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A transcription factor pulse can prime chromatin for heritable transcriptional memory

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE72488 | GEO | 2016/12/21

SECONDARY ACCESSION(S): PRJNA294144

REPOSITORIES: GEO

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A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory.

Project description:Short-term and long-term transcriptional memory is the phenomenon whereby the kinetics or magnitude of gene induction is enhanced following a prior induction period. Short-term memory persists within one cell generation or in postmitotic cells, while long-term memory can survive multiple rounds of cell division. We have developed a tissue culture model to study the epigenetic basis for long-term transcriptional memory (LTTM) and subsequently used this model to better understand the epigenetic mechanisms that enable heritable memory of temporary stimuli. We find that a pulse of transcription factor CCAAT/enhancer-binding protein alpha (C/EBPα) induces LTTM on a subset of target genes that survives nine cell divisions. The chromatin landscape at genes that acquire LTTM is more repressed than at those genes that do not exhibit memory, akin to a latent state. We show through chromatin immunoprecipitation (ChIP) and chemical inhibitor studies that RNA polymerase II (Pol II) elongation is important for establishing memory in this model but that Pol II itself is not retained as part of the memory mechanism. More generally, our work reveals that a transcription factor involved in lineage specification can induce LTTM and that failure to rerepress chromatin is one epigenetic mechanism underlying transcriptional memory.

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A transcription factor pulse can prime chromatin for heritable transcriptional memory [RNAseq]

Project description:To indentify genes displaying long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed RNAseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any genes respond more/faster in a second stimulation than in the first.

2016-12-21 | GSE72487 | GEO

A transcription factor pulse can prime chromatin for heritable transcriptional memory [ChIPseq]

Project description:To investigate the epigenetic control of long-term transcriptionnal memory (LTTM) we used a trans-differentiation system where Bcell are reprogramed into macrophages upon induction of the transcription factor Cebpa. We performed ChIPseq in untreated Bcells, after 12h of Cebpa induction and after 6days of “wash” of Cebpa, to see if any proteins/histone marks are retained.

2016-12-21 | GSE72486 | GEO

A transcription factor pulse can prime chromatin for heritable transcriptional memory

Project description:A transcription factor pulse can prime chromatin for heritable transcriptional memory

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Heritable chromatin structure: mapping "memory" in histones H3 and H4.

Project description:Telomeric position effect in Saccharomyces cerevisiae is a chromatin-mediated phenomenon in which telomere proximal genes are repressed (silenced) in a heritable, but reversible, fashion. Once a transcriptional state (active or silenced) is established, however, there is a strong tendency for that state to be propagated. Twenty-five years ago, H. Weintraub and colleagues suggested that such heritability could be mediated by posttranslational modification of chromatin [Weintraub, H., Flint, S. J., Leffak, I. M., Groudine, M. & Grainger, R. M. (1977) Cold Spring Harbor Symp. Quant. Biol. 42, 401-407]. To identify potential sites within the chromatin that might act as sources of "memory" for the heritable transmission, we performed a genetic screen to isolate mutant alleles of the histones H3 and H4 genes that would "lock" telomeric marker genes into a silenced state. We identified mutations in the NH(2)-terminal tail and core of both histones; most of the amino acid changes mapped adjacent to lysines that are known sites of acetylation or methylation. We developed a method using MS to quantify the level of acetylation at each lysine within the histone H4 NH(2)-terminal tail in these mutants. We discovered that each of these mutants had a dramatic reduction in the level of acetylation at lysine 12 within the histone H4 tail. We propose that this lysine serves as a "memory mark" for propagating the expression state of a telomeric gene: when it is unacetylated, silent chromatin will be inherited; when it is acetylated an active state will be inherited.

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HP1BP3, a chromatin retention factor for co-transcriptional microRNA processing

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-07-24 | E-GEOD-77856 | biostudies-arrayexpress

Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-02-02 | GSE211610 | GEO

Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Epigenetic Memory Is Not Intrinsic To Transcription Factor-Mediated Reprogramming

Project description:This SuperSeries is composed of the SubSeries listed below.