes with the Gypsy Retrotransposon Insulator Sequence

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Nucleosomes unfold completely at a transcriptionally active promoter

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

HUMAN GENOME: A Low Number Wins the GeneSweep Pool

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1173084

DNA structural variability as a factor in gene expression and evolution

28 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/15918906

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-6-126

0 references

DBLP publication ID

journals/bmcbi/GanapathiSSKDSBB05

1 reference

DBLP Dataset 2021-01-02