Chromatin loop anchors contain core structural components of the gene expression machinery in maize (Record no. 63351)
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| 000 -LEADER | |
|---|---|
| fixed length control field | 03721nab|a22003857a|4500 |
| 001 - CONTROL NUMBER | |
| control field | 63351 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MX-TxCIM |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20211006085222.0 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 200910s2021||||xxk|||p|op||||00||0|eng|d |
| 022 ## - INTERNATIONAL STANDARD SERIAL NUMBER | |
| International Standard Serial Number | 1471-2164 |
| 024 8# - OTHER STANDARD IDENTIFIER | |
| Standard number or code | https://doi.org/10.1186/s12864-020-07324-0 |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | MX-TxCIM |
| 041 ## - LANGUAGE CODE | |
| Language code of text/sound track or separate title | eng |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| Personal name | Deschamps, S. |
| 9 (RLIN) | 18522 |
| 245 10 - TITLE STATEMENT | |
| Title | Chromatin loop anchors contain core structural components of the gene expression machinery in maize |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT) | |
| Place of publication, distribution, etc. | London (United Kingdom) : |
| Name of publisher, distributor, etc. | BioMed Central, |
| Date of publication, distribution, etc. | 2021. |
| 500 ## - GENERAL NOTE | |
| General note | Peer review |
| 500 ## - GENERAL NOTE | |
| General note | Open Access |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc. | Background: Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heterochromatic regions marked by higher repeat content, but little is known on their spatial organization and genome-wide occurrence in relation to transcriptional activity. Results: Here, ultra-deep Hi-C sequencing of maize B73 leaf tissue was combined with gene expression and open chromatin sequencing for chromatin loop discovery and correlation with hierarchical topologically-associating domains (TADs) and transcriptional activity. A majority of all anchors are shared between multiple loops from previous public maize high-resolution interactome datasets, suggesting a highly dynamic environment, with a conserved set of anchors involved in multiple interaction networks. Chromatin loop interiors are marked by higher repeat contents than the anchors flanking them. A small fraction of high-resolution interaction anchors, fully embedded in larger chromatin loops, co-locate with active genes and putative protein-binding sites. Combinatorial analyses indicate that all anchors studied here co-locate with at least 81.5% of expressed genes and 74% of open chromatin regions. Approximately 38% of all Hi-C chromatin loops are fully embedded within hierarchical TAD-like domains, while the remaining ones share anchors with domain boundaries or with distinct domains. Those various loop types exhibit specific patterns of overlap for open chromatin regions and expressed genes, but no apparent pattern of gene expression. In addition, up to 63% of all unique variants derived from a prior public maize eQTL dataset overlap with Hi-C loop anchors. Anchor annotation suggests that < 7% of all loops detected here are potentially devoid of any genes or regulatory elements. The overall organization of chromatin loop anchors in the maize genome suggest a loop modeling system hypothesized to resemble phase separation of repeat-rich regions. Conclusions: Sets of conserved chromatin loop anchors mapping to hierarchical domains contains core structural components of the gene expression machinery in maize. The data presented here will be a useful reference to further investigate their function in regard to the formation of transcriptional complexes and the regulation of transcriptional activity in the maize genome. |
| 546 ## - LANGUAGE NOTE | |
| Language note | Text in English |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Topical term or geographic name as entry element | Maize |
| Miscellaneous information | AGROVOC |
| Source of heading or term | |
| 9 (RLIN) | 1173 |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 14145 |
| Topical term or geographic name as entry element | Chromatin |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 9041 |
| Topical term or geographic name as entry element | RNA Sequence |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 8835 |
| Topical term or geographic name as entry element | Gene Expression |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18523 |
| Personal name | Crow, J.A. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18524 |
| Personal name | Chaidir, N. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18525 |
| Personal name | Peterson-Burch, B. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18526 |
| Personal name | Kumar, S. |
| 700 0# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18527 |
| Personal name | Haining Lin |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 18528 |
| Personal name | Zastrow-Hayes, G. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 17716 |
| Personal name | May, G.D. |
| 773 0# - HOST ITEM ENTRY | |
| Title | BMC Genomics |
| Related parts | v. 22, art. 23 |
| Place, publisher, and date of publication | London (United Kingdom) : BioMed Central, 2021. |
| International Standard Serial Number | 1471-2164 |
| Record control number | u56896 |
| 856 4# - ELECTRONIC LOCATION AND ACCESS | |
| Link text | Click here to access online |
| Uniform Resource Identifier | https://doi.org/10.1186/s12864-020-07324-0 |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Koha item type | Article |
| Suppress in OPAC | No |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Date last seen | Total Checkouts | Price effective from | Koha item type | Lost status | Source of classification or shelving scheme | Damaged status | Not for loan | Collection code | Withdrawn status | Home library | Current library | Date acquired |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 02/17/2021 | 02/17/2021 | Article | Not Lost | Dewey Decimal Classification | Reprints Collection | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Knowledge Center: John Woolston Library | 02/17/2021 |