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  • 1
    Online Resource
    Online Resource
    The Company of Biologists ; 2022
    In:  Development Vol. 149, No. 22 ( 2022-11-15)
    In: Development, The Company of Biologists, Vol. 149, No. 22 ( 2022-11-15)
    Type of Medium: Online Resource
    ISSN: 0950-1991 , 1477-9129
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2022
    detail.hit.zdb_id: 2007916-3
    SSG: 12
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  • 2
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 380, No. 6643 ( 2023-04-28)
    Abstract: Human accelerated regions (HARs) are evolutionarily conserved sequences that acquired an unexpectedly high number of nucleotide substitutions in the human genome since divergence from our common ancestor with chimpanzees. Prior work has established that many HARs are gene regulatory enhancers that function during embryonic development, particularly in neurodevelopment, and that most HARs show signatures of positive selection. However, the events that caused the sudden change in selective pressures on HARs remain a mystery. RATIONALE Because HARs acquired many substitutions in our ancestors after millions of years of extreme constraint across diverse mammals, we reasoned that their conserved roles in regulating development of the brain and other organs must have changed during human evolution. One mechanism that could drive such a functional shift is enhancer hijacking, whereby the target gene repertoire of a noncoding sequence is changed through alterations in three-dimensional genome folding. The regulatory information encoded in a hijacked enhancer would likely need to change to avoid deleterious expression of the altered target gene while also possibly supporting modified expression patterns. Structural variants—large genomic insertions, deletions, and rearrangements—are the greatest sources of sequence differences between the human and chimpanzee genomes, and they have the potential to affect how a region of the genome folds and localizes in the nucleus. We therefore hypothesized that some HARs were generated through enhancer hijacking triggered by nearby human-specific structural variants (hsSVs). RESULTS We leveraged an alignment of hundreds of mammalian genomes plus a Nextflow pipeline that we wrote for automating the detection of lineage-specific accelerated regions to identify 312 high-confidence HARs (zooHARs). Through massively parallel reporter assays and machine learning integration of hundreds of epigenomic datasets, we showed that many zooHARs function as neurodevelopmental enhancers and that their human substitutions alter transcription factor binding sites, consistent with previous studies. We further mapped zooHARs to specific cell types and tissues using single-cell open chromatin and gene expression data, and we found that they represent a more diverse set of neurodevelopmental processes than a parallel set of chimpanzee accelerated regions. To test the enhancer hijacking hypothesis, we first examined the three-dimensional neighborhoods of zooHARs using publicly available chromatin capture (Hi-C) data, finding a significant enrichment of zooHARs in domains with hsSVs. This motivated us to use deep learning to predict how hsSVs changed genome folding in the human versus the chimpanzee genomes. We found that 30% of zooHARs occur within 500 kb of an hsSV that substantially alters local chromatin interactions, and we confirmed this association in Hi-C data that we generated in human and chimpanzee neural progenitor cells. Finally, we showed that chromatin domains containing zooHARs and hsSVs are enriched for genes differentially expressed in human versus chimpanzee neurodevelopment. CONCLUSION The origin of many HARs may be explained by human-specific structural variants that altered three-dimensional genome folding, causing evolutionarily conserved enhancers to adapt to different target genes and regulatory domains. Example of HAR enhancer hijacking. The HAR is nearby and regulates gene A, but not gene B, as the chimpanzee genome folds. An insertion in the human genome brings the HAR closer to gene B, causing expression of gene B. The HAR adapts to being in gene B’s regulatory domain through substitutions to previously conserved nucleotides.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    RVK:
    RVK:
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 3
    In: eLife, eLife Sciences Publications, Ltd, Vol. 10 ( 2021-06-01)
    Abstract: The ability to sense pain is critical to our survival. Normally, pain is provoked by intense heat or cold temperatures, strong force or a chemical stimulus, for example, capsaicin, the pain-provoking substance in chili peppers. However, if nerve fibers in the arms or legs are damaged, pain can occur in response to touch or pressure stimuli that are normally painless. This hypersensitivity is called mechanical allodynia. A protein called calcitonin gene-related peptide, or CGRP, has been implicated in mechanical allodynia and other chronic pain conditions, such as migraine. CGRP is found in, and released from, the neurons that receive and transmit pain messages from tissues, such as skin and muscles, to the spinal cord. However, only a few distinct groups of CGRP-expressing neurons have been identified and it is unclear if these nerve cells also contribute to mechanical allodynia. To investigate this, Löken et al. genetically engineered mice so that all nerve cells containing CGRP produced red fluorescent light when illuminated with a laser. This included a previously unexplored group of CGRP-expressing neurons found in a part of the spinal cord that is known to receive information about non-painful stimuli. Using neuroanatomical methods, Löken et al. monitored the activity of these neurons in response to various stimuli, before and after a partial nerve injury. This partial injury was induced via a surgery that cut off a few, but not all, branches of a key leg nerve. The experiments showed that in their normal state, the CGRP-expressing neurons hardly responded to mechanical stimulation. In fact, it was difficult to establish what they normally respond to. However, after a nerve injury, brushing the mice’s skin evoked significant activity in these cells. Moreover, when these CGRP cells were artificially stimulated, the stimulation induced hypersensitivity to mechanical stimuli, even when the mice had no nerve damage. These results suggest that this group of neurons, which are normally suppressed, can become hyperexcitable and contribute to the development of mechanical allodynia. In summary, Löken et al. have identified a group of nerve cells in the spinal cord that process mechanical information and contribute to touch-evoked pain. Future studies will identify the nerve circuits that are targeted by CGRP released from these nerve cells. These circuits represent a new therapeutic target for managing chronic pain conditions related to nerve damage, specifically mechanical allodynia, which is the most common complaint of patients with chronic pain.
    Type of Medium: Online Resource
    ISSN: 2050-084X
    Language: English
    Publisher: eLife Sciences Publications, Ltd
    Publication Date: 2021
    detail.hit.zdb_id: 2687154-3
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  • 4
    In: The CRISPR Journal, Mary Ann Liebert Inc
    Type of Medium: Online Resource
    ISSN: 2573-1599 , 2573-1602
    Language: English
    Publisher: Mary Ann Liebert Inc
    Publication Date: 2023
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  • 5
    Online Resource
    Online Resource
    Elsevier BV ; 2024
    In:  Cell Stem Cell Vol. 31, No. 1 ( 2024-01), p. 3-4
    In: Cell Stem Cell, Elsevier BV, Vol. 31, No. 1 ( 2024-01), p. 3-4
    Type of Medium: Online Resource
    ISSN: 1934-5909
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2024
    detail.hit.zdb_id: 2375356-0
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