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| Status |
Public on Apr 20, 2015 |
| Title |
Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem cell (ESC) biology, although the functions of specific lncRNAs, and the molecular mechanisms through which they act, remain unclear. Here, we demonstrate discrete and opposing roles for the lncRNA transcript Haunt and its genomic locus in regulating the HOXA gene cluster during ESC differentiation. Reducing or enhancing Haunt expression, with minimal disruption of the Haunt locus, led to up- or down-regulation of HOXA genes, respectively. In contrast, increasingly large genomic deletions within the Haunt locus attenuated HOXA activation. The Haunt DNA locus contains potential enhancers of HOXA activation, whereas Haunt RNA acts to prevent aberrant HOXA expression. This work reveals a multi-faceted model of lncRNA-mediated transcriptional regulation of the HOXA cluster, with distinct roles for a lncRNA transcript and its genomic locus, while illustrating the power of rapid CRISPR/Cas9-based genome editing for assigning lncRNA functions.
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| Overall design |
All RNA-seq(s) were designed to reveal the differentially expressed genes among different stages of ESCs differentiation, or differentially expressed genes between wild-type or Haunt or HOXA mutant cells during RA-induced differentiation. All ChIRP-Seq were used to reveal the DNA or RNA targets of Haunt before or after RA treatment.
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| Contributor(s) |
Yin Y, Lu J, Shen X |
| Citation(s) |
25891907 |
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| Submission date |
Jun 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
jinlong lu |
| E-mail(s) |
bioyuyang@hotmail.com
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| Phone |
5853098469
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| Organization name |
University of Rochester
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| Lab |
Gorbunova & Seluanov Labs
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| Street address |
213 Hutchinson Hall
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| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14627 |
| Country |
USA |
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| Platforms (3) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (54)
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| Relations |
| BioProject |
PRJNA252812 |
| SRA |
SRP044012 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58514_ESCs_RNA-Seq_profile.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE58514_GSM1604235_GSM1604254_Haunt_RA_RNA_profiling.xlsx |
17.7 Mb |
(ftp)(http) |
XLSX |
| GSE58514_RAW.tar |
385.8 Mb |
(http)(custom) |
TAR (of BEDGRAPH, BIGWIG) |
| GSE58514_mRNA_profiling_Haunt_58_kb_KO_RA_differentiation.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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