Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes

Arvind Raghavan, Rachel L. Ogilvie, Cavan Reilly, Michelle L. Abelson, Shalini Raghavan, Jayprakash Vasdewani, Mitchell Krathwohl, Paul R. Bohjanen

Research output: Contribution to journalReview article

169 Citations (Scopus)

Abstract

We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.

Original languageEnglish (US)
Pages (from-to)5529-5538
Number of pages10
JournalNucleic acids research
Volume30
Issue number24
DOIs
StatePublished - Dec 15 2002

Fingerprint

RNA Stability
Genome
T-Lymphocytes
Anti-Idiotypic Antibodies
RNA
Gene Expression
Cell Surface Receptors
Dactinomycin
Oligonucleotide Array Sequence Analysis
Signal Transduction
Cell Cycle
Transcription Factors
Apoptosis
Cytokines
Technology
Proteins

Cite this

Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. / Raghavan, Arvind; Ogilvie, Rachel L.; Reilly, Cavan; Abelson, Michelle L.; Raghavan, Shalini; Vasdewani, Jayprakash; Krathwohl, Mitchell; Bohjanen, Paul R.

In: Nucleic acids research, Vol. 30, No. 24, 15.12.2002, p. 5529-5538.

Research output: Contribution to journalReview article

Raghavan, A, Ogilvie, RL, Reilly, C, Abelson, ML, Raghavan, S, Vasdewani, J, Krathwohl, M & Bohjanen, PR 2002, 'Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes', Nucleic acids research, vol. 30, no. 24, pp. 5529-5538. https://doi.org/10.1093/nar/gkf682
Raghavan, Arvind ; Ogilvie, Rachel L. ; Reilly, Cavan ; Abelson, Michelle L. ; Raghavan, Shalini ; Vasdewani, Jayprakash ; Krathwohl, Mitchell ; Bohjanen, Paul R. / Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. In: Nucleic acids research. 2002 ; Vol. 30, No. 24. pp. 5529-5538.
@article{9a78376c269142a39aa624d09237b209,
title = "Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes",
abstract = "We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.",
author = "Arvind Raghavan and Ogilvie, {Rachel L.} and Cavan Reilly and Abelson, {Michelle L.} and Shalini Raghavan and Jayprakash Vasdewani and Mitchell Krathwohl and Bohjanen, {Paul R.}",
year = "2002",
month = "12",
day = "15",
doi = "10.1093/nar/gkf682",
language = "English (US)",
volume = "30",
pages = "5529--5538",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "24",

}

TY - JOUR

T1 - Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes

AU - Raghavan, Arvind

AU - Ogilvie, Rachel L.

AU - Reilly, Cavan

AU - Abelson, Michelle L.

AU - Raghavan, Shalini

AU - Vasdewani, Jayprakash

AU - Krathwohl, Mitchell

AU - Bohjanen, Paul R.

PY - 2002/12/15

Y1 - 2002/12/15

N2 - We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.

AB - We used microarray technology to measure mRNA decay rates in resting and activated T lymphocytes in order to better understand the role of mRNA decay in regulating gene expression. Purified human T lymphocytes were stimulated for 3 h with medium alone, with an anti-CD3 antibody, or with a combination of anti-CD3 and anti-CD28 antibodies. Actinomycin D was added to arrest transcription, and total cellular RNA was collected at discrete time points over a 2 h period. RNA from each point was analyzed using Affymetrix oligonucleotide arrays and a first order decay model was used to determine the half-lives of approximately 6000 expressed transcripts. We identified hundreds of short-lived transcripts encoding important regulatory proteins including cytokines, cell surface receptors, signal transduction regulators, transcription factors, cell cycle regulators and regulators of apoptosis. Approximately 100 of these short-lived transcripts contained ARE-like sequences. We also identified numerous transcripts that exhibited stimulus-dependent changes in mRNA decay. In particular, we identified hundreds of transcripts whose steady-state levels were repressed following T cell activation and were either unstable in the resting state or destabilized following cellular activation. Thus, rapid mRNA degradation appears to be an important mechanism for turning gene expression off in an activation-dependent manner.

UR - http://www.scopus.com/inward/record.url?scp=0037115826&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0037115826&partnerID=8YFLogxK

U2 - 10.1093/nar/gkf682

DO - 10.1093/nar/gkf682

M3 - Review article

VL - 30

SP - 5529

EP - 5538

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 24

ER -