scholarly journals A noncatalytic activity of the H4K20 demethylase DPY-21 regulates condensin DC binding

2021 ◽  
Author(s):  
Laura Breimann ◽  
Ana Karina Morao ◽  
Jun Kim ◽  
David Jimenez ◽  
Nina Maryn ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Dosage Compensation ◽  
Fluorescence Recovery After Photobleaching ◽  
Null Mutant ◽  
X Chromosomes ◽  
Mobility Separation ◽  
C Elegans ◽  
Catalytic Role ◽  
Mobile Fraction

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Unlike cohesin, in vivo regulators of condensin binding dynamics remain unclear. Here we addressed this question using C. elegans condensin DC, which specifically binds to and represses transcription of both X chromosomes in hermaphrodites for dosage compensation. Mutants of several chromatin modifiers that regulate H4K20me and H4K16ac cause varying degrees of X chromosome derepression. We used fluorescence recovery after photobleaching (FRAP) to analyze how these modifiers regulate condensin DC binding dynamics in vivo. We established FRAP using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. The greatest effect on condensin DC dynamics was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of the complex reduced from ~30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Separation of catalytic and non-catalytic activity is also supported by Hi-C data in the dpy-21 null mutant. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.

scholarly journals The H4K20 demethylase DPY-21 regulates the dynamics of condensin DC binding

2021 ◽  
Author(s):  
Laura Breimann ◽  
Ana Karina Morao ◽  
Jun Kim ◽  
David Sebastian Jimenez ◽  
Nina Maryn ◽  
...  
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
Transcriptional Repression ◽  
Fluorescence Recovery After Photobleaching ◽  
Null Mutant ◽  
Wild Type ◽  
X Chromosomes ◽  
C Elegans ◽  
Catalytic Role ◽  
Mobile Fraction

Condensin is a multi-subunit SMC complex that binds to and compacts chromosomes. Here we addressed the regulation of condensin binding dynamics using C. elegans condensin DC, which represses X chromosomes in hermaphrodites for dosage compensation. We established fluorescence recovery after photobleaching (FRAP) using the SMC4 homolog DPY-27 and showed that a well-characterized ATPase mutation abolishes its binding. Next, we performed FRAP in the background of several chromatin modifier mutants that cause varying degrees of X-chromosome derepression. The greatest effect was in a null mutant of the H4K20me2 demethylase DPY-21, where the mobile fraction of condensin DC reduced from ∼30% to 10%. In contrast, a catalytic mutant of dpy-21 did not regulate condensin DC mobility. Hi-C data in the dpy-21 null mutant showed little change compared to wild type, uncoupling Hi-C measured long-range DNA contacts from transcriptional repression of the X chromosomes. Together, our results indicate that DPY-21 has a non-catalytic role in regulating the dynamics of condensin DC binding, which is important for transcription repression.

SDC-3 coordinates the assembly of a dosage compensation complex on the nematode X chromosome

Development ◽  
1997 ◽  
Vol 124 (5) ◽  
pp. 1019-1031 ◽  
Author(s):  
T.L. Davis ◽  
B.J. Meyer
Keyword(s):  
Zinc Finger ◽  
X Chromosome ◽  
Dosage Compensation ◽  
Protein Complex ◽  
Terminal Region ◽  
X Chromosomes ◽  
C Elegans ◽  
Amino Terminal ◽  
Zinc Finger Motifs ◽  
Specific Association

X chromosome expression in C. elegans is controlled by a chromosome-wide regulatory process called dosage compensation that specifically reduces by half the level of transcripts made from each hermaphrodite X chromosome. This process equalizes X expression between the sexes (XX hermaphrodites and XO males), despite their two-fold difference in X chromosome dose, and thereby prevents sex-specific lethality. Dosage compensation is achieved by a protein complex that associates with X in a sex-specific fashion to modulate gene expression. SDC-3, a protein that coordinately controls both sex determination and dosage compensation, activates dosage compensation by directing the dosage compensation protein complex to the hermaphrodite X chromosomes. We show that SDC-3 coordinates this assembly through its own sex-specific association with X. SDC-3 in turn requires other members of the dosage compensation gene hierarchy for its stability and its X localization. In addition, SDC-3 requires its own zinc finger motifs and an amino-terminal region for its X association. Our experiments suggest the possible involvement of zinc finger motifs in X chromosome recognition and the amino-terminal region in interactions with other dosage compensation proteins.

