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| Status |
Public on Sep 06, 2020 |
| Title |
Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
While Hox genes encode for similar transcription factors (TFs), they induce different fates across body axes. We sought to understand how Hox TF genomic binding preferences relate to their patterning activities during neuronal differentiation. To generate the required neuronal diversity for locomotor activity, Hox TFs specify spinal motor neuron and interneuron subtypes along the rostro-caudal axis. Our data revelated that Hoxc6 and Hoxc8 of the central group induce limb-innervating fates by binding to the same sites. On the other hand, the posterior group Hox genes assign different positional identities: Hoxc9 (thoracic), Hoxc10 (limb-innervating) and Hox13 (axial elongation termination) by binding to distinct sites with the same primary motif. We find that their genomic binding distributions are explained by differential abilities to bind to previously inaccessible chromatin. Thus, the vertebrate posterior Hox expansion and its associated patterning diversification is the product of their differential abilities to associate with less accessible chromatin.
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| Overall design |
RNA-Seq was used to investigate global gene expression prior to and upon Hox TF induction during ESC-to-MN differentiation
Please note that each processed data file was generated from all replicates and is linked to the corresponding rep1 sample records.
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| Contributor(s) |
Bulajić M, Srivastava D, Dasen JS, Wichterle H, Mahony S, Mazzoni EO |
| Citation(s) |
33028607 |
| |
| Submission date |
Dec 19, 2019 |
| Last update date |
Dec 06, 2020 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
|
| Phone |
814-865-3008
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| Organization name |
Penn State University
|
| Department |
Biochemistry & Molecular Biology
|
| Lab |
Shaun Mahony
|
| Street address |
404 South Frear Bldg
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (18)
|
| GSM4226466 |
RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate1 |
| GSM4226467 |
RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate2 |
| GSM4226468 |
RNAseq in EB-Day2[D0+RA+SAG][iCre]_replicate3 |
| GSM4226469 |
RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate1 |
| GSM4226470 |
RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate2 |
| GSM4226471 |
RNAseq in EB-Day4[D0+RA+SAG][noDox(iFlag.Hoxc6)]_replicate3 |
| GSM4226472 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 1 |
| GSM4226473 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 2 |
| GSM4226474 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc6)] replicate 3 |
| GSM4226475 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 1 |
| GSM4226476 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 2 |
| GSM4226477 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc8)] replicate 3 |
| GSM4226478 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 1 |
| GSM4226479 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 2 |
| GSM4226480 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc9)] replicate 3 |
| GSM4226481 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 1 |
| GSM4226482 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 2 |
| GSM4226483 |
RNAseq in EB-Day4[D0+RA+SAG][D2+48hDox(iFlag.Hoxc10)] replicate 3 |
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| This SubSeries is part of SuperSeries: |
| GSE142379 |
Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin |
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| Relations |
| BioProject |
PRJNA596779 |
| SRA |
SRP238220 |
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