Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA322456 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Variable chromatin secondary structures in live cells revealed by radiation-induced spatially correlated DNA cleavage mapping [RICC-Seq]
| PRJNA322621 | ENA
Project description:Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping
| PRJNA322612 | ENA
Project description:Chromatin structure at the length scale encompassing nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this chromatin secondary structure remains poorly understood compared to the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Unbiased analysis of RICC-seq DNA fragments in 1 Mb windows reveals a similar fragment length profile across the genome, with regional enrichment of characteristic fragments spanning tri-nucleosome units in heterochromatin. We observe differences in nucleosome-nucleosome contacts among euchromatin, H3K27me3-marked heterochromatin, and H3k9me3-marked heterochromatin. After calibrating RICC-seq signal to 3D distances, we show that compact 2-start helical fiber structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked heterochromatin, while non-compact zig-zags and other extended structures are preferred in open chromatin. Our data support a model of heterochromatin condensation in native, intact nuclei consistent with longitudinal compaction of two-start helical fibers.
2016-12-26 | GSE81806 | GEO
Project description:Chromatin structure at the length scale encompassing nucleosome-nucleosome interactions is thought to play a crucial role in regulating transcription and access to DNA. However, this chromatin secondary structure remains poorly understood compared to the primary structure of single nucleosomes or the tertiary structure of long-range looping interactions. Here we report the first genome-wide map of chromatin conformation in human cells at the 1-3 nucleosome (50-500 bp) scale, obtained using ionizing radiation-induced spatially correlated cleavage of DNA with sequencing (RICC-seq). Unbiased analysis of RICC-seq DNA fragments in 1 Mb windows reveals a similar fragment length profile across the genome, with regional enrichment of characteristic fragments spanning tri-nucleosome units in heterochromatin. We observe differences in nucleosome-nucleosome contacts among euchromatin, H3K27me3-marked heterochromatin, and H3k9me3-marked heterochromatin. After calibrating RICC-seq signal to 3D distances, we show that compact 2-start helical fiber structures with stacked alternating nucleosomes are consistent with RICC-seq fragmentation patterns from H3K9me3-marked heterochromatin, while non-compact zig-zags and other extended structures are preferred in open chromatin. Our data support a model of heterochromatin condensation in native, intact nuclei consistent with longitudinal compaction of two-start helical fibers.
2016-12-26 | GSE81736 | GEO
Project description:The high-throughput DICER cleavage assays were conducted shRNA variants containing different sequences. We showcase a comprehensive cleavage activity of DICER on different shRNAs containing different secondary structures.
2022-02-21 | GSE182701 | GEO
Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
2025-01-15 | GSE275081 | GEO
Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
2025-01-15 | GSE275076 | GEO
Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
2025-01-15 | GSE275074 | GEO
Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
2025-01-15 | GSE275080 | GEO
Project description:RNA endonucleases are the rate-limiting initiator of decay for many bacterial mRNAs. However, the positions of cleavage and their sequence determinants remain elusive even for the well-studied Bacillus subtilis. Here we present two complementary approaches – transcriptome-wide mapping of endoribonucleolytic activity and deep mutational scanning of RNA cleavage sites – that reveal distinct rules governing the specificity among B. subtilis endoribonucleases. Detection of RNA terminal nucleotides in both 5′- and 3′-exonuclease-deficient cells revealed >103 putative endonucleolytic cleavage sites with single-nucleotide resolution. We found a surprisingly weak consensus for RNase Y targets, a contrastingly strong primary sequence motif for EndoA targets, and long-range intramolecular secondary structures for RNase III targets. Deep mutational analysis of RNase Y cleavage sites showed that the specificity is governed by many disjointed sequence features, each with mild contributions. Our results highlight the delocalized nature of mRNA stability determinants and provide a strategy for elucidating endoribonuclease specificity in vivo.
2025-01-15 | GSE275077 | GEO