scholarly journals Topoisomerases I and II facilitate condensin DC translocation to organize and repress X chromosomes in C. elegans

2021 ◽  
Author(s):  
Ana Karina Morao ◽  
Jun Kim ◽  
Daniel Obaji ◽  
Siyu Sun ◽  
Sevinc Ercan
Keyword(s):  
Long Range ◽  
X Chromosome ◽  
Molecular Motors ◽  
Topoisomerase Ii ◽  
Dna Looping ◽  
Loop Formation ◽  
X Chromosomes ◽  
C Elegans ◽  
And Control

Condensin complexes are evolutionarily conserved molecular motors that translocate along DNA and form loops. While condensin-mediated DNA looping is thought to direct the chain-passing activity of topoisomerase II to separate sister chromatids, it is not known if topological constraints in turn regulate loop formation in vivo. Here we applied auxin inducible degradation of topoisomerases I and II to determine how DNA topology affects the translocation of an X chromosome specific condensin that represses transcription for dosage compensation in C. elegans (condensin DC). We found that both topoisomerases colocalize with condensin DC and control its movement at different genomic scales. TOP-2 depletion hindered condensin DC translocation over long distances, resulting in accumulation around its X-specific recruitment sites and shorter Hi-C interactions. In contrast, TOP-1 depletion did not affect long-range spreading but resulted in accumulation of condensin DC within expressed gene bodies. Both TOP-1 and TOP-2 depletions resulted in X chromosome transcriptional upregulation indicating that condensin DC translocation at both scales is required for its function in gene repression. Together the distinct effects of TOP-1 and TOP-2 on condensin DC distribution revealed two distinct modes of condensin DC association with chromatin: long-range translocation that requires decatenation/unknotting of DNA and short-range translocation across genes that requires resolution of transcription-induced supercoiling.

scholarly journals Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans

2021 ◽  
Author(s):  
David Sebastian Jimenez ◽  
Jun Kim ◽  
Bhavana Ragipani ◽  
Bo Zhang ◽  
Lena Annika Street ◽  
...  
Keyword(s):  
Chromosome Segregation ◽  
X Chromosome ◽  
Molecular Motors ◽  
Sequence Motif ◽  
X Chromosomes ◽  
C Elegans ◽  
Eukaryotic Chromosome ◽  
Multiple Copies

AbstractCondensins are molecular motors that compact DNA for chromosome segregation and gene regulation. In vitro experiments have begun to elucidate the mechanics of condensin function but how condensin loading and translocation along DNA controls eukaryotic chromosome structure in vivo remains poorly understood. To address this question, we took advantage of a specialized condensin, which organizes the 3D conformation of X chromosomes to mediate dosage compensation (DC) in C. elegans. Condensin DC is recruited and spreads from a small number of recruitment elements on the X chromosome (rex). We found that ectopic insertion of rex sites on an autosome leads to bidirectional spreading of the complex over hundreds of kilobases. On the X chromosome, strong rex sites contain multiple copies of a 12-bp sequence motif and act as TAD borders. Inserting a strong rex and ectopically recruiting the complex on the X chromosome or an autosome creates a loop-anchored TAD. Unlike the CTCF system, which controls TAD formation by cohesin, direction of the 12-bp motif does not control the specificity of loops. In an X;V fusion chromosome, condensin DC linearly spreads into V and increases 3D DNA contacts, but fails to form TADs in the absence of rex sites. Finally, we provide in vivo evidence for the loop extrusion hypothesis by targeting multiple dCas9-Suntag complexes to an X chromosome repeat region. Consistent with linear translocation along DNA, condensin DC accumulates at the block site. Together, our results support a model whereby strong rex sites act as insulation elements through recruitment and bidirectional spreading of condensin DC molecules and form loop-anchored TADs.

