Decoding chromosome organization using CheC-PLS: chromosome conformation by proximity labeling and long-read sequencing DOI Creative Commons

Xu Kewei,

Yichen Zhang, James G. Baldwin-Brown

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 3, 2024

Abstract Genomic approaches have provided detailed insight into chromosome architecture. However, commonly deployed techniques do not preserve connectivity-based information, leaving large-scale genome organization poorly characterized. Here, we developed CheC-PLS: a proximity-labeling technique that indelibly marks, and then decodes, protein-associated sites. CheC-PLS tethers dam methyltransferase to protein of interest, followed by Nanopore sequencing identify methylated bases - indicative in vivo proximity along reads >100kb. As proof-of-concept analyzed, budding yeast, cohesin-based meiotic backbone organizes chromatin an array loops. Our data recapitulates previously obtained association patterns, and, importantly, exposes variability between cells. Single read reveals cohesin translocation on DNA anchoring onto unique regions, define the internal ribosomal locus. versatile technique, which also isolated nuclei with nanobodies, promises illuminate diverse chromosomal processes describing conformations single chromosomes.

Язык: Английский

Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes DOI Creative Commons
Francisco Rodríguez-Algarra,

E. T. Whittaker,

Sandra del Castillo

и другие.

BioEssays, Год журнала: 2025, Номер unknown

Опубликована: Янв. 20, 2025

ABSTRACT Although genome‐scale analyses have provided insights into the connection between genetic variability and complex human phenotypes, much trait variation is still not fully understood. Genetic within repetitive elements, such as multi‐copy, multi‐locus ribosomal DNA (rDNA), has emerged a potential contributor to variation. Whereas rDNA was long believed be largely uniform species, recent studies revealed substantial in locus, both across individuals. This variation, which takes form of copy number, structural arrangement, sequence differences, been found associated with phenotypes. review summarizes what currently known about its causes, association phenotypic outcomes, highlighting technical challenges field faces solutions proposed address them. Finally, we suggest experimental approaches that can help clarify elusive mechanisms underlying consequences

Язык: Английский

Процитировано

1
Spontaneous and environment induced genomic alterations in yeast model DOI Creative Commons
Kejing Li, Lei S. Qi,

Ying-Xuan Zhu

и другие.

Cell Insight, Год журнала: 2024, Номер 4(1), С. 100209 - 100209

Опубликована: Сен. 26, 2024

Язык: Английский

Процитировано

3
A hidden intrinsic ability of bicistronic expression based on a novel translation reinitiation mechanism in yeast DOI Creative Commons
Yiwen Sun, Ralph Bock, Zhichao Li

и другие.

Nucleic Acids Research, Год журнала: 2025, Номер 53(6)

Опубликована: Март 20, 2025

Abstract Gene organization in operons and co-expression as polycistronic transcripts is characteristic of prokaryotes. With the evolution eukaryotic translation machinery, operon structure expression polycistrons were largely abandoned. Whether eukaryotes still possess ability to express polycistrons, how they functionally activate bacterial acquired by horizontal DNA transfer unknown. Here, we demonstrate that a polycistron can be rapidly activated yeast induction bicistronic under selection. We show induced downstream cistron transcript based on novel type reinitiation mediated 80S ribosome triggered inefficient stop codon recognition, stable independent cis-elements. These results provide key insights into epigenetic mechanism pathway activation. also developed strain efficiently expresses constructs, but does not carry any genomic sequence change, utilized this synthesize high-value metabolite from construct. Together, our reveal capacity bicistrons previously unrecognized pathway. While normally hidden, it selection improve fitness.

Язык: Английский

Процитировано

0
Decoding chromosome organization using CheC-PLS: chromosome conformation by proximity labeling and long-read sequencing DOI Creative Commons

Xu Kewei,

Yichen Zhang, James G. Baldwin-Brown

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 3, 2024

Abstract Genomic approaches have provided detailed insight into chromosome architecture. However, commonly deployed techniques do not preserve connectivity-based information, leaving large-scale genome organization poorly characterized. Here, we developed CheC-PLS: a proximity-labeling technique that indelibly marks, and then decodes, protein-associated sites. CheC-PLS tethers dam methyltransferase to protein of interest, followed by Nanopore sequencing identify methylated bases - indicative in vivo proximity along reads >100kb. As proof-of-concept analyzed, budding yeast, cohesin-based meiotic backbone organizes chromatin an array loops. Our data recapitulates previously obtained association patterns, and, importantly, exposes variability between cells. Single read reveals cohesin translocation on DNA anchoring onto unique regions, define the internal ribosomal locus. versatile technique, which also isolated nuclei with nanobodies, promises illuminate diverse chromosomal processes describing conformations single chromosomes.

Язык: Английский

Процитировано

0