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Update Literature (#177)
## Description This PR introduces changes from automated literature retrieval followed by manual curation. ## Major Changes - Done ## Minor Changes - Some rewording and website updates ## Checklist - [x] Check I've included all literature since the last "Literature Update" PR (may need to diff against an earlier version) - [x] Check for updates to existing loci - [x] Check for potential new loci - [x] Add any changes to `STRchive-loci.json` as commits to this branch/PR - [x] If anything needs to be discussed further before adding to STRchive, add it to [Discussions](https://github.com/dashnowlab/STRchive/discussions) - [x] Check all tests pass e.g. the website built - [x] Check that the website preview looks good - [x] Update the STRchive version in `CITATION.cff`, format X.Y.Z. If any major changes, increment Y. If only minor changes, increment Z. If the breaking change (rare), increment X. - [x] Ask someone to review this PR --------- Co-authored-by: hdashnow <3794821+hdashnow@users.noreply.github.com> Co-authored-by: Harriet Dashnow <h.dashnow@gmail.com>
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‎CITATION.cff‎

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title: STRchive
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version: 2.4.2
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version: 2.4.3
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date-released: "2025-04-28"
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url: https://github.com/dashnowlab/STRchive
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authors:

‎README.md‎

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- Laurel Hiatt
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- Akshay Avvaru
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- Vincent Rubinetti
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- Macayla Weiner
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## Contributing
2021

‎data/STRchive-citations.json‎

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‎data/STRchive-loci.json‎

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‎data/literature/AR01.txt‎

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‎data/literature/ATN101.txt‎

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‎data/literature/ATXN1001.txt‎

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@@ -3,7 +3,7 @@ PMID- 40067487
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OWN - NLM
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STAT- MEDLINE
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DCOM- 20250311
6-
LR - 20250311
6+
LR - 20250418
77
IS - 1432-1459 (Electronic)
88
IS - 0340-5354 (Linking)
99
VI - 272
@@ -154,9 +154,8 @@ SO - J Neurol. 2025 Mar 11;272(4):261. doi: 10.1007/s00415-025-13003-5.
154154

155155
PMID- 39820777
156156
OWN - NLM
157-
STAT- MEDLINE
158-
DCOM- 20250117
159-
LR - 20250311
157+
STAT- In-Process
158+
LR - 20250501
160159
IS - 1473-4230 (Electronic)
161160
IS - 1473-4222 (Linking)
162161
VI - 24
@@ -3720,6 +3719,126 @@ PST - ppublish
37203719
SO - Proc Natl Acad Sci U S A. 2011 Feb 15;108(7):2843-8. doi:
37213720
10.1073/pnas.1009409108. Epub 2011 Jan 31.
37223721

3722+
PMID- 20065034
3723+
OWN - NLM
3724+
STAT- MEDLINE
3725+
DCOM- 20100409
3726+
LR - 20211020
3727+
IS - 1098-5549 (Electronic)
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IS - 0270-7306 (Print)
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IS - 0270-7306 (Linking)
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VI - 30
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IP - 6
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DP - 2010 Mar
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TI - The DNA unwinding element binding protein DUE-B interacts with Cdc45 in
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preinitiation complex formation.
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PG - 1495-507
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LID - 10.1128/MCB.00710-09 [doi]
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AB - Template unwinding during DNA replication initiation requires the loading of the
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MCM helicase activator Cdc45 at replication origins. We show that Cdc45 interacts
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with the DNA unwinding element (DUE) binding protein DUE-B and that these
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proteins localize to the DUEs of active replication origins. DUE-B and Cdc45 are
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not bound at the inactive c-myc replicator in the absence of a functional DUE or
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at the recently identified ataxin 10 (ATX10) origin, which is silent before
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disease-related (ATTCT)(n) repeat length expansion of its DUE sequence, despite
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the presence of the origin recognition complex (ORC) and MCM proteins at these
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origins. Addition of a heterologous DUE to the ectopic c-myc origin, or expansion
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of the ATX10 DUE, leads to origin activation, DUE-B binding, and Cdc45 binding.
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DUE-B, Cdc45, and topoisomerase IIbeta binding protein 1 (TopBP1) form complexes
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in cell extracts and when expressed from baculovirus vectors. During replication
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in Xenopus egg extracts, DUE-B and Cdc45 bind to chromatin with similar kinetics,
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and DUE-B immunodepletion blocks replication and the loading of Cdc45 and a
3751+
fraction of TopBP1. The coordinated binding of DUE-B and Cdc45 to origins and the
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physical interactions of DUE-B, Cdc45, and TopBP1 suggest that complexes of these
3753+
proteins are necessary for replication initiation.
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FAU - Chowdhury, A
3755+
AU - Chowdhury A
3756+
AD - Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine,
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Wright State University, Dayton, Ohio 45435, USA.
3758+
FAU - Liu, G
3759+
AU - Liu G
3760+
FAU - Kemp, M
3761+
AU - Kemp M
3762+
FAU - Chen, X
3763+
AU - Chen X
3764+
FAU - Katrangi, N
3765+
AU - Katrangi N
3766+
FAU - Myers, S
3767+
AU - Myers S
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FAU - Ghosh, M
3769+
AU - Ghosh M
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FAU - Yao, J
3771+
AU - Yao J
3772+
FAU - Gao, Y
3773+
AU - Gao Y
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FAU - Bubulya, P
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AU - Bubulya P
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FAU - Leffak, M
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AU - Leffak M
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LA - eng
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GR - R01 GM053819/GM/NIGMS NIH HHS/United States
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GR - R15 GM084407/GM/NIGMS NIH HHS/United States
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GR - GM82995/GM/NIGMS NIH HHS/United States
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GR - R01 GM082995/GM/NIGMS NIH HHS/United States
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GR - GM53819/GM/NIGMS NIH HHS/United States
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PT - Journal Article
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PT - Research Support, N.I.H., Extramural
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PT - Research Support, Non-U.S. Gov't
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DEP - 20100111
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PL - United States
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TA - Mol Cell Biol
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JT - Molecular and cellular biology
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JID - 8109087
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RN - 0 (CDC45 protein, human)
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RN - 0 (Carrier Proteins)
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RN - 0 (Cell Cycle Proteins)
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RN - 0 (Chromatin)
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RN - 0 (DNA-Binding Proteins)
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RN - 0 (DTD1 protein, human)
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RN - 0 (Nuclear Proteins)
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RN - 0 (ORC2 protein, human)
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RN - 0 (Origin Recognition Complex)
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RN - 0 (Saccharomyces cerevisiae Proteins)
3802+
RN - 0 (Sld3 protein, S cerevisiae)
3803+
RN - 0 (TOPBP1 protein, human)
3804+
SB - IM
3805+
MH - Amino Acid Sequence
3806+
MH - Animals
3807+
MH - Carrier Proteins/metabolism
3808+
MH - Cell Cycle Proteins/chemistry/*metabolism
3809+
MH - Chromatin/metabolism
3810+
MH - DNA-Binding Proteins/chemistry/*metabolism
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MH - Fluorescent Antibody Technique
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MH - HCT116 Cells
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MH - HeLa Cells
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MH - Humans
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MH - Intracellular Space/metabolism
3816+
MH - Models, Biological
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MH - Molecular Sequence Data
3818+
MH - Nuclear Proteins/metabolism
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MH - Origin Recognition Complex/metabolism
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MH - Phosphorylation
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MH - Protein Binding
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MH - Protein Transport
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MH - *Replication Origin
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MH - Saccharomyces cerevisiae Proteins/chemistry
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MH - Xenopus
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PMC - PMC2832489
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EDAT- 2010/01/13 06:00
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MHDA- 2010/04/10 06:00
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PMCR- 2010/09/01
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CRDT- 2010/01/13 06:00
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PHST- 2010/01/13 06:00 [entrez]
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PHST- 2010/01/13 06:00 [pubmed]
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PHST- 2010/04/10 06:00 [medline]
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PHST- 2010/09/01 00:00 [pmc-release]
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AID - MCB.00710-09 [pii]
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AID - 0710-09 [pii]
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AID - 10.1128/MCB.00710-09 [doi]
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PST - ppublish
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SO - Mol Cell Biol. 2010 Mar;30(6):1495-507. doi: 10.1128/MCB.00710-09. Epub 2010 Jan
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11.
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37233842
PMID- 19651850
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OWN - NLM
37253844
STAT- MEDLINE

‎data/literature/ATXN101.txt‎

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22
PMID- 39820777
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OWN - NLM
4-
STAT- MEDLINE
5-
DCOM- 20250117
6-
LR - 20250311
4+
STAT- In-Process
5+
LR - 20250501
76
IS - 1473-4230 (Electronic)
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IS - 1473-4222 (Linking)
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‎data/literature/ATXN201.txt‎

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2+
PMID- 40220918
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OWN - NLM
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STAT- MEDLINE
5+
DCOM- 20250424
6+
LR - 20250424
7+
IS - 1095-953X (Electronic)
8+
IS - 0969-9961 (Linking)
9+
VI - 209
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DP - 2025 Jun 1
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TI - ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2
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depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation.
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PG - 106903
14+
LID - S0969-9961(25)00119-6 [pii]
15+
LID - 10.1016/j.nbd.2025.106903 [doi]
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AB - The cytoplasmic Ataxin-2 (ATXN2) protein associates with TDP-43 in stress
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granules (SG) where RNA quality control occurs. Mutations in this pathway
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underlie Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis.
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In contrast, Ataxin-2-like (ATXN2L) is predominantly perinuclear, more abundant,
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and essential for embryonic life. Its sequestration into ATXN2 aggregates may
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contribute to disease. In this study, we utilized two approaches to clarify the
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roles of ATXN2L. First, we identified interactors through co-immunoprecipitation
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in both wild-type and ATXN2L-null murine embryonic fibroblasts. Second, we
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assessed the proteome profile effects using mass spectrometry in these cells.
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Additionally, we examined the accumulation of ATXN2L interactors in the SCA2
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mouse model, Atxn2-CAG100-KnockIn (KIN). We observed that RNA-binding proteins,
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including PABPN1, NUFIP2, MCRIP2, RBMS1, LARP1, PTBP1, FMR1, RPS20, FUBP3, MBNL2,
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ZMAT3, SFPQ, CSDE1, HNRNPK, and HNRNPDL, exhibit a stronger association with
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ATXN2L compared to established interactors like ATXN2, PABPC1, LSM12, and G3BP2.
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Additionally, ATXN2L interacted with components of the actin complex, such as
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SYNE2, LMOD1, ACTA2, FYB, and GOLGA3. We noted that oxidative stress increased
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HNRNPK but decreased SYNE2 association, which likely reflects the relocalization
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of SG. Proteome profiling revealed that NUFIP2 and SYNE2 are depleted in
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ATXN2L-null fibroblasts. Furthermore, NUFIP2 homodimers and SYNE1 accumulate
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during the ATXN2 aggregation process in KIN 14-month-old spinal cord tissues. The
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functions of ATXN2L and its interactors are therefore critical in RNA granule
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trafficking and surveillance, particularly for the maintenance of differentiated
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neurons.
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CI - Copyright (c) 2025 The Author(s). Published by Elsevier Inc. All rights reserved.
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FAU - Key, Jana
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AU - Key J
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Almaguer-Mederos, Luis-Enrique
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AU - Almaguer-Mederos LE
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Kandi, Arvind Reddy
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AU - Kandi AR
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Sen, Nesli-Ece
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AU - Sen NE
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Gispert, Suzana
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AU - Gispert S
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Kopf, Gabriele
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AU - Kopf G
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany.
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FAU - Meierhofer, David
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AU - Meierhofer D
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AD - Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin,
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Germany.
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FAU - Auburger, Georg
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AU - Auburger G
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AD - Goethe University Frankfurt, University Hospital, Clinic of Neurology,
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Experimental Neurology, Heinrich- Hoffmann-Str. 7, 60528 Frankfurt am Main,
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Germany; Institute for Clinical Neuroanatomy, Dr. Senckenberg Anatomy,
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Fachbereich Medizin, Goethe University Frankfurt, Frankfurt am Main, Germany.
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Electronic address: auburger@em.uni-frankfurt.de.
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LA - eng
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PT - Journal Article
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DEP - 20250411
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PL - United States
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TA - Neurobiol Dis
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JT - Neurobiology of disease
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JID - 9500169
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RN - 0 (Ataxin-2)
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RN - 0 (RNA-Binding Proteins)
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RN - 0 (Atxn2 protein, mouse)
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RN - 0 (Nerve Tissue Proteins)
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RN - 0 (Peptides)
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SB - IM
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MH - Animals
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MH - Mice
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MH - *Ataxin-2/metabolism/genetics
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MH - Humans
98+
MH - *RNA-Binding Proteins/metabolism
99+
MH - Fibroblasts/metabolism
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MH - Spinocerebellar Ataxias/metabolism/genetics
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MH - *Nerve Tissue Proteins/metabolism/genetics
102+
MH - Peptides/metabolism/genetics
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MH - Mice, Knockout
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OTO - NOTNLM
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OT - RNA-binding proteins
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OT - Spinocerebellar Ataxia
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OT - actin cytoskeleton
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OT - interactome profiling
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OT - proteome profiling
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OT - ribonucleoprotein complexes
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OT - stress granules
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COIS- Declaration of competing interest The authors report no competing interests.
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EDAT- 2025/04/13 00:44
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MHDA- 2025/04/24 06:27
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CRDT- 2025/04/12 19:34
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PHST- 2025/02/27 00:00 [received]
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PHST- 2025/04/04 00:00 [revised]
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PHST- 2025/04/04 00:00 [accepted]
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PHST- 2025/04/24 06:27 [medline]
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PHST- 2025/04/13 00:44 [pubmed]
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PHST- 2025/04/12 19:34 [entrez]
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AID - S0969-9961(25)00119-6 [pii]
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AID - 10.1016/j.nbd.2025.106903 [doi]
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PST - ppublish
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SO - Neurobiol Dis. 2025 Jun 1;209:106903. doi: 10.1016/j.nbd.2025.106903. Epub 2025
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Apr 11.
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2128
PMID- 40004498
3129
OWN - NLM
4130
STAT- MEDLINE
@@ -476,9 +602,8 @@ SO - Int J Mol Sci. 2025 Jan 23;26(3):933. doi: 10.3390/ijms26030933.
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477603
PMID- 39820777
478604
OWN - NLM
479-
STAT- MEDLINE
480-
DCOM- 20250117
481-
LR - 20250311
605+
STAT- In-Process
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LR - 20250501
482607
IS - 1473-4230 (Electronic)
483608
IS - 1473-4222 (Linking)
484609
VI - 24
@@ -612,8 +737,8 @@ SO - Cerebellum. 2025 Jan 16;24(2):33. doi: 10.1007/s12311-024-01784-w.
612737
PMID- 39812846
613738
OWN - NLM
614739
STAT- MEDLINE
615-
DCOM- 20250115
616-
LR - 20250215
740+
DCOM- 20250501
741+
LR - 20250501
617742
IS - 1432-1459 (Electronic)
618743
IS - 0340-5354 (Linking)
619744
VI - 272
@@ -740,16 +865,17 @@ SB - IM
740865
MH - Humans
741866
MH - Male
742867
MH - Female
743-
MH - Adult
744868
MH - Middle Aged
869+
MH - Adult
745870
MH - Retrospective Studies
746871
MH - Cross-Sectional Studies
872+
MH - *Genetic Testing
747873
MH - Aged
874+
MH - *Spinocerebellar Degenerations/diagnosis/genetics
748875
MH - Young Adult
749-
MH - *Genetic Testing/methods
750-
MH - Adolescent
751876
MH - High-Throughput Nucleotide Sequencing
752-
MH - Italy
877+
MH - Adolescent
878+
MH - Spinocerebellar Ataxias/diagnosis/genetics
753879
OTO - NOTNLM
754880
OT - Cerebellar ataxia
755881
OT - Diagnostic yield
@@ -774,8 +900,8 @@ SO - J Neurol. 2025 Jan 15;272(2):111. doi: 10.1007/s00415-024-12772-9.
774900
PMID- 39804470
775901
OWN - NLM
776902
STAT- MEDLINE
777-
DCOM- 20250113
778-
LR - 20250113
903+
DCOM- 20250430
904+
LR - 20250430
779905
IS - 1364-6753 (Electronic)
780906
IS - 1364-6745 (Linking)
781907
VI - 26
@@ -869,21 +995,21 @@ JT - Neurogenetics
869995
JID - 9709714
870996
RN - 0 (ATXN2 protein, human)
871997
RN - 0 (Ataxin-2)
872-
RN - 26700-71-0 (polyglutamine)
873998
RN - 0 (Peptides)
999+
RN - 26700-71-0 (polyglutamine)
8741000
SB - IM
8751001
MH - Humans
8761002
MH - *Amyotrophic Lateral Sclerosis/genetics
8771003
MH - Malaysia
878-
MH - *Ataxin-2/genetics
8791004
MH - Male
1005+
MH - *Ataxin-2/genetics
8801006
MH - Female
8811007
MH - Middle Aged
8821008
MH - *Trinucleotide Repeat Expansion/genetics
8831009
MH - Adult
8841010
MH - Aged
885-
MH - Peptides/genetics
8861011
MH - Asian People/genetics
1012+
MH - *Peptides/genetics
8871013
MH - Genetic Predisposition to Disease
8881014
OTO - NOTNLM
8891015
OT - ATXN2

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