Chromatin architecture mapping by multiplex proximity tagging DOI Open Access

Axel Delamarre,

Benton M. Bailey,

Jennifer Yavid

и другие.

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

Опубликована: Ноя. 12, 2024

Abstract Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate 3D space. Using this – Proximity Copy Paste (PCP) mapped the connectivity of individual nucleosomes Saccharomyces cerevisiae. By analyzing nucleosome positions spacing on single molecule fibers, show is predominantly organized into regularly spaced arrays can be positioned or delocalized. Basic features are generally explained by gene size transcription. PCP also map long-range, multi-way interactions provide first direct evidence supporting model metaphase chromosomes compacted cohesin loop clustering. Analyzing single-molecule nuclease footprinting data define distinct states within mixed population non-canonical nucleosomes, notably Overlapping-Di-Nucleosomes (OLDN) stable feature chromatin. versatile allowing detection locally over large distance at high-resolution experiment.

Язык: Английский

DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions DOI Creative Commons
Yi Li, James Lee, Lu Bai

и другие.

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Май 22, 2024

Abstract 3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those promoters and distal enhancers. Here, we present M ethyltransferase T argeting-based chromosome A rchitecture C apture (MTAC), method that maps the contacts target site (viewpoint) rest in budding yeast with high resolution sensitivity. MTAC detects hundreds intra- inter-chromosomal within nucleosome-depleted regions (NDRs) cannot be captured by 4C, Hi-C, or Micro-C. By applying various viewpoints, find (1) most long-distance detected reflect tethering nuclear pore complexes (NPCs), (2) genes co-regulated methionine assemble into clusters near NPCs upon activation, (3) mediated condensin, mating locus forms highly specific interaction recombination enhancer (RE) mating-type manner, (4) correlation signals among NDRs reveal spatial mixing segregation genome. Overall, these results demonstrate powerful tool resolve fine-scale provide insights

Язык: Английский

Процитировано

9
High plasticity of ribosomal DNA organization in budding yeast DOI Creative Commons
Shuangying Jiang, Zelin Cai, Yun Wang

и другие.

Cell Reports, Год журнала: 2024, Номер 43(2), С. 113742 - 113742

Опубликована: Фев. 1, 2024

In eukaryotic genomes, rDNA generally resides as a highly repetitive and dynamic structure, making it difficult to study. Here, synthetic array on chromosome III in budding yeast was constructed serve the sole source of rRNA. Utilizing loxPsym site within each repeat Cre recombinase, we were able reduce copy number few eight copies. Additionally, strains with two or three arrays found that presence multiple did not affect formation single nucleolus. Although alteration position impact three-dimensional genome additional had no deleterious influence cell growth transcriptomes. Overall, this study sheds light high plasticity organization opens up opportunities for future engineering.

Язык: Английский

Процитировано

4
Molecular mechanism targeting condensin for chromosome condensation DOI Creative Commons
Menglu Wang, Daniel Robertson, Juan Zou

и другие.

The EMBO Journal, Год журнала: 2024, Номер unknown

Опубликована: Дек. 17, 2024

Genomes are organised into DNA loops by the Structural Maintenance of Chromosomes (SMC) proteins. SMCs establish functional chromosomal sub-domains for repair, gene expression and chromosome segregation, but how SMC activity is specifically targeted unclear. Here, we define molecular mechanism targeting condensin complex to specific regions in budding yeast. A conserved pocket on HAWK subunit Ycg1 binds receptors carrying a related motif, CR1. In early mitosis, CR1 motifs Sgo1 Lrs4 recruit pericentromeres rDNA, facilitate sister kinetochore biorientation rDNA condensation, respectively. We additionally find that arm condensation begins as kinetochores come under tension, manner dependent pocket. propose multiple CR1-containing proteins chromosomes identify several additional candidates based their sequence. Overall, uncover targets functionalise domains achieve accurate segregation during mitosis.

Язык: Английский

Процитировано

2
Molecular basis for condensin enrichment at pericentromeres DOI Creative Commons
Menglu Wang, Juan Zou, Christos Spanos

и другие.

