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Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans

Kim, Jun ; Jimenez, David S ; Ragipani, Bhavana ; [weitere]

eLife Sciences Publications, Ltd ; 2022

In: eLife Vol. 11 ( 2022-11-04)

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In: eLife, eLife Sciences Publications, Ltd, Vol. 11 ( 2022-11-04)

Kurzfassung: Condensins are molecular motors that compact DNA via linear translocation. In Caenorhabditis elegans , the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of r ecruitment e lements on the X -chromosome ( rex ) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a ‘ super rex ’ composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to the formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.

Materialart: Online-Ressource

ISSN: 2050-084X

URL: Article

DOI: 10.7554/eLife.68745

Sprache: Englisch

Verlag: eLife Sciences Publications, Ltd

Publikationsdatum: 2022

ZDB Id: 2687154-3

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Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans

Kramer, Maxwell ; Kranz, Anna-Lena ; Su, Amanda ; [weitere]

Public Library of Science (PLoS) ; 2015

In: PLOS Genetics Vol. 11, No. 12 ( 2015-12-7), p. e1005698-

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In: PLOS Genetics, Public Library of Science (PLoS), Vol. 11, No. 12 ( 2015-12-7), p. e1005698-

Materialart: Online-Ressource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1005698

DOI: 10.1371/journal.pgen.1005698.g001

DOI: 10.1371/journal.pgen.1005698.g002

DOI: 10.1371/journal.pgen.1005698.g003

DOI: 10.1371/journal.pgen.1005698.g004

DOI: 10.1371/journal.pgen.1005698.g005

DOI: 10.1371/journal.pgen.1005698.g006

DOI: 10.1371/journal.pgen.1005698.g007

DOI: 10.1371/journal.pgen.1005698.g008

DOI: 10.1371/journal.pgen.1005698.s001

DOI: 10.1371/journal.pgen.1005698.s002

DOI: 10.1371/journal.pgen.1005698.s003

DOI: 10.1371/journal.pgen.1005698.s004

DOI: 10.1371/journal.pgen.1005698.s005

DOI: 10.1371/journal.pgen.1005698.s006

DOI: 10.1371/journal.pgen.1005698.s007

DOI: 10.1371/journal.pgen.1005698.s008

DOI: 10.1371/journal.pgen.1005698.s009

DOI: 10.1371/journal.pgen.1005698.s010

DOI: 10.1371/journal.pgen.1005698.s011

DOI: 10.1371/journal.pgen.1005698.s012

DOI: 10.1371/journal.pgen.1005698.s013

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2015

ZDB Id: 2186725-2

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Correction: Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans

Kramer, Maxwell ; Kranz, Anna-Lena ; Su, Amanda ; [weitere]

Public Library of Science (PLoS) ; 2016

In: PLOS Genetics Vol. 12, No. 2 ( 2016-2-22), p. e1005899-

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In: PLOS Genetics, Public Library of Science (PLoS), Vol. 12, No. 2 ( 2016-2-22), p. e1005899-

Materialart: Online-Ressource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1005899

Sprache: Englisch

Verlag: Public Library of Science (PLoS)

Publikationsdatum: 2016

ZDB Id: 2186725-2

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Recent ultra-rare inherited variants implicate new autism candidate risk genes

Wilfert, Amy B. ; Turner, Tychele N. ; Murali, Shwetha C. ; [weitere]

Springer Science and Business Media LLC ; 2021

In: Nature Genetics Vol. 53, No. 8 ( 2021-08), p. 1125-1134

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 53, No. 8 ( 2021-08), p. 1125-1134

Materialart: Online-Ressource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-021-00899-8

RVK:

XA 10000

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2021

ZDB Id: 1494946-5

SSG: 12

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Detection of long repeat expansions from PCR-free whole-genome sequence data

Dolzhenko, Egor ; van Vugt, Joke J.F.A. ; Shaw, Richard J. ; [weitere]

Cold Spring Harbor Laboratory ; 2017

In: Genome Research Vol. 27, No. 11 ( 2017-11), p. 1895-1903

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In: Genome Research, Cold Spring Harbor Laboratory, Vol. 27, No. 11 ( 2017-11), p. 1895-1903

Kurzfassung: Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00] ) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.

Materialart: Online-Ressource

ISSN: 1088-9051 , 1549-5469

URL: Article

DOI: 10.1101/gr.225672.117

RVK:

XA 10000

Sprache: Englisch

Verlag: Cold Spring Harbor Laboratory

Publikationsdatum: 2017

ZDB Id: 1483456-X

SSG: 12

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Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis

Weinstock, Joshua S. ; Gopakumar, Jayakrishnan ; Burugula, Bala Bharathi ; [weitere]

Springer Science and Business Media LLC ; 2023

In: Nature Vol. 616, No. 7958 ( 2023-04-27), p. 755-763

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In: Nature, Springer Science and Business Media LLC, Vol. 616, No. 7958 ( 2023-04-27), p. 755-763

Materialart: Online-Ressource

ISSN: 0028-0836 , 1476-4687

URL: Article

DOI: 10.1038/s41586-023-05806-1

RVK:

TA 1000

RVK:

UA 1000

RVK:

WA 15000

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2023

ZDB Id: 120714-3

ZDB Id: 1413423-8

SSG: 11

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A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies

Li, Zilin ; Li, Xihao ; Zhou, Hufeng ; [weitere]

Springer Science and Business Media LLC ; 2022

In: Nature Methods Vol. 19, No. 12 ( 2022-12), p. 1599-1611

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In: Nature Methods, Springer Science and Business Media LLC, Vol. 19, No. 12 ( 2022-12), p. 1599-1611

Materialart: Online-Ressource

ISSN: 1548-7091 , 1548-7105

URL: Article

DOI: 10.1038/s41592-022-01640-x

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2022

ZDB Id: 2163081-1

SSG: 12

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Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies

Li, Xihao ; Quick, Corbin ; Zhou, Hufeng ; [weitere]

Springer Science and Business Media LLC ; 2023

In: Nature Genetics Vol. 55, No. 1 ( 2023-01), p. 154-164

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 55, No. 1 ( 2023-01), p. 154-164

Materialart: Online-Ressource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-022-01225-6

RVK:

XA 10000

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2023

ZDB Id: 1494946-5

SSG: 12

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A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response

Luo, Yang ; Kanai, Masahiro ; Choi, Wanson ; [weitere]

Springer Science and Business Media LLC ; 2021

In: Nature Genetics Vol. 53, No. 10 ( 2021-10), p. 1504-1516

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 53, No. 10 ( 2021-10), p. 1504-1516

Materialart: Online-Ressource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-021-00935-7

RVK:

XA 10000

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2021

ZDB Id: 1494946-5

SSG: 12

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Assessing the contribution of rare variants to complex trait heritability from whole-genome sequence data

Wainschtein, Pierrick ; Jain, Deepti ; Zheng, Zhili ; [weitere]

Springer Science and Business Media LLC ; 2022

In: Nature Genetics Vol. 54, No. 3 ( 2022-03), p. 263-273

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 54, No. 3 ( 2022-03), p. 263-273

Materialart: Online-Ressource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-021-00997-7

RVK:

XA 10000

Sprache: Englisch

Verlag: Springer Science and Business Media LLC

Publikationsdatum: 2022

ZDB Id: 1494946-5

SSG: 12

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