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Series GSE272387

Query DataSets for GSE272387

Status

Public on Jul 18, 2024

Title

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length [RNA-seq gastruloid]

Organism

Experiment type

Expression profiling by high throughput sequencing
Third-party reanalysis

Summary

In mammals, tail length is controlled by several genetic determinants, amongst which Hox13 genes located at the posterior extremities of Hox clusters, whose main function are to terminate the extension of the body axis. In this view, the precise timing in the transcriptional activation of these genes may impact upon body length. Unlike other Hox clusters, HoxB lacks all posterior genes between Hoxb9 and Hoxb13, two genes separated by a ca. 70 kb large DNA segment containing an unusually high number of CTCF sites, suggesting it isolates Hoxb13 from the rest of the cluster, thereby delaying its negative impact on trunk extension. We deleted the spacer DNA to induce a potential heterochronic gain of function of Hoxb13 at physiological concentration and observed a shortening of the tail as well as other abnormal phenotypes, which were all rescued by inactivating Hoxb13 in-cis with the deletion. A comparable gain of function was observed in mutant ES cells grown as pseudo-embryos in vitro, which allowed us to examine in details the importance of both the number and the orientation of CTCF sites in the insulating activity of the DNA spacer. A short cassette containing all the CTCF sites was sufficient to insulate Hoxb13 from the rest of HoxB and additional modifications of this CTCF cassette showed that two CTCF sites in convergent orientations are already capable of importantly delaying Hoxb13 activation in these conditions. We discuss the relative importance of genomic distance versus number and orientation of CTCF sites in preventing Hoxb13 to be activated too early during trunk extension and hence to modulate tail length.

Overall design

RNA-seq of HoxB mutated gastruloids

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The table below lists GEO accessions reused/reanalyzed for this study.
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Contributor(s)

Bochaton C, Rekaik H, Lopez-Delisle L, Zakany J, Duboule D

Citation missing

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Submission date

Jul 16, 2024

Last update date

Jul 19, 2024

Contact name

Lucille Lopez-Delisle

E-mail(s)

lucille.delisle@epfl.ch

Organization name

EPFL

Street address

Station 19

City

Lausanne

ZIP/Postal code

1015

Country

Switzerland

Platforms (3)

GPL19057	Illumina NextSeq 500 (Mus musculus)
GPL21103	Illumina HiSeq 4000 (Mus musculus)
GPL24247	Illumina NovaSeq 6000 (Mus musculus)

Samples (26)

More...

GSM8399806	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 1
GSM8399807	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 2
GSM8399808	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 3

GSM8399809	RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10) gastruloids replicate 1
GSM8399810	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS5-10) gastruloids replicate 1
GSM8399811	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS5-10) gastruloids replicate 2
GSM8399812	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS8-10) gastruloids replicate 1
GSM8399813	RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS8-10) gastruloids replicate 1
GSM8399814	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS7-10) gastruloids replicate 1
GSM8399815	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Del(CBS7-10) gastruloids replicate 2
GSM8399816	RNA-seq of 96h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1
GSM8399817	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1
GSM8399818	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 2
GSM8399819	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 3
GSM8399820	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 4
GSM8399821	RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1
GSM8399822	RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 2
GSM8399823	RNA-seq of 168h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 1 gastruloids replicate 1
GSM8399824	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 2 gastruloids replicate 1
GSM8399825	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10) clone 2 gastruloids replicate 2
GSM8399826	RNA-seq of 120h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10):Del(CBS7-10) gastruloids replicate 1
GSM8399827	RNA-seq of 144h HoxB Del/Del(i9-13):Ins(CBS5-10):Inv(CBS5-10):Del(CBS7-10) gastruloids replicate 1
GSM8399828	RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 1
GSM8399829	RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 2
GSM8399830	RNA-seq of 120h HoxB Del/Del(i9-13) gastruloids replicate 3
GSM8399831	RNA-seq of 144h HoxB Del/Del(i9-13) gastruloids replicate 1

This SubSeries is part of SuperSeries:

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length

Relations

Reanalysis of

Reanalysis of

Reanalysis of

Reanalysis of

BioProject

TABLE OF REANALYZED/REUSED DATA - header descriptions
GEO Series	Link for GEO Series
GEO Sample	Link for GEO Sample
SRA Experiment	SRA Run Selector link for SRA Experiment
BioSample	SRA Run Selector link for BioSample
BioProject	SRA Run Selector link for BioProject
Sample title	Title of GEO Sample record

Data table
GEO Series	GEO Sample	SRA Experiment	BioSample	BioProject	Sample title
GSE205781	GSM6226308	SRX15651622	SAMN28944768	PRJNA847581	RNA-seq of wt stembryos at 120h, Time-course_rep1
GSE205781	GSM6226309	SRX15651623	SAMN28944767	PRJNA847581	RNA-seq of wt stembryos at 120h, Time-course_rep2
GSE205781	GSM6226314	SRX15651628	SAMN28944762	PRJNA847581	RNA-seq of wt stembryos at 144h, Time-course_rep1
GSE205781	GSM6226315	SRX15651629	SAMN28944761	PRJNA847581	RNA-seq of wt stembryos at 144h, Time-course_rep2

Total number of rows: 4

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE272387_AllCufflinks_Simplified.txt.gz	3.4 Mb	(ftp)(http)	TXT
GSE272387_AllHTSeqCounts.txt.gz	1.2 Mb	(ftp)(http)	TXT
GSE272387_RAW.tar	3.1 Gb	(http)(custom)	TAR (of BW)
GSE272387_RNAseq_wt_120h_rep1_Uniq_fwd_norm.bw	61.3 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_120h_rep1_Uniq_rev_norm.bw	60.2 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_120h_rep2_Uniq_fwd_norm.bw	55.6 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_120h_rep2_Uniq_rev_norm.bw	54.6 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_144h_rep1_Uniq_fwd_norm.bw	57.1 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_144h_rep1_Uniq_rev_norm.bw	56.4 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_144h_rep2_Uniq_fwd_norm.bw	41.2 Mb	(ftp)(http)	BW
GSE272387_RNAseq_wt_144h_rep2_Uniq_rev_norm.bw	40.7 Mb	(ftp)(http)	BW
SRA Run Selector
Raw data are available in SRA

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