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

Опубликована: Март 28, 2024

Summary Faithful chromosome segregation requires packaging of the genome on both global and local scales. Condensin plays a crucial role at pericentromeres to resist spindle forces ensure bioriented attachment kinetochores microtubules in mitosis. Here we demonstrate that budding yeast condensin is recruited through direct interaction between its Ycg1 subunit pericentromeric adaptor protein, shugoshin (Sgo1). We identify Short Linear Motif (SLiM), termed CR1, within C-terminal region Sgo1 which inserts into conserved pocket Ycg1. Disruption this interface abolishes Sgo1-condensin interaction, prevents recruitment results defective sister kinetochore biorientation Similar motifs CR1 are found known potential binding partners broadly conserved, including mammalian homolog CAP-G. Overall, uncover molecular mechanism targets define specialized chromosomal domain.

Язык: Английский

Процитировано

1
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions DOI Creative Commons
Yi Li, James Lee, Lu Bai

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Дек. 27, 2023

Abstract 3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those promoters and distal enhancers. Here, we present M ethyltransferase T argeting-based chromosome A rchitecture C apture (MTAC), method that maps the contacts target site (viewpoint) rest in budding yeast with high resolution sensitivity. MTAC detects hundreds intra-and inter-chromosomal within nucleosome-depleted regions (NDRs) cannot be captured by 4C, Hi-C, or Micro-C. By applying various viewpoints, find 1) tethering nuclear pore complex (NPC) is major mechanism mediates long-distance yeast, 2) genes co-regulated methionine assemble into clusters near NPCs upon activation, 3) mediated condensin, mating locus forms highly specific interaction recombination enhancer (RE) mating-type manner, 4) correlation signals among NDRs reveal spatial mixing segregation genome. Overall, these results demonstrate powerful tool resolve fine-scale provide insights

Язык: Английский

Процитировано

1
Budding Yeast Cap Analysis of Gene Expression Dataset of Two Cell Types DOI Creative Commons
Kei Kawakami, Shin‐ichi Maeda,

Yoshiko Tanimoto

и другие.

Genes & Genetic Systems, Год журнала: 2024, Номер 99(0), С. n/a - n/a

Опубликована: Янв. 1, 2024

The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying chromatin regulation with high-resolution genome-wide analyses. Since newly generated data are often compared publicly available datasets, expanding our dataset repertoire will be beneficial the field. Information on transcription start sites (TSSs) determined at base pair resolution essential elucidating mechanisms of and related regulation, yet no datasets that cover two different cell types available. Here, we present a CAGE (cap analysis gene expression) a-cells α-cells grown in defined rich media. Cell type-specific genes were differentially expressed as expected, ensuring reliability data. Some TSSs medium-specific or detected due to unrecognized chromosome rearrangement. By comparing nucleosome map, major primarily found +1 nucleosomes, peak approximately 30 bp from promoter-proximal end nucleosome. DDBJ/GEA.

Язык: Английский

Процитировано

0
Chromatin architecture mapping by multiplex proximity tagging DOI Open Access

Axel Delamarre,

Benton M. Bailey,

Jennifer Yavid

и другие.

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

Опубликована: Ноя. 12, 2024

Abstract Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed novel proximity-tagging method which assigns unique DNA barcodes to molecules that associate 3D space. Using this – Proximity Copy Paste (PCP) mapped the connectivity of individual nucleosomes Saccharomyces cerevisiae. By analyzing nucleosome positions spacing on single molecule fibers, show is predominantly organized into regularly spaced arrays can be positioned or delocalized. Basic features are generally explained by gene size transcription. PCP also map long-range, multi-way interactions provide first direct evidence supporting model metaphase chromosomes compacted cohesin loop clustering. Analyzing single-molecule nuclease footprinting data define distinct states within mixed population non-canonical nucleosomes, notably Overlapping-Di-Nucleosomes (OLDN) stable feature chromatin. versatile allowing detection locally over large distance at high-resolution experiment.

Язык: Английский

Процитировано

0