Faculty Opinions recommendation of The dynamic architecture of Hox gene clusters.

Summary paragraphPolycomb-group (PcG) proteins are conserved chromatin factors that maintain the silencing of key developmental genes, notably the Hox gene clusters, outside of their expression domains [1-3]. Polycomb repressive complex 2 (PRC2) trimethylates lysine K27 of histone H3 [4], and PRC1 collaborates with PRC2 in gene silencing. Genome-wide studies have revealed large H3K27me3 chromatin domains bound by PcG proteins, and Polycomb domains fold into distinct nuclear structures [5-9]. Although PRC1 is involved in chromatin compaction [10-16], it is unknown whether PRC1-dependent transcriptional silencing is a consequence of its role on higher-order chromatin folding. This is because depletion of PRC1 proteins typically induces both chromatin unfolding and ectopic transcription, and ectopic transcription can open chromatin by itself. To disentangle these two components, we analysed the temporal effects of two PRC1 proteins, Polyhomeotic (Ph) and Polycomb (Pc), on Hox gene clusters during Drosophila embryogenesis. We show that the absence of Ph or Pc affects the higher-order chromatin folding of Hox clusters prior to ectopic Hox gene transcription, demonstrating that PRC1 primary function during early embryogenesis is to compact its target chromatin. During later embryogenesis, we observed further chromatin opening at Hox complexes in both Ph and Pc mutants, which was coupled to strong deregulation of Hox genes at this stage of development. Moreover, the differential effects of Ph and Pc on Hox cluster folding matches the differences in ectopic Hox gene expression observed in these two mutants, suggesting that the degree of Hox derepression in PcG mutants depends on the degree of structural constraints imposed by each PcG component. In summary, our data demonstrate that binding of PRC1 to large genomic domains during early embryogenesis induces the formation of compact chromatin to prevent ectopic gene expression at later time-points. Thus, epigenetic mechanisms such as Polycomb mediated silencing act by folding chromatin domains and impose an architectural layer to gene regulation.

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Evolutionary Genomics of Hox Gene Clusters

HOX Gene Expression ◽

10.1007/978-0-387-68990-6_5 ◽

2007 ◽

pp. 68-90 ◽

Cited By ~ 1

Author(s):

Sonja J. Prohaska ◽

Peter F. Stadler ◽

Günter P. Wagner

Keyword(s):

Gene Clusters ◽

Evolutionary Genomics ◽

Hox Gene

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The CALM/AF10 Fusion: Molecular Analysis of the Fusion Transcripts in 13 Cases of AML and ALL; Gene Expression Profiling Reveals HOX Gene Deregulation.

Blood ◽

10.1182/blood.v104.11.2895.2895 ◽

2004 ◽

Vol 104 (11) ◽

pp. 2895-2895 ◽

Cited By ~ 1

Author(s):

Alexandre Krause ◽

Alexander Kohlmann ◽

Torsten Haferlach ◽

Claudia Schoch ◽

Susanne Schnittger ◽

...

Keyword(s):

Gene Expression ◽

Fusion Protein ◽

Hox Genes ◽

Lymphoblastic Leukemia ◽

Critical Role ◽

Gene Clusters ◽

Dominant Negative ◽

Nucleotide Position ◽

Gamma Delta ◽

Hox Gene

Abstract The t(10;11)(p13;q14) is a recurring translocation associated with the CALM/AF10 fusion gene which is found in undifferentiated leukemia, acute myeloid leukemia, acute lymphoblastic leukemia and malignant lymphoma with poor prognosis. The CALM/AF10 fusion protein was reported to be the most common fusion protein in T-ALL with TCR gamma delta rearrangement. We have analyzed samples from 9 patients with different types of leukemia: case 1 (AML M2), case 2 (AML M0), case 3 (Pre T-ALL), case 4 (Acute Undifferentiated Leukemia), case 5 (PreT-ALL), case 6 and 7 (ProT-ALL), case 8 (T-ALL), case 9 (AML), with a t(10;11) translocation suggesting a CALM/AF10-rearrangement. The samples were analyzed for the presence of the CALM/AF10 and AF10/CALM mRNA by RT-PCR and sequence analysis. All these patients were found positive for the CALM/AF10 fusion. In addition, we analyzed a series of twenty-nine patients with T-ALL with gamma delta rearrangement. Among these patients, four were positive for CALM/AF10 transcripts, indicating a high incidence of CALM/AF10 fusions in this group of leukemia. We found three different breakpoints in CALM at nucleotide 1926, 2091 and a new exon, with 106 bases inserted after nt 2064 of CALM in patient 4. In AF10 four breakpoints were identified: at nucleotide position 424, 589, 883 and 979. In seven patients it was also possible to amplify the reciprocal AF10/CALM fusion transcript (case 1, 3, 4, 8, 9, 10 and 11). There was no correlation between disease phenotype and breakpoint location. The patients were 5 to 46 years old (median 25). Ten CALM/AF10 positive patients were further analyzed using oligonucleotide microarrays representing 33,000 different genes (U133 set, Affymetrix). Analysis of microarray gene expression signatures of these patients revealed high expression levels of the homeobox gene MEIS1 and the HOXA cluster genes HOXA1, HOXA4, HOXA5, HOXA7, HOXA9, and HOXA10. The overexpression of HOX genes seen in these CALM/AF10 positive leukemias is reminiscent of the pattern seen in leukemias with rearrangements of the MLL gene, and complex aberrant karyotypes suggesting a common effector pathway (i.e. HOX gene deregulation) for these diverse leukemias. It is known that alhambra, the Drosophila homologue of AF10 can act on polycomb group responsive elements, which play a critical role in the regulation of the HOX gene clusters. It is thus conceivable that the CALM/AF10 fusion proteins acts in a dominant negative fashion on wild type AF10 function relieving the repression that is presumably normally exerted by AF10 on the expression of HOX genes.

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