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Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression

Overview of attention for article published in BMC Genomics, January 2015
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  • Above-average Attention Score compared to outputs of the same age (53rd percentile)
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6 tweeters

Citations

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30 Dimensions

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58 Mendeley
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Title
Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression
Published in
BMC Genomics, January 2015
DOI 10.1186/1471-2164-16-s5-s5
Pubmed ID
Authors

Lucia L Peixoto, Mathieu E Wimmer, Shane G Poplawski, Jennifer C Tudor, Charles A Kenworthy, Shichong Liu, Keiko Mizuno, Benjamin A Garcia, Nancy R Zhang, K Giese, Ted Abel

Abstract

A fundamental question in neuroscience is how memories are stored and retrieved in the brain. Long-term memory formation requires transcription, translation and epigenetic processes that control gene expression. Thus, characterizing genome-wide the transcriptional changes that occur after memory acquisition and retrieval is of broad interest and importance. Genome-wide technologies are commonly used to interrogate transcriptional changes in discovery-based approaches. Their ability to increase scientific insight beyond traditional candidate gene approaches, however, is usually hindered by batch effects and other sources of unwanted variation, which are particularly hard to control in the study of brain and behavior. We examined genome-wide gene expression after contextual conditioning in the mouse hippocampus, a brain region essential for learning and memory, at all the time-points in which inhibiting transcription has been shown to impair memory formation. We show that most of the variance in gene expression is not due to conditioning and that by removing unwanted variance through additional normalization we are able provide novel biological insights. In particular, we show that genes downregulated by memory acquisition and retrieval impact different functions: chromatin assembly and RNA processing, respectively. Levels of histone 2A variant H2AB are reduced only following acquisition, a finding we confirmed using quantitative proteomics. On the other hand, splicing factor Rbfox1 and NMDA receptor-dependent microRNA miR-219 are only downregulated after retrieval, accompanied by an increase in protein levels of miR-219 target CAMKIIγ. We provide a thorough characterization of coding and non-coding gene expression during long-term memory formation. We demonstrate that unwanted variance dominates the signal in transcriptional studies of learning and memory and introduce the removal of unwanted variance through normalization as a necessary step for the analysis of genome-wide transcriptional studies in the context of brain and behavior. We show for the first time that histone variants are downregulated after memory acquisition, and splicing factors and microRNAs after memory retrieval. Our results provide mechanistic insights into the molecular basis of cognition by highlighting the differential involvement of epigenetic mechanisms, such as histone variants and post-transcriptional RNA regulation, after acquisition and retrieval of memory.

Twitter Demographics

The data shown below were collected from the profiles of 6 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 58 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 3 5%
Netherlands 1 2%
Unknown 54 93%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 22%
Researcher 12 21%
Student > Master 7 12%
Student > Bachelor 7 12%
Professor 6 10%
Other 13 22%
Readers by discipline Count As %
Agricultural and Biological Sciences 20 34%
Neuroscience 13 22%
Unspecified 9 16%
Biochemistry, Genetics and Molecular Biology 7 12%
Psychology 5 9%
Other 4 7%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 June 2015.
All research outputs
#2,304,359
of 5,190,687 outputs
Outputs from BMC Genomics
#2,285
of 4,705 outputs
Outputs of similar age
#77,609
of 173,107 outputs
Outputs of similar age from BMC Genomics
#166
of 258 outputs
Altmetric has tracked 5,190,687 research outputs across all sources so far. This one has received more attention than most of these and is in the 54th percentile.
So far Altmetric has tracked 4,705 research outputs from this source. They receive a mean Attention Score of 3.8. This one is in the 48th percentile – i.e., 48% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 173,107 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 53% of its contemporaries.
We're also able to compare this research output to 258 others from the same source and published within six weeks on either side of this one. This one is in the 31st percentile – i.e., 31% of its contemporaries scored the same or lower than it.