DPY-30, a nuclear protein essential early in embryogenesis for Caenorhabditis elegans dosage compensation

Development ◽  
1995 ◽  
Vol 121 (10) ◽  
pp. 3323-3334 ◽  
Author(s):  
D.R. Hsu ◽  
P.T. Chuang ◽  
B.J. Meyer
Keyword(s):  
Amino Acids ◽  
Dosage Compensation ◽  
Nuclear Protein ◽  
Rna Binding ◽  
Rna Binding Protein ◽  
X Chromosomes ◽  
Transcript Levels ◽  
C Elegans ◽  
Morphological Defects ◽  
Specific Association

DPY-30 is an essential component of the C. elegans dosage compensation machinery that reduces X chromosome transcript levels in hermaphrodites (XX). DPY-30 is required for the sex-specific association of DPY-27 (a chromosome condensation protein homolog) with the hermaphrodite X chromosomes. Loss of dpy-30 activity results in XX-specific lethality. We demonstrate that dpy-30 encodes a novel nuclear protein of 123 amino acids that is present in both hermaphrodites and males (XO) throughout development. DPY-30 itself is not associated with the X chromosomes, nor is its pattern of expression perturbed by mutations in the gene hierarchy that controls dosage compensation. Therefore, DPY-30 is a ubiquitous factor that is likely to promote the hermaphrodite-specific association of DPY-27 with X by affecting the activity of a sex-specific dosage compensation gene. In XO animals, DPY-30 is required for developmental processes other than dosage compensation: coordinated movement, normal body size, correct tail morphology and mating behavior. We demonstrate that rescue of both the XX-specific lethality and the XO-specific morphological defects caused by dpy-30 mutations can be achieved by inducing dpy-30 transcripts either in the mother or in the embryo through the end of gastrulation. dpy-30 appears to be cotranscribed in an operon with a novel RNA-binding protein.

scholarly journals Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Sarah Elizabeth Albritton ◽  
Anna-Lena Kranz ◽  
Lara Heermans Winterkorn ◽  
Lena Annika Street ◽  
Sevinc Ercan
Keyword(s):  
Dosage Compensation ◽  
Regulatory Elements ◽  
Secondary Site ◽  
Open Chromatin ◽  
Sequence Motifs ◽  
Genomic Context ◽  
Long Distance ◽  
X Chromosomes ◽  
Single Chromosome ◽  
C Elegans

In many organisms, it remains unclear how X chromosomes are specified for dosage compensation, since DNA sequence motifs shown to be important for dosage compensation complex (DCC) recruitment are themselves not X-specific. Here, we addressed this problem in C. elegans. We found that the DCC recruiter, SDC-2, is required to maintain open chromatin at a small number of primary DCC recruitment sites, whose sequence and genomic context are X-specific. Along the X, primary recruitment sites are interspersed with secondary sites, whose function is X-dependent. A secondary site can ectopically recruit the DCC when additional recruitment sites are inserted either in tandem or at a distance (>30 kb). Deletion of a recruitment site on the X results in reduced DCC binding across several megabases surrounded by topologically associating domain (TAD) boundaries. Our work elucidates that hierarchy and long-distance cooperativity between gene-regulatory elements target a single chromosome for regulation.

scholarly journals Dual Roles for Nuclear RNAi Argonautes in C. elegans Dosage Compensation

2021 ◽  
Author(s):  
Michael B Davis ◽  
Bahaar Chawla ◽  
Eshna Jash ◽  
Lillian E. Tushman ◽  
Rebecca A. Haines ◽  
...  
Keyword(s):  
X Chromosome ◽  
Dosage Compensation ◽  
Dual Roles ◽  
Independent Manner ◽  
X Chromosomes ◽  
C Elegans ◽  
Gene Regulatory ◽  
Subsequent Activation ◽  
Nuclear Rnai ◽  
Transcriptional Output

Dosage compensation involves chromosome-wide gene regulatory mechanisms which impact higher order chromatin structure and are crucial for organismal health. Using a genetic approach, we identified Argonaute genes which promote dosage compensation in C. elegans. Dosage compensation in C. elegans hermaphrodites is initiated by the silencing of xol-1 and subsequent activation of the Dosage Compensation Complex (DCC) which binds to both hermaphrodite X chromosomes and reduces transcriptional output by twofold. A hallmark phenotype of dosage compensation mutants is decondensation of the X chromosomes. We characterized this phenotype in Argonaute mutants using X chromosome paint probe and fluorescence microscopy. We found that while nuclear Argonaute mutants hrde-1 and nrde-3 exhibit de-repression of xol-1 transcripts, they also effect X chromosome condensation in a xol-1-independent manner. We also characterized the physiological contribution of Argonaute genes to dosage compensation using genetic assays and find that hrde-1 and nrde-3, together with the piRNA Argonaute prg-1, contribute to healthy dosage compensation both upstream and downstream of xol-1.

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