Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer

Zhi Mei Liu, Julia B. George-Raizen, Shuyu Li, Katherine C. Meyers, Mee Young Chang, William T. Garrard

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

To identify new regulatory elements within the mouse Igκ locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Igκ transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the Vκ gene closest to the Jκ region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a Vκ gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Igκ gene locus, including NF-κB and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.

Original languageEnglish (US)
Pages (from-to)32640-32649
Number of pages10
JournalJournal of Biological Chemistry
Volume277
Issue number36
DOIs
StatePublished - Sep 6 2002

Fingerprint

Immunoglobulin Genes
B-Lymphoid Precursor Cells
Chromatin
Transfection
Genes
E-Box Elements
Yeast Artificial Chromosomes
Plasmacytoma
Deoxyribonuclease I
Assays
Transgenes
Cells
Introns
B-Lymphocytes
Chromosomes
Cell Line
Yeast
DNA

ASJC Scopus subject areas

  • Biochemistry

Cite this

Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer. / Liu, Zhi Mei; George-Raizen, Julia B.; Li, Shuyu; Meyers, Katherine C.; Chang, Mee Young; Garrard, William T.

In: Journal of Biological Chemistry, Vol. 277, No. 36, 06.09.2002, p. 32640-32649.

Research output: Contribution to journalArticle

Liu, Zhi Mei ; George-Raizen, Julia B. ; Li, Shuyu ; Meyers, Katherine C. ; Chang, Mee Young ; Garrard, William T. / Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer. In: Journal of Biological Chemistry. 2002 ; Vol. 277, No. 36. pp. 32640-32649.
@article{735f4fe20dff4f9da9ebe1f4bcc33dda,
title = "Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer",
abstract = "To identify new regulatory elements within the mouse Igκ locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Igκ transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the Vκ gene closest to the Jκ region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a Vκ gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Igκ gene locus, including NF-κB and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.",
author = "Liu, {Zhi Mei} and George-Raizen, {Julia B.} and Shuyu Li and Meyers, {Katherine C.} and Chang, {Mee Young} and Garrard, {William T.}",
year = "2002",
month = "9",
day = "6",
doi = "10.1074/jbc.M204065200",
language = "English (US)",
volume = "277",
pages = "32640--32649",
journal = "Journal of Biological Chemistry",
issn = "0021-9258",
publisher = "American Society for Biochemistry and Molecular Biology Inc.",
number = "36",

}

TY - JOUR

T1 - Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer

AU - Liu, Zhi Mei

AU - George-Raizen, Julia B.

AU - Li, Shuyu

AU - Meyers, Katherine C.

AU - Chang, Mee Young

AU - Garrard, William T.

PY - 2002/9/6

Y1 - 2002/9/6

N2 - To identify new regulatory elements within the mouse Igκ locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Igκ transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the Vκ gene closest to the Jκ region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a Vκ gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Igκ gene locus, including NF-κB and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.

AB - To identify new regulatory elements within the mouse Igκ locus, we have mapped DNase I hypersensitive sites (HSs) in the chromatin of B cell lines arrested at different stages of differentiation. We have focused on two regions encompassing 50 kilobases suspected to contain new regulatory elements based on our previous high level expression results with yeast artificial chromosome-based mouse Igκ transgenes. This approach has revealed a cluster of HSs within the 18-kilobase intervening sequence, which we cloned and sequenced in its entirety, between the Vκ gene closest to the Jκ region. These HSs exhibit pro/pre-B cell-specific transcriptional silencing of a Vκ gene promoter in transient transfection assays. We also identified a plasmacytoma cell-specific HS in the far downstream region of the locus, which in analogous transient transfection assays proved to be a powerful transcriptional enhancer. Deletional analyses reveal that for each element multiple DNA segments cooperate to achieve either silencing or enhancement. The enhancer sequence is conserved in the human Igκ gene locus, including NF-κB and E-box sites that are important for the activity. In summary, our results pinpoint the locations of presumptive regulatory elements for future knockout studies to define their functional roles in the native locus.

UR - http://www.scopus.com/inward/record.url?scp=0037031831&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0037031831&partnerID=8YFLogxK

U2 - 10.1074/jbc.M204065200

DO - 10.1074/jbc.M204065200

M3 - Article

C2 - 12080064

AN - SCOPUS:0037031831

VL - 277

SP - 32640

EP - 32649

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

SN - 0021-9258

IS - 36

